From 893ce11acc4b3fcf7e74a713f66e6ee23586a29d Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 2 Nov 2023 00:01:14 -0400
Subject: [PATCH 01/21] Add persistentToggle composable.  This can be used for
 persisting the toggled state of particular sections in the UI.

---
 client/src/composables/persistentToggle.ts | 28 ++++++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 client/src/composables/persistentToggle.ts

diff --git a/client/src/composables/persistentToggle.ts b/client/src/composables/persistentToggle.ts
new file mode 100644
index 000000000000..6b9b414aea1a
--- /dev/null
+++ b/client/src/composables/persistentToggle.ts
@@ -0,0 +1,28 @@
+import { type Ref, ref, watch } from "vue";
+
+interface ToggleStateInterface {
+    toggled: Ref<boolean>;
+    toggle: () => void;
+}
+
+export function usePersistentToggle(uniqueId: string): ToggleStateInterface{
+    const localStorageKey = `toggle-state-${uniqueId}`;
+
+    // Retrieve the toggled state from localStorage if available, otherwise default to false
+    const toggled = ref<boolean>(localStorage.getItem(localStorageKey) === "true");
+
+    // Watch for changes in the toggled state and persist them to localStorage
+    watch(toggled, (newVal: boolean) => {
+        localStorage.setItem(localStorageKey, String(newVal));
+    });
+
+    // Expose a function for toggling state
+    const toggle = () => {
+        toggled.value = !toggled.value;
+    };
+
+    return {
+        toggled,
+        toggle,
+    };
+}

From 129d3c24a6b0a18dc781f05563b392b9b245a848 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 6 Nov 2023 14:01:17 -0500
Subject: [PATCH 02/21] Add basic collapse to heading -- work on styling...

---
 client/src/components/Common/Heading.vue   | 9 +++++++++
 client/src/composables/persistentToggle.ts | 2 +-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/client/src/components/Common/Heading.vue b/client/src/components/Common/Heading.vue
index 815680b6dc88..8454314c276c 100644
--- a/client/src/components/Common/Heading.vue
+++ b/client/src/components/Common/Heading.vue
@@ -14,10 +14,14 @@ interface Props {
     inline?: boolean;
     size?: "xl" | "lg" | "md" | "sm" | "text";
     icon?: string | [string, string];
+    collapsible?: boolean;
+    collapsed?: boolean;
 }
 
 const props = defineProps<Props>();
 
+defineEmits(["click"]);
+
 const sizeClass = computed(() => {
     return `h-${props.size ?? "lg"}`;
 });
@@ -37,6 +41,10 @@ const element = computed(() => {
         <div class="stripe"></div>
         <component :is="element" :class="[sizeClass, props.bold ? 'font-weight-bold' : '']">
             <slot />
+            <FontAwesomeIcon
+                v-if="collapsible"
+                :icon="collapsed ? 'chevron-down' : 'chevron-up'"
+                @click="$emit('click')" />
         </component>
         <div class="stripe"></div>
     </div>
@@ -47,6 +55,7 @@ const element = computed(() => {
         :class="[sizeClass, props.bold ? 'font-weight-bold' : '', props.inline ? 'inline' : '']">
         <FontAwesomeIcon v-if="props.icon" :icon="props.icon" />
         <slot />
+        <FontAwesomeIcon v-if="collapsible" :icon="collapsed ? 'chevron-down' : 'chevron-up'" @click="$emit('click')" />
     </component>
 </template>
 
diff --git a/client/src/composables/persistentToggle.ts b/client/src/composables/persistentToggle.ts
index 6b9b414aea1a..154f4c2b4a42 100644
--- a/client/src/composables/persistentToggle.ts
+++ b/client/src/composables/persistentToggle.ts
@@ -5,7 +5,7 @@ interface ToggleStateInterface {
     toggle: () => void;
 }
 
-export function usePersistentToggle(uniqueId: string): ToggleStateInterface{
+export function usePersistentToggle(uniqueId: string): ToggleStateInterface {
     const localStorageKey = `toggle-state-${uniqueId}`;
 
     // Retrieve the toggled state from localStorage if available, otherwise default to false

From 75cbcab6df2f6d645b6064c9de4c21a2759f6e6f Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 6 Nov 2023 14:08:10 -0500
Subject: [PATCH 03/21] Swap AWSEstimate to use persistentToggle

---
 .../src/components/JobMetrics/AwsEstimate.vue | 34 ++++++++++++-------
 1 file changed, 21 insertions(+), 13 deletions(-)

diff --git a/client/src/components/JobMetrics/AwsEstimate.vue b/client/src/components/JobMetrics/AwsEstimate.vue
index da194e56a6d4..ae8e4a686609 100644
--- a/client/src/components/JobMetrics/AwsEstimate.vue
+++ b/client/src/components/JobMetrics/AwsEstimate.vue
@@ -1,6 +1,10 @@
 <script setup lang="ts">
 import { computed } from "vue";
 
+import { usePersistentToggle } from "@/composables/persistentToggle";
+
+import Heading from "@/components/Common/Heading.vue";
+
 const props = defineProps<{
     jobRuntimeInSeconds: number;
     coresAllocated: number;
@@ -20,6 +24,8 @@ const props = defineProps<{
     }[];
 }>();
 
+const { toggled, toggle } = usePersistentToggle("aws-estimate");
+
 const computedAwsEstimate = computed(() => {
     const { coresAllocated, jobRuntimeInSeconds, memoryAllocatedInMebibyte } = props;
 
@@ -50,24 +56,26 @@ const computedAwsEstimate = computed(() => {
 
 <template>
     <div v-if="computedAwsEstimate" id="aws-estimate" class="mt-4">
-        <h2>AWS estimate</h2>
+        <Heading h2 size="md" separator collapsible :collapsed="toggled" @click="toggle()">AWS estimate</Heading>
 
-        <strong id="aws-cost">{{ computedAwsEstimate.price }} USD</strong>
+        <template v-if="!toggled">
+            <strong id="aws-cost">{{ computedAwsEstimate.price }} USD</strong>
 
-        <br />
+            <br />
 
-        This job requested {{ computedAwsEstimate.requestedVCpuCount }} core(s) and
-        {{ computedAwsEstimate.memory.toFixed(3) }} GiB of memory. Given this information, the smallest EC2 machine we
-        could find is:
+            This job requested {{ computedAwsEstimate.requestedVCpuCount }} core(s) and
+            {{ computedAwsEstimate.memory.toFixed(3) }} GiB of memory. Given this information, the smallest EC2 machine
+            we could find is:
 
-        <span id="aws-name">{{ computedAwsEstimate.instance.name }}</span>
-        (<span id="aws-mem">{{ computedAwsEstimate.instance.mem }}</span> GB /
-        <span id="aws-vcpus">{{ computedAwsEstimate.instance.vCpuCount }}</span> vCPUs /
-        <span id="aws-cpu">{{ computedAwsEstimate.instance.cpu.map(({ cpuModel }) => cpuModel).join(", ") }}</span
-        >). This instance is priced at {{ computedAwsEstimate.instance.price }} USD/hour.
+            <span id="aws-name">{{ computedAwsEstimate.instance.name }}</span>
+            (<span id="aws-mem">{{ computedAwsEstimate.instance.mem }}</span> GB /
+            <span id="aws-vcpus">{{ computedAwsEstimate.instance.vCpuCount }}</span> vCPUs /
+            <span id="aws-cpu">{{ computedAwsEstimate.instance.cpu.map(({ cpuModel }) => cpuModel).join(", ") }}</span
+            >). This instance is priced at {{ computedAwsEstimate.instance.price }} USD/hour.
 
-        <br />
+            <br />
 
-        &ast;Please note, that these numbers are only estimates, all jobs are always free of charge for all users.
+            &ast;Please note, that these numbers are only estimates, all jobs are always free of charge for all users.
+        </template>
     </div>
 </template>

From 1fd74e1bbcfdb6335295ea10fa84e0ccd1486c81 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 6 Nov 2023 14:11:00 -0500
Subject: [PATCH 04/21] Swap CarbonEmissions to use header sizing inline with
 rest of dataset/job details

---
 .../components/JobMetrics/CarbonEmissions/CarbonEmissions.vue   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/JobMetrics/CarbonEmissions/CarbonEmissions.vue b/client/src/components/JobMetrics/CarbonEmissions/CarbonEmissions.vue
index f124643cecbc..c3776997534c 100644
--- a/client/src/components/JobMetrics/CarbonEmissions/CarbonEmissions.vue
+++ b/client/src/components/JobMetrics/CarbonEmissions/CarbonEmissions.vue
@@ -270,7 +270,7 @@ function getEnergyNeededText(energyNeededInKiloWattHours: number) {
 
 <template v-if="carbonEmissions && carbonEmissionsComparisons">
     <div class="mt-4">
-        <Heading h2 separator inline bold> Carbon Footprint </Heading>
+        <Heading h2 separator size="md" inline> Carbon Footprint </Heading>
 
         <section class="carbon-emission-values my-4">
             <div class="emissions-grid">

From 397d4ff756e7b9f597c7775ab8491ab509ab0883 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 6 Nov 2023 14:13:46 -0500
Subject: [PATCH 05/21] Swap CarbonEmissions sections to use persistentToggle

---
 .../JobMetrics/CarbonEmissions/CarbonEmissions.vue     | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/client/src/components/JobMetrics/CarbonEmissions/CarbonEmissions.vue b/client/src/components/JobMetrics/CarbonEmissions/CarbonEmissions.vue
index c3776997534c..aec2aac1f80f 100644
--- a/client/src/components/JobMetrics/CarbonEmissions/CarbonEmissions.vue
+++ b/client/src/components/JobMetrics/CarbonEmissions/CarbonEmissions.vue
@@ -5,6 +5,8 @@ import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import type { GetComponentPropTypes } from "types/utilityTypes";
 import { computed, unref } from "vue";
 
+import { usePersistentToggle } from "@/composables/persistentToggle";
+
 import * as carbonEmissionsConstants from "./carbonEmissionConstants.js";
 
 import BarChart from "./BarChart.vue";
@@ -34,6 +36,8 @@ const props = withDefaults(defineProps<CarbonEmissionsProps>(), {
     memoryAllocatedInMebibyte: 0,
 });
 
+const { toggled, toggle } = usePersistentToggle("carbonEmissions");
+
 const carbonEmissions = computed(() => {
     const memoryPowerUsed = carbonEmissionsConstants.memoryPowerUsage;
     const runtimeInHours = props.jobRuntimeInSeconds / (60 * 60); // Convert to hours
@@ -270,9 +274,11 @@ function getEnergyNeededText(energyNeededInKiloWattHours: number) {
 
 <template v-if="carbonEmissions && carbonEmissionsComparisons">
     <div class="mt-4">
-        <Heading h2 separator size="md" inline> Carbon Footprint </Heading>
+        <Heading h2 separator size="md" inline collapsible :collapsed="toggled" @click="toggle()">
+            Carbon Footprint
+        </Heading>
 
-        <section class="carbon-emission-values my-4">
+        <section v-if="!toggled" class="carbon-emission-values my-4">
             <div class="emissions-grid">
                 <!-- Carbon Footprint Totals -->
                 <CarbonEmissionsCard

From 1706027a09513e7a90a72d9bf2b5691e4a83d1e9 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 6 Nov 2023 14:23:55 -0500
Subject: [PATCH 06/21] Make entire header text + chevron clickable.

---
 client/src/components/Common/Heading.vue | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/client/src/components/Common/Heading.vue b/client/src/components/Common/Heading.vue
index 8454314c276c..290845ac296a 100644
--- a/client/src/components/Common/Heading.vue
+++ b/client/src/components/Common/Heading.vue
@@ -39,12 +39,9 @@ const element = computed(() => {
 <template>
     <div v-if="props.separator" class="separator heading">
         <div class="stripe"></div>
-        <component :is="element" :class="[sizeClass, props.bold ? 'font-weight-bold' : '']">
+        <component :is="element" :class="[sizeClass, props.bold ? 'font-weight-bold' : '']" @click="$emit('click')">
             <slot />
-            <FontAwesomeIcon
-                v-if="collapsible"
-                :icon="collapsed ? 'chevron-down' : 'chevron-up'"
-                @click="$emit('click')" />
+            <FontAwesomeIcon v-if="collapsible" :icon="collapsed ? 'chevron-down' : 'chevron-up'" />
         </component>
         <div class="stripe"></div>
     </div>
@@ -52,10 +49,11 @@ const element = computed(() => {
         :is="element"
         v-else
         class="heading"
-        :class="[sizeClass, props.bold ? 'font-weight-bold' : '', props.inline ? 'inline' : '']">
+        :class="[sizeClass, props.bold ? 'font-weight-bold' : '', props.inline ? 'inline' : '']"
+        @click="$emit('click')">
         <FontAwesomeIcon v-if="props.icon" :icon="props.icon" />
         <slot />
-        <FontAwesomeIcon v-if="collapsible" :icon="collapsed ? 'chevron-down' : 'chevron-up'" @click="$emit('click')" />
+        <FontAwesomeIcon v-if="collapsible" :icon="collapsed ? 'chevron-down' : 'chevron-up'" />
     </component>
 </template>
 

From cee7cd83f569520d377d32cec97367a7ed98b2f3 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 6 Nov 2023 14:33:26 -0500
Subject: [PATCH 07/21] Make entire header clickable for collapsible headers

---
 client/src/components/Common/Heading.vue | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Common/Heading.vue b/client/src/components/Common/Heading.vue
index 290845ac296a..e7ad0cdb5007 100644
--- a/client/src/components/Common/Heading.vue
+++ b/client/src/components/Common/Heading.vue
@@ -39,7 +39,10 @@ const element = computed(() => {
 <template>
     <div v-if="props.separator" class="separator heading">
         <div class="stripe"></div>
-        <component :is="element" :class="[sizeClass, props.bold ? 'font-weight-bold' : '']" @click="$emit('click')">
+        <component
+            :is="element"
+            :class="[sizeClass, props.bold ? 'font-weight-bold' : '', props.collapsible ? 'collapsible' : '']"
+            @click="$emit('click')">
             <slot />
             <FontAwesomeIcon v-if="collapsible" :icon="collapsed ? 'chevron-down' : 'chevron-up'" />
         </component>
@@ -49,7 +52,12 @@ const element = computed(() => {
         :is="element"
         v-else
         class="heading"
-        :class="[sizeClass, props.bold ? 'font-weight-bold' : '', props.inline ? 'inline' : '']"
+        :class="[
+            sizeClass,
+            props.bold ? 'font-weight-bold' : '',
+            props.inline ? 'inline' : '',
+            props.collapsible ? 'collapsible' : '',
+        ]"
         @click="$emit('click')">
         <FontAwesomeIcon v-if="props.icon" :icon="props.icon" />
         <slot />
@@ -76,6 +84,10 @@ h1, h2, h3, h4, h5, h6 {
     }
 }
 
+.collapsible {
+    cursor: pointer;
+}
+
 .separator {
     display: grid;
     grid-template-columns: 1rem auto 1fr;

From 8d200f1b9a0e8e8bf19ae29f8313d7ee263aae28 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 9 Nov 2023 09:02:13 -0500
Subject: [PATCH 08/21] Refactor Heading collapse property to be
 open/closed/none, to avoid having separate 'collapsible' and 'collapsed'
 props.

---
 client/src/components/Common/Heading.vue        | 17 +++++++++++++----
 .../src/components/JobMetrics/AwsEstimate.vue   |  4 +++-
 .../CarbonEmissions/CarbonEmissions.vue         |  2 +-
 3 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/client/src/components/Common/Heading.vue b/client/src/components/Common/Heading.vue
index e7ad0cdb5007..873c5478a22a 100644
--- a/client/src/components/Common/Heading.vue
+++ b/client/src/components/Common/Heading.vue
@@ -14,11 +14,12 @@ interface Props {
     inline?: boolean;
     size?: "xl" | "lg" | "md" | "sm" | "text";
     icon?: string | [string, string];
-    collapsible?: boolean;
-    collapsed?: boolean;
+    collapse?: "open" | "closed" | "none";
 }
 
-const props = defineProps<Props>();
+const props = withDefaults(defineProps<Props>(), {
+    collapse: "none",
+});
 
 defineEmits(["click"]);
 
@@ -26,6 +27,14 @@ const sizeClass = computed(() => {
     return `h-${props.size ?? "lg"}`;
 });
 
+const collapsible = computed(() => {
+    return props.collapse !== "none";
+});
+
+const collapsed = computed(() => {
+    return props.collapse === "closed";
+});
+
 const element = computed(() => {
     for (const key of ["h1", "h2", "h3", "h4", "h5", "h6"]) {
         if (props[key as keyof typeof props]) {
@@ -41,7 +50,7 @@ const element = computed(() => {
         <div class="stripe"></div>
         <component
             :is="element"
-            :class="[sizeClass, props.bold ? 'font-weight-bold' : '', props.collapsible ? 'collapsible' : '']"
+            :class="[sizeClass, props.bold ? 'font-weight-bold' : '', collapsible ? 'collapsible' : '']"
             @click="$emit('click')">
             <slot />
             <FontAwesomeIcon v-if="collapsible" :icon="collapsed ? 'chevron-down' : 'chevron-up'" />
diff --git a/client/src/components/JobMetrics/AwsEstimate.vue b/client/src/components/JobMetrics/AwsEstimate.vue
index ae8e4a686609..76170db0e990 100644
--- a/client/src/components/JobMetrics/AwsEstimate.vue
+++ b/client/src/components/JobMetrics/AwsEstimate.vue
@@ -56,7 +56,9 @@ const computedAwsEstimate = computed(() => {
 
 <template>
     <div v-if="computedAwsEstimate" id="aws-estimate" class="mt-4">
-        <Heading h2 size="md" separator collapsible :collapsed="toggled" @click="toggle()">AWS estimate</Heading>
+        <Heading h2 size="md" separator :collapse="toggled ? 'closed' : 'open'" @click="toggle()">
+            AWS estimate
+        </Heading>
 
         <template v-if="!toggled">
             <strong id="aws-cost">{{ computedAwsEstimate.price }} USD</strong>
diff --git a/client/src/components/JobMetrics/CarbonEmissions/CarbonEmissions.vue b/client/src/components/JobMetrics/CarbonEmissions/CarbonEmissions.vue
index aec2aac1f80f..8d4efc8314cc 100644
--- a/client/src/components/JobMetrics/CarbonEmissions/CarbonEmissions.vue
+++ b/client/src/components/JobMetrics/CarbonEmissions/CarbonEmissions.vue
@@ -274,7 +274,7 @@ function getEnergyNeededText(energyNeededInKiloWattHours: number) {
 
 <template v-if="carbonEmissions && carbonEmissionsComparisons">
     <div class="mt-4">
-        <Heading h2 separator size="md" inline collapsible :collapsed="toggled" @click="toggle()">
+        <Heading h2 separator size="md" inline :collapse="toggled ? 'closed' : 'open'" @click="toggle()">
             Carbon Footprint
         </Heading>
 

From 90f3003f96b161e62d8fbe159ee6f06f5ef5a4b0 Mon Sep 17 00:00:00 2001
From: Dannon <dannon.baker@gmail.com>
Date: Fri, 10 Nov 2023 06:18:50 -0500
Subject: [PATCH 09/21] Apply suggestions from code review

Co-authored-by: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
---
 client/src/components/Common/Heading.vue   |  2 +-
 client/src/composables/persistentToggle.ts | 13 ++++---------
 2 files changed, 5 insertions(+), 10 deletions(-)

diff --git a/client/src/components/Common/Heading.vue b/client/src/components/Common/Heading.vue
index 873c5478a22a..a82885d59418 100644
--- a/client/src/components/Common/Heading.vue
+++ b/client/src/components/Common/Heading.vue
@@ -65,7 +65,7 @@ const element = computed(() => {
             sizeClass,
             props.bold ? 'font-weight-bold' : '',
             props.inline ? 'inline' : '',
-            props.collapsible ? 'collapsible' : '',
+            collapsible ? 'collapsible' : '',
         ]"
         @click="$emit('click')">
         <FontAwesomeIcon v-if="props.icon" :icon="props.icon" />
diff --git a/client/src/composables/persistentToggle.ts b/client/src/composables/persistentToggle.ts
index 154f4c2b4a42..a9c0920304d9 100644
--- a/client/src/composables/persistentToggle.ts
+++ b/client/src/composables/persistentToggle.ts
@@ -1,4 +1,6 @@
-import { type Ref, ref, watch } from "vue";
+import { type Ref } from "vue";
+
+import { useUserLocalStorage } from "./userLocalStorage";
 
 interface ToggleStateInterface {
     toggled: Ref<boolean>;
@@ -7,14 +9,7 @@ interface ToggleStateInterface {
 
 export function usePersistentToggle(uniqueId: string): ToggleStateInterface {
     const localStorageKey = `toggle-state-${uniqueId}`;
-
-    // Retrieve the toggled state from localStorage if available, otherwise default to false
-    const toggled = ref<boolean>(localStorage.getItem(localStorageKey) === "true");
-
-    // Watch for changes in the toggled state and persist them to localStorage
-    watch(toggled, (newVal: boolean) => {
-        localStorage.setItem(localStorageKey, String(newVal));
-    });
+    const toggled = useUserLocalStorage(localStorageKey, true);
 
     // Expose a function for toggling state
     const toggle = () => {

From 281aa57be60a99095945d0276bb5c9c618947926 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 10 Nov 2023 13:47:30 -0500
Subject: [PATCH 10/21] Shift collapse toggle indicator before Header slot
 contents.

---
 client/src/components/Common/Heading.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Common/Heading.vue b/client/src/components/Common/Heading.vue
index a82885d59418..8f069c7b5591 100644
--- a/client/src/components/Common/Heading.vue
+++ b/client/src/components/Common/Heading.vue
@@ -52,8 +52,8 @@ const element = computed(() => {
             :is="element"
             :class="[sizeClass, props.bold ? 'font-weight-bold' : '', collapsible ? 'collapsible' : '']"
             @click="$emit('click')">
-            <slot />
             <FontAwesomeIcon v-if="collapsible" :icon="collapsed ? 'chevron-down' : 'chevron-up'" />
+            <slot />
         </component>
         <div class="stripe"></div>
     </div>
@@ -69,8 +69,8 @@ const element = computed(() => {
         ]"
         @click="$emit('click')">
         <FontAwesomeIcon v-if="props.icon" :icon="props.icon" />
-        <slot />
         <FontAwesomeIcon v-if="collapsible" :icon="collapsed ? 'chevron-down' : 'chevron-up'" />
+        <slot />
     </component>
 </template>
 

From 36179559a6810ee17a990b15bd23f54bd4e793f7 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 10 Nov 2023 14:27:27 -0500
Subject: [PATCH 11/21] Swap to the double chevron we use elsewhere, use a
 link-variant button.  The click bubbles up to the parent, so the header is
 fully clickable and the button is tab navigable for accessibility.

---
 client/src/components/Common/Heading.vue | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Common/Heading.vue b/client/src/components/Common/Heading.vue
index 8f069c7b5591..57d909e128ef 100644
--- a/client/src/components/Common/Heading.vue
+++ b/client/src/components/Common/Heading.vue
@@ -52,7 +52,10 @@ const element = computed(() => {
             :is="element"
             :class="[sizeClass, props.bold ? 'font-weight-bold' : '', collapsible ? 'collapsible' : '']"
             @click="$emit('click')">
-            <FontAwesomeIcon v-if="collapsible" :icon="collapsed ? 'chevron-down' : 'chevron-up'" />
+            <b-button v-if="collapsible" variant="link" size="sm">
+                <icon v-if="collapsed" fixed-width icon="angle-double-down" />
+                <icon v-else fixed-width icon="angle-double-up" />
+            </b-button>
             <slot />
         </component>
         <div class="stripe"></div>
@@ -68,8 +71,11 @@ const element = computed(() => {
             collapsible ? 'collapsible' : '',
         ]"
         @click="$emit('click')">
+        <b-button v-if="collapsible" variant="link" size="sm">
+            <icon v-if="collapsed" fixed-width icon="angle-double-down" />
+            <icon v-else fixed-width icon="angle-double-up" />
+        </b-button>
         <FontAwesomeIcon v-if="props.icon" :icon="props.icon" />
-        <FontAwesomeIcon v-if="collapsible" :icon="collapsed ? 'chevron-down' : 'chevron-up'" />
         <slot />
     </component>
 </template>

From 228a3ac793fb9b36a3aab6b5099ea2cebc114a06 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 10 Nov 2023 14:36:53 -0500
Subject: [PATCH 12/21] Drop invalid/unused prop on awsestimate.

---
 client/src/components/JobMetrics/JobMetrics.vue | 1 -
 1 file changed, 1 deletion(-)

diff --git a/client/src/components/JobMetrics/JobMetrics.vue b/client/src/components/JobMetrics/JobMetrics.vue
index accbc853642e..469dc3062e73 100644
--- a/client/src/components/JobMetrics/JobMetrics.vue
+++ b/client/src/components/JobMetrics/JobMetrics.vue
@@ -203,7 +203,6 @@ const estimatedServerInstance = computed(() => {
         <AwsEstimate
             v-if="jobRuntimeInSeconds && coresAllocated && ec2Instances && shouldShowAwsEstimate"
             :ec2-instances="ec2Instances"
-            :should-show-aws-estimate="shouldShowAwsEstimate"
             :job-runtime-in-seconds="jobRuntimeInSeconds"
             :cores-allocated="coresAllocated"
             :memory-allocated-in-mebibyte="memoryAllocatedInMebibyte" />

From 805b675c25bc0d219d9026b27d34ef448d565016 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 5 Mar 2024 09:39:23 -0500
Subject: [PATCH 13/21] Swap default toggle state to 'not toggled', adjust
 awsestimate

---
 client/src/composables/persistentToggle.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/composables/persistentToggle.ts b/client/src/composables/persistentToggle.ts
index a9c0920304d9..3a1247dbb916 100644
--- a/client/src/composables/persistentToggle.ts
+++ b/client/src/composables/persistentToggle.ts
@@ -9,7 +9,7 @@ interface ToggleStateInterface {
 
 export function usePersistentToggle(uniqueId: string): ToggleStateInterface {
     const localStorageKey = `toggle-state-${uniqueId}`;
-    const toggled = useUserLocalStorage(localStorageKey, true);
+    const toggled = useUserLocalStorage(localStorageKey, false);
 
     // Expose a function for toggling state
     const toggle = () => {

From fb34f0f9d362e21811b225bcf4801fd57170f4f9 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 5 Mar 2024 15:18:30 -0500
Subject: [PATCH 14/21] Use first column for toggle when separator+collapsible

---
 client/src/components/Common/Heading.vue | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/client/src/components/Common/Heading.vue b/client/src/components/Common/Heading.vue
index 57d909e128ef..cb46df1b3c7c 100644
--- a/client/src/components/Common/Heading.vue
+++ b/client/src/components/Common/Heading.vue
@@ -47,15 +47,15 @@ const element = computed(() => {
 
 <template>
     <div v-if="props.separator" class="separator heading">
-        <div class="stripe"></div>
+        <b-button v-if="collapsible" variant="link" size="sm" @click="$emit('click')">
+            <icon v-if="collapsed" fixed-width icon="angle-double-down" />
+            <icon v-else fixed-width icon="angle-double-up" />
+        </b-button>
+        <div v-else class="stripe"></div>
         <component
             :is="element"
             :class="[sizeClass, props.bold ? 'font-weight-bold' : '', collapsible ? 'collapsible' : '']"
             @click="$emit('click')">
-            <b-button v-if="collapsible" variant="link" size="sm">
-                <icon v-if="collapsed" fixed-width icon="angle-double-down" />
-                <icon v-else fixed-width icon="angle-double-up" />
-            </b-button>
             <slot />
         </component>
         <div class="stripe"></div>

From 4a6958e059fd9ba25d226bdcfcae59594d401207 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 24 Apr 2024 16:43:34 +0200
Subject: [PATCH 15/21] Refactoring + stronger type annotations in file sources

---
 lib/galaxy/files/__init__.py               |  61 ++++++++---
 lib/galaxy/files/sources/__init__.py       | 114 ++++++++++++++++-----
 lib/galaxy/files/sources/_pyfilesystem2.py |  36 +++++--
 lib/galaxy/files/sources/_rdm.py           |   4 +-
 lib/galaxy/files/sources/base64.py         |  15 ++-
 lib/galaxy/files/sources/drs.py            |  19 +++-
 lib/galaxy/files/sources/ftp.py            |  16 ++-
 lib/galaxy/files/sources/http.py           |  15 ++-
 lib/galaxy/files/sources/invenio.py        |  12 ++-
 lib/galaxy/files/sources/posix.py          |  34 ++++--
 lib/galaxy/files/sources/s3fs.py           |  34 ++++--
 lib/galaxy/files/sources/util.py           |   4 +-
 lib/galaxy/job_execution/setup.py          |   6 +-
 lib/galaxy/jobs/__init__.py                |   4 +-
 lib/galaxy/managers/remote_files.py        |   8 +-
 lib/galaxy/model/store/__init__.py         |   6 +-
 lib/galaxy/tools/parameters/basic.py       |   4 +-
 test/unit/files/_util.py                   |  46 +++++++--
 18 files changed, 329 insertions(+), 109 deletions(-)

diff --git a/lib/galaxy/files/__init__.py b/lib/galaxy/files/__init__.py
index f58f158ee38c..6ddf924f4089 100644
--- a/lib/galaxy/files/__init__.py
+++ b/lib/galaxy/files/__init__.py
@@ -3,10 +3,12 @@
 from collections import defaultdict
 from typing import (
     Any,
+    Callable,
     Dict,
     List,
     NamedTuple,
     Optional,
+    Protocol,
     Set,
 )
 
@@ -121,7 +123,7 @@ def get_file_source_path(self, uri):
         path = file_source.to_relative_path(uri)
         return FileSourcePath(file_source, path)
 
-    def validate_uri_root(self, uri: str, user_context: "ProvidesUserFileSourcesUserContext"):
+    def validate_uri_root(self, uri: str, user_context: "FileSourcesUserContext"):
         # validate a URI against Galaxy's configuration, environment, and the current
         # user. Throw appropriate exception if there is a problem with the files source
         # referenced by the URI.
@@ -164,7 +166,7 @@ def looks_like_uri(self, path_or_uri):
     def plugins_to_dict(
         self,
         for_serialization: bool = False,
-        user_context: Optional["FileSourceDictifiable"] = None,
+        user_context: "OptionalUserContext" = None,
         browsable_only: Optional[bool] = False,
         include_kind: Optional[Set[PluginKind]] = None,
         exclude_kind: Optional[Set[PluginKind]] = None,
@@ -183,9 +185,7 @@ def plugins_to_dict(
             rval.append(el)
         return rval
 
-    def to_dict(
-        self, for_serialization: bool = False, user_context: Optional["FileSourceDictifiable"] = None
-    ) -> Dict[str, Any]:
+    def to_dict(self, for_serialization: bool = False, user_context: "OptionalUserContext" = None) -> Dict[str, Any]:
         return {
             "file_sources": self.plugins_to_dict(for_serialization=for_serialization, user_context=user_context),
             "config": self._file_sources_config.to_dict(),
@@ -224,30 +224,59 @@ def __init__(
         super().__init__(FileSourcePluginsConfig())
 
 
-class FileSourceDictifiable(Dictifiable):
+class DictifiableFilesSourceContext(Protocol):
+    @property
+    def role_names(self) -> Set[str]: ...
+
+    @property
+    def group_names(self) -> Set[str]: ...
+
+    @property
+    def file_sources(self) -> ConfiguredFileSources: ...
+
+    def to_dict(
+        self, view: str = "collection", value_mapper: Optional[Dict[str, Callable]] = None
+    ) -> Dict[str, Any]: ...
+
+
+class FileSourceDictifiable(Dictifiable, DictifiableFilesSourceContext):
     dict_collection_visible_keys = ("email", "username", "ftp_dir", "preferences", "is_admin")
 
-    def to_dict(self, view="collection", value_mapper=None):
+    def to_dict(self, view="collection", value_mapper: Optional[Dict[str, Callable]] = None) -> Dict[str, Any]:
         rval = super().to_dict(view=view, value_mapper=value_mapper)
         rval["role_names"] = list(self.role_names)
         rval["group_names"] = list(self.group_names)
         return rval
 
+
+class FileSourcesUserContext(DictifiableFilesSourceContext, Protocol):
+
     @property
-    def role_names(self) -> Set[str]:
-        raise NotImplementedError
+    def email(self) -> str: ...
 
     @property
-    def group_names(self) -> Set[str]:
-        raise NotImplementedError
+    def username(self) -> str: ...
 
     @property
-    def file_sources(self):
-        """Return other filesources available in the system, for chained filesource resolution"""
-        raise NotImplementedError
+    def ftp_dir(self) -> str: ...
+
+    @property
+    def preferences(self) -> Dict[str, Any]: ...
+
+    @property
+    def is_admin(self) -> bool: ...
+
+    @property
+    def user_vault(self) -> Dict[str, Any]: ...
+
+    @property
+    def app_vault(self) -> Dict[str, Any]: ...
+
+
+OptionalUserContext = Optional[FileSourcesUserContext]
 
 
-class ProvidesUserFileSourcesUserContext(FileSourceDictifiable):
+class ProvidesFileSourcesUserContext(FileSourcesUserContext, FileSourceDictifiable):
     """Implement a FileSourcesUserContext from a Galaxy ProvidesUserContext (e.g. trans)."""
 
     def __init__(self, trans, **kwargs):
@@ -306,7 +335,7 @@ def file_sources(self):
         return self.trans.app.file_sources
 
 
-class DictFileSourcesUserContext(FileSourceDictifiable):
+class DictFileSourcesUserContext(FileSourcesUserContext, FileSourceDictifiable):
     def __init__(self, **kwd):
         self._kwd = kwd
 
diff --git a/lib/galaxy/files/sources/__init__.py b/lib/galaxy/files/sources/__init__.py
index c0a79e7abe67..ae5a59299d78 100644
--- a/lib/galaxy/files/sources/__init__.py
+++ b/lib/galaxy/files/sources/__init__.py
@@ -9,8 +9,11 @@
 from typing import (
     Any,
     ClassVar,
+    List,
     Optional,
     Set,
+    TYPE_CHECKING,
+    Union,
 )
 
 from typing_extensions import (
@@ -33,6 +36,12 @@
 DEFAULT_SCHEME = "gxfiles"
 DEFAULT_WRITABLE = False
 
+if TYPE_CHECKING:
+    from galaxy.files import (
+        FileSourcesUserContext,
+        OptionalUserContext,
+    )
+
 
 class PluginKind(str, Enum):
     """Enum to distinguish between different kinds or categories of plugins."""
@@ -140,6 +149,9 @@ class RemoteFile(RemoteEntry, TFileClass):
     ctime: str
 
 
+AnyRemoteEntry = Union[RemoteDirectory, RemoteFile]
+
+
 class SingleFileSource(metaclass=abc.ABCMeta):
     """
     Represents a protocol handler for a single remote file that can be read by or written to by Galaxy.
@@ -160,12 +172,16 @@ def get_writable(self) -> bool:
         """Return a boolean indicating whether this target is writable."""
 
     @abc.abstractmethod
-    def user_has_access(self, user_context) -> bool:
+    def user_has_access(self, user_context: "OptionalUserContext") -> bool:
         """Return a boolean indicating whether the user can access the FileSource."""
 
     @abc.abstractmethod
     def realize_to(
-        self, source_path: str, native_path: str, user_context=None, opts: Optional[FilesSourceOptions] = None
+        self,
+        source_path: str,
+        native_path: str,
+        user_context: "OptionalUserContext" = None,
+        opts: Optional[FilesSourceOptions] = None,
     ):
         """Realize source path (relative to uri root) to local file system path.
 
@@ -174,14 +190,18 @@ def realize_to(
         :param native_path: local path to write to. e.g. `/tmp/myfile.txt`
         :type native_path: str
         :param user_context: A user context , defaults to None
-        :type user_context: FileSourceDictifiable, optional
+        :type user_context: OptionalUserContext, optional
         :param opts: A set of options to exercise additional control over the realize_to method. Filesource specific, defaults to None
         :type opts: Optional[FilesSourceOptions], optional
         """
 
     @abc.abstractmethod
     def write_from(
-        self, target_path: str, native_path: str, user_context=None, opts: Optional[FilesSourceOptions] = None
+        self,
+        target_path: str,
+        native_path: str,
+        user_context: "OptionalUserContext" = None,
+        opts: Optional[FilesSourceOptions] = None,
     ):
         """Write file at native path to target_path (relative to uri root).
 
@@ -232,7 +252,7 @@ def to_relative_path(self, url: str) -> str:
         returned unchanged."""
 
     @abc.abstractmethod
-    def to_dict(self, for_serialization=False, user_context=None) -> FilesSourceProperties:
+    def to_dict(self, for_serialization=False, user_context: "OptionalUserContext" = None) -> FilesSourceProperties:
         """Return a dictified representation of this FileSource instance.
 
         If ``user_context`` is supplied, properties should be written so user
@@ -254,7 +274,13 @@ def get_uri_root(self) -> str:
         """Return a prefix for the root (e.g. gxfiles://prefix/)."""
 
     @abc.abstractmethod
-    def list(self, path="/", recursive=False, user_context=None, opts: Optional[FilesSourceOptions] = None) -> dict:
+    def list(
+        self,
+        path="/",
+        recursive=False,
+        user_context: "OptionalUserContext" = None,
+        opts: Optional[FilesSourceOptions] = None,
+    ) -> List[AnyRemoteEntry]:
         """Return dictionary of 'Directory's and 'File's."""
 
 
@@ -287,7 +313,7 @@ def get_scheme(self) -> str:
     def get_writable(self) -> bool:
         return self.writable
 
-    def user_has_access(self, user_context) -> bool:
+    def user_has_access(self, user_context: "OptionalUserContext") -> bool:
         if user_context is None and self.user_context_required:
             return False
         return (
@@ -315,7 +341,7 @@ def score_url_match(self, url: str) -> int:
         root = self.get_uri_root()
         return len(root) if root in url else 0
 
-    def uri_from_path(self, path) -> str:
+    def uri_from_path(self, path: str) -> str:
         uri_root = self.get_uri_root()
         return uri_join(uri_root, path)
 
@@ -335,7 +361,7 @@ def _parse_common_config_opts(self, kwd: FilesSourceProperties):
         kwd.pop("browsable", None)
         return kwd
 
-    def to_dict(self, for_serialization=False, user_context=None) -> FilesSourceProperties:
+    def to_dict(self, for_serialization=False, user_context: "OptionalUserContext" = None) -> FilesSourceProperties:
         rval: FilesSourceProperties = {
             "id": self.id,
             "type": self.plugin_type,
@@ -361,27 +387,45 @@ def to_dict_time(self, ctime):
             return ctime.strftime("%m/%d/%Y %I:%M:%S %p")
 
     @abc.abstractmethod
-    def _serialization_props(self, user_context=None) -> FilesSourceProperties:
+    def _serialization_props(self, user_context: "OptionalUserContext" = None) -> FilesSourceProperties:
         """Serialize properties needed to recover plugin configuration.
         Used in to_dict method if for_serialization is True.
         """
 
-    def list(self, path="/", recursive=False, user_context=None, opts: Optional[FilesSourceOptions] = None):
+    def list(
+        self,
+        path="/",
+        recursive=False,
+        user_context: "OptionalUserContext" = None,
+        opts: Optional[FilesSourceOptions] = None,
+    ) -> List[AnyRemoteEntry]:
         self._check_user_access(user_context)
         return self._list(path, recursive, user_context, opts)
 
-    def _list(self, path="/", recursive=False, user_context=None, opts: Optional[FilesSourceOptions] = None):
+    def _list(
+        self,
+        path="/",
+        recursive=False,
+        user_context: "OptionalUserContext" = None,
+        opts: Optional[FilesSourceOptions] = None,
+    ):
         pass
 
     def create_entry(
-        self, entry_data: EntryData, user_context=None, opts: Optional[FilesSourceOptions] = None
+        self,
+        entry_data: EntryData,
+        user_context: "OptionalUserContext" = None,
+        opts: Optional[FilesSourceOptions] = None,
     ) -> Entry:
         self._ensure_writeable()
         self._check_user_access(user_context)
         return self._create_entry(entry_data, user_context, opts)
 
     def _create_entry(
-        self, entry_data: EntryData, user_context=None, opts: Optional[FilesSourceOptions] = None
+        self,
+        entry_data: EntryData,
+        user_context: "OptionalUserContext" = None,
+        opts: Optional[FilesSourceOptions] = None,
     ) -> Entry:
         """Create a new entry (directory) in the file source.
 
@@ -390,21 +434,45 @@ def _create_entry(
         """
         raise NotImplementedError()
 
-    def write_from(self, target_path, native_path, user_context=None, opts: Optional[FilesSourceOptions] = None):
+    def write_from(
+        self,
+        target_path: str,
+        native_path: str,
+        user_context: "OptionalUserContext" = None,
+        opts: Optional[FilesSourceOptions] = None,
+    ):
         self._ensure_writeable()
         self._check_user_access(user_context)
         self._write_from(target_path, native_path, user_context=user_context, opts=opts)
 
     @abc.abstractmethod
-    def _write_from(self, target_path, native_path, user_context=None, opts: Optional[FilesSourceOptions] = None):
+    def _write_from(
+        self,
+        target_path: str,
+        native_path: str,
+        user_context: "OptionalUserContext" = None,
+        opts: Optional[FilesSourceOptions] = None,
+    ):
         pass
 
-    def realize_to(self, source_path, native_path, user_context=None, opts: Optional[FilesSourceOptions] = None):
+    def realize_to(
+        self,
+        source_path: str,
+        native_path: str,
+        user_context: "OptionalUserContext" = None,
+        opts: Optional[FilesSourceOptions] = None,
+    ):
         self._check_user_access(user_context)
         self._realize_to(source_path, native_path, user_context, opts=opts)
 
     @abc.abstractmethod
-    def _realize_to(self, source_path, native_path, user_context=None, opts: Optional[FilesSourceOptions] = None):
+    def _realize_to(
+        self,
+        source_path: str,
+        native_path: str,
+        user_context: "OptionalUserContext" = None,
+        opts: Optional[FilesSourceOptions] = None,
+    ):
         pass
 
     def _ensure_writeable(self):
@@ -420,7 +488,7 @@ def _check_user_access(self, user_context):
         if user_context is not None and not self.user_has_access(user_context):
             raise ItemAccessibilityException(f"User {user_context.username} has no access to file source.")
 
-    def _evaluate_prop(self, prop_val: Any, user_context):
+    def _evaluate_prop(self, prop_val: Any, user_context: "OptionalUserContext"):
         rval = prop_val
         if isinstance(prop_val, str) and "$" in prop_val:
             template_context = dict(
@@ -436,12 +504,12 @@ def _evaluate_prop(self, prop_val: Any, user_context):
 
         return rval
 
-    def _user_has_required_roles(self, user_context) -> bool:
+    def _user_has_required_roles(self, user_context: "FileSourcesUserContext") -> bool:
         if self.requires_roles:
             return self._evaluate_security_rules(self.requires_roles, user_context.role_names)
         return True
 
-    def _user_has_required_groups(self, user_context) -> bool:
+    def _user_has_required_groups(self, user_context: "FileSourcesUserContext") -> bool:
         if self.requires_groups:
             return self._evaluate_security_rules(self.requires_groups, user_context.group_names)
         return True
@@ -464,7 +532,7 @@ def _get_error_msg_for(rule_name: str) -> str:
             raise ConfigurationError(_get_error_msg_for("requires_groups"))
 
 
-def uri_join(*args):
+def uri_join(*args: str) -> str:
     # url_join doesn't work with non-standard scheme
     if "://" in (arg0 := args[0]):
         scheme, path = arg0.split("://", 1)
@@ -474,6 +542,6 @@ def uri_join(*args):
     return rval
 
 
-def slash_join(*args):
+def slash_join(*args: str) -> str:
     # https://codereview.stackexchange.com/questions/175421/joining-strings-to-form-a-url
     return "/".join(arg.strip("/") for arg in args)
diff --git a/lib/galaxy/files/sources/_pyfilesystem2.py b/lib/galaxy/files/sources/_pyfilesystem2.py
index efdb5ac79ca8..671753368aa3 100644
--- a/lib/galaxy/files/sources/_pyfilesystem2.py
+++ b/lib/galaxy/files/sources/_pyfilesystem2.py
@@ -3,9 +3,7 @@
 import logging
 import os
 from typing import (
-    Any,
     ClassVar,
-    Dict,
     List,
     Optional,
     Type,
@@ -20,7 +18,9 @@
     AuthenticationRequired,
     MessageException,
 )
+from galaxy.files import OptionalUserContext
 from . import (
+    AnyRemoteEntry,
     BaseFilesSource,
     FilesSourceOptions,
     FilesSourceProperties,
@@ -42,15 +42,21 @@ def __init__(self, **kwd: Unpack[FilesSourceProperties]):
         self._props = props
 
     @abc.abstractmethod
-    def _open_fs(self, user_context=None, opts: Optional[FilesSourceOptions] = None):
+    def _open_fs(self, user_context: OptionalUserContext = None, opts: Optional[FilesSourceOptions] = None):
         """Subclasses must instantiate a PyFilesystem2 handle for this file system."""
 
-    def _list(self, path="/", recursive=False, user_context=None, opts: Optional[FilesSourceOptions] = None):
+    def _list(
+        self,
+        path="/",
+        recursive=False,
+        user_context: OptionalUserContext = None,
+        opts: Optional[FilesSourceOptions] = None,
+    ) -> List[AnyRemoteEntry]:
         """Return dictionary of 'Directory's and 'File's."""
         try:
             with self._open_fs(user_context=user_context, opts=opts) as h:
                 if recursive:
-                    res: List[Dict[str, Any]] = []
+                    res: List[AnyRemoteEntry] = []
                     for p, dirs, files in h.walk(path):
                         to_dict = functools.partial(self._resource_info_to_dict, p)
                         res.extend(map(to_dict, dirs))
@@ -67,11 +73,23 @@ def _list(self, path="/", recursive=False, user_context=None, opts: Optional[Fil
         except fs.errors.FSError as e:
             raise MessageException(f"Problem listing file source path {path}. Reason: {e}") from e
 
-    def _realize_to(self, source_path, native_path, user_context=None, opts: Optional[FilesSourceOptions] = None):
+    def _realize_to(
+        self,
+        source_path: str,
+        native_path: str,
+        user_context: OptionalUserContext = None,
+        opts: Optional[FilesSourceOptions] = None,
+    ):
         with open(native_path, "wb") as write_file:
             self._open_fs(user_context=user_context, opts=opts).download(source_path, write_file)
 
-    def _write_from(self, target_path, native_path, user_context=None, opts: Optional[FilesSourceOptions] = None):
+    def _write_from(
+        self,
+        target_path: str,
+        native_path: str,
+        user_context: OptionalUserContext = None,
+        opts: Optional[FilesSourceOptions] = None,
+    ):
         with open(native_path, "rb") as read_file:
             openfs = self._open_fs(user_context=user_context, opts=opts)
             dirname = fs.path.dirname(target_path)
@@ -79,7 +97,7 @@ def _write_from(self, target_path, native_path, user_context=None, opts: Optiona
                 openfs.makedirs(dirname)
             openfs.upload(target_path, read_file)
 
-    def _resource_info_to_dict(self, dir_path, resource_info):
+    def _resource_info_to_dict(self, dir_path, resource_info) -> AnyRemoteEntry:
         name = resource_info.name
         path = os.path.join(dir_path, name)
         uri = self.uri_from_path(path)
@@ -96,7 +114,7 @@ def _resource_info_to_dict(self, dir_path, resource_info):
                 "path": path,
             }
 
-    def _serialization_props(self, user_context=None):
+    def _serialization_props(self, user_context: OptionalUserContext = None):
         effective_props = {}
         for key, val in self._props.items():
             effective_props[key] = self._evaluate_prop(val, user_context=user_context)
diff --git a/lib/galaxy/files/sources/_rdm.py b/lib/galaxy/files/sources/_rdm.py
index 8cd6d8523e26..3c3400c13f8d 100644
--- a/lib/galaxy/files/sources/_rdm.py
+++ b/lib/galaxy/files/sources/_rdm.py
@@ -8,7 +8,7 @@
 from typing_extensions import Unpack
 
 from galaxy.exceptions import AuthenticationRequired
-from galaxy.files import ProvidesUserFileSourcesUserContext
+from galaxy.files import OptionalUserContext
 from galaxy.files.sources import (
     BaseFilesSource,
     FilesSourceProperties,
@@ -19,8 +19,6 @@
 
 log = logging.getLogger(__name__)
 
-OptionalUserContext = Optional[ProvidesUserFileSourcesUserContext]
-
 
 class RDMFilesSourceProperties(FilesSourceProperties):
     url: str
diff --git a/lib/galaxy/files/sources/base64.py b/lib/galaxy/files/sources/base64.py
index 98f48ef287ed..968ae499ac5f 100644
--- a/lib/galaxy/files/sources/base64.py
+++ b/lib/galaxy/files/sources/base64.py
@@ -4,6 +4,7 @@
 
 from typing_extensions import Unpack
 
+from galaxy.files import OptionalUserContext
 from . import (
     BaseFilesSource,
     FilesSourceOptions,
@@ -30,14 +31,22 @@ def __init__(self, **kwd: Unpack[FilesSourceProperties]):
         self._props = props
 
     def _realize_to(
-        self, source_path: str, native_path: str, user_context=None, opts: Optional[FilesSourceOptions] = None
+        self,
+        source_path: str,
+        native_path: str,
+        user_context: OptionalUserContext = None,
+        opts: Optional[FilesSourceOptions] = None,
     ):
         with open(native_path, "wb") as temp:
             temp.write(base64.b64decode(source_path[len("base64://") :]))
             temp.flush()
 
     def _write_from(
-        self, target_path: str, native_path: str, user_context=None, opts: Optional[FilesSourceOptions] = None
+        self,
+        target_path: str,
+        native_path: str,
+        user_context: OptionalUserContext = None,
+        opts: Optional[FilesSourceOptions] = None,
     ):
         raise NotImplementedError()
 
@@ -47,7 +56,7 @@ def score_url_match(self, url: str):
         else:
             return 0
 
-    def _serialization_props(self, user_context=None):
+    def _serialization_props(self, user_context: OptionalUserContext = None):
         effective_props = {}
         for key, val in self._props.items():
             effective_props[key] = self._evaluate_prop(val, user_context=user_context)
diff --git a/lib/galaxy/files/sources/drs.py b/lib/galaxy/files/sources/drs.py
index 590bfd4666b3..00f1a3643385 100644
--- a/lib/galaxy/files/sources/drs.py
+++ b/lib/galaxy/files/sources/drs.py
@@ -8,6 +8,7 @@
 
 from typing_extensions import Unpack
 
+from galaxy.files import OptionalUserContext
 from . import (
     BaseFilesSource,
     FilesSourceOptions,
@@ -48,7 +49,13 @@ def __init__(self, **kwd: Unpack[FilesSourceProperties]):
     def _allowlist(self):
         return self._file_sources_config.fetch_url_allowlist
 
-    def _realize_to(self, source_path, native_path, user_context=None, opts: Optional[FilesSourceOptions] = None):
+    def _realize_to(
+        self,
+        source_path: str,
+        native_path: str,
+        user_context: OptionalUserContext = None,
+        opts: Optional[FilesSourceOptions] = None,
+    ):
         props = self._serialization_props(user_context)
         headers = props.pop("http_headers", {}) or {}
         fetch_drs_to_file(
@@ -60,7 +67,13 @@ def _realize_to(self, source_path, native_path, user_context=None, opts: Optiona
             force_http=self._force_http,
         )
 
-    def _write_from(self, target_path, native_path, user_context=None, opts: Optional[FilesSourceOptions] = None):
+    def _write_from(
+        self,
+        target_path: str,
+        native_path: str,
+        user_context: OptionalUserContext = None,
+        opts: Optional[FilesSourceOptions] = None,
+    ):
         raise NotImplementedError()
 
     def score_url_match(self, url: str):
@@ -69,7 +82,7 @@ def score_url_match(self, url: str):
         else:
             return 0
 
-    def _serialization_props(self, user_context=None) -> DRSFilesSourceProperties:
+    def _serialization_props(self, user_context: OptionalUserContext = None) -> DRSFilesSourceProperties:
         effective_props = {}
         for key, val in self._props.items():
             effective_props[key] = self._evaluate_prop(val, user_context=user_context)
diff --git a/lib/galaxy/files/sources/ftp.py b/lib/galaxy/files/sources/ftp.py
index f2877f648392..5df4066e615d 100644
--- a/lib/galaxy/files/sources/ftp.py
+++ b/lib/galaxy/files/sources/ftp.py
@@ -1,5 +1,7 @@
 import urllib.parse
 
+from galaxy.files import OptionalUserContext
+
 try:
     from fs.ftpfs import FTPFS
 except ImportError:
@@ -30,14 +32,18 @@ class FtpFilesSource(PyFilesystem2FilesSource):
     required_module = FTPFS
     required_package = "fs.ftpfs"
 
-    def _open_fs(self, user_context=None, opts: Optional[FilesSourceOptions] = None):
+    def _open_fs(self, user_context: OptionalUserContext = None, opts: Optional[FilesSourceOptions] = None):
         props = self._serialization_props(user_context)
         extra_props: FTPFilesSourceProperties = cast(FTPFilesSourceProperties, opts.extra_props or {} if opts else {})
         handle = FTPFS(**{**props, **extra_props})
         return handle
 
     def _realize_to(
-        self, source_path: str, native_path: str, user_context=None, opts: Optional[FilesSourceOptions] = None
+        self,
+        source_path: str,
+        native_path: str,
+        user_context: OptionalUserContext = None,
+        opts: Optional[FilesSourceOptions] = None,
     ):
         extra_props: FTPFilesSourceProperties
         if opts and opts.extra_props:
@@ -49,7 +55,11 @@ def _realize_to(
         super()._realize_to(path, native_path, user_context=user_context, opts=opts)
 
     def _write_from(
-        self, target_path: str, native_path: str, user_context=None, opts: Optional[FilesSourceOptions] = None
+        self,
+        target_path: str,
+        native_path: str,
+        user_context: OptionalUserContext = None,
+        opts: Optional[FilesSourceOptions] = None,
     ):
         extra_props: FTPFilesSourceProperties
         if opts and opts.extra_props:
diff --git a/lib/galaxy/files/sources/http.py b/lib/galaxy/files/sources/http.py
index 0e538baec1dc..ed4ae1ea8d33 100644
--- a/lib/galaxy/files/sources/http.py
+++ b/lib/galaxy/files/sources/http.py
@@ -10,6 +10,7 @@
 
 from typing_extensions import Unpack
 
+from galaxy.files import OptionalUserContext
 from galaxy.files.uris import validate_non_local
 from galaxy.util import (
     DEFAULT_SOCKET_TIMEOUT,
@@ -56,7 +57,11 @@ def _allowlist(self):
         return self._file_sources_config.fetch_url_allowlist
 
     def _realize_to(
-        self, source_path: str, native_path: str, user_context=None, opts: Optional[FilesSourceOptions] = None
+        self,
+        source_path: str,
+        native_path: str,
+        user_context: OptionalUserContext = None,
+        opts: Optional[FilesSourceOptions] = None,
     ):
         props = self._serialization_props(user_context)
         extra_props: HTTPFilesSourceProperties = cast(HTTPFilesSourceProperties, opts.extra_props or {} if opts else {})
@@ -73,11 +78,15 @@ def _realize_to(
             )
 
     def _write_from(
-        self, target_path: str, native_path: str, user_context=None, opts: Optional[FilesSourceOptions] = None
+        self,
+        target_path: str,
+        native_path: str,
+        user_context: OptionalUserContext = None,
+        opts: Optional[FilesSourceOptions] = None,
     ):
         raise NotImplementedError()
 
-    def _serialization_props(self, user_context=None) -> HTTPFilesSourceProperties:
+    def _serialization_props(self, user_context: OptionalUserContext = None) -> HTTPFilesSourceProperties:
         effective_props = {}
         for key, val in self._props.items():
             effective_props[key] = self._evaluate_prop(val, user_context=user_context)
diff --git a/lib/galaxy/files/sources/invenio.py b/lib/galaxy/files/sources/invenio.py
index 8b237960878c..8406e4630694 100644
--- a/lib/galaxy/files/sources/invenio.py
+++ b/lib/galaxy/files/sources/invenio.py
@@ -4,6 +4,7 @@
 import urllib.request
 from typing import (
     Any,
+    cast,
     Dict,
     List,
     Optional,
@@ -17,7 +18,9 @@
     Unpack,
 )
 
+from galaxy.files import OptionalUserContext
 from galaxy.files.sources import (
+    AnyRemoteEntry,
     DEFAULT_SCHEME,
     Entry,
     EntryData,
@@ -26,7 +29,6 @@
     RemoteFile,
 )
 from galaxy.files.sources._rdm import (
-    OptionalUserContext,
     RDMFilesSource,
     RDMFilesSourceProperties,
     RDMRepositoryInteractor,
@@ -145,13 +147,15 @@ def _list(
         recursive=True,
         user_context: OptionalUserContext = None,
         opts: Optional[FilesSourceOptions] = None,
-    ):
+    ) -> List[AnyRemoteEntry]:
         writeable = opts and opts.writeable or False
         is_root_path = path == "/"
         if is_root_path:
-            return self.repository.get_records(writeable, user_context)
+            records = self.repository.get_records(writeable, user_context)
+            return cast(List[AnyRemoteEntry], records)
         record_id = self.get_record_id_from_path(path)
-        return self.repository.get_files_in_record(record_id, writeable, user_context)
+        files = self.repository.get_files_in_record(record_id, writeable, user_context)
+        return cast(List[AnyRemoteEntry], files)
 
     def _create_entry(
         self,
diff --git a/lib/galaxy/files/sources/posix.py b/lib/galaxy/files/sources/posix.py
index a844cf68b553..331dc7860671 100644
--- a/lib/galaxy/files/sources/posix.py
+++ b/lib/galaxy/files/sources/posix.py
@@ -2,8 +2,6 @@
 import os
 import shutil
 from typing import (
-    Any,
-    Dict,
     List,
     Optional,
 )
@@ -11,12 +9,14 @@
 from typing_extensions import Unpack
 
 from galaxy import exceptions
+from galaxy.files import OptionalUserContext
 from galaxy.util.path import (
     safe_contains,
     safe_path,
     safe_walk,
 )
 from . import (
+    AnyRemoteEntry,
     BaseFilesSource,
     FilesSourceOptions,
     FilesSourceProperties,
@@ -53,14 +53,20 @@ def __init__(self, **kwd: Unpack[PosixFilesSourceProperties]):
         self.delete_on_realize = props.get("delete_on_realize", DEFAULT_DELETE_ON_REALIZE)
         self.allow_subdir_creation = props.get("allow_subdir_creation", DEFAULT_ALLOW_SUBDIR_CREATION)
 
-    def _list(self, path="/", recursive=True, user_context=None, opts: Optional[FilesSourceOptions] = None):
+    def _list(
+        self,
+        path="/",
+        recursive=True,
+        user_context: OptionalUserContext = None,
+        opts: Optional[FilesSourceOptions] = None,
+    ) -> List[AnyRemoteEntry]:
         if not self.root:
             raise exceptions.ItemAccessibilityException("Listing files at file:// URLs has been disabled.")
         dir_path = self._to_native_path(path, user_context=user_context)
         if not self._safe_directory(dir_path):
             raise exceptions.ObjectNotFound(f"The specified directory does not exist [{dir_path}].")
         if recursive:
-            res: List[Dict[str, Any]] = []
+            res: List[AnyRemoteEntry] = []
             effective_root = self._effective_root(user_context)
             for p, dirs, files in safe_walk(dir_path, allowlist=self._allowlist):
                 rel_dir = os.path.relpath(p, effective_root)
@@ -74,7 +80,11 @@ def _list(self, path="/", recursive=True, user_context=None, opts: Optional[File
             return list(map(to_dict, res))
 
     def _realize_to(
-        self, source_path: str, native_path: str, user_context=None, opts: Optional[FilesSourceOptions] = None
+        self,
+        source_path: str,
+        native_path: str,
+        user_context: OptionalUserContext = None,
+        opts: Optional[FilesSourceOptions] = None,
     ):
         if not self.root and (not user_context or not user_context.is_admin):
             raise exceptions.ItemAccessibilityException("Writing to file:// URLs has been disabled.")
@@ -94,7 +104,11 @@ def _realize_to(
             shutil.move(source_native_path, native_path)
 
     def _write_from(
-        self, target_path: str, native_path: str, user_context=None, opts: Optional[FilesSourceOptions] = None
+        self,
+        target_path: str,
+        native_path: str,
+        user_context: OptionalUserContext = None,
+        opts: Optional[FilesSourceOptions] = None,
     ):
         effective_root = self._effective_root(user_context)
         target_native_path = self._to_native_path(target_path, user_context=user_context)
@@ -118,16 +132,16 @@ def _write_from(
         shutil.copyfile(native_path, target_native_path_part)
         os.rename(target_native_path_part, target_native_path)
 
-    def _to_native_path(self, source_path: str, user_context=None):
+    def _to_native_path(self, source_path: str, user_context: OptionalUserContext = None):
         source_path = os.path.normpath(source_path)
         if source_path.startswith("/"):
             source_path = source_path[1:]
         return os.path.join(self._effective_root(user_context), source_path)
 
-    def _effective_root(self, user_context=None):
+    def _effective_root(self, user_context: OptionalUserContext = None):
         return self._evaluate_prop(self.root or "/", user_context=user_context)
 
-    def _resource_info_to_dict(self, dir: str, name: str, user_context=None):
+    def _resource_info_to_dict(self, dir: str, name: str, user_context: OptionalUserContext = None) -> AnyRemoteEntry:
         rel_path = os.path.normpath(os.path.join(dir, name))
         full_path = self._to_native_path(rel_path, user_context=user_context)
         uri = self.uri_from_path(rel_path)
@@ -155,7 +169,7 @@ def _safe_directory(self, directory):
             return False
         return True
 
-    def _serialization_props(self, user_context=None) -> PosixFilesSourceProperties:
+    def _serialization_props(self, user_context: OptionalUserContext = None) -> PosixFilesSourceProperties:
         return {
             # abspath needed because will be used by external Python from
             # a job working directory
diff --git a/lib/galaxy/files/sources/s3fs.py b/lib/galaxy/files/sources/s3fs.py
index 687eb1881ea6..d9954ea20b32 100644
--- a/lib/galaxy/files/sources/s3fs.py
+++ b/lib/galaxy/files/sources/s3fs.py
@@ -2,16 +2,16 @@
 import logging
 import os
 from typing import (
-    Any,
     cast,
-    Dict,
     List,
     Optional,
 )
 
 from typing_extensions import Unpack
 
+from galaxy.files import OptionalUserContext
 from . import (
+    AnyRemoteEntry,
     FilesSourceOptions,
     FilesSourceProperties,
 )
@@ -55,13 +55,19 @@ def __init__(self, **kwd: Unpack[S3FsFilesSourceProperties]):
         if self._endpoint_url:
             self._props.update({"client_kwargs": {"endpoint_url": self._endpoint_url}})
 
-    def _list(self, path="/", recursive=True, user_context=None, opts: Optional[FilesSourceOptions] = None):
+    def _list(
+        self,
+        path="/",
+        recursive=True,
+        user_context: OptionalUserContext = None,
+        opts: Optional[FilesSourceOptions] = None,
+    ) -> List[AnyRemoteEntry]:
         _props = self._serialization_props(user_context)
         # we need to pop the 'bucket' here, because the argument is not recognised in a downstream function
         _bucket_name = _props.pop("bucket", "")
         fs = self._open_fs(props=_props, opts=opts)
         if recursive:
-            res: List[Dict[str, Any]] = []
+            res: List[AnyRemoteEntry] = []
             bucket_path = self._bucket_path(_bucket_name, path)
             for p, dirs, files in fs.walk(bucket_path, detail=True):
                 to_dict = functools.partial(self._resource_info_to_dict, p)
@@ -74,14 +80,26 @@ def _list(self, path="/", recursive=True, user_context=None, opts: Optional[File
             to_dict = functools.partial(self._resource_info_to_dict, path)
             return list(map(to_dict, res))
 
-    def _realize_to(self, source_path, native_path, user_context=None, opts: Optional[FilesSourceOptions] = None):
+    def _realize_to(
+        self,
+        source_path: str,
+        native_path: str,
+        user_context: OptionalUserContext = None,
+        opts: Optional[FilesSourceOptions] = None,
+    ):
         _props = self._serialization_props(user_context)
         _bucket_name = _props.pop("bucket", "")
         fs = self._open_fs(props=_props, opts=opts)
         bucket_path = self._bucket_path(_bucket_name, source_path)
         fs.download(bucket_path, native_path)
 
-    def _write_from(self, target_path, native_path, user_context=None, opts: Optional[FilesSourceOptions] = None):
+    def _write_from(
+        self,
+        target_path,
+        native_path,
+        user_context: OptionalUserContext = None,
+        opts: Optional[FilesSourceOptions] = None,
+    ):
         _props = self._serialization_props(user_context)
         _bucket_name = _props.pop("bucket", "")
         fs = self._open_fs(props=_props, opts=opts)
@@ -100,7 +118,7 @@ def _open_fs(self, props: FilesSourceProperties, opts: Optional[FilesSourceOptio
         fs = s3fs.S3FileSystem(**{**props, **extra_props})
         return fs
 
-    def _resource_info_to_dict(self, dir_path: str, resource_info):
+    def _resource_info_to_dict(self, dir_path: str, resource_info) -> AnyRemoteEntry:
         name = os.path.basename(resource_info["name"])
         path = os.path.join(dir_path, name)
         uri = self.uri_from_path(path)
@@ -117,7 +135,7 @@ def _resource_info_to_dict(self, dir_path: str, resource_info):
                 "path": path,
             }
 
-    def _serialization_props(self, user_context=None) -> S3FsFilesSourceProperties:
+    def _serialization_props(self, user_context: OptionalUserContext = None) -> S3FsFilesSourceProperties:
         effective_props = {}
         for key, val in self._props.items():
             effective_props[key] = self._evaluate_prop(val, user_context=user_context)
diff --git a/lib/galaxy/files/sources/util.py b/lib/galaxy/files/sources/util.py
index 0616910b76ff..b43a05e303de 100644
--- a/lib/galaxy/files/sources/util.py
+++ b/lib/galaxy/files/sources/util.py
@@ -12,7 +12,7 @@
 from galaxy import exceptions
 from galaxy.files import (
     ConfiguredFileSources,
-    FileSourceDictifiable,
+    FileSourcesUserContext,
 )
 from galaxy.files.sources import FilesSourceOptions
 from galaxy.files.sources.http import HTTPFilesSourceProperties
@@ -79,7 +79,7 @@ def _get_access_info(obj_url: str, access_method: dict, headers=None) -> Tuple[s
 def fetch_drs_to_file(
     drs_uri: str,
     target_path: TargetPathT,
-    user_context: FileSourceDictifiable,
+    user_context: Optional[FileSourcesUserContext],
     force_http=False,
     retry_options: Optional[RetryOptions] = None,
     headers: Optional[dict] = None,
diff --git a/lib/galaxy/job_execution/setup.py b/lib/galaxy/job_execution/setup.py
index 934dd528e74a..4d2f54842c48 100644
--- a/lib/galaxy/job_execution/setup.py
+++ b/lib/galaxy/job_execution/setup.py
@@ -17,7 +17,7 @@
 from galaxy.files import (
     ConfiguredFileSources,
     DictFileSourcesUserContext,
-    ProvidesUserFileSourcesUserContext,
+    FileSourcesUserContext,
 )
 from galaxy.job_execution.datasets import (
     DatasetPath,
@@ -109,13 +109,13 @@ def __init__(
         check_job_script_integrity_count: int,
         check_job_script_integrity_sleep: float,
         file_sources_dict: Dict[str, Any],
-        user_context: Union[ProvidesUserFileSourcesUserContext, Dict["str", Any]],
+        user_context: Union[FileSourcesUserContext, Dict[str, Any]],
         tool_source: Optional[str] = None,
         tool_source_class: Optional["str"] = "XmlToolSource",
         tool_dir: Optional[str] = None,
         is_task: bool = False,
     ):
-        user_context_instance: Union[ProvidesUserFileSourcesUserContext, DictFileSourcesUserContext]
+        user_context_instance: FileSourcesUserContext
         self.file_sources_dict = file_sources_dict
         if isinstance(user_context, dict):
             user_context_instance = DictFileSourcesUserContext(**user_context, file_sources=self.file_sources)
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 5ba851359c92..302e53c1c3b4 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -38,7 +38,7 @@
     ObjectInvalid,
     ObjectNotFound,
 )
-from galaxy.files import ProvidesUserFileSourcesUserContext
+from galaxy.files import ProvidesFileSourcesUserContext
 from galaxy.job_execution.actions.post import ActionBox
 from galaxy.job_execution.compute_environment import SharedComputeEnvironment
 from galaxy.job_execution.output_collect import (
@@ -1060,7 +1060,7 @@ def job_io(self):
         if self._job_io is None:
             job = self.get_job()
             work_request = WorkRequestContext(self.app, user=job.user, galaxy_session=job.galaxy_session)
-            user_context = ProvidesUserFileSourcesUserContext(work_request)
+            user_context = ProvidesFileSourcesUserContext(work_request)
             tool_source = self.tool and self.tool.tool_source.to_string()
             self._job_io = JobIO(
                 sa_session=self.sa_session,
diff --git a/lib/galaxy/managers/remote_files.py b/lib/galaxy/managers/remote_files.py
index 2be2274dbc70..4abccb8d9229 100644
--- a/lib/galaxy/managers/remote_files.py
+++ b/lib/galaxy/managers/remote_files.py
@@ -10,7 +10,7 @@
 from galaxy.files import (
     ConfiguredFileSources,
     FileSourcePath,
-    ProvidesUserFileSourcesUserContext,
+    ProvidesFileSourcesUserContext,
 )
 from galaxy.files.sources import (
     FilesSourceOptions,
@@ -53,7 +53,7 @@ def index(
     ) -> AnyRemoteFilesListResponse:
         """Returns a list of remote files available to the user."""
 
-        user_file_source_context = ProvidesUserFileSourcesUserContext(user_ctx)
+        user_file_source_context = ProvidesFileSourcesUserContext(user_ctx)
         default_recursive = False
         default_format = RemoteFilesFormat.uri
 
@@ -143,7 +143,7 @@ def get_files_source_plugins(
         exclude_kind: Optional[Set[PluginKind]] = None,
     ):
         """Display plugin information for each of the gxfiles:// URI targets available."""
-        user_file_source_context = ProvidesUserFileSourcesUserContext(user_context)
+        user_file_source_context = ProvidesFileSourcesUserContext(user_context)
         browsable_only = True if browsable_only is None else browsable_only
         plugins_dict = self._file_sources.plugins_to_dict(
             user_context=user_file_source_context,
@@ -160,7 +160,7 @@ def _file_sources(self) -> ConfiguredFileSources:
     def create_entry(self, user_ctx: ProvidesUserContext, entry_data: CreateEntryPayload) -> CreatedEntryResponse:
         """Create an entry (directory or record) in a remote files location."""
         target = entry_data.target
-        user_file_source_context = ProvidesUserFileSourcesUserContext(user_ctx)
+        user_file_source_context = ProvidesFileSourcesUserContext(user_ctx)
         self._file_sources.validate_uri_root(target, user_context=user_file_source_context)
         file_source_path = self._file_sources.get_file_source_path(target)
         file_source = file_source_path.file_source
diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index dbca1f250f33..7033a91ab176 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -57,7 +57,7 @@
 )
 from galaxy.files import (
     ConfiguredFileSources,
-    ProvidesUserFileSourcesUserContext,
+    ProvidesFileSourcesUserContext,
 )
 from galaxy.files.uris import stream_url_to_file
 from galaxy.model.base import (
@@ -1902,7 +1902,7 @@ def __init__(
             sessionless = True
             security = IdEncodingHelper(id_secret="randomdoesntmatter")
 
-        self.user_context = ProvidesUserFileSourcesUserContext(user_context)
+        self.user_context = ProvidesFileSourcesUserContext(user_context)
         self.file_sources = file_sources
         self.serialize_jobs = serialize_jobs
         self.sessionless = sessionless
@@ -3033,7 +3033,7 @@ def source_to_import_store(
         if source_uri.startswith("file://"):
             source_uri = source_uri[len("file://") :]
         if "://" in source_uri:
-            user_context = ProvidesUserFileSourcesUserContext(user_context)
+            user_context = ProvidesFileSourcesUserContext(user_context)
             source_uri = stream_url_to_file(
                 source_uri, app.file_sources, prefix="gx_import_model_store", user_context=user_context
             )
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 0ec2a659e86c..698e97cd8ee4 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -25,7 +25,7 @@
 from webob.compat import cgi_FieldStorage
 
 from galaxy import util
-from galaxy.files import ProvidesUserFileSourcesUserContext
+from galaxy.files import ProvidesFileSourcesUserContext
 from galaxy.managers.dbkeys import read_dbnames
 from galaxy.model import (
     cached_id,
@@ -2633,7 +2633,7 @@ def validate(self, value, trans=None):
         file_source = file_source_path.file_source
         if file_source is None:
             raise ParameterValueError(f"'{value}' is not a valid file source uri.", self.name)
-        user_context = ProvidesUserFileSourcesUserContext(trans)
+        user_context = ProvidesFileSourcesUserContext(trans)
         user_has_access = file_source.user_has_access(user_context)
         if not user_has_access:
             raise ParameterValueError(f"The user cannot access {value}.", self.name)
diff --git a/test/unit/files/_util.py b/test/unit/files/_util.py
index 5da87676b120..9b23a7005f48 100644
--- a/test/unit/files/_util.py
+++ b/test/unit/files/_util.py
@@ -6,6 +6,7 @@
 from galaxy.files import (
     ConfiguredFileSources,
     DictFileSourcesUserContext,
+    OptionalUserContext,
 )
 from galaxy.files.plugins import FileSourcePluginsConfig
 
@@ -13,7 +14,7 @@
 TEST_EMAIL = "alice@galaxyproject.org"
 
 
-def serialize_and_recover(file_sources_o, user_context=None):
+def serialize_and_recover(file_sources_o: ConfiguredFileSources, user_context: OptionalUserContext = None):
     as_dict = file_sources_o.to_dict(for_serialization=True, user_context=user_context)
     file_sources = ConfiguredFileSources.from_dict(as_dict)
     return file_sources
@@ -33,14 +34,24 @@ def find(dir_list, class_=None, name=None):
     return None
 
 
-def list_root(file_sources, uri, recursive, user_context=None):
+def list_root(
+    file_sources: ConfiguredFileSources,
+    uri: str,
+    recursive: bool,
+    user_context: OptionalUserContext = None,
+):
     file_source_pair = file_sources.get_file_source_path(uri)
     file_source = file_source_pair.file_source
     res = file_source.list("/", recursive=recursive, user_context=user_context)
     return res
 
 
-def list_dir(file_sources, uri, recursive, user_context=None):
+def list_dir(
+    file_sources: ConfiguredFileSources,
+    uri: str,
+    recursive: bool,
+    user_context: OptionalUserContext = None,
+):
     file_source_pair = file_sources.get_file_source_path(uri)
     file_source = file_source_pair.file_source
     print(file_source_pair.path)
@@ -82,7 +93,9 @@ def user_context_fixture(user_ftp_dir=None, role_names=None, group_names=None, i
     return user_context
 
 
-def realize_to_temp_file(file_sources, uri, user_context=None):
+def realize_to_temp_file(
+    file_sources: ConfiguredFileSources, uri: str, user_context: OptionalUserContext = None
+) -> str:
     file_source_path = file_sources.get_file_source_path(uri)
     with tempfile.NamedTemporaryFile(mode="r") as temp:
         file_source_path.file_source.realize_to(file_source_path.path, temp.name, user_context=user_context)
@@ -91,7 +104,12 @@ def realize_to_temp_file(file_sources, uri, user_context=None):
             return realized_contents
 
 
-def assert_realizes_as(file_sources, uri, expected, user_context=None):
+def assert_realizes_as(
+    file_sources: ConfiguredFileSources,
+    uri: str,
+    expected: str,
+    user_context: OptionalUserContext = None,
+):
     realized_contents = realize_to_temp_file(file_sources, uri, user_context=user_context)
     if realized_contents != expected:
         raise AssertionError(
@@ -99,7 +117,12 @@ def assert_realizes_as(file_sources, uri, expected, user_context=None):
         )
 
 
-def assert_realizes_contains(file_sources, uri, expected, user_context=None):
+def assert_realizes_contains(
+    file_sources: ConfiguredFileSources,
+    uri: str,
+    expected: str,
+    user_context: OptionalUserContext = None,
+):
     realized_contents = realize_to_temp_file(file_sources, uri, user_context=user_context)
     if expected not in realized_contents:
         raise AssertionError(
@@ -107,7 +130,9 @@ def assert_realizes_contains(file_sources, uri, expected, user_context=None):
         )
 
 
-def assert_realizes_throws_exception(file_sources, uri, user_context=None) -> Exception:
+def assert_realizes_throws_exception(
+    file_sources: ConfiguredFileSources, uri: str, user_context: OptionalUserContext = None
+) -> Exception:
     exception = None
     try:
         realize_to_temp_file(file_sources, uri, user_context=user_context)
@@ -117,7 +142,12 @@ def assert_realizes_throws_exception(file_sources, uri, user_context=None) -> Ex
     return exception
 
 
-def write_from(file_sources, uri, content, user_context=None):
+def write_from(
+    file_sources: ConfiguredFileSources,
+    uri: str,
+    content: str,
+    user_context: OptionalUserContext = None,
+):
     file_source_path = file_sources.get_file_source_path(uri)
     with tempfile.NamedTemporaryFile(mode="w") as f:
         f.write(content)

From b11506af0c748089d418c83adfc8ce166e62ed31 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 27 Apr 2024 14:22:24 -0400
Subject: [PATCH 16/21] Potential selenium fix.

---
 lib/galaxy/selenium/navigates_galaxy.py | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/selenium/navigates_galaxy.py b/lib/galaxy/selenium/navigates_galaxy.py
index de765d0375fe..9791c999cb45 100644
--- a/lib/galaxy/selenium/navigates_galaxy.py
+++ b/lib/galaxy/selenium/navigates_galaxy.py
@@ -153,6 +153,14 @@ def _retry(*args, **kwds):
     return _retry
 
 
+def retry_index_during_transitions():
+
+    def exception_check(e):
+        return exception_seems_to_indicate_transition(e) or isinstance(e, IndexError)
+
+    return partial(retry_during_transitions, exception_check=exception_check)
+
+
 def edit_details(f, scope=".history-index"):
     """Open the editor, run the edits, hit the save button"""
 
@@ -1421,7 +1429,12 @@ def workflow_card_elements(self):
         return self.components.workflows.workflow_card.all()
 
     def workflow_card_element(self, workflow_index=0):
-        return self.workflow_card_elements()[workflow_index]
+
+        @retry_index_during_transitions()
+        def fetch():
+            return self.workflow_card_elements()[workflow_index]
+
+        return fetch()
 
     @retry_during_transitions
     def workflow_index_column_text(self, column_index, workflow_index=0):

From 0e89124a13cb8a95db4d74fdc9e6780d7abc0e6e Mon Sep 17 00:00:00 2001
From: galaxybot <galaxybot@users.noreply.github.com>
Date: Sat, 27 Apr 2024 03:26:22 +0000
Subject: [PATCH 17/21] Update Python dependencies

---
 lib/galaxy/dependencies/dev-requirements.txt     | 16 ++++++++--------
 .../dependencies/pinned-lint-requirements.txt    |  4 ++--
 lib/galaxy/dependencies/pinned-requirements.txt  |  8 ++++----
 .../pinned-typecheck-requirements.txt            |  4 ++--
 4 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index f963631db7b0..59178ed6dc9d 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -9,7 +9,7 @@ axe-selenium-python==2.1.6 ; python_version >= "3.8" and python_version < "3.13"
 babel==2.14.0 ; python_version >= "3.8" and python_version < "3.13"
 backports-tarfile==1.1.1 ; python_version >= "3.8" and python_version < "3.12"
 backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
-black==24.4.0 ; python_version >= "3.8" and python_version < "3.13"
+black==24.4.2 ; python_version >= "3.8" and python_version < "3.13"
 build==1.2.1 ; python_version >= "3.8" and python_version < "3.13"
 cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
 certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -19,9 +19,9 @@ click==8.1.7 ; python_version >= "3.8" and python_version < "3.13"
 codespell==2.2.6 ; python_version >= "3.8" and python_version < "3.13"
 colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt")
 contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
-coverage[toml]==7.4.4 ; python_version >= "3.8" and python_version < "3.13"
+coverage[toml]==7.5.0 ; python_version >= "3.8" and python_version < "3.13"
 cryptography==42.0.5 ; python_version >= "3.8" and python_version < "3.13"
-cwltest==2.5.20240304113812 ; python_version >= "3.8" and python_version < "3.13"
+cwltest==2.5.20240425111257 ; python_version >= "3.8" and python_version < "3.13"
 cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
 darker==2.1.1 ; python_version >= "3.8" and python_version < "3.13"
 darkgraylib==1.2.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -56,7 +56,7 @@ jinja2==3.1.3 ; python_version >= "3.8" and python_version < "3.13"
 jsonschema-specifications==2023.12.1 ; python_version >= "3.9" and python_version < "3.13"
 jsonschema==4.20.0 ; python_version >= "3.9" and python_version < "3.13"
 junit-xml==1.9 ; python_version >= "3.8" and python_version < "3.13"
-keyring==25.1.0 ; python_version >= "3.8" and python_version < "3.13"
+keyring==25.2.0 ; python_version >= "3.8" and python_version < "3.13"
 kiwisolver==1.4.5 ; python_version >= "3.8" and python_version < "3.13"
 lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13"
 markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -83,7 +83,7 @@ pbr==6.0.0 ; python_version >= "3.9" and python_version < "3.13"
 pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
 pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 pkginfo==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
-platformdirs==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
+platformdirs==4.2.1 ; python_version >= "3.8" and python_version < "3.13"
 playwright==1.43.0 ; python_version >= "3.8" and python_version < "3.13"
 pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -119,7 +119,7 @@ pywin32-ctypes==0.2.2 ; python_version >= "3.8" and python_version < "3.13" and
 pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
 rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
 readme-renderer==43.0 ; python_version >= "3.8" and python_version < "3.13"
-referencing==0.34.0 ; python_version >= "3.9" and python_version < "3.13"
+referencing==0.35.0 ; python_version >= "3.9" and python_version < "3.13"
 requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
 responses==0.25.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -133,7 +133,7 @@ schema-salad==8.5.20240410123758 ; python_version >= "3.8" and python_version <
 scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
 scipy==1.13.0 ; python_version >= "3.9" and python_version < "3.13"
 secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
-selenium==4.19.0 ; python_version >= "3.8" and python_version < "3.13"
+selenium==4.20.0 ; python_version >= "3.8" and python_version < "3.13"
 seletools==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
 setuptools==69.5.1 ; python_version >= "3.8" and python_version < "3.13"
 six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -160,7 +160,7 @@ tomli==2.0.1 ; python_version >= "3.8" and python_full_version <= "3.11.0a6"
 trio-websocket==0.11.1 ; python_version >= "3.8" and python_version < "3.13"
 trio==0.25.0 ; python_version >= "3.8" and python_version < "3.13"
 tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
-twill==3.2.3 ; python_version >= "3.8" and python_version < "3.13"
+twill==3.2.4 ; python_version >= "3.8" and python_version < "3.13"
 twine==5.0.0 ; python_version >= "3.8" and python_version < "3.13"
 typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"
 tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt
index fea2eeeb9fa8..951a6bf4792f 100644
--- a/lib/galaxy/dependencies/pinned-lint-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt
@@ -1,7 +1,7 @@
 attrs==23.2.0
 flake8==7.0.0
-flake8-bugbear==24.4.21
+flake8-bugbear==24.4.26
 mccabe==0.7.0
 pycodestyle==2.11.1
 pyflakes==3.2.0
-ruff==0.4.1
+ruff==0.4.2
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 37b51a528176..007384ec0854 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -122,7 +122,7 @@ oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13"
 packaging==24.0 ; python_version >= "3.8" and python_version < "3.13"
 paramiko==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
 parsley==1.3 ; python_version >= "3.8" and python_version < "3.13"
-paste==3.9.0 ; python_version >= "3.8" and python_version < "3.13"
+paste==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
 pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pebble==5.0.7 ; python_version >= "3.8" and python_version < "3.13"
 pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -148,7 +148,7 @@ pylibmagic==0.5.0 ; python_version >= "3.8" and python_version < "3.13"
 pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 pyparsing==3.1.2 ; python_version >= "3.8" and python_version < "3.13"
 pyreadline3==3.4.1 ; sys_platform == "win32" and python_version >= "3.8" and python_version < "3.13"
-pysam==0.22.0 ; python_version >= "3.8" and python_version < "3.13"
+pysam==0.22.1 ; python_version >= "3.8" and python_version < "3.13"
 python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_version < "3.13"
 python-magic==0.4.27 ; python_version >= "3.8" and python_version < "3.13"
 python-multipart==0.0.9 ; python_version >= "3.8" and python_version < "3.13"
@@ -157,7 +157,7 @@ pytz==2024.1 ; python_version >= "3.8" and python_version < "3.13"
 pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
 pyzmq==26.0.2 ; python_version >= "3.8" and python_version < "3.13"
 rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
-referencing==0.34.0 ; python_version >= "3.8" and python_version < "3.13"
+referencing==0.35.0 ; python_version >= "3.8" and python_version < "3.13"
 refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.13"
 regex==2024.4.16 ; python_version >= "3.8" and python_version < "3.13"
 repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.13"
@@ -178,7 +178,7 @@ setuptools==69.5.1 ; python_version >= "3.8" and python_version < "3.13"
 shellescape==3.8.1 ; python_version >= "3.8" and python_version < "3.13"
 six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
-social-auth-core==4.5.3 ; python_version >= "3.8" and python_version < "3.13"
+social-auth-core==4.5.4 ; python_version >= "3.8" and python_version < "3.13"
 sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
 spython==0.3.13 ; python_version >= "3.8" and python_version < "3.13"
 sqlalchemy==2.0.29 ; python_version >= "3.8" and python_version < "3.13"
diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
index 014e6a3a3cb5..99e1264d74fd 100644
--- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
@@ -3,7 +3,7 @@ cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" and platform_
 cryptography==42.0.5 ; python_version >= "3.8" and python_version < "3.13"
 lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
-mypy==1.9.0 ; python_version >= "3.8" and python_version < "3.13"
+mypy==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
 pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
 pydantic-core==2.18.2 ; python_version >= "3.8" and python_version < "3.13"
 pydantic==2.7.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -20,6 +20,6 @@ types-pkg-resources==0.1.3 ; python_version >= "3.8" and python_version < "3.13"
 types-python-dateutil==2.9.0.20240316 ; python_version >= "3.8" and python_version < "3.13"
 types-pyyaml==6.0.12.20240311 ; python_version >= "3.8" and python_version < "3.13"
 types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.13"
-types-six==1.16.21.20240311 ; python_version >= "3.8" and python_version < "3.13"
+types-six==1.16.21.20240425 ; python_version >= "3.8" and python_version < "3.13"
 types-urllib3==1.26.25.14 ; python_version >= "3.8" and python_version < "3.13"
 typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"

From 0629908541043d93063df8832c8f94d6d41bb3ca Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Sat, 27 Apr 2024 16:03:22 +0100
Subject: [PATCH 18/21] Fix new UP031 errors from ruff 0.4.2

---
 .../webhooks/demo/tour_generator/__init__.py  | 28 ++++-----
 doc/parse_gx_xsd.py                           | 32 +++++-----
 lib/galaxy/actions/library.py                 |  2 +-
 lib/galaxy/auth/providers/ldap_ad.py          |  4 +-
 lib/galaxy/config/__init__.py                 |  5 +-
 lib/galaxy/datatypes/binary.py                | 14 ++---
 .../interval_to_bedstrict_converter.py        |  2 +-
 .../converters/maf_to_fasta_converter.py      | 11 ++--
 .../converters/wiggle_to_simple_converter.py  |  2 +-
 lib/galaxy/datatypes/interval.py              |  6 +-
 lib/galaxy/datatypes/neo4j.py                 |  3 +-
 lib/galaxy/datatypes/proteomics.py            |  2 +-
 lib/galaxy/datatypes/qiime2.py                |  4 +-
 lib/galaxy/datatypes/registry.py              |  5 +-
 lib/galaxy/datatypes/tabular.py               |  2 +-
 lib/galaxy/datatypes/tracks.py                |  3 +-
 lib/galaxy/datatypes/xml.py                   |  2 +-
 lib/galaxy/job_execution/actions/post.py      |  4 +-
 lib/galaxy/jobs/__init__.py                   |  3 +-
 lib/galaxy/jobs/runners/__init__.py           |  2 +-
 lib/galaxy/jobs/runners/aws.py                |  2 +-
 lib/galaxy/jobs/runners/pbs.py                |  4 +-
 .../jobs/runners/state_handlers/resubmit.py   |  4 +-
 lib/galaxy/jobs/runners/util/cli/job/lsf.py   |  2 +-
 lib/galaxy/jobs/runners/util/pykube_util.py   |  2 +-
 lib/galaxy/managers/interactivetool.py        |  9 +--
 lib/galaxy/managers/markdown_parse.py         |  4 +-
 lib/galaxy/managers/markdown_util.py          | 10 +--
 lib/galaxy/managers/users.py                  |  2 +-
 lib/galaxy/model/__init__.py                  |  7 +--
 lib/galaxy/model/deferred.py                  |  4 +-
 lib/galaxy/model/store/__init__.py            |  2 +-
 lib/galaxy/objectstore/__init__.py            |  4 +-
 lib/galaxy/objectstore/rucio_extra_clients.py | 14 ++---
 lib/galaxy/selenium/sizzle.py                 | 13 ++--
 lib/galaxy/tool_shed/tools/tool_validator.py  |  7 +--
 lib/galaxy/tool_shed/util/shed_util_common.py |  2 +-
 lib/galaxy/tool_util/deps/brew_exts.py        |  4 +-
 .../tool_util/deps/mulled/mulled_build.py     |  2 +-
 lib/galaxy/tool_util/parser/xml.py            |  3 +-
 lib/galaxy/tools/__init__.py                  |  6 +-
 .../tools/error_reports/plugins/gitlab.py     |  2 +-
 lib/galaxy/util/markdown.py                   |  2 +-
 lib/galaxy/util/topsort.py                    |  2 +-
 .../web/framework/middleware/profile.py       |  2 +-
 lib/galaxy/webapps/base/webapp.py             |  2 +-
 .../webapps/galaxy/controllers/admin.py       |  6 +-
 .../webapps/galaxy/controllers/dataset.py     |  2 +-
 .../webapps/galaxy/controllers/history.py     |  8 +--
 lib/galaxy/webapps/galaxy/controllers/page.py |  4 +-
 .../webapps/galaxy/controllers/tool_runner.py |  4 +-
 .../galaxy/controllers/visualization.py       |  2 +-
 lib/galaxy/workflow/modules.py                |  4 +-
 lib/galaxy/workflow/refactor/execute.py       |  4 +-
 lib/galaxy_test/api/test_libraries.py         |  2 +-
 .../dependencies/attribute_handlers.py        |  4 +-
 .../metadata/repository_metadata_manager.py   |  6 +-
 lib/tool_shed/repository_types/util.py        | 22 +++----
 lib/tool_shed/test/base/twilltestcase.py      | 10 ++-
 ...st_0440_deleting_dependency_definitions.py | 44 +++++++------
 lib/tool_shed/util/shed_util_common.py        | 10 +--
 lib/tool_shed/webapp/controllers/user.py      | 13 ++--
 scripts/api/common.py                         | 10 +--
 scripts/api/data_manager_example_execute.py   |  4 +-
 scripts/api/display.py                        |  2 +-
 scripts/api/example_watch_folder.py           |  8 +--
 .../filter_failed_datasets_from_collection.py |  3 +-
 scripts/api/history_create_history.py         |  2 +-
 scripts/api/history_delete_history.py         |  2 +-
 .../api/import_library_dataset_to_history.py  |  2 +-
 scripts/api/library_create_folder.py          |  2 +-
 scripts/api/library_create_library.py         |  2 +-
 scripts/api/library_upload_from_import_dir.py |  2 +-
 scripts/api/load_data_with_metadata.py        |  4 +-
 ...eset_metadata_on_installed_repositories.py |  2 +-
 scripts/api/workflow_delete.py                |  2 +-
 scripts/api/workflow_execute.py               |  2 +-
 scripts/api/workflow_execute_parameters.py    |  2 +-
 scripts/api/workflow_import.py                |  4 +-
 .../api/workflow_import_from_file_rpark.py    |  2 +-
 scripts/apply_tags.py                         |  6 +-
 scripts/build_toolbox.py                      |  2 +-
 scripts/check_python.py                       |  7 ++-
 .../admin_cleanup_datasets.py                 | 10 +--
 scripts/cleanup_datasets/pgcleanup.py         | 18 +++---
 scripts/config_sample_to_kwalify.py           |  8 +--
 scripts/db_shell.py                           |  6 +-
 scripts/drmaa_external_killer.py              |  2 +-
 scripts/drmaa_external_runner.py              |  6 +-
 scripts/dump_library_paths.py                 |  4 +-
 scripts/external_chown_script.py              |  6 +-
 scripts/grt/export.py                         |  2 +-
 scripts/loc_files/create_all_fasta_loc.py     | 61 ++++++++-----------
 scripts/microbes/create_bacteria_loc_file.py  | 14 ++---
 scripts/microbes/create_nib_seq_loc_file.py   |  4 +-
 scripts/microbes/harvest_bacteria.py          | 36 +++++------
 scripts/pages_identifier_conversion.py        |  4 +-
 scripts/runtime_stats.py                      | 24 ++++----
 scripts/set_user_disk_usage.py                |  4 +-
 scripts/tests_markdown.py                     |  4 +-
 scripts/tool_shed/api/common.py               |  6 +-
 scripts/tool_shed/api/create_categories.py    |  4 +-
 scripts/tool_shed/api/create_users.py         |  6 +-
 ...deprecate_repositories_without_metadata.py |  8 +--
 scripts/tools/re_escape_output.py             |  2 +-
 scripts/update_shed_config_path.py            |  4 +-
 .../chained_dyndest_rules/module2/rules.py    |  2 +-
 .../chained_dyndest_rules/module3/rules.py    |  2 +-
 .../integration/test_repository_operations.py |  4 +-
 test/integration/test_structured_dataset.py   | 10 +--
 .../gen_history_export_test_artifacts.py      |  2 +-
 test/manual/workflows_scaling.py              |  6 +-
 test/unit/app/queue_worker/conftest.py        |  2 +-
 test/unit/app/test_markdown_validate.py       |  2 +-
 test/unit/app/tools/conftest.py               |  2 +-
 test/unit/app/tools/test_wrappers.py          | 13 ++--
 test/unit/config/test_path_resolves_to.py     |  6 +-
 test/unit/data/test_model_copy.py             |  4 +-
 test/unit/data/test_quota.py                  |  2 +-
 test/unit/files/test_posix.py                 |  2 +-
 test/unit/objectstore/test_objectstore.py     |  2 +-
 test/unit/tool_shed/test_shed_index.py        |  2 +-
 .../unit/tool_util/mulled/test_mulled_list.py |  4 +-
 test/unit/tool_util/test_tool_deps.py         | 16 +++--
 test/unit/util/test_lazy_process.py           |  2 +-
 test/unit/util/test_rule_utils.py             |  4 +-
 test/unit/util/test_sqlite_utils.py           |  4 +-
 127 files changed, 381 insertions(+), 425 deletions(-)

diff --git a/config/plugins/webhooks/demo/tour_generator/__init__.py b/config/plugins/webhooks/demo/tour_generator/__init__.py
index 16219c91b402..3e5e39bb1d18 100644
--- a/config/plugins/webhooks/demo/tour_generator/__init__.py
+++ b/config/plugins/webhooks/demo/tour_generator/__init__.py
@@ -59,7 +59,7 @@ def _upload_test_data(self):
                 filename = test_datasets[input_name]
                 input_path = self._tool.test_data_path(filename)
                 if not input_path:
-                    raise ValueError('Test dataset "%s" doesn\'t exist.' % input_name)
+                    raise ValueError(f'Test dataset "{input_name}" doesn\'t exist.')
                 upload_tool = self._trans.app.toolbox.get_tool("upload1")
                 filename = os.path.basename(input_path)
                 with open(input_path, "rb") as f:
@@ -92,12 +92,12 @@ def _upload_test_data(self):
 
     def _generate_tour(self):
         """Generate a tour."""
-        tour_name = self._tool.name + " Tour"
+        tour_name = f"{self._tool.name} Tour"
         test_inputs = self._test.inputs.keys()
         steps = [
             {
                 "title": tour_name,
-                "content": "This short tour will guide you through the <b>" + self._tool.name + "</b> tool.",
+                "content": f"This short tour will guide you through the <b>{self._tool.name}</b> tool.",
                 "orphan": True,
             }
         ]
@@ -107,26 +107,26 @@ def _generate_tour(self):
                 continue
             step = {
                 "title": input.label,
-                "element": "[id='form-element-%s']" % name,
+                "element": f"[id='form-element-{name}']",
                 "placement": "right",
                 "content": "",
             }
             if input.type == "text":
                 if name in test_inputs:
                     param = self._test.inputs[name]
-                    step["content"] = "Enter value(s): <b>%s</b>" % param
+                    step["content"] = f"Enter value(s): <b>{param}</b>"
                 else:
                     step["content"] = "Enter a value"
             elif input.type == "integer" or input.type == "float":
                 if name in test_inputs:
                     num_param = self._test.inputs[name][0]
-                    step["content"] = "Enter number: <b>%s</b>" % num_param
+                    step["content"] = f"Enter number: <b>{num_param}</b>"
                 else:
                     step["content"] = "Enter a number"
             elif input.type == "boolean":
                 if name in test_inputs:
                     choice = "Yes" if self._test.inputs[name][0] is True else "No"
-                    step["content"] = "Choose <b>%s</b>" % choice
+                    step["content"] = f"Choose <b>{choice}</b>"
                 else:
                     step["content"] = "Choose Yes/No"
             elif input.type == "select":
@@ -138,7 +138,7 @@ def _generate_tour(self):
                                 params.append(option[0])
                 if params:
                     select_param = ", ".join(params)
-                    step["content"] = "Select parameter(s): <b>%s</b>" % select_param
+                    step["content"] = f"Select parameter(s): <b>{select_param}</b>"
                 else:
                     step["content"] = "Select a parameter"
             elif input.type == "data":
@@ -151,7 +151,7 @@ def _generate_tour(self):
             elif input.type == "conditional":
                 param_id = f"{input.name}|{input.test_param.name}"
                 step["title"] = input.test_param.label
-                step["element"] = "[id='form-element-%s']" % param_id
+                step["element"] = f"[id='form-element-{param_id}']"
                 params = []
                 if param_id in self._test.inputs.keys():
                     for option in input.test_param.static_options:
@@ -173,24 +173,24 @@ def _generate_tour(self):
                                 step_msg = f"Select dataset: <b>{hid}: {dataset}</b>"
                             else:
                                 case_params = ", ".join(self._test.inputs[tour_id])
-                                step_msg = "Select parameter(s): " + "<b>%s</b>" % case_params
+                                step_msg = f"Select parameter(s): <b>{case_params}</b>"
                             cond_case_steps.append(
                                 {
                                     "title": case_title,
-                                    "element": "[id='form-element-%s']" % tour_id,
+                                    "element": f"[id='form-element-{tour_id}']",
                                     "placement": "right",
                                     "content": step_msg,
                                 }
                             )
                 if params:
                     cond_param = ", ".join(params)
-                    step["content"] = "Select parameter(s): <b>%s</b>" % cond_param
+                    step["content"] = f"Select parameter(s): <b>{cond_param}</b>"
                 else:
                     step["content"] = "Select a parameter"
             elif input.type == "data_column":
                 if name in test_inputs:
                     column_param = self._test.inputs[name][0]
-                    step["content"] = "Select <b>Column: %s</b>" % column_param
+                    step["content"] = f"Select <b>Column: {column_param}</b>"
                 else:
                     step["content"] = "Select a column"
             else:
@@ -210,7 +210,7 @@ def _generate_tour(self):
         self._tour = {
             "title_default": tour_name,
             "name": tour_name,
-            "description": self._tool.name + " " + self._tool.description,
+            "description": f"{self._tool.name} {self._tool.description}",
             "steps": steps,
         }
 
diff --git a/doc/parse_gx_xsd.py b/doc/parse_gx_xsd.py
index d1453f86870b..e34a9ba89afd 100644
--- a/doc/parse_gx_xsd.py
+++ b/doc/parse_gx_xsd.py
@@ -34,7 +34,7 @@ def main():
 
 
 class Tag:
-    def __init__(self, line):
+    def __init__(self, line: str):
         assert line.startswith("$tag:")
         line_parts = line.split(" ")
         first_part = line_parts[0]
@@ -52,12 +52,12 @@ def __init__(self, line):
 
     @property
     def _pretty_title(self):
-        return " > ".join("``%s``" % p for p in self.title.split("|"))
+        return " > ".join(f"``{p}``" for p in self.title.split("|"))
 
     def build_help(self):
         tag = xmlschema_doc.find(self.xpath)
         if tag is None:
-            raise Exception("Could not find xpath for %s" % self.xpath)
+            raise Exception(f"Could not find xpath for {self.xpath}")
 
         tag_help = StringIO()
         tag_help.write("## " + self._pretty_title)
@@ -98,7 +98,7 @@ def _build_tag(tag, hide_attributes):
                     doc = _doc_or_none(element)
                     if doc is None:
                         doc = _doc_or_none(_type_el(element))
-                    assert doc is not None, "Documentation for %s is empty" % element.attrib["name"]
+                    assert doc is not None, f"Documentation for {element.attrib['name']} is empty"
                     doc = doc.strip()
 
                     element_el = _find_tag_el(element)
@@ -110,10 +110,9 @@ def _build_tag(tag, hide_attributes):
     if best_practices := _get_bp_link(annotation_el):
         tag_help.write("\n\n### Best Practices\n")
         tag_help.write(
-            """
-Find the Intergalactic Utilities Commision suggested best practices for this
-element [here](%s)."""
-            % best_practices
+            f"""
+Find the Intergalactic Utilities Commission suggested best practices for this
+element [here]({best_practices})."""
         )
     tag_help.write(_build_attributes_table(tag, attributes, hide_attributes))
 
@@ -140,7 +139,7 @@ def _get_bp_link(annotation_el):
     anchor = annotation_el.attrib.get("{http://galaxyproject.org/xml/1.0}best_practices", None)
     link = None
     if anchor:
-        link = "https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#%s" % anchor
+        link = f"https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#{anchor}"
     return link
 
 
@@ -149,7 +148,7 @@ def _build_attributes_table(tag, attributes, hide_attributes=False, attribute_na
     attribute_table.write("\n\n")
     if attributes and not hide_attributes:
         header_prefix = "#" * header_level
-        attribute_table.write("\n%s Attributes\n\n" % header_prefix)
+        attribute_table.write(f"\n{header_prefix} Attributes\n\n")
         attribute_table.write("Attribute | Details | Required\n")
         attribute_table.write("--- | --- | ---\n")
         for attribute in attributes:
@@ -159,7 +158,7 @@ def _build_attributes_table(tag, attributes, hide_attributes=False, attribute_na
             details = _doc_or_none(attribute)
             if details is None:
                 type_el = _type_el(attribute)
-                assert type_el is not None, "No details or type found for %s" % name
+                assert type_el is not None, f"No details or type found for {name}"
                 details = _doc_or_none(type_el)
                 annotation_el = type_el.find("{http://www.w3.org/2001/XMLSchema}annotation")
             else:
@@ -170,10 +169,7 @@ def _build_attributes_table(tag, attributes, hide_attributes=False, attribute_na
             details = details.replace("|", "\\|").strip()
             best_practices = _get_bp_link(annotation_el)
             if best_practices:
-                details += (
-                    """ Find the Intergalactic Utilities Commision suggested best practices for this element [here](%s)."""
-                    % best_practices
-                )
+                details += f""" Find the Intergalactic Utilities Commission suggested best practices for this element [here]({best_practices})."""
 
             attribute_table.write(f"``{name}`` | {details} | {use}\n")
     return attribute_table.getvalue()
@@ -204,7 +200,7 @@ def _find_attributes(tag):
     for attribute_group in attribute_groups:
         attribute_group_name = attribute_group.get("ref")
         attribute_group_def = xmlschema_doc.find(
-            "//{http://www.w3.org/2001/XMLSchema}attributeGroup/[@name='%s']" % attribute_group_name
+            f"//{{http://www.w3.org/2001/XMLSchema}}attributeGroup/[@name='{attribute_group_name}']"
         )
         attributes.extend(_find_attributes(attribute_group_def))
     return attributes
@@ -219,9 +215,9 @@ def _find_tag_el(tag):
 
 def _type_el(tag):
     element_type = tag.attrib["type"]
-    type_el = xmlschema_doc.find("//{http://www.w3.org/2001/XMLSchema}complexType/[@name='%s']" % element_type)
+    type_el = xmlschema_doc.find(f"//{{http://www.w3.org/2001/XMLSchema}}complexType/[@name='{element_type}']")
     if type_el is None:
-        type_el = xmlschema_doc.find("//{http://www.w3.org/2001/XMLSchema}simpleType/[@name='%s']" % element_type)
+        type_el = xmlschema_doc.find(f"//{{http://www.w3.org/2001/XMLSchema}}simpleType/[@name='{element_type}']")
     return type_el
 
 
diff --git a/lib/galaxy/actions/library.py b/lib/galaxy/actions/library.py
index 5962474bbf20..72b651e1869a 100644
--- a/lib/galaxy/actions/library.py
+++ b/lib/galaxy/actions/library.py
@@ -265,7 +265,7 @@ def _check_path_paste_params(self, params):
             if not os.path.exists(path):
                 bad_paths.append(path)
         if bad_paths:
-            message = 'Invalid paths: "%s".' % '", "'.join(bad_paths)
+            message = 'Invalid paths: "{}".'.format('", "'.join(bad_paths))
             response_code = 400
             return None, response_code, message
         return None
diff --git a/lib/galaxy/auth/providers/ldap_ad.py b/lib/galaxy/auth/providers/ldap_ad.py
index 180f925556c5..5c7e5974100a 100644
--- a/lib/galaxy/auth/providers/ldap_ad.py
+++ b/lib/galaxy/auth/providers/ldap_ad.py
@@ -135,8 +135,8 @@ def check_config(self, username, email, options):
         self.role_search_attribute = options.get(self.role_search_option)
         if self.auto_create_roles_or_groups and self.role_search_attribute is None:
             raise ConfigurationError(
-                "If 'auto-create-roles' or 'auto-create-groups' is True, a '%s' attribute has to"
-                " be provided." % self.role_search_option
+                f"If 'auto-create-roles' or 'auto-create-groups' is True, a '{self.role_search_option}' attribute has to"
+                " be provided."
             )
 
         return ok, failure_mode
diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index c69009d47315..e3da3e743e55 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -944,7 +944,8 @@ def _process_config(self, kwargs: Dict[str, Any]) -> None:
                     log.warning(
                         "The path '%s' for the 'sanitize_allowlist_file' config option is "
                         "deprecated and will be no longer checked in a future release. Please consult "
-                        "the latest version of the sample configuration file." % deprecated
+                        "the latest version of the sample configuration file.",
+                        deprecated,
                     )
                     _sanitize_allowlist_path = deprecated
                     break
@@ -965,7 +966,7 @@ def _process_config(self, kwargs: Dict[str, Any]) -> None:
         )
         # Searching data libraries
         self.ftp_upload_dir_template = kwargs.get(
-            "ftp_upload_dir_template", "${ftp_upload_dir}%s${ftp_upload_dir_identifier}" % os.path.sep
+            "ftp_upload_dir_template", f"${{ftp_upload_dir}}{os.path.sep}${{ftp_upload_dir_identifier}}"
         )
         # Support older library-specific path paste option but just default to the new
         # allow_path_paste value.
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 679cc6da19db..6e6a5d570177 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -2089,7 +2089,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return "HDF5 Model (%s)" % (nice_size(dataset.get_size()))
+            return f"HDF5 Model ({nice_size(dataset.get_size())})"
 
     def display_data(
         self,
@@ -4258,7 +4258,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return "Binary pretext file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary pretext file ({nice_size(dataset.get_size())})"
 
 
 class JP2(Binary):
@@ -4302,7 +4302,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return "Binary JPEG 2000 file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary JPEG 2000 file ({nice_size(dataset.get_size())})"
 
 
 class Npz(CompressedArchive):
@@ -4356,7 +4356,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return "Binary Numpy npz file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary Numpy npz file ({nice_size(dataset.get_size())})"
 
 
 class HexrdImagesNpz(Npz):
@@ -4433,7 +4433,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return "Binary Numpy npz file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary Numpy npz file ({nice_size(dataset.get_size())})"
 
 
 class HexrdEtaOmeNpz(Npz):
@@ -4495,7 +4495,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return "Binary Numpy npz file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary Numpy npz file ({nice_size(dataset.get_size())})"
 
 
 class FITS(Binary):
@@ -4624,4 +4624,4 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
         try:
             return dataset.peek
         except Exception:
-            return "Binary numpy file (%s)" % (nice_size(dataset.get_size()))
+            return f"Binary numpy file ({nice_size(dataset.get_size())})"
diff --git a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
index ea2d1b013138..1e343d32ae8b 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
+++ b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
@@ -181,7 +181,7 @@ def __main__():
                     fields = [str(item) for item in (region.chrom, region.start, region.end, name, 0, region.strand)]
                     if force_num_columns is not None and len(fields) != force_num_columns:
                         fields = force_bed_field_count(fields, count, force_num_columns)
-                    out.write("%s\n" % "\t".join(fields))
+                    out.write("{}\n".format("\t".join(fields)))
                 except Exception:
                     skipped_lines += 1
                     if first_skipped_line is None:
diff --git a/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py b/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
index 0b968f3c7537..aa7252ba1128 100644
--- a/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
+++ b/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
@@ -24,11 +24,12 @@ def __main__():
                 else:
                     spec_counts[spec] += 1
                 out.write(
-                    "%s\n"
-                    % maf_utilities.get_fasta_header(
-                        c,
-                        {"block_index": count, "species": spec, "sequence_index": spec_counts[spec]},
-                        suffix="%s_%i_%i" % (spec, count, spec_counts[spec]),
+                    "{}\n".format(
+                        maf_utilities.get_fasta_header(
+                            c,
+                            {"block_index": count, "species": spec, "sequence_index": spec_counts[spec]},
+                            suffix="%s_%i_%i" % (spec, count, spec_counts[spec]),
+                        )
                     )
                 )
                 out.write(f"{c.text}\n")
diff --git a/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
index 853d57e0172c..66aa9028e58d 100644
--- a/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
+++ b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
@@ -20,7 +20,7 @@ def main():
     with open(sys.argv[1]) as in_file, open(sys.argv[2], "w") as out_file:
         try:
             for fields in bx.wiggle.IntervalReader(UCSCOutWrapper(in_file)):
-                out_file.write("%s\n" % "\t".join(map(str, fields)))
+                out_file.write("{}\n".format("\t".join(map(str, fields))))
         except UCSCLimitException:
             # Wiggle data was truncated, at the very least need to warn the user.
             sys.stderr.write(
diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index 2fbac3ff7abe..ee323163c885 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -289,18 +289,18 @@ def as_ucsc_display_file(self, dataset: DatasetProtocol, **kwd) -> Union[FileObj
                     if t < len(elems):
                         strand = cast(str, elems[t])
                     tmp = [elems[c], elems[s], elems[e], name, "0", strand]
-                    fh.write("%s\n" % "\t".join(tmp))
+                    fh.write("{}\n".format("\t".join(tmp)))
             elif n >= 0:  # name column (should) exists
                 for i, elems in enumerate(compression_utils.file_iter(dataset.get_file_name())):
                     name = "region_%i" % i
                     if n >= 0 and n < len(elems):
                         name = cast(str, elems[n])
                     tmp = [elems[c], elems[s], elems[e], name]
-                    fh.write("%s\n" % "\t".join(tmp))
+                    fh.write("{}\n".format("\t".join(tmp)))
             else:
                 for elems in compression_utils.file_iter(dataset.get_file_name()):
                     tmp = [elems[c], elems[s], elems[e]]
-                    fh.write("%s\n" % "\t".join(tmp))
+                    fh.write("{}\n".format("\t".join(tmp)))
             return compression_utils.get_fileobj(fh.name, mode="rb")
 
     def display_peek(self, dataset: DatasetProtocol) -> str:
diff --git a/lib/galaxy/datatypes/neo4j.py b/lib/galaxy/datatypes/neo4j.py
index 608b19c0d9c5..0d6fec174dee 100644
--- a/lib/galaxy/datatypes/neo4j.py
+++ b/lib/galaxy/datatypes/neo4j.py
@@ -30,9 +30,8 @@ def generate_primary_file(self, dataset: HasExtraFilesAndMetadata) -> str:
         """
         # self.regenerate_primary_file(dataset)
         rval = [
-            "<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\
+            f"<html><head><title>Files for Composite Dataset ({self.file_ext})</title></head><p/>\
             This composite dataset is composed of the following files:<p/><ul>"
-            % (self.file_ext)
         ]
         for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
             opt_text = ""
diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index d691e98f0bfc..f9b30ca3bcfd 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -714,7 +714,7 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
             if not line.startswith("<?"):
                 break
         # pattern match <root or <ns:root for any ns string
-        pattern = r"<(\w*:)?%s" % self.root
+        pattern = rf"<(\w*:)?{self.root}"
         return re.search(pattern, line) is not None
 
     def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
diff --git a/lib/galaxy/datatypes/qiime2.py b/lib/galaxy/datatypes/qiime2.py
index 0b998bf69c5e..deaaf6a3da47 100644
--- a/lib/galaxy/datatypes/qiime2.py
+++ b/lib/galaxy/datatypes/qiime2.py
@@ -258,10 +258,10 @@ def _get_uuid(path):
     if len(roots) == 0:
         raise ValueError("Archive does not have a visible root directory.")
     if len(roots) > 1:
-        raise ValueError("Archive has multiple root directories: %r" % roots)
+        raise ValueError(f"Archive has multiple root directories: {roots!r}")
     uuid = roots.pop()
     if not _is_uuid4(uuid):
-        raise ValueError("Archive root directory name %r is not a valid version 4 " "UUID." % uuid)
+        raise ValueError(f"Archive root directory name {uuid!r} is not a valid version 4 UUID.")
     return uuid
 
 
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index f91eada60a4b..671f30d82e16 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -971,9 +971,8 @@ def get_extension(self, elem):
         # If extension is not None and is uppercase or mixed case, we need to lowercase it
         if extension is not None and not extension.islower():
             self.log.debug(
-                "%s is not lower case, that could cause troubles in the future. \
-            Please change it to lower case"
-                % extension
+                "%s is not lower case, that could cause troubles in the future. Please change it to lower case",
+                extension,
             )
             extension = extension.lower()
         return extension
diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index 5865235cfd44..b9b79f046511 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -1075,7 +1075,7 @@ def merge(split_files: List[str], output_file: str) -> None:
     def validate(self, dataset: DatasetProtocol, **kwd) -> DatatypeValidation:
         def validate_row(row):
             if len(row) < 8:
-                raise Exception("Not enough columns in row %s" % row.join("\t"))
+                raise Exception("Not enough columns in row {}".format(row.join("\t")))
 
         validate_tabular(dataset.get_file_name(), sep="\t", validate_row=validate_row, comment_designator="#")
         return DatatypeValidation.validated()
diff --git a/lib/galaxy/datatypes/tracks.py b/lib/galaxy/datatypes/tracks.py
index 0fccbba26d15..e32b035abd4f 100644
--- a/lib/galaxy/datatypes/tracks.py
+++ b/lib/galaxy/datatypes/tracks.py
@@ -36,9 +36,8 @@ def generate_primary_file(self, dataset: HasExtraFilesAndMetadata) -> str:
         cannot rename the datasets here - they come with the default unfortunately
         """
         rval = [
-            "<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\
+            f"<html><head><title>Files for Composite Dataset ({self.file_ext})</title></head><p/>\
             This composite dataset is composed of the following files:<p/><ul>"
-            % (self.file_ext)
         ]
         for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
             opt_text = ""
diff --git a/lib/galaxy/datatypes/xml.py b/lib/galaxy/datatypes/xml.py
index a5148336bf80..d3060c93ad9d 100644
--- a/lib/galaxy/datatypes/xml.py
+++ b/lib/galaxy/datatypes/xml.py
@@ -49,7 +49,7 @@ def _has_root_element_in_prefix(self, file_prefix: FilePrefix, root: str) -> boo
             if not line.startswith("<?"):
                 break
         # pattern match <root or <ns:root for any ns string
-        pattern = r"^<(\w*:)?%s" % root
+        pattern = rf"^<(\w*:)?{root}"
         return re.match(pattern, line) is not None
 
     def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
diff --git a/lib/galaxy/job_execution/actions/post.py b/lib/galaxy/job_execution/actions/post.py
index 75b03cd3e9e6..408ea2accb6c 100644
--- a/lib/galaxy/job_execution/actions/post.py
+++ b/lib/galaxy/job_execution/actions/post.py
@@ -231,11 +231,11 @@ def _gen_new_name(self, action, input_names, replacement_dict):
                     elif operation == "lower":
                         replacement = replacement.lower()
 
-                new_name = new_name.replace("#{%s}" % to_be_replaced, replacement)
+                new_name = new_name.replace(f"#{{{to_be_replaced}}}", replacement)
 
             if replacement_dict:
                 for k, v in replacement_dict.items():
-                    new_name = new_name.replace("${%s}" % k, v)
+                    new_name = new_name.replace(f"${{{k}}}", v)
 
         return new_name
 
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 5ba851359c92..8b0984886312 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -2169,8 +2169,7 @@ def check_limits(self, runtime=None):
                     )
                     return (
                         JobState.runner_states.OUTPUT_SIZE_LIMIT,
-                        "Job output file grew too large (greater than %s), please try different inputs or parameters"
-                        % util.nice_size(self.app.job_config.limits.output_size),
+                        f"Job output file grew too large (greater than {util.nice_size(self.app.job_config.limits.output_size)}), please try different inputs or parameters",
                     )
         if self.app.job_config.limits.walltime_delta is not None and runtime is not None:
             if runtime > self.app.job_config.limits.walltime_delta:
diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py
index e87d7c1b0091..54ae6f27f464 100644
--- a/lib/galaxy/jobs/runners/__init__.py
+++ b/lib/galaxy/jobs/runners/__init__.py
@@ -169,7 +169,7 @@ def run_next(self):
                 try:
                     action_str = f"galaxy.jobs.runners.{self.__class__.__name__.lower()}.{name}"
                     action_timer = self.app.execution_timer_factory.get_timer(
-                        f"internals.{action_str}", "job runner action %s for job ${job_id} executed" % (action_str)
+                        f"internals.{action_str}", f"job runner action {action_str} for job ${{job_id}} executed"
                     )
                     method(arg)
                     log.trace(action_timer.to_str(job_id=job_id))
diff --git a/lib/galaxy/jobs/runners/aws.py b/lib/galaxy/jobs/runners/aws.py
index ee0284fe0f23..57b8dae427fa 100644
--- a/lib/galaxy/jobs/runners/aws.py
+++ b/lib/galaxy/jobs/runners/aws.py
@@ -528,7 +528,7 @@ def parse_destination_params(self, params):
             parsed_params[k] = mapper(value)  # type: ignore[operator]
         if check_required:
             raise AWSBatchRunnerException(
-                "AWSBatchJobRunner requires the following params to be provided: %s." % (", ".join(check_required))
+                "AWSBatchJobRunner requires the following params to be provided: {}.".format(", ".join(check_required))
             )
 
         # parse Platform
diff --git a/lib/galaxy/jobs/runners/pbs.py b/lib/galaxy/jobs/runners/pbs.py
index a1012d1a3705..4ab56c460ff5 100644
--- a/lib/galaxy/jobs/runners/pbs.py
+++ b/lib/galaxy/jobs/runners/pbs.py
@@ -13,7 +13,7 @@
     PBS_IMPORT_MESSAGE = (
         "The Python pbs-python package is required to use "
         "this feature, please install it or correct the "
-        "following error:\nImportError %s" % str(exc)
+        f"following error:\nImportError {exc}"
     )
 
 from galaxy import (
@@ -514,7 +514,7 @@ def stop_job(self, job_wrapper):
         try:
             pbs_server_name = self.__get_pbs_server(job.destination_params)
             if pbs_server_name is None:
-                log.debug("(%s) Job queued but no destination stored in job params, cannot delete" % job_tag)
+                log.debug("(%s) Job queued but no destination stored in job params, cannot delete", job_tag)
                 return
             c = pbs.pbs_connect(util.smart_str(pbs_server_name))
             if c <= 0:
diff --git a/lib/galaxy/jobs/runners/state_handlers/resubmit.py b/lib/galaxy/jobs/runners/state_handlers/resubmit.py
index b6bea8e3f467..172237a32f66 100644
--- a/lib/galaxy/jobs/runners/state_handlers/resubmit.py
+++ b/lib/galaxy/jobs/runners/state_handlers/resubmit.py
@@ -62,7 +62,7 @@ def _handle_resubmit_definitions(resubmit_definitions, app, job_runner, job_stat
         # Is destination needed here, might these be serialized to the database?
         destination = resubmit.get("environment") or resubmit.get("destination")
         log.info(
-            "%s Job will be resubmitted to '%s' because %s at " "the '%s' destination",
+            "%s Job will be resubmitted to '%s' because %s at the '%s' destination",
             job_log_prefix,
             destination,
             MESSAGES[runner_state],
@@ -106,7 +106,7 @@ def _handle_resubmit_definitions(resubmit_definitions, app, job_runner, job_stat
         if job.params is None:
             job.params = {}
         job_state.runner_state_handled = True
-        info = "This job was resubmitted to the queue because %s on its " "compute resource." % MESSAGES[runner_state]
+        info = f"This job was resubmitted to the queue because {MESSAGES[runner_state]} on its compute resource."
         job_runner.mark_as_resubmitted(job_state, info=info)
         return
 
diff --git a/lib/galaxy/jobs/runners/util/cli/job/lsf.py b/lib/galaxy/jobs/runners/util/cli/job/lsf.py
index 2a5903e4b486..36842bb51bb5 100644
--- a/lib/galaxy/jobs/runners/util/cli/job/lsf.py
+++ b/lib/galaxy/jobs/runners/util/cli/job/lsf.py
@@ -52,7 +52,7 @@ def submit(self, script_file):
         # This should be really handled outside with something like
         # parse_external. Currently CLI runner expect this to just send it in the last position
         # of the string.
-        return "bsub <%s | awk '{ print $2}' | sed 's/[<>]//g'" % script_file
+        return f"bsub <{script_file} | awk '{{ print $2}}' | sed 's/[<>]//g'"
 
     def delete(self, job_id):
         return f"bkill {job_id}"
diff --git a/lib/galaxy/jobs/runners/util/pykube_util.py b/lib/galaxy/jobs/runners/util/pykube_util.py
index 699df65398ac..6fc2c039f741 100644
--- a/lib/galaxy/jobs/runners/util/pykube_util.py
+++ b/lib/galaxy/jobs/runners/util/pykube_util.py
@@ -25,7 +25,7 @@
     K8S_IMPORT_MESSAGE = (
         "The Python pykube package is required to use "
         "this feature, please install it or correct the "
-        "following error:\nImportError %s" % str(exc)
+        f"following error:\nImportError {exc}"
     )
 
 log = logging.getLogger(__name__)
diff --git a/lib/galaxy/managers/interactivetool.py b/lib/galaxy/managers/interactivetool.py
index 4892091eee99..8cec876ba561 100644
--- a/lib/galaxy/managers/interactivetool.py
+++ b/lib/galaxy/managers/interactivetool.py
@@ -69,7 +69,7 @@ def save(self, key, key_type, token, host, port, info=None):
                 try:
                     # Create table
                     c.execute(
-                        """CREATE TABLE %s
+                        f"""CREATE TABLE {DATABASE_TABLE_NAME}
                                  (key text,
                                   key_type text,
                                   token text,
@@ -78,7 +78,6 @@ def save(self, key, key_type, token, host, port, info=None):
                                   info text,
                                   PRIMARY KEY (key, key_type)
                                   )"""
-                        % (DATABASE_TABLE_NAME)
                     )
                 except Exception:
                     pass
@@ -90,11 +89,9 @@ def save(self, key, key_type, token, host, port, info=None):
                         key_type,
                     ),
                 )
-                insert = """INSERT INTO %s
+                insert = f"""INSERT INTO {DATABASE_TABLE_NAME}
                             (key, key_type, token, host, port, info)
-                            VALUES (?, ?, ?, ?, ?, ?)""" % (
-                    DATABASE_TABLE_NAME
-                )
+                            VALUES (?, ?, ?, ?, ?, ?)"""
                 c.execute(
                     insert,
                     (
diff --git a/lib/galaxy/managers/markdown_parse.py b/lib/galaxy/managers/markdown_parse.py
index ab52141fa4e2..7eeef2ba482d 100644
--- a/lib/galaxy/managers/markdown_parse.py
+++ b/lib/galaxy/managers/markdown_parse.py
@@ -71,10 +71,10 @@ class DynamicArguments:
     "invocation_inputs": [],
 }
 GALAXY_FLAVORED_MARKDOWN_CONTAINERS = list(VALID_ARGUMENTS.keys())
-GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX = r"(?P<container>%s)" % "|".join(GALAXY_FLAVORED_MARKDOWN_CONTAINERS)
+GALAXY_FLAVORED_MARKDOWN_CONTAINER_REGEX = r"(?P<container>{})".format("|".join(GALAXY_FLAVORED_MARKDOWN_CONTAINERS))
 
 ARG_VAL_REGEX = r"""[\w_\-]+|\"[^\"]+\"|\'[^\']+\'"""
-FUNCTION_ARG = r"\s*[\w\|]+\s*=\s*(?:%s)\s*" % ARG_VAL_REGEX
+FUNCTION_ARG = rf"\s*[\w\|]+\s*=\s*(?:{ARG_VAL_REGEX})\s*"
 # embed commas between arguments
 FUNCTION_MULTIPLE_ARGS = rf"(?P<firstargcall>{FUNCTION_ARG})(?P<restargcalls>(?:,{FUNCTION_ARG})*)"
 FUNCTION_MULTIPLE_ARGS_PATTERN = re.compile(FUNCTION_MULTIPLE_ARGS)
diff --git a/lib/galaxy/managers/markdown_util.py b/lib/galaxy/managers/markdown_util.py
index af1adc7f6856..009aae3ea762 100644
--- a/lib/galaxy/managers/markdown_util.py
+++ b/lib/galaxy/managers/markdown_util.py
@@ -67,11 +67,11 @@
 log = logging.getLogger(__name__)
 
 ARG_VAL_CAPTURED_REGEX = r"""(?:([\w_\-\|]+)|\"([^\"]+)\"|\'([^\']+)\')"""
-OUTPUT_LABEL_PATTERN = re.compile(r"output=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX)
-INPUT_LABEL_PATTERN = re.compile(r"input=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX)
-STEP_LABEL_PATTERN = re.compile(r"step=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX)
-PATH_LABEL_PATTERN = re.compile(r"path=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX)
-SIZE_PATTERN = re.compile(r"size=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX)
+OUTPUT_LABEL_PATTERN = re.compile(rf"output=\s*{ARG_VAL_CAPTURED_REGEX}\s*")
+INPUT_LABEL_PATTERN = re.compile(rf"input=\s*{ARG_VAL_CAPTURED_REGEX}\s*")
+STEP_LABEL_PATTERN = re.compile(rf"step=\s*{ARG_VAL_CAPTURED_REGEX}\s*")
+PATH_LABEL_PATTERN = re.compile(rf"path=\s*{ARG_VAL_CAPTURED_REGEX}\s*")
+SIZE_PATTERN = re.compile(rf"size=\s*{ARG_VAL_CAPTURED_REGEX}\s*")
 # STEP_OUTPUT_LABEL_PATTERN = re.compile(r'step_output=([\w_\-]+)/([\w_\-]+)')
 UNENCODED_ID_PATTERN = re.compile(
     r"(history_id|workflow_id|history_dataset_id|history_dataset_collection_id|job_id|implicit_collection_jobs_id|invocation_id)=([\d]+)"
diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index eea8ca6d4d0e..1d7ceaeb9bbd 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -195,7 +195,7 @@ def purge(self, user, flush=True):
                 "The configuration of this Galaxy instance does not allow admins to delete or purge users."
             )
         if not user.deleted:
-            raise exceptions.MessageException("User '%s' has not been deleted, so they cannot be purged." % user.email)
+            raise exceptions.MessageException(f"User '{user.email}' has not been deleted, so they cannot be purged.")
         private_role = self.app.security_agent.get_private_user_role(user)
         # Delete History
         for active_history in user.active_histories:
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index d28fcb08353d..4cb9358961c9 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -612,13 +612,10 @@ def calculate_user_disk_usage_statements(user_id, quota_source_map, for_sqlite=F
     if default_usage_dataset_condition.strip():
         default_usage_dataset_condition = f"AND ( {default_usage_dataset_condition} )"
     default_usage = UNIQUE_DATASET_USER_USAGE.format(and_dataset_condition=default_usage_dataset_condition)
-    default_usage = (
-        """
-UPDATE galaxy_user SET disk_usage = (%s)
+    default_usage = f"""
+UPDATE galaxy_user SET disk_usage = ({default_usage})
 WHERE id = :id
 """
-        % default_usage
-    )
     params = {"id": user_id}
     if default_exclude_ids:
         params["exclude_object_store_ids"] = default_exclude_ids
diff --git a/lib/galaxy/model/deferred.py b/lib/galaxy/model/deferred.py
index e7c009ad3645..d73517fb756a 100644
--- a/lib/galaxy/model/deferred.py
+++ b/lib/galaxy/model/deferred.py
@@ -61,9 +61,9 @@ def __init__(self, staging_directory: str):
         self._staging_directory = staging_directory
 
     def transient_paths_for(self, old_dataset: Dataset) -> TransientDatasetPaths:
-        external_filename_basename = "dataset_%s.dat" % str(old_dataset.uuid)
+        external_filename_basename = f"dataset_{old_dataset.uuid}.dat"
         external_filename = os.path.join(self._staging_directory, external_filename_basename)
-        external_extras_basename = "dataset_%s_files" % str(old_dataset.uuid)
+        external_extras_basename = f"dataset_{old_dataset.uuid}_files"
         external_extras = os.path.join(self._staging_directory, external_extras_basename)
         return TransientDatasetPaths(external_filename, external_extras, self._staging_directory)
 
diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index dbca1f250f33..e337858493f4 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -1621,7 +1621,7 @@ def _read_list_if_exists(self, file_name: str, required: bool = False) -> List[D
             attrs = load(open(file_name))
         else:
             if required:
-                raise Exception("Failed to find file [%s] in model store archive" % file_name)
+                raise Exception(f"Failed to find file [{file_name}] in model store archive")
             attrs = []
         return attrs
 
diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index da023ee13bee..62d49420e5e6 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -1513,8 +1513,8 @@ def wraps(self, *args, **kwargs):
                 if c.__name__ == "DiskObjectStore":
                     return getattr(c, func.__name__)(self, *args, **kwargs)
             raise Exception(
-                "Could not call DiskObjectStore's %s method, does your "
-                "Object Store plugin inherit from DiskObjectStore?" % func.__name__
+                f"Could not call DiskObjectStore's {func.__name__} method, does your "
+                "Object Store plugin inherit from DiskObjectStore?"
             )
 
     return wraps
diff --git a/lib/galaxy/objectstore/rucio_extra_clients.py b/lib/galaxy/objectstore/rucio_extra_clients.py
index 36ff04981b3f..500366ee3618 100644
--- a/lib/galaxy/objectstore/rucio_extra_clients.py
+++ b/lib/galaxy/objectstore/rucio_extra_clients.py
@@ -35,7 +35,7 @@ def _delete_item(self, item, forced_schemes, ignore_availability):
             if not self.rses.get(rse):
                 rse_settings = self.rses.setdefault(rse, rsemgr.get_rse_info(rse, vo=self.client.vo))
                 if not ignore_availability and rse_settings["availability_delete"] != 1:
-                    logger(logging.DEBUG, "%s is not available for deletion. No actions have been taken" % rse)
+                    logger(logging.DEBUG, "%s is not available for deletion. No actions have been taken", rse)
                     continue
 
             # protocol handling and deletion
@@ -52,8 +52,8 @@ def _delete_item(self, item, forced_schemes, ignore_availability):
                     success = True
                 except Exception as error:
                     logger(logging.WARNING, "Delete attempt failed")
-                    logger(logging.INFO, "Exception: %s" % str(error), exc_info=True)
-            logger(logging.DEBUG, "Successfully deleted dataset %s" % pfn)
+                    logger(logging.INFO, "Exception: %s", error, exc_info=True)
+            logger(logging.DEBUG, "Successfully deleted dataset %s", pfn)
 
 
 class InPlaceIngestClient(UploadClient):
@@ -107,7 +107,7 @@ def ingest(self, items, summary_file_path=None, traces_copy_out=None, ignore_ava
             if not self.rses.get(rse):
                 rse_settings = self.rses.setdefault(rse, rsemgr.get_rse_info(rse, vo=self.client.vo))
                 if not ignore_availability and rse_settings["availability_write"] != 1:
-                    raise RSEWriteBlocked("%s is not available for writing. No actions have been taken" % rse)
+                    raise RSEWriteBlocked(f"{rse} is not available for writing. No actions have been taken")
 
             dataset_scope = file.get("dataset_scope")
             dataset_name = file.get("dataset_name")
@@ -120,7 +120,7 @@ def ingest(self, items, summary_file_path=None, traces_copy_out=None, ignore_ava
             registered_file_dids.add(f"{file['did_scope']}:{file['did_name']}")
         wrong_dids = registered_file_dids.intersection(registered_dataset_dids)
         if len(wrong_dids):
-            raise InputValidationError("DIDs used to address both files and datasets: %s" % str(wrong_dids))
+            raise InputValidationError(f"DIDs used to address both files and datasets: {wrong_dids}")
         logger(logging.DEBUG, "Input validation done.")
 
         # clear this set again to ensure that we only try to register datasets once
@@ -129,7 +129,7 @@ def ingest(self, items, summary_file_path=None, traces_copy_out=None, ignore_ava
         summary = []
         for file in files:
             basename = file["basename"]
-            logger(logging.INFO, "Preparing upload for file %s" % basename)
+            logger(logging.INFO, "Preparing upload for file %s", basename)
 
             pfn = file.get("pfn")
 
@@ -169,7 +169,7 @@ def ingest(self, items, summary_file_path=None, traces_copy_out=None, ignore_ava
             trace["transferEnd"] = time.time()
             trace["clientState"] = "DONE"
             file["state"] = "A"
-            logger(logging.INFO, "Successfully uploaded file %s" % basename)
+            logger(logging.INFO, "Successfully uploaded file %s", basename)
             self._send_trace(trace)
 
             if summary_file_path:
diff --git a/lib/galaxy/selenium/sizzle.py b/lib/galaxy/selenium/sizzle.py
index 94d9e903b6ae..f3421c697255 100644
--- a/lib/galaxy/selenium/sizzle.py
+++ b/lib/galaxy/selenium/sizzle.py
@@ -87,22 +87,19 @@ def find_elements_by_sizzle(driver, sizzle_selector: str):
 
 
 def _inject_sizzle(driver, sizzle_url, timeout):
-    script = (
-        """
-        if(typeof(window.$) != "undefined") {
+    script = f"""
+        if(typeof(window.$) != "undefined") {{
             // Just reuse jQuery if it is available, avoids potential amd problems
             // that have cropped up with Galaxy for instance.
             window.Sizzle = window.$;
-        } else {
+        }} else {{
             var _s = document.createElement("script");
             _s.type = "text/javascript";
-            _s.src = "%s";
+            _s.src = "{sizzle_url}";
             var _h = document.getElementsByTagName("head")[0];
             _h.appendChild(_s);
-        }
+        }}
     """
-        % sizzle_url
-    )
     driver.execute_script(script)
     wait = WebDriverWait(driver, timeout)
     wait.until(lambda d: _is_sizzle_loaded(d), f"Can't inject Sizzle in {timeout} seconds")
diff --git a/lib/galaxy/tool_shed/tools/tool_validator.py b/lib/galaxy/tool_shed/tools/tool_validator.py
index 1d2780c81d3d..a73af2230c9e 100644
--- a/lib/galaxy/tool_shed/tools/tool_validator.py
+++ b/lib/galaxy/tool_shed/tools/tool_validator.py
@@ -70,10 +70,9 @@ def check_tool_input_params(self, repo_dir, tool_config_name, tool, sample_files
                                 sample_found = True
                                 break
                         if not sample_found:
-                            correction_msg = f"This file refers to a file named <b>{str(index_file_name)}</b>.  "
-                            correction_msg += (
-                                "Upload a file named <b>%s.sample</b> to the repository to correct this error."
-                                % str(index_file_name)
+                            correction_msg = (
+                                f"This file refers to a file named <b>{index_file_name}</b>.  "
+                                f"Upload a file named <b>{index_file_name}.sample</b> to the repository to correct this error."
                             )
                             invalid_files_and_errors_tups.append((tool_config_name, correction_msg))
         return invalid_files_and_errors_tups
diff --git a/lib/galaxy/tool_shed/util/shed_util_common.py b/lib/galaxy/tool_shed/util/shed_util_common.py
index cb16ee71e918..43a1e652b110 100644
--- a/lib/galaxy/tool_shed/util/shed_util_common.py
+++ b/lib/galaxy/tool_shed/util/shed_util_common.py
@@ -163,7 +163,7 @@ def set_image_paths(app, text, encoded_repository_id=None, tool_shed_repository=
         # settings like .. images:: http_files/images/help.png
         for match in re.findall(".. image:: (?!http)/?(.+)", text):
             text = text.replace(match, match.replace("/", "%2F"))
-        text = re.sub(r"\.\. image:: (?!https?://)/?(.+)", r".. image:: %s/\1" % route_to_images, text)
+        text = re.sub(r"\.\. image:: (?!https?://)/?(.+)", rf".. image:: {route_to_images}/\1", text)
     return text
 
 
diff --git a/lib/galaxy/tool_util/deps/brew_exts.py b/lib/galaxy/tool_util/deps/brew_exts.py
index 0f56b279251a..ce2adb760743 100755
--- a/lib/galaxy/tool_util/deps/brew_exts.py
+++ b/lib/galaxy/tool_util/deps/brew_exts.py
@@ -387,9 +387,9 @@ def modify_environ(self, environ):
         if self.action == "set" or not environ.get(self.variable, ""):
             environ[self.variable] = self.__eval("${value}")
         elif self.action == "prepend":
-            environ[self.variable] = self.__eval("${value}:%s" % environ[self.variable])
+            environ[self.variable] = self.__eval(f"${{value}}:{environ[self.variable]}")
         else:
-            environ[self.variable] = self.__eval("%s:${value}" % environ[self.variable])
+            environ[self.variable] = self.__eval(f"{environ[self.variable]}:${{value}}")
 
     def __eval(self, template):
         return string.Template(template).safe_substitute(
diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_build.py b/lib/galaxy/tool_util/deps/mulled/mulled_build.py
index bcbf1bfdf0bc..be956c84a8b9 100644
--- a/lib/galaxy/tool_util/deps/mulled/mulled_build.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_build.py
@@ -307,7 +307,7 @@ def mull_targets(
         conda_bin = "mamba"
         if mamba_version is None:
             mamba_version = ""
-    involucro_args.extend(["-set", "CONDA_BIN=%s" % conda_bin])
+    involucro_args.extend(["-set", f"CONDA_BIN={conda_bin}"])
     if conda_version is not None or mamba_version is not None:
         mamba_test = "true"
         specs = []
diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
index ef39fd2ac2d4..57d22e34750e 100644
--- a/lib/galaxy/tool_util/parser/xml.py
+++ b/lib/galaxy/tool_util/parser/xml.py
@@ -1133,7 +1133,8 @@ def parse_stdio_regexes(self, stdio_elem):
                         log.warning(
                             "Tool id %s: unable to determine if tool "
                             "stream source scanning is output, error, "
-                            "or both. Defaulting to use both." % self.id
+                            "or both. Defaulting to use both.",
+                            self.id,
                         )
                         regex.stdout_match = True
                         regex.stderr_match = True
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 917464e5b45d..6e64d3a11011 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2103,7 +2103,7 @@ def validate_inputs(input, value, error, parent, context, prefixed_name, prefixe
                             )
                         parent[input.name] = value
                     except Exception:
-                        messages[prefixed_name] = "Attempt to replace invalid value for '%s' failed." % (prefixed_label)
+                        messages[prefixed_name] = f"Attempt to replace invalid value for '{prefixed_label}' failed."
                 else:
                     messages[prefixed_name] = error
 
@@ -2315,7 +2315,7 @@ def to_archive(self):
                     if os.path.exists(filesystem_path):
                         tarball_files.append((filesystem_path, tarball_path))
                         image_found = True
-                        tool_xml = tool_xml.replace("${static_path}/%s" % tarball_path, tarball_path)
+                        tool_xml = tool_xml.replace(f"${{static_path}}/{tarball_path}", tarball_path)
         # If one or more tool help images were found, add the modified tool XML to the tarball instead of the original.
         if image_found:
             with tempfile.NamedTemporaryFile(mode="w", suffix=".xml", delete=False) as fh2:
@@ -2684,7 +2684,7 @@ def _compare_tool_version(self, job):
             )
             if tool is None:
                 raise exceptions.MessageException(
-                    "This dataset was created by an obsolete tool (%s). Can't re-run." % tool_id
+                    f"This dataset was created by an obsolete tool ({tool_id}). Can't re-run."
                 )
             if (self.id != tool_id and self.old_id != tool_id) or self.version != tool_version:
                 if self.id == tool_id:
diff --git a/lib/galaxy/tools/error_reports/plugins/gitlab.py b/lib/galaxy/tools/error_reports/plugins/gitlab.py
index b8f2d923bade..3540154dfca5 100644
--- a/lib/galaxy/tools/error_reports/plugins/gitlab.py
+++ b/lib/galaxy/tools/error_reports/plugins/gitlab.py
@@ -154,7 +154,7 @@ def submit_report(self, dataset, job, tool, **kwargs):
                         gl_emailquery = self.gitlab.users.list(search=gl_useremail)
                         log.debug(f"GitLab error reporting - User list: {gl_emailquery}")
                         if len(gl_emailquery) > 0:
-                            log.debug("GitLab error reporting - Last Committer user ID: %s" % gl_emailquery[0].get_id())
+                            log.debug("GitLab error reporting - Last Committer user ID: %s", gl_emailquery[0].get_id())
                             self.git_username_id_cache[gl_useremail] = gl_emailquery[0].get_id()
                     gl_userid = self.git_username_id_cache.get(gl_useremail, None)
 
diff --git a/lib/galaxy/util/markdown.py b/lib/galaxy/util/markdown.py
index 3ebaab42202f..fa142df66776 100644
--- a/lib/galaxy/util/markdown.py
+++ b/lib/galaxy/util/markdown.py
@@ -2,7 +2,7 @@
 
 
 def literal_via_fence(content):
-    return "\n%s\n" % "\n".join(f"    {line}" for line in content.splitlines())
+    return "\n{}\n".format("\n".join(f"    {line}" for line in content.splitlines()))
 
 
 def indicate_data_truncated():
diff --git a/lib/galaxy/util/topsort.py b/lib/galaxy/util/topsort.py
index 38bdf40c4bd4..64a1338fa1a4 100644
--- a/lib/galaxy/util/topsort.py
+++ b/lib/galaxy/util/topsort.py
@@ -168,7 +168,7 @@ def topsort(pairlist):
             for y in successors[x]:
                 numpreds[y] = numpreds[y] - 1
                 if numpreds[y] == 0:
-                    answer.append(y)  # noqa: B038
+                    answer.append(y)
             # following "del" isn't needed; just makes
             # CycleError details easier to grasp
             del successors[x]
diff --git a/lib/galaxy/web/framework/middleware/profile.py b/lib/galaxy/web/framework/middleware/profile.py
index da2d4c9f9a8a..649ec2933596 100644
--- a/lib/galaxy/web/framework/middleware/profile.py
+++ b/lib/galaxy/web/framework/middleware/profile.py
@@ -171,7 +171,7 @@ def func_std_string(func_name):
         # special case for built-in functions
         name = func_name[2]
         if name.startswith("<") and name.endswith(">"):
-            return "{%s}" % name[1:-1]
+            return f"{{{name[1:-1]}}}"
         else:
             return name
     else:
diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index 0029bb70a7e6..0cd502606613 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -144,7 +144,7 @@ def build_apispec(self):
             if rule.routepath.endswith(".:(format)") or not rule.routepath.startswith("api/"):
                 continue
             # Try to replace routes various ways to encode variables with simple swagger {form}
-            swagger_path = "/%s" % RE_URL.sub(r"{\1}", rule.routepath)
+            swagger_path = "/{}".format(RE_URL.sub(r"{\1}", rule.routepath))
             controller = rule.defaults.get("controller", "")
             action = rule.defaults.get("action", "")
             # Get the list of methods for the route
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py
index 0070c9be7c56..7e788bb1cc0f 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin.py
@@ -534,7 +534,7 @@ def manage_users_and_groups_for_quota(self, trans, payload=None, **kwd):
                     in_groups.append(trans.security.encode_id(group.id))
                 all_groups.append((group.name, trans.security.encode_id(group.id)))
             return {
-                "title": "Quota '%s'" % quota.name,
+                "title": f"Quota '{quota.name}'",
                 "message": "Quota '%s' is currently associated with %d user(s) and %d group(s)."
                 % (quota.name, len(in_users), len(in_groups)),
                 "status": "info",
@@ -797,7 +797,7 @@ def manage_users_and_groups_for_role(self, trans, payload=None, **kwd):
                     in_groups.append(trans.security.encode_id(group.id))
                 all_groups.append((group.name, trans.security.encode_id(group.id)))
             return {
-                "title": "Role '%s'" % role.name,
+                "title": f"Role '{role.name}'",
                 "message": "Role '%s' is currently associated with %d user(s) and %d group(s)."
                 % (role.name, len(in_users), len(in_groups)),
                 "status": "info",
@@ -902,7 +902,7 @@ def manage_users_and_roles_for_group(self, trans, payload=None, **kwd):
                     in_roles.append(trans.security.encode_id(role.id))
                 all_roles.append((role.name, trans.security.encode_id(role.id)))
             return {
-                "title": "Group '%s'" % group.name,
+                "title": f"Group '{group.name}'",
                 "message": "Group '%s' is currently associated with %d user(s) and %d role(s)."
                 % (group.name, len(in_users), len(in_roles)),
                 "status": "info",
diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
index 69f25c42866a..e1c2f5b79a9a 100644
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -332,7 +332,7 @@ def get_edit(self, trans, dataset_id=None, **kwd):
             }
         else:
             return self.message_exception(
-                trans, "You do not have permission to edit this dataset's ( id: %s ) information." % str(dataset_id)
+                trans, f"You do not have permission to edit this dataset's ( id: {dataset_id} ) information."
             )
 
     @web.expose_api_anonymous
diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py
index fd3f1a036f20..3db60f29ad2a 100644
--- a/lib/galaxy/webapps/galaxy/controllers/history.py
+++ b/lib/galaxy/webapps/galaxy/controllers/history.py
@@ -155,7 +155,7 @@ def permissions(self, trans, payload=None, **kwd):
                         "value": [trans.security.encode_id(role.id) for role in in_roles],
                     }
                 )
-            return {"title": "Change default dataset permissions for history '%s'" % history.name, "inputs": inputs}
+            return {"title": f"Change default dataset permissions for history '{history.name}'", "inputs": inputs}
         else:
             self.history_manager.error_unless_mutable(history)
             permissions = {}
@@ -164,7 +164,7 @@ def permissions(self, trans, payload=None, **kwd):
                 in_roles = [trans.sa_session.get(Role, trans.security.decode_id(x)) for x in in_roles]
                 permissions[trans.app.security_agent.get_action(action.action)] = in_roles
             trans.app.security_agent.history_set_default_permissions(history, permissions)
-            return {"message": "Default history '%s' dataset permissions have been changed." % history.name}
+            return {"message": f"Default history '{history.name}' dataset permissions have been changed."}
 
     @web.legacy_expose_api
     @web.require_login("make datasets private")
@@ -286,10 +286,10 @@ def rename(self, trans, payload=None, **kwd):
                 new_name = payload.get("name_%i" % i)
                 # validate name is empty
                 if not isinstance(new_name, str) or not new_name.strip():
-                    messages.append("You must specify a valid name for History '%s'." % cur_name)
+                    messages.append(f"You must specify a valid name for History '{cur_name}'.")
                 # skip if not the owner
                 elif h.user_id != user.id:
-                    messages.append("History '%s' does not appear to belong to you." % cur_name)
+                    messages.append(f"History '{cur_name}' does not appear to belong to you.")
                 # skip if it wouldn't be a change
                 elif new_name != cur_name:
                     h.name = new_name
diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py
index 0d4d11b993e6..b222c7a6be3e 100644
--- a/lib/galaxy/webapps/galaxy/controllers/page.py
+++ b/lib/galaxy/webapps/galaxy/controllers/page.py
@@ -100,7 +100,7 @@ def create(self, trans, payload=None, **kwd):
             }
         else:
             page = self.page_manager.create_page(trans, CreatePagePayload(**payload))
-            return {"message": "Page '%s' successfully created." % page.title, "status": "success"}
+            return {"message": f"Page '{page.title}' successfully created.", "status": "success"}
 
     @web.legacy_expose_api
     @web.require_login("edit pages")
@@ -159,7 +159,7 @@ def edit(self, trans, payload=None, **kwd):
                 trans.sa_session.add(p)
                 with transaction(trans.sa_session):
                     trans.sa_session.commit()
-            return {"message": "Attributes of '%s' successfully saved." % p.title, "status": "success"}
+            return {"message": f"Attributes of '{p.title}' successfully saved.", "status": "success"}
 
     @web.expose
     @web.require_login()
diff --git a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
index f85e9b2d9a30..d3337bb8e602 100644
--- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
+++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
@@ -46,9 +46,9 @@ def __get_tool(self, tool_id, tool_version=None, get_loaded_tools_by_lineage=Fal
     def index(self, trans, tool_id=None, from_noframe=None, **kwd):
         def __tool_404__():
             log.debug("index called with tool id '%s' but no such tool exists", tool_id)
-            trans.log_event("Tool id '%s' does not exist" % tool_id)
+            trans.log_event(f"Tool id '{tool_id}' does not exist")
             trans.response.status = 404
-            return trans.show_error_message("Tool '%s' does not exist." % (escape(tool_id)))
+            return trans.show_error_message(f"Tool '{escape(tool_id)}' does not exist.")
 
         # tool id not available, redirect to main page
         if tool_id is None:
diff --git a/lib/galaxy/webapps/galaxy/controllers/visualization.py b/lib/galaxy/webapps/galaxy/controllers/visualization.py
index 157cfde250d2..3928d2e6f02d 100644
--- a/lib/galaxy/webapps/galaxy/controllers/visualization.py
+++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py
@@ -225,7 +225,7 @@ def edit(self, trans, payload=None, **kwd):
                 trans.sa_session.add(v)
                 with transaction(trans.sa_session):
                     trans.sa_session.commit()
-            return {"message": "Attributes of '%s' successfully saved." % v.title, "status": "success"}
+            return {"message": f"Attributes of '{v.title}' successfully saved.", "status": "success"}
 
     # ------------------------- registry.
     @web.expose
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index e1fcaceeefba..46926aaca35c 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -138,7 +138,7 @@ def to_cwl(value, hda_references, step):
         # I think the following two checks are needed but they may
         # not be needed.
         if not value.dataset.in_ready_state():
-            why = "dataset [%s] is needed for valueFrom expression and is non-ready" % value.id
+            why = f"dataset [{value.id}] is needed for valueFrom expression and is non-ready"
             raise DelayedWorkflowEvaluation(why=why)
         if not value.is_ok:
             raise FailWorkflowEvaluation(
@@ -190,7 +190,7 @@ def from_cwl(value, hda_references, progress: "WorkflowProgress"):
             # This is going to re-file -> HDA this each iteration I think, not a good
             # implementation.
             return progress.raw_to_galaxy(value)
-        assert value["location"].startswith("step_input://"), "Invalid location %s" % value
+        assert value["location"].startswith("step_input://"), f"Invalid location {value}"
         return hda_references[int(value["location"][len("step_input://") :]) - 1]
     elif isinstance(value, dict):
         raise NotImplementedError()
diff --git a/lib/galaxy/workflow/refactor/execute.py b/lib/galaxy/workflow/refactor/execute.py
index d35cbbbc7785..fc38a9351468 100644
--- a/lib/galaxy/workflow/refactor/execute.py
+++ b/lib/galaxy/workflow/refactor/execute.py
@@ -251,7 +251,7 @@ def _apply_extract_input(self, action: ExtractInputAction, execution: RefactorAc
     def _apply_extract_untyped_parameter(self, action: ExtractUntypedParameter, execution: RefactorActionExecution):
         untyped_parameter_name = action.name
         new_label = action.label or untyped_parameter_name
-        target_value = "${%s}" % untyped_parameter_name
+        target_value = f"${{{untyped_parameter_name}}}"
 
         target_tool_inputs = []
         rename_pjas = []
@@ -330,7 +330,7 @@ def callback(input, prefixed_name, context, value=None, **kwargs):
             if untyped_parameter_name != new_label:
                 action_arguments = rename_pja.get("action_arguments")
                 old_newname = action_arguments["newname"]
-                new_newname = old_newname.replace(target_value, "${%s}" % new_label)
+                new_newname = old_newname.replace(target_value, f"${{{new_label}}}")
                 action_arguments["newname"] = new_newname
 
         optional = False
diff --git a/lib/galaxy_test/api/test_libraries.py b/lib/galaxy_test/api/test_libraries.py
index cd1c67926d29..440d004db146 100644
--- a/lib/galaxy_test/api/test_libraries.py
+++ b/lib/galaxy_test/api/test_libraries.py
@@ -194,7 +194,7 @@ def test_create_library_dataset_bootstrap_user(self, library_name="private_datas
         library = self.library_populator.new_private_library(library_name)
         payload, files = self.library_populator.create_dataset_request(library, file_type="txt", contents="create_test")
         create_response = self.galaxy_interactor.post(
-            "libraries/%s/contents" % library["id"], payload, files=files, key=self.master_api_key
+            f"libraries/{library['id']}/contents", payload, files=files, key=self.master_api_key
         )
         self._assert_status_code_is(create_response, 400)
 
diff --git a/lib/tool_shed/dependencies/attribute_handlers.py b/lib/tool_shed/dependencies/attribute_handlers.py
index 87cba9e1a6fd..2d72abd48e17 100644
--- a/lib/tool_shed/dependencies/attribute_handlers.py
+++ b/lib/tool_shed/dependencies/attribute_handlers.py
@@ -137,8 +137,8 @@ def handle_elem(self, elem):
                     elem.attrib["changeset_revision"] = lastest_installable_changeset_revision
                     altered = True
                 else:
-                    error_message = "Invalid latest installable changeset_revision %s " % str(
-                        lastest_installable_changeset_revision
+                    error_message = (
+                        f"Invalid latest installable changeset_revision {lastest_installable_changeset_revision} "
                     )
                     error_message += f"retrieved for repository {name} owned by {owner}.  "
             else:
diff --git a/lib/tool_shed/metadata/repository_metadata_manager.py b/lib/tool_shed/metadata/repository_metadata_manager.py
index 41fdf8da1821..31a1fc45cac0 100644
--- a/lib/tool_shed/metadata/repository_metadata_manager.py
+++ b/lib/tool_shed/metadata/repository_metadata_manager.py
@@ -1036,10 +1036,10 @@ def set_repository_metadata(self, host, content_alert_str="", **kwd):
                         changeset_revisions.append(changeset_revision)
                 self._add_tool_versions(repository_id, repository_metadata, changeset_revisions)
         elif len(repo) == 1 and not self.invalid_file_tups:
-            message = "Revision <b>%s</b> includes no Galaxy utilities for which metadata can " % str(
-                self.repository.tip()
+            message = (
+                f"Revision <b>{self.repository.tip()}</b> includes no Galaxy utilities for which metadata can "
+                "be defined so this revision cannot be automatically installed into a local Galaxy instance."
             )
-            message += "be defined so this revision cannot be automatically installed into a local Galaxy instance."
             status = "error"
         if self.invalid_file_tups:
             message = tool_util.generate_message_for_invalid_tools(
diff --git a/lib/tool_shed/repository_types/util.py b/lib/tool_shed/repository_types/util.py
index dc2751eebc16..fff61e6778f2 100644
--- a/lib/tool_shed/repository_types/util.py
+++ b/lib/tool_shed/repository_types/util.py
@@ -43,26 +43,18 @@ def generate_message_for_repository_type_change(app, repository):
         repository_suite_definition_type_class = app.repository_types_registry.get_class_by_label(
             REPOSITORY_SUITE_DEFINITION
         )
-        message += (
-            "This repository currently contains a single file named <b>%s</b>.  If the intent of this repository is "
-            % REPOSITORY_DEPENDENCY_DEFINITION_FILENAME
-        )
-        message += "to define relationships to a collection of repositories that contain related Galaxy utilities with "
-        message += (
-            "no plans to add additional files, consider setting its type to <b>%s</b>.<br/>"
-            % repository_suite_definition_type_class.label
+        message = (
+            f"This repository currently contains a single file named <b>{REPOSITORY_DEPENDENCY_DEFINITION_FILENAME}</b>.  If the intent of this repository is "
+            "to define relationships to a collection of repositories that contain related Galaxy utilities with "
+            f"no plans to add additional files, consider setting its type to <b>{repository_suite_definition_type_class.label}</b>.<br/>"
         )
     elif repository.can_change_type_to(app, TOOL_DEPENDENCY_DEFINITION):
         tool_dependency_definition_type_class = app.repository_types_registry.get_class_by_label(
             TOOL_DEPENDENCY_DEFINITION
         )
-        message += (
-            "This repository currently contains a single file named <b>%s</b>.  If additional files will "
-            % TOOL_DEPENDENCY_DEFINITION_FILENAME
-        )
-        message += (
-            "not be added to this repository, consider setting its type to <b>%s</b>.<br/>"
-            % tool_dependency_definition_type_class.label
+        message = (
+            f"This repository currently contains a single file named <b>{TOOL_DEPENDENCY_DEFINITION_FILENAME}</b>.  If additional files will "
+            f"not be added to this repository, consider setting its type to <b>{tool_dependency_definition_type_class.label}</b>.<br/>"
         )
     return message
 
diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index 30d6525ec192..87eaf2c3ab8d 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -2048,9 +2048,7 @@ def assert_has():
     def _assert_repo_has_tool_with_id(
         self, installed_repository: galaxy_model.ToolShedRepository, tool_id: str
     ) -> None:
-        assert "tools" in installed_repository.metadata_, (
-            "No valid tools were defined in %s." % installed_repository.name
-        )
+        assert "tools" in installed_repository.metadata_, f"No valid tools were defined in {installed_repository.name}."
         tools = installed_repository.metadata_["tools"]
         found_it = False
         for tool in tools:  # type:ignore[attr-defined]
@@ -2064,9 +2062,9 @@ def _assert_repo_has_tool_with_id(
     def _assert_repo_has_invalid_tool_in_file(
         self, installed_repository: galaxy_model.ToolShedRepository, name: str
     ) -> None:
-        assert "invalid_tools" in installed_repository.metadata_, (
-            "No invalid tools were defined in %s." % installed_repository.name
-        )
+        assert (
+            "invalid_tools" in installed_repository.metadata_
+        ), f"No invalid tools were defined in {installed_repository.name}."
         invalid_tools = installed_repository.metadata_["invalid_tools"]
         found_it = name in invalid_tools
         assert found_it, f"Did not find invalid tool file {name} in {invalid_tools}"
diff --git a/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py b/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py
index 9eb9d9b7aa94..4b540f71584e 100644
--- a/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py
+++ b/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py
@@ -165,15 +165,14 @@ def test_0025_delete_repository_dependency(self):
         new_changeset_revision = self.get_repository_tip(repository)
         # Check that the old changeset revision is still downloadable.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, old_changeset_revision)
-        assert metadata_record.downloadable, (
-            "The revision of %s that contains repository_dependencies.xml is no longer downloadable." % repository.name
-        )
+        assert (
+            metadata_record.downloadable
+        ), f"The revision of {repository.name} that contains repository_dependencies.xml is no longer downloadable."
         # Check that the new tip is also downloadable.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, new_changeset_revision)
-        assert metadata_record.downloadable, (
-            "The revision of %s that does not contain repository_dependencies.xml is not downloadable."
-            % repository.name
-        )
+        assert (
+            metadata_record.downloadable
+        ), f"The revision of {repository.name} that does not contain repository_dependencies.xml is not downloadable."
         # Verify that there are only two downloadable revisions.
         assert (
             len(self._db_repository(repository).downloadable_revisions) == 2
@@ -279,14 +278,14 @@ def test_0050_delete_complex_repository_dependency(self):
         new_changeset_revision = self.get_repository_tip(repository)
         # Check that the old changeset revision is still downloadable.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, old_changeset_revision)
-        assert metadata_record.downloadable, (
-            "The revision of %s that contains tool_dependencies.xml is no longer downloadable." % repository.name
-        )
+        assert (
+            metadata_record.downloadable
+        ), f"The revision of {repository.name} that contains tool_dependencies.xml is no longer downloadable."
         # Check that the new tip is also downloadable.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, new_changeset_revision)
-        assert metadata_record.downloadable, (
-            "The revision of %s that does not contain tool_dependencies.xml is not downloadable." % repository.name
-        )
+        assert (
+            metadata_record.downloadable
+        ), f"The revision of {repository.name} that does not contain tool_dependencies.xml is not downloadable."
         # Verify that there are only two downloadable revisions.
         assert (
             len(self._db_repository(repository).downloadable_revisions) == 2
@@ -331,9 +330,9 @@ def test_0060_delete_bwa_tool_dependency_definition(self):
         assert old_changeset_revision != new_changeset_revision
         # Check that the old changeset revision is still downloadable.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, old_changeset_revision)
-        assert metadata_record.downloadable, (
-            "The revision of %s that contains tool_dependencies.xml is no longer downloadable." % repository.name
-        )
+        assert (
+            metadata_record.downloadable
+        ), f"The revision of {repository.name} that contains tool_dependencies.xml is no longer downloadable."
         # Check that the new tip does not have a metadata revision.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, new_changeset_revision)
         # If a changeset revision does not have metadata, the above method will return None.
@@ -364,15 +363,14 @@ def test_0065_reupload_bwa_tool_dependency_definition(self):
         new_changeset_revision = self.get_repository_tip(repository)
         # Check that the old changeset revision is still downloadable.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, old_changeset_revision)
-        assert metadata_record is None, (
-            "The revision of %s that does not contain tool_dependencies.xml should not be downloadable, but is."
-            % repository.name
-        )
+        assert (
+            metadata_record is None
+        ), f"The revision of {repository.name} that does not contain tool_dependencies.xml should not be downloadable, but is."
         # Check that the new tip is also downloadable.
         metadata_record = self._get_repository_metadata_by_changeset_revision(repository, new_changeset_revision)
-        assert metadata_record.downloadable, (
-            "The revision of %s that contains tool_dependencies.xml is not downloadable." % repository.name
-        )
+        assert (
+            metadata_record.downloadable
+        ), f"The revision of {repository.name} that contains tool_dependencies.xml is not downloadable."
         # Verify that there are only two downloadable revisions.
         assert (
             len(self._db_repository(repository).downloadable_revisions) == 1
diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py
index a6cab6cc954d..b3fbbb477532 100644
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -136,20 +136,14 @@ def get_repository_file_contents(app: "ToolShedApp", file_path: str, repository_
                 safe_str = f"{safe_str}{basic_util.to_html_string(line)}"
                 # Stop reading after string is larger than MAX_CONTENT_SIZE.
                 if len(safe_str) > MAX_CONTENT_SIZE:
-                    large_str = (
-                        "<br/>File contents truncated because file size is larger than maximum viewing size of %s<br/>"
-                        % util.nice_size(MAX_CONTENT_SIZE)
-                    )
+                    large_str = f"<br/>File contents truncated because file size is larger than maximum viewing size of {util.nice_size(MAX_CONTENT_SIZE)}<br/>"
                     safe_str = f"{safe_str}{large_str}"
                     break
 
         if len(safe_str) > basic_util.MAX_DISPLAY_SIZE:
             # Eliminate the middle of the file to display a file no larger than basic_util.MAX_DISPLAY_SIZE.
             # This may not be ideal if the file is larger than MAX_CONTENT_SIZE.
-            join_by_str = (
-                "<br/><br/>...some text eliminated here because file size is larger than maximum viewing size of %s...<br/><br/>"
-                % util.nice_size(basic_util.MAX_DISPLAY_SIZE)
-            )
+            join_by_str = f"<br/><br/>...some text eliminated here because file size is larger than maximum viewing size of {util.nice_size(basic_util.MAX_DISPLAY_SIZE)}...<br/><br/>"
             safe_str = util.shrink_string_by_size(
                 safe_str,
                 basic_util.MAX_DISPLAY_SIZE,
diff --git a/lib/tool_shed/webapp/controllers/user.py b/lib/tool_shed/webapp/controllers/user.py
index 2740ee9f6c7d..eb9a11878eba 100644
--- a/lib/tool_shed/webapp/controllers/user.py
+++ b/lib/tool_shed/webapp/controllers/user.py
@@ -85,8 +85,9 @@ def login(self, trans, refresh_frames=None, **kwd):
         if not success and not user and trans.app.config.require_login:
             if trans.app.config.allow_user_creation:
                 create_account_str = (
-                    "  If you don't already have an account, <a href='%s'>you may create one</a>."
-                    % web.url_for(controller="user", action="create", cntrller="user")
+                    "  If you don't already have an account, <a href='{}'>you may create one</a>.".format(
+                        web.url_for(controller="user", action="create", cntrller="user")
+                    )
                 )
                 header = REQUIRE_LOGIN_TEMPLATE % ("Galaxy tool shed", create_account_str)
             else:
@@ -243,9 +244,9 @@ def reset_password(self, trans, email=None, **kwd):
             if not message:
                 # Default to a non-userinfo-leaking response message
                 message = (
-                    "Your reset request for %s has been received.  "
+                    f"Your reset request for {escape(email)} has been received.  "
                     "Please check your email account for more instructions.  "
-                    "If you do not receive an email shortly, please contact an administrator." % (escape(email))
+                    "If you do not receive an email shortly, please contact an administrator."
                 )
                 reset_user = get_user_by_email(trans.sa_session, email, trans.app.model.User)
                 if not reset_user:
@@ -476,9 +477,7 @@ def change_password(self, trans, token=None, id=None, **kwd):
     @web.expose
     def logout(self, trans, logout_all=False, **kwd):
         trans.handle_user_logout(logout_all=logout_all)
-        message = 'You have been logged out.<br>To log in again <a target="_top" href="%s">go to the home page</a>.' % (
-            url_for("/")
-        )
+        message = f'You have been logged out.<br>To log in again <a target="_top" href="{url_for("/")}">go to the home page</a>.'
         if trans.app.config.use_remote_user and trans.app.config.remote_user_logout_href:
             trans.response.send_redirect(trans.app.config.remote_user_logout_href)
         else:
diff --git a/scripts/api/common.py b/scripts/api/common.py
index 9dca44f367fb..7a9cc62b6ec9 100644
--- a/scripts/api/common.py
+++ b/scripts/api/common.py
@@ -36,7 +36,7 @@ def get(api_key, url):
     try:
         return json.loads(urlopen(url).read())
     except ValueError as e:
-        print("URL did not return JSON data: %s" % e)
+        print(f"URL did not return JSON data: {e}")
         sys.exit(1)
 
 
@@ -87,14 +87,14 @@ def display(api_key, url, return_formatted=True):
         print("------------------")
         for n, i in enumerate(r):
             if isinstance(i, str):
-                print("  %s" % i)
+                print(f"  {i}")
             else:
                 # All collection members should have a name in the response.
                 # url is optional
                 if "url" in i:
                     print("#%d: %s" % (n + 1, i.pop("url")))
                 if "name" in i:
-                    print("  name: %s" % i.pop("name"))
+                    print(f"  name: {i.pop('name')}")
                 try:
                     for k, v in i.items():
                         print(f"  {k}: {v}")
@@ -112,7 +112,7 @@ def display(api_key, url, return_formatted=True):
     elif isinstance(r, str):
         print(r)
     else:
-        print("response is unknown type: %s" % type(r))
+        print(f"response is unknown type: {type(r)}")
 
 
 def submit(api_key, url, data, return_formatted=True):
@@ -143,7 +143,7 @@ def submit(api_key, url, data, return_formatted=True):
                 else:
                     print("----")
                 if "name" in i:
-                    print("  name: %s" % i.pop("name"))
+                    print(f"  name: {i.pop('name')}")
                 for k, v in i.items():
                     print(f"  {k}: {v}")
             else:
diff --git a/scripts/api/data_manager_example_execute.py b/scripts/api/data_manager_example_execute.py
index 5e7e7dc28843..9ece98404625 100644
--- a/scripts/api/data_manager_example_execute.py
+++ b/scripts/api/data_manager_example_execute.py
@@ -47,7 +47,7 @@ def run_tool(tool_id, history_id, params, api_key, galaxy_url, wait=True, sleep_
 
 
 def get_dataset_state(hda_id, api_key, galaxy_url):
-    datasets_url = urljoin(galaxy_url, "api/datasets/%s" % hda_id)
+    datasets_url = urljoin(galaxy_url, f"api/datasets/{hda_id}")
     dataset_info = get(api_key, datasets_url)
     return dataset_info["state"]
 
@@ -117,7 +117,7 @@ def dataset_is_terminal(hda_id, api_key, galaxy_url):
                 wait=False,
             )
         else:
-            "dbkey (%s) was specified more than once, skipping additional specification." % (dbkey)
+            f"dbkey ({dbkey}) was specified more than once, skipping additional specification."
 
     print("Genomes Queued for downloading.")
 
diff --git a/scripts/api/display.py b/scripts/api/display.py
index d46266c2a9ce..6e3513e9d284 100755
--- a/scripts/api/display.py
+++ b/scripts/api/display.py
@@ -9,7 +9,7 @@
 try:
     display(*sys.argv[1:3])
 except TypeError as e:
-    print("usage: %s key url" % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url")
     print(e)
     sys.exit(1)
 except URLError as e:
diff --git a/scripts/api/example_watch_folder.py b/scripts/api/example_watch_folder.py
index dd11c594022f..5e12bfd530d6 100755
--- a/scripts/api/example_watch_folder.py
+++ b/scripts/api/example_watch_folder.py
@@ -33,11 +33,11 @@ def main(api_key, api_url, in_folder, out_folder, data_library, workflow):
         lib_create_data = {"name": data_library}
         library = submit(api_key, api_url + "libraries", lib_create_data, return_formatted=False)
         library_id = library[0]["id"]
-    folders = display(api_key, api_url + "libraries/%s/contents" % library_id, return_formatted=False)
+    folders = display(api_key, api_url + f"libraries/{library_id}/contents", return_formatted=False)
     for f in folders:
         if f["name"] == "/":
             library_folder_id = f["id"]
-    workflow = display(api_key, api_url + "workflows/%s" % workflow, return_formatted=False)
+    workflow = display(api_key, api_url + f"workflows/{workflow}", return_formatted=False)
     if not workflow:
         print("Workflow %s not found, terminating.")
         sys.exit(1)
@@ -57,7 +57,7 @@ def main(api_key, api_url, in_folder, out_folder, data_library, workflow):
                 data["upload_option"] = "upload_paths"
                 data["filesystem_paths"] = fullpath
                 data["create_type"] = "file"
-                libset = submit(api_key, api_url + "libraries/%s/contents" % library_id, data, return_formatted=False)
+                libset = submit(api_key, api_url + f"libraries/{library_id}/contents", data, return_formatted=False)
                 # TODO Handle this better, but the datatype isn't always
                 # set for the followup workflow execution without this
                 # pause.
@@ -88,6 +88,6 @@ def main(api_key, api_url, in_folder, out_folder, data_library, workflow):
         data_library = sys.argv[5]
         workflow = sys.argv[6]
     except IndexError:
-        print("usage: %s key url in_folder out_folder data_library workflow" % os.path.basename(sys.argv[0]))
+        print(f"usage: {os.path.basename(sys.argv[0])} key url in_folder out_folder data_library workflow")
         sys.exit(1)
     main(api_key, api_url, in_folder, out_folder, data_library, workflow)
diff --git a/scripts/api/filter_failed_datasets_from_collection.py b/scripts/api/filter_failed_datasets_from_collection.py
index 87fc85f30578..1e66a8b7648d 100644
--- a/scripts/api/filter_failed_datasets_from_collection.py
+++ b/scripts/api/filter_failed_datasets_from_collection.py
@@ -16,8 +16,7 @@
 
 if len(sys.argv) < 5:
     print(
-        "Usage: %s <GalaxyUrl> <ApiKey> <HistoryName (must be unique)> <CollectionHistoryId (i.e. the simple integer id)>"
-        % sys.argv[0]
+        f"Usage: {sys.argv[0]} <GalaxyUrl> <ApiKey> <HistoryName (must be unique)> <CollectionHistoryId (i.e. the simple integer id)>"
     )
     exit(0)
 
diff --git a/scripts/api/history_create_history.py b/scripts/api/history_create_history.py
index 210311324e60..df576a9cd9ba 100644
--- a/scripts/api/history_create_history.py
+++ b/scripts/api/history_create_history.py
@@ -8,7 +8,7 @@
 try:
     assert sys.argv[2]
 except IndexError:
-    print("usage: %s key url [name] " % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url [name] ")
     sys.exit(1)
 try:
     data = {}
diff --git a/scripts/api/history_delete_history.py b/scripts/api/history_delete_history.py
index 2c48d5a45331..6b11b2bbffff 100644
--- a/scripts/api/history_delete_history.py
+++ b/scripts/api/history_delete_history.py
@@ -8,7 +8,7 @@
 try:
     assert sys.argv[2]
 except IndexError:
-    print("usage: %s key url [purge (true/false)] " % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url [purge (true/false)] ")
     sys.exit(1)
 try:
     data = {}
diff --git a/scripts/api/import_library_dataset_to_history.py b/scripts/api/import_library_dataset_to_history.py
index 75d0e8a9095e..c3440c5de51b 100644
--- a/scripts/api/import_library_dataset_to_history.py
+++ b/scripts/api/import_library_dataset_to_history.py
@@ -10,7 +10,7 @@
     data = {}
     data["from_ld_id"] = sys.argv[3]
 except IndexError:
-    print("usage: %s key url library_file_id" % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url library_file_id")
     print("    library_file_id is from /api/libraries/<library_id>/contents/<library_file_id>")
     sys.exit(1)
 
diff --git a/scripts/api/library_create_folder.py b/scripts/api/library_create_folder.py
index 8df85a5f46d9..e77bc27511d3 100755
--- a/scripts/api/library_create_folder.py
+++ b/scripts/api/library_create_folder.py
@@ -11,7 +11,7 @@
     data["name"] = sys.argv[4]
     data["create_type"] = "folder"
 except IndexError:
-    print("usage: %s key url folder_id name [description]" % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url folder_id name [description]")
     sys.exit(1)
 try:
     data["description"] = sys.argv[5]
diff --git a/scripts/api/library_create_library.py b/scripts/api/library_create_library.py
index b9485c2b1554..514a7129cded 100755
--- a/scripts/api/library_create_library.py
+++ b/scripts/api/library_create_library.py
@@ -9,7 +9,7 @@
     data = {}
     data["name"] = sys.argv[3]
 except IndexError:
-    print("usage: %s key url name [description] [synopsys]" % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url name [description] [synopsys]")
     sys.exit(1)
 try:
     data["description"] = sys.argv[4]
diff --git a/scripts/api/library_upload_from_import_dir.py b/scripts/api/library_upload_from_import_dir.py
index 09a42a91d127..a9678eb5937e 100755
--- a/scripts/api/library_upload_from_import_dir.py
+++ b/scripts/api/library_upload_from_import_dir.py
@@ -18,7 +18,7 @@
     data["upload_option"] = "upload_directory"
     data["create_type"] = "file"
 except IndexError:
-    print("usage: %s key url folder_id file_type server_dir dbkey" % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url folder_id file_type server_dir dbkey")
     sys.exit(1)
 
 submit(sys.argv[1], sys.argv[2], data)
diff --git a/scripts/api/load_data_with_metadata.py b/scripts/api/load_data_with_metadata.py
index 47e6a7080f12..ee24fbc0f2f5 100755
--- a/scripts/api/load_data_with_metadata.py
+++ b/scripts/api/load_data_with_metadata.py
@@ -39,7 +39,7 @@ def load_file(fullpath, api_key, api_url, library_id, library_folder_id, uuid_fi
     if uuid_field is not None and uuid_field in ext_meta:
         data["uuid"] = ext_meta[uuid_field]
 
-    libset = submit(api_key, api_url + "libraries/%s/contents" % library_id, data, return_formatted=True)
+    libset = submit(api_key, api_url + f"libraries/{library_id}/contents", data, return_formatted=True)
     print(libset)
 
 
@@ -54,7 +54,7 @@ def main(api_key, api_url, in_folder, data_library, uuid_field=None):
         lib_create_data = {"name": data_library}
         library = submit(api_key, api_url + "libraries", lib_create_data, return_formatted=False)
         library_id = library["id"]
-    folders = display(api_key, api_url + "libraries/%s/contents" % library_id, return_formatted=False)
+    folders = display(api_key, api_url + f"libraries/{library_id}/contents", return_formatted=False)
     for f in folders:
         if f["name"] == "/":
             library_folder_id = f["id"]
diff --git a/scripts/api/reset_metadata_on_installed_repositories.py b/scripts/api/reset_metadata_on_installed_repositories.py
index 150f809c0a44..69cdd09d8cb7 100644
--- a/scripts/api/reset_metadata_on_installed_repositories.py
+++ b/scripts/api/reset_metadata_on_installed_repositories.py
@@ -15,7 +15,7 @@
 
 def main(options):
     base_galaxy_url = options.galaxy_url.rstrip("/")
-    url = "%s/api/tool_shed_repositories/reset_metadata_on_installed_repositories" % base_galaxy_url
+    url = f"{base_galaxy_url}/api/tool_shed_repositories/reset_metadata_on_installed_repositories"
     submit(options.api, url, {})
 
 
diff --git a/scripts/api/workflow_delete.py b/scripts/api/workflow_delete.py
index 9972a9b1359c..3ccea68a017d 100644
--- a/scripts/api/workflow_delete.py
+++ b/scripts/api/workflow_delete.py
@@ -17,7 +17,7 @@
 try:
     assert sys.argv[2]
 except IndexError:
-    print("usage: %s key url [purge (true/false)] " % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url [purge (true/false)] ")
     sys.exit(1)
 try:
     data = {}
diff --git a/scripts/api/workflow_execute.py b/scripts/api/workflow_execute.py
index 18824704d92e..a8def8bf8867 100755
--- a/scripts/api/workflow_execute.py
+++ b/scripts/api/workflow_execute.py
@@ -24,7 +24,7 @@ def main():
             step, src, ds_id = v.split("=")
             data["ds_map"][step] = {"src": src, "id": ds_id}
     except IndexError:
-        print("usage: %s key url workflow_id history step=src=dataset_id" % os.path.basename(sys.argv[0]))
+        print(f"usage: {os.path.basename(sys.argv[0])} key url workflow_id history step=src=dataset_id")
         sys.exit(1)
     submit(sys.argv[1], sys.argv[2], data)
 
diff --git a/scripts/api/workflow_execute_parameters.py b/scripts/api/workflow_execute_parameters.py
index 280976f8d3f5..a9693869ee21 100644
--- a/scripts/api/workflow_execute_parameters.py
+++ b/scripts/api/workflow_execute_parameters.py
@@ -46,7 +46,7 @@ def main():
                     print("TOOL ID ERROR:")
 
     except IndexError:
-        print("usage: %s key url workflow_id history step=src=dataset_id" % os.path.basename(sys.argv[0]))
+        print(f"usage: {os.path.basename(sys.argv[0])} key url workflow_id history step=src=dataset_id")
         sys.exit(1)
     submit(sys.argv[1], sys.argv[2], data)
 
diff --git a/scripts/api/workflow_import.py b/scripts/api/workflow_import.py
index 1f78d9567518..98d1a68e6b69 100755
--- a/scripts/api/workflow_import.py
+++ b/scripts/api/workflow_import.py
@@ -14,14 +14,14 @@
 def main():
     api_key = sys.argv[1]
     api_base_url = sys.argv[2]
-    api_url = "%s/api/workflows" % api_base_url
+    api_url = f"{api_base_url}/api/workflows"
     try:
         data = {}
         data["installed_repository_file"] = sys.argv[3]
         if len(sys.argv) > 4 and sys.argv[4] == "--add_to_menu":
             data["add_to_menu"] = True
     except IndexError:
-        print("usage: %s key galaxy_url workflow_file" % os.path.basename(sys.argv[0]))
+        print(f"usage: {os.path.basename(sys.argv[0])} key galaxy_url workflow_file")
         sys.exit(1)
     submit(api_key, api_url, data, return_formatted=False)
 
diff --git a/scripts/api/workflow_import_from_file_rpark.py b/scripts/api/workflow_import_from_file_rpark.py
index 31242d8b25db..47508311c765 100644
--- a/scripts/api/workflow_import_from_file_rpark.py
+++ b/scripts/api/workflow_import_from_file_rpark.py
@@ -20,7 +20,7 @@ def openWorkflow(in_file):
 try:
     assert sys.argv[2]
 except IndexError:
-    print("usage: %s key url [name] " % os.path.basename(sys.argv[0]))
+    print(f"usage: {os.path.basename(sys.argv[0])} key url [name] ")
     sys.exit(1)
 try:
     data = {}
diff --git a/scripts/apply_tags.py b/scripts/apply_tags.py
index fa4ebb258bb3..bec742db8ab9 100644
--- a/scripts/apply_tags.py
+++ b/scripts/apply_tags.py
@@ -29,12 +29,12 @@ def read_galaxy_history(self):
             try:
                 update_history = history.show_history(self.history_id)
             except Exception as exception:
-                print("Some problem occurred with history: %s" % self.history_id)
+                print(f"Some problem occurred with history: {self.history_id}")
                 print(exception)
                 return
         update_history_id = update_history["id"]
-        print("History name: %s" % update_history["name"])
-        print("History id: %s" % update_history_id)
+        print(f"History name: {update_history['name']}")
+        print(f"History id: {update_history_id}")
         self.find_dataset_parents_update_tags(history, job, update_history_id)
 
     def find_dataset_parents_update_tags(self, history, job, history_id):
diff --git a/scripts/build_toolbox.py b/scripts/build_toolbox.py
index d471bc9b8d77..f26e571dcb9e 100644
--- a/scripts/build_toolbox.py
+++ b/scripts/build_toolbox.py
@@ -141,7 +141,7 @@ def scanfiles(filenamelist):
             newtoolelement = ET.Element("tool", attrib)
             toolboxpositionelements = toolelement.findall("toolboxposition")
             if not toolboxpositionelements:
-                print("DBG> %s has no toolboxposition" % fn)
+                print(f"DBG> {fn} has no toolboxposition")
             else:
                 for toolboxpositionelement in toolboxpositionelements:
                     toolbox.add(newtoolelement, toolboxpositionelement)
diff --git a/scripts/check_python.py b/scripts/check_python.py
index 62a8cfbfa59e..766d67904fe2 100644
--- a/scripts/check_python.py
+++ b/scripts/check_python.py
@@ -3,6 +3,8 @@
 message to stderr and returns 1
 """
 
+from __future__ import print_function  # noqa: UP010
+
 import sys
 
 
@@ -13,13 +15,12 @@ def check_python():
     else:
         version_string = ".".join(str(_) for _ in sys.version_info[:3])
         msg = (
-            """\
-ERROR: Your Python version is: %s
+            """ERROR: Your Python version is: %s
 Galaxy is currently supported on Python >=3.8 .
 To run Galaxy, please install a supported Python version.
 If a supported version is already installed but is not your default,
 https://docs.galaxyproject.org/en/latest/admin/python.html contains instructions
-on how to force Galaxy to use a different version."""
+on how to force Galaxy to use a different version."""  # noqa: UP031
             % version_string
         )
         print(msg, file=sys.stderr)
diff --git a/scripts/cleanup_datasets/admin_cleanup_datasets.py b/scripts/cleanup_datasets/admin_cleanup_datasets.py
index f9050c58e87e..5c78ff0382b3 100755
--- a/scripts/cleanup_datasets/admin_cleanup_datasets.py
+++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py
@@ -151,7 +151,7 @@ def main():
     template_file = args.template
     if template_file is None:
         default_template = os.path.join(scriptdir, "admin_cleanup_deletion_template.txt")
-        sample_template_file = "%s.sample" % default_template
+        sample_template_file = f"{default_template}.sample"
         if os.path.exists(default_template):
             template_file = default_template
         elif os.path.exists(sample_template_file):
@@ -164,7 +164,7 @@ def main():
                 "found, please specify template as an option (--template)."
             )
     elif not os.path.exists(template_file):
-        parser.error("Specified template file (%s) not found." % template_file)
+        parser.error(f"Specified template file ({template_file}) not found.")
 
     config = galaxy.config.Configuration(**app_properties)
 
@@ -273,9 +273,9 @@ def administrative_delete_datasets(
         subject = "Galaxy Server Cleanup " "- %d datasets DELETED" % len(dataset_list)
         fromaddr = config.email_from
         print()
-        print("From: %s" % fromaddr)
-        print("To: %s" % email)
-        print("Subject: %s" % subject)
+        print(f"From: {fromaddr}")
+        print(f"To: {email}")
+        print(f"Subject: {subject}")
         print("----------")
         print(msgtext)
         if not info_only:
diff --git a/scripts/cleanup_datasets/pgcleanup.py b/scripts/cleanup_datasets/pgcleanup.py
index 7ff09d7c4a5a..325cd6b24b08 100755
--- a/scripts/cleanup_datasets/pgcleanup.py
+++ b/scripts/cleanup_datasets/pgcleanup.py
@@ -143,22 +143,22 @@ def __open_log(self):
         else:
             logf = os.path.join(self._log_dir, self.name + ".log")
         if self._dry_run:
-            log.info("--dry-run specified, logging changes to stderr instead of log file: %s" % logf)
+            log.info("--dry-run specified, logging changes to stderr instead of log file: %s", logf)
             h = set_log_handler()
         else:
-            log.info("Opening log file: %s" % logf)
+            log.info("Opening log file: %s", logf)
             h = set_log_handler(filename=logf)
         h.setLevel(logging.DEBUG if self._debug else logging.INFO)
         h.setFormatter(LevelFormatter())
         self.__log = logging.getLogger(self.name)
         self.__log.addHandler(h)
         self.__log.propagate = False
-        m = ("==== Log opened: %s " % datetime.datetime.now().isoformat()).ljust(72, "=")
+        m = (f"==== Log opened: {datetime.datetime.now().isoformat()} ").ljust(72, "=")
         self.__log.info(m)
-        self.__log.info(f"Epoch time for this action: {self._epoch_time}")
+        self.__log.info("Epoch time for this action: %s", self._epoch_time)
 
     def __close_log(self):
-        m = ("==== Log closed: %s " % datetime.datetime.now().isoformat()).ljust(72, "=")
+        m = (f"==== Log closed: {datetime.datetime.now().isoformat()} ").ljust(72, "=")
         self.log.info(m)
         self.__log = None
 
@@ -1221,7 +1221,7 @@ def conn(self):
             self.__conn = psycopg2.connect(cursor_factory=NamedTupleCursor, **args)
             # TODO: is this per session or cursor?
             if self.args.work_mem is not None:
-                log.info("Setting work_mem to %s" % self.args.work_mem)
+                log.info("Setting work_mem to %s", self.args.work_mem)
                 self.__conn.cursor().execute("SET work_mem TO %s", (self.args.work_mem,))
         return self.__conn
 
@@ -1271,7 +1271,7 @@ def __parse_args(self):
             nargs="*",
             metavar="ACTION",
             default=[],
-            help="Action(s) to perform, chosen from: %s" % ", ".join(sorted(self.actions.keys())),
+            help="Action(s) to perform, chosen from: {}".format(", ".join(sorted(self.actions.keys()))),
         )
         self.args = parser.parse_args()
 
@@ -1292,7 +1292,7 @@ def __validate_actions(self):
         ok = True
         for name in self.args.actions:
             if name not in self.actions.keys():
-                log.error("Unknown action in sequence: %s" % name)
+                log.error("Unknown action in sequence: %s", name)
                 ok = False
         if not ok:
             log.critical("Exiting due to previous error(s)")
@@ -1381,7 +1381,7 @@ def run(self):
             self.__current_action = name
             with cls(self) as action:
                 self._run_action(action)
-            log.info("Finished %s" % name)
+            log.info("Finished %s", name)
 
 
 if __name__ == "__main__":
diff --git a/scripts/config_sample_to_kwalify.py b/scripts/config_sample_to_kwalify.py
index 5ced81c081fa..6d7357751c06 100644
--- a/scripts/config_sample_to_kwalify.py
+++ b/scripts/config_sample_to_kwalify.py
@@ -55,14 +55,14 @@ def print_line(line):
             type = "str"
     if default == "None":
         default = None
-    print_line("%s:" % key)
-    print_line("  type: %s" % type)
+    print_line(f"{key}:")
+    print_line(f"  type: {type}")
     if default is not None:
-        print_line("  default: %s" % default)
+        print_line(f"  default: {default}")
     # print_line("  required: false")
     print_line("  desc: |")
     for line in current_section_desc:
-        print_line("    %s" % line)
+        print_line(f"    {line}")
     print_line("")
 
 
diff --git a/scripts/db_shell.py b/scripts/db_shell.py
index e1a1da3455bc..44e8803f58de 100644
--- a/scripts/db_shell.py
+++ b/scripts/db_shell.py
@@ -85,7 +85,7 @@ def render_literal_value(self, value, type_):
             """
             if isinstance(value, str):
                 value = value.replace("'", "''")
-                return "'%s'" % value
+                return f"'{value}'"
             elif value is None:
                 return "NULL"
             elif isinstance(value, (float, int)):
@@ -93,10 +93,10 @@ def render_literal_value(self, value, type_):
             elif isinstance(value, decimal.Decimal):
                 return str(value)
             elif isinstance(value, datetime.datetime):
-                return "TO_DATE('%s','YYYY-MM-DD HH24:MI:SS')" % value.strftime("%Y-%m-%d %H:%M:%S")
+                return f"TO_DATE('{value.strftime('%Y-%m-%d %H:%M:%S')}','YYYY-MM-DD HH24:MI:SS')"
 
             else:
-                raise NotImplementedError("Don't know how to literal-quote value %r" % value)
+                raise NotImplementedError(f"Don't know how to literal-quote value {value!r}")
 
     compiler = LiteralCompiler(dialect, statement)
     print(compiler.process(statement))
diff --git a/scripts/drmaa_external_killer.py b/scripts/drmaa_external_killer.py
index e7c53b18df05..f07d5477c421 100755
--- a/scripts/drmaa_external_killer.py
+++ b/scripts/drmaa_external_killer.py
@@ -14,7 +14,7 @@
 
 def validate_paramters():
     if len(sys.argv) < 3:
-        sys.stderr.write("usage: %s [job ID] [user uid]\n" % sys.argv[0])
+        sys.stderr.write(f"usage: {sys.argv[0]} [job ID] [user uid]\n")
         exit(1)
 
     jobID = sys.argv[1]
diff --git a/scripts/drmaa_external_runner.py b/scripts/drmaa_external_runner.py
index eba22c466efb..c07e164721a9 100755
--- a/scripts/drmaa_external_runner.py
+++ b/scripts/drmaa_external_runner.py
@@ -50,14 +50,14 @@ def get_user_id_by_name(username):
     try:
         pw = pwd.getpwnam(username)
     except KeyError:
-        sys.stderr.write("error: User name (%s) is not valid.\n" % username)
+        sys.stderr.write(f"error: User name ({username}) is not valid.\n")
         exit(1)
     return pw.pw_uid
 
 
 def json_file_exists(json_filename):
     if not os.path.exists(json_filename):
-        sys.stderr.write("error: JobTemplate file (%s) doesn't exist\n" % (json_filename))
+        sys.stderr.write(f"error: JobTemplate file ({json_filename}) doesn't exist\n")
         exit(1)
 
     return True
@@ -70,7 +70,7 @@ def validate_paramters():
         sys.argv.remove("--assign_all_groups")
 
     if len(sys.argv) < 3:
-        sys.stderr.write("usage: %s [USER-ID] [JSON-JOB-TEMPLATE-FILE]\n" % sys.argv[0])
+        sys.stderr.write(f"usage: {sys.argv[0]} [USER-ID] [JSON-JOB-TEMPLATE-FILE]\n")
         exit(1)
 
     userid = sys.argv[1]
diff --git a/scripts/dump_library_paths.py b/scripts/dump_library_paths.py
index 504b348eb2fa..4f0aacc04548 100644
--- a/scripts/dump_library_paths.py
+++ b/scripts/dump_library_paths.py
@@ -138,11 +138,11 @@ def _get_library_dataset_paths(args, kwargs):
         filename = object_store.get_filename(dataset)
         files_dir = dataset.get_extra_files_path()
         if (args.exists and object_store.exists(dataset)) or not args.exists:
-            output.write("%s\n" % _path(filename, args))
+            output.write(f"{_path(filename, args)}\n")
         elif args.exists:
             log.warning("Missing %s", filename)
         if files_dir and os.path.exists(files_dir):
-            output.write("%s\n" % _path(files_dir, args))
+            output.write(f"{_path(files_dir, args)}\n")
         last_library = library
     output.close()
 
diff --git a/scripts/external_chown_script.py b/scripts/external_chown_script.py
index 2032e5dd90cb..a08116b94a48 100755
--- a/scripts/external_chown_script.py
+++ b/scripts/external_chown_script.py
@@ -15,7 +15,7 @@
 
 def validate_parameters():
     if len(sys.argv) < 4:
-        sys.stderr.write("usage: %s path user_name gid\n" % sys.argv[0])
+        sys.stderr.write(f"usage: {sys.argv[0]} path user_name gid\n")
         exit(1)
 
     path = os.path.abspath(sys.argv[1])
@@ -28,7 +28,7 @@ def validate_parameters():
                 allowed = True
                 break
     if not allowed:
-        sys.stderr.write("owner and group modifications in %s are not allowed\n" % path)
+        sys.stderr.write(f"owner and group modifications in {path} are not allowed\n")
         sys.exit(1)
 
     galaxy_user_name = sys.argv[2]
@@ -44,7 +44,7 @@ def main():
         (stdoutdata, stderrdata) = p.communicate()
         exitcode = p.returncode
         if exitcode != 0:
-            sys.exit("external_chown_script: could not chown\ncmd was %s\n" % " ".join(cmd))
+            sys.exit("external_chown_script: could not chown\ncmd was {}\n".format(" ".join(cmd)))
 
 
 if __name__ == "__main__":
diff --git a/scripts/grt/export.py b/scripts/grt/export.py
index c5e15276b98e..aaa0da2d502d 100644
--- a/scripts/grt/export.py
+++ b/scripts/grt/export.py
@@ -56,7 +56,7 @@ def kw_metrics(job):
 
 def round_to_2sd(number):
     if number:
-        return str(int(float("%.2g" % number)))
+        return str(int(float(f"{number:.2g}")))
     else:
         return "-1"
 
diff --git a/scripts/loc_files/create_all_fasta_loc.py b/scripts/loc_files/create_all_fasta_loc.py
index e785b01509ce..cf891e081ac2 100644
--- a/scripts/loc_files/create_all_fasta_loc.py
+++ b/scripts/loc_files/create_all_fasta_loc.py
@@ -272,16 +272,16 @@ def __main__():
         paths_to_look_in = [os.path.join(options.genome_dir, "%s")]
 
     # say what we're looking in
-    print("\nLooking in:\n\t%s" % "\n\t".join(p % "<build_name>" for p in paths_to_look_in))
-    poss_names = ["<build_name>%s" % _ for _ in variants]
-    print("for files that are named %s" % ", ".join(poss_names[:-1]), end=" ")
+    print("\nLooking in:\n\t{}".format("\n\t".join(p % "<build_name>" for p in paths_to_look_in)))
+    poss_names = [f"<build_name>{_}" for _ in variants]
+    print("for files that are named {}".format(", ".join(poss_names[:-1])), end=" ")
     if len(poss_names) > 1:
-        print("or %s" % poss_names[-1], end=" ")
+        print(f"or {poss_names[-1]}", end=" ")
     if len(options.fasta_exts) == 1:
-        print("with the extension %s." % ", ".join(fasta_exts[:-1]))
+        print("with the extension {}.".format(", ".join(fasta_exts[:-1])))
     else:
         print("with the extension {} or {}.".format(", ".join(fasta_exts[:-1]), fasta_exts[-1]))
-    print("\nSkipping the following:\n\t%s" % "\n\t".join(exemptions))
+    print("\nSkipping the following:\n\t{}".format("\n\t".join(exemptions)))
 
     # get column names
     col_values = []
@@ -350,40 +350,33 @@ def __main__():
 
     # output results
     print(
-        "\nThere were %s fasta files found that were not included because they did not have the expected file names."
-        % len(unmatching_fasta_paths)
+        f"\nThere were {len(unmatching_fasta_paths)} fasta files found that were not included because they did not have the expected file names."
     )
-    print("%s fasta files were found and listed.\n" % len(fasta_locs.keys()))
+    print(f"{len(fasta_locs.keys())} fasta files were found and listed.\n")
 
     # output unmatching fasta files
     if options.unmatching_fasta and unmatching_fasta_paths:
-        open(options.unmatching_fasta, "wb").write("%s\n" % "\n".join(unmatching_fasta_paths))
+        open(options.unmatching_fasta, "wb").write("{}\n".format("\n".join(unmatching_fasta_paths)))
 
     # output loc file
-    if options.append:
-        all_fasta_loc = open(loc_path, "ab")
-    else:
-        all_fasta_loc = open(loc_path, "wb")
-    # put sample loc file text at top of file if appropriate
-    if sample_text:
-        if options.loc_sample_name:
-            all_fasta_loc.write("%s\n" % open(options.loc_sample_name, "rb").read().strip())
-        else:
-            all_fasta_loc.write("%s\n" % open("%s.sample" % loc_path, "rb").read().strip())
-    # output list of fasta files in alphabetical order
-    fasta_bases = list(fasta_locs.keys())
-    fasta_bases.sort(key=str.upper)
-    for fb in fasta_bases:
-        out_line = []
-        for col in col_values:
-            try:
-                out_line.append(fasta_locs[fb][col])
-            except KeyError:
-                raise Exception("Unexpected column (%s) encountered" % col)
-        if out_line:
-            all_fasta_loc.write("%s\n" % "\t".join(out_line))
-    # close up output loc file
-    all_fasta_loc.close()
+    with open(loc_path, "ab" if options.append else "wb") as all_fasta_loc:
+        # put sample loc file text at top of file if appropriate
+        if sample_text:
+            loc_sample_name = options.loc_sample_name if options.loc_sample_name else f"{loc_path}.sample"
+            with open(loc_sample_name, "rb") as loc_sample_name_fh:
+                all_fasta_loc.write(f"{loc_sample_name_fh.read().strip()}\n")
+        # output list of fasta files in alphabetical order
+        fasta_bases = list(fasta_locs.keys())
+        fasta_bases.sort(key=str.upper)
+        for fb in fasta_bases:
+            out_line = []
+            for col in col_values:
+                try:
+                    out_line.append(fasta_locs[fb][col])
+                except KeyError:
+                    raise Exception(f"Unexpected column ({col}) encountered")
+            if out_line:
+                all_fasta_loc.write("{}\n".format("\t".join(out_line)))
 
 
 if __name__ == "__main__":
diff --git a/scripts/microbes/create_bacteria_loc_file.py b/scripts/microbes/create_bacteria_loc_file.py
index f9dae93dbd1e..ea12b7cb57ee 100644
--- a/scripts/microbes/create_bacteria_loc_file.py
+++ b/scripts/microbes/create_bacteria_loc_file.py
@@ -95,11 +95,11 @@ def __main__():
                     chr["chromosome"],
                     "sequence",
                     "fasta",
-                    os.path.join(org["base_dir"], "%s.fna" % chr["chromosome"]),
+                    os.path.join(org["base_dir"], f"{chr['chromosome']}.fna"),
                 )
             )
             # GeneMark
-            if os.path.exists(os.path.join(org["base_dir"], "%s.GeneMark.bed" % chr["chromosome"])):
+            if os.path.exists(os.path.join(org["base_dir"], f"{chr['chromosome']}.GeneMark.bed")):
                 print(
                     "DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(
                         build,
@@ -109,11 +109,11 @@ def __main__():
                         chr["chromosome"],
                         "GeneMark",
                         "bed",
-                        os.path.join(org["base_dir"], "%s.GeneMark.bed" % chr["chromosome"]),
+                        os.path.join(org["base_dir"], f"{chr['chromosome']}.GeneMark.bed"),
                     )
                 )
             # GenMarkHMM
-            if os.path.exists(os.path.join(org["base_dir"], "%s.GeneMarkHMM.bed" % chr["chromosome"])):
+            if os.path.exists(os.path.join(org["base_dir"], f"{chr['chromosome']}.GeneMarkHMM.bed")):
                 print(
                     "DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(
                         build,
@@ -123,11 +123,11 @@ def __main__():
                         chr["chromosome"],
                         "GeneMarkHMM",
                         "bed",
-                        os.path.join(org["base_dir"], "%s.GeneMarkHMM.bed" % chr["chromosome"]),
+                        os.path.join(org["base_dir"], f"{chr['chromosome']}.GeneMarkHMM.bed"),
                     )
                 )
             # Glimmer3
-            if os.path.exists(os.path.join(org["base_dir"], "%s.Glimmer3.bed" % chr["chromosome"])):
+            if os.path.exists(os.path.join(org["base_dir"], f"{chr['chromosome']}.Glimmer3.bed")):
                 print(
                     "DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(
                         build,
@@ -137,7 +137,7 @@ def __main__():
                         chr["chromosome"],
                         "Glimmer3",
                         "bed",
-                        os.path.join(org["base_dir"], "%s.Glimmer3.bed" % chr["chromosome"]),
+                        os.path.join(org["base_dir"], f"{chr['chromosome']}.Glimmer3.bed"),
                     )
                 )
 
diff --git a/scripts/microbes/create_nib_seq_loc_file.py b/scripts/microbes/create_nib_seq_loc_file.py
index 3a79d9b84e5d..1ced877e34de 100644
--- a/scripts/microbes/create_nib_seq_loc_file.py
+++ b/scripts/microbes/create_nib_seq_loc_file.py
@@ -74,8 +74,8 @@ def __main__():
         for chr in org["chrs"]:
             chr = org["chrs"][chr]
 
-            fasta_file = os.path.join(org["base_dir"], "%s.fna" % chr["chromosome"])
-            nib_out_file = os.path.join(seq_path, "%s.nib " % chr["chromosome"])
+            fasta_file = os.path.join(org["base_dir"], f"{chr['chromosome']}.fna")
+            nib_out_file = os.path.join(seq_path, f"{chr['chromosome']}.nib ")
             # create nibs using faToNib binary
             # TODO: when bx supports writing nib, use it here instead
             command = f"faToNib {fasta_file} {nib_out_file}"
diff --git a/scripts/microbes/harvest_bacteria.py b/scripts/microbes/harvest_bacteria.py
index a94ae088dbae..89a4b59df51e 100644
--- a/scripts/microbes/harvest_bacteria.py
+++ b/scripts/microbes/harvest_bacteria.py
@@ -158,18 +158,18 @@ def process_FASTA(filename, org_num, refseq):
     fasta = "".join(fasta)
 
     # Create Chrom Info File:
-    chrom_info_file = open(os.path.join(os.path.split(filename)[0], "%s.info" % refseq), "wb+")
+    chrom_info_file = open(os.path.join(os.path.split(filename)[0], f"{refseq}.info"), "wb+")
     chrom_info_file.write(f"chromosome={refseq}\nname={chr_name}\nlength={len(fasta)}\norganism={org_num}\n")
     try:
-        chrom_info_file.write("gi=%s\n" % accesions["gi"])
+        chrom_info_file.write(f"gi={accesions['gi']}\n")
     except Exception:
         chrom_info_file.write("gi=None\n")
     try:
-        chrom_info_file.write("gb=%s\n" % accesions["gb"])
+        chrom_info_file.write(f"gb={accesions['gb']}\n")
     except Exception:
         chrom_info_file.write("gb=None\n")
     try:
-        chrom_info_file.write("refseq=%s\n" % refseq)
+        chrom_info_file.write(f"refseq={refseq}\n")
     except Exception:
         chrom_info_file.write("refseq=None\n")
     chrom_info_file.close()
@@ -191,7 +191,7 @@ def process_Glimmer3(filename, org_num, refseq):
     except Exception as e:
         print("Converting Glimmer3 to bed FAILED! For chrom:", refseq, "file:", filename, e)
         glimmer3_bed = []
-    glimmer3_bed_file = open(os.path.join(os.path.split(filename)[0], "%s.Glimmer3.bed" % refseq), "wb+")
+    glimmer3_bed_file = open(os.path.join(os.path.split(filename)[0], f"{refseq}.Glimmer3.bed"), "wb+")
     glimmer3_bed_file.write("\n".join(glimmer3_bed))
     glimmer3_bed_file.close()
 
@@ -202,7 +202,7 @@ def process_GeneMarkHMM(filename, org_num, refseq):
     except Exception as e:
         print("Converting GeneMarkHMM to bed FAILED! For chrom:", refseq, "file:", filename, e)
         geneMarkHMM_bed = []
-    geneMarkHMM_bed_bed_file = open(os.path.join(os.path.split(filename)[0], "%s.GeneMarkHMM.bed" % refseq), "wb+")
+    geneMarkHMM_bed_bed_file = open(os.path.join(os.path.split(filename)[0], f"{refseq}.GeneMarkHMM.bed"), "wb+")
     geneMarkHMM_bed_bed_file.write("\n".join(geneMarkHMM_bed))
     geneMarkHMM_bed_bed_file.close()
 
@@ -213,7 +213,7 @@ def process_GeneMark(filename, org_num, refseq):
     except Exception as e:
         print("Converting GeneMark to bed FAILED! For chrom:", refseq, "file:", filename, e)
         geneMark_bed = []
-    geneMark_bed_bed_file = open(os.path.join(os.path.split(filename)[0], "%s.GeneMark.bed" % refseq), "wb+")
+    geneMark_bed_bed_file = open(os.path.join(os.path.split(filename)[0], f"{refseq}.GeneMark.bed"), "wb+")
     geneMark_bed_bed_file.write("\n".join(geneMark_bed))
     geneMark_bed_bed_file.close()
 
@@ -228,9 +228,9 @@ def __main__():
 
     try:
         os.mkdir(base_dir)
-        print("path '%s' has been created" % base_dir)
+        print(f"path '{base_dir}' has been created")
     except Exception:
-        print("path '%s' seems to already exist" % base_dir)
+        print(f"path '{base_dir}' seems to already exist")
 
     for org_num, name, chroms, kingdom, group, _, _, info_url, ftp_url in iter_genome_projects():
         if chroms is None:
@@ -240,7 +240,7 @@ def __main__():
             org_dir = os.path.join(base_dir, org_num)
             os.mkdir(org_dir)
         except Exception:
-            print("Organism %s already exists on disk, skipping" % org_num)
+            print(f"Organism {org_num} already exists on disk, skipping")
             continue
 
         # get ftp contents
@@ -254,14 +254,14 @@ def __main__():
                 print("Org:", org_num, "chrom:", refseq, "[", time.time() - start_time, "seconds elapsed. ]")
 
         # Create org info file
-        info_file = open(os.path.join(org_dir, "%s.info" % org_num), "wb+")
-        info_file.write("genome project id=%s\n" % org_num)
-        info_file.write("name=%s\n" % name)
-        info_file.write("kingdom=%s\n" % kingdom)
-        info_file.write("group=%s\n" % group)
-        info_file.write("chromosomes=%s\n" % ",".join(chroms))
-        info_file.write("info url=%s\n" % info_url)
-        info_file.write("ftp url=%s\n" % ftp_url)
+        info_file = open(os.path.join(org_dir, f"{org_num}.info"), "wb+")
+        info_file.write(f"genome project id={org_num}\n")
+        info_file.write(f"name={name}\n")
+        info_file.write(f"kingdom={kingdom}\n")
+        info_file.write(f"group={group}\n")
+        info_file.write("chromosomes={}\n".format(",".join(chroms)))
+        info_file.write(f"info url={info_url}\n")
+        info_file.write(f"ftp url={ftp_url}\n")
         info_file.close()
 
     print("Finished Harvesting", "[", time.time() - start_time, "seconds elapsed. ]")
diff --git a/scripts/pages_identifier_conversion.py b/scripts/pages_identifier_conversion.py
index b290206ecbe8..8aaee5f2247c 100644
--- a/scripts/pages_identifier_conversion.py
+++ b/scripts/pages_identifier_conversion.py
@@ -58,11 +58,11 @@ def main(argv):
                     with transaction(session):
                         session.commit()
                 else:
-                    print("Modifying revision %s." % p.id)
+                    print(f"Modifying revision {p.id}.")
                     print(difflib.unified_diff(p.content, newcontent))
         except Exception:
             logging.exception(
-                "Error parsing page, rolling changes back and skipping revision %s.  Please report this error." % p.id
+                "Error parsing page, rolling changes back and skipping revision %s.  Please report this error.", p.id
             )
             session.rollback()
 
diff --git a/scripts/runtime_stats.py b/scripts/runtime_stats.py
index dd11460a2f0e..9e6c9e5277aa 100755
--- a/scripts/runtime_stats.py
+++ b/scripts/runtime_stats.py
@@ -90,7 +90,7 @@ def parse_arguments():
     parser.add_argument("-M", "--max", type=int, default=-1, help="Ignore runtimes greater than MAX seconds")
     parser.add_argument("-u", "--user", help="Return stats for only this user (id, email, " "or username)")
     parser.add_argument(
-        "-s", "--source", default="metrics", help="Runtime data source (SOURCES: %s)" % ", ".join(DATA_SOURCES)
+        "-s", "--source", default="metrics", help="Runtime data source (SOURCES: {})".format(", ".join(DATA_SOURCES))
     )
     args = parser.parse_args()
 
@@ -144,13 +144,13 @@ def query(
             if row:
                 user_id = row[0]
             else:
-                print("Invalid user: %s" % user)
+                print(f"Invalid user: {user}")
                 sys.exit(1)
 
     if like:
-        query_tool_id = "%%/%s/%%" % tool_id
+        query_tool_id = f"%/{tool_id}/%"
     elif "/" in tool_id and not re.match(r"\d+\.\d+", tool_id.split("/")[-1]):
-        query_tool_id = "%s%%" % tool_id
+        query_tool_id = f"{tool_id}%"
         like = True
     else:
         query_tool_id = tool_id
@@ -187,14 +187,14 @@ def query(
         if min > 0 and max > 0:
             time_clause = """WHERE ctimes[1] - ctimes[2] > interval %s
           AND ctimes[1] - ctimes[2] < interval %s"""
-            sql_args.append("%s seconds" % min)
-            sql_args.append("%s seconds" % max)
+            sql_args.append(f"{min} seconds")
+            sql_args.append(f"{max} seconds")
         elif min > 0:
             time_clause = "WHERE ctimes[1] - ctimes[2] > interval %s"
-            sql_args.append("%s seconds" % min)
+            sql_args.append(f"{min} seconds")
         elif max > 0:
             time_clause = "WHERE ctimes[1] - ctimes[2] < interval %s"
-            sql_args.append("%s seconds" % max)
+            sql_args.append(f"{max} seconds")
         else:
             time_clause = ""
         sql = HISTORY_SQL
@@ -218,7 +218,7 @@ def query(
         return
 
     if user:
-        print("Displaying statistics for user %s" % user)
+        print(f"Displaying statistics for user {user}")
 
     stats = (
         ("Mean runtime", numpy.mean(times)),
@@ -229,11 +229,11 @@ def query(
 
     for name, seconds in stats:
         hours, minutes = nice_times(seconds)
-        msg = name + " is %0.0f seconds" % seconds
+        msg = name + f" is {seconds:0.0f} seconds"
         if minutes:
-            msg += " (=%0.2f minutes)" % minutes
+            msg += f" (={minutes:0.2f} minutes)"
         if hours:
-            msg += " (=%0.2f hours)" % hours
+            msg += f" (={hours:0.2f} hours)"
         print(msg)
 
 
diff --git a/scripts/set_user_disk_usage.py b/scripts/set_user_disk_usage.py
index b23b159b0ca8..9c10d3c8f554 100755
--- a/scripts/set_user_disk_usage.py
+++ b/scripts/set_user_disk_usage.py
@@ -62,9 +62,9 @@ def quotacheck(sa_session, users, engine, object_store):
         print("none")
     else:
         if new > current:
-            print("+%s" % (nice_size(new - current)))
+            print(f"+{nice_size(new - current)}")
         else:
-            print("-%s" % (nice_size(current - new)))
+            print(f"-{nice_size(current - new)}")
 
 
 if __name__ == "__main__":
diff --git a/scripts/tests_markdown.py b/scripts/tests_markdown.py
index 1b6fb8edd2c4..1fc53003affd 100644
--- a/scripts/tests_markdown.py
+++ b/scripts/tests_markdown.py
@@ -244,10 +244,10 @@ def summarize_counter(c):
             continue
 
         endpoint_summary = {"total_time": summarize_times(timings), "label": endpoint[len("api.") :]}
-        sql_times = "sql.%s" % endpoint
+        sql_times = f"sql.{endpoint}"
         if sql_times in timing:
             endpoint_summary["sql_time"] = summarize_times(timing[sql_times])
-        sql_queries = "sqlqueries.%s" % endpoint
+        sql_queries = f"sqlqueries.{endpoint}"
         if sql_queries in counter:
             endpoint_summary["sql_queries"] = summarize_counter(counter[sql_queries])
         api_endpoints[endpoint] = endpoint_summary
diff --git a/scripts/tool_shed/api/common.py b/scripts/tool_shed/api/common.py
index 16ad847ec524..fb1ec34bba2f 100644
--- a/scripts/tool_shed/api/common.py
+++ b/scripts/tool_shed/api/common.py
@@ -35,7 +35,7 @@ def display(url, api_key=None, return_formatted=True):
             if "url" in i:
                 print("#%d: %s" % (n + 1, i.pop("url")))
             if "name" in i:
-                print("  name: %s" % i.pop("name"))
+                print(f"  name: {i.pop('name')}")
             for k, v in i.items():
                 print(f"  {k}: {v}")
         print()
@@ -47,7 +47,7 @@ def display(url, api_key=None, return_formatted=True):
         for k, v in r.items():
             print(f"{k}: {v}")
     else:
-        print("response is unknown type: %s" % type(r))
+        print(f"response is unknown type: {type(r)}")
 
 
 def get(url, api_key=None):
@@ -100,7 +100,7 @@ def submit(url, data, api_key=None, return_formatted=True):
                 else:
                     print("----")
                 if "name" in i:
-                    print("  name: %s" % i.pop("name"))
+                    print(f"  name: {i.pop('name')}")
                 for k, v in i.items():
                     print(f"  {k}: {v}")
             else:
diff --git a/scripts/tool_shed/api/create_categories.py b/scripts/tool_shed/api/create_categories.py
index 86c76a1200f8..6f6a7a5a3389 100644
--- a/scripts/tool_shed/api/create_categories.py
+++ b/scripts/tool_shed/api/create_categories.py
@@ -31,7 +31,7 @@ def main(options):
     from_tool_shed = options.from_tool_shed.rstrip("/")
     to_tool_shed = options.to_tool_shed.rstrip("/")
     # Get the categories from the specified Tool Shed.
-    url = "%s/api/categories" % from_tool_shed
+    url = f"{from_tool_shed}/api/categories"
     category_dicts = get(url)
     create_response_dicts = []
     for category_dict in category_dicts:
@@ -39,7 +39,7 @@ def main(options):
         description = category_dict.get("description", None)
         if name is not None and description is not None:
             data = dict(name=name, description=description)
-            url = "%s/api/categories" % to_tool_shed
+            url = f"{to_tool_shed}/api/categories"
             try:
                 response = submit(url, data, api_key)
             except Exception as e:
diff --git a/scripts/tool_shed/api/create_users.py b/scripts/tool_shed/api/create_users.py
index dea8adef38fc..5a6e3f7fa860 100644
--- a/scripts/tool_shed/api/create_users.py
+++ b/scripts/tool_shed/api/create_users.py
@@ -32,16 +32,16 @@ def main(options):
     from_tool_shed = options.from_tool_shed.rstrip("/")
     to_tool_shed = options.to_tool_shed.rstrip("/")
     # Get the users from the specified Tool Shed.
-    url = "%s/api/users" % from_tool_shed
+    url = f"{from_tool_shed}/api/users"
     user_dicts = get(url)
     create_response_dicts = []
     for user_dict in user_dicts:
         username = user_dict.get("username", None)
         if username is not None:
-            email = "%s@test.org" % username
+            email = f"{username}@test.org"
             password = "testuser"
             data = dict(email=email, password=password, username=username)
-            url = "%s/api/users" % to_tool_shed
+            url = f"{to_tool_shed}/api/users"
             try:
                 response = submit(url, data, api_key)
             except Exception as e:
diff --git a/scripts/tool_shed/deprecate_repositories_without_metadata.py b/scripts/tool_shed/deprecate_repositories_without_metadata.py
index beddab51dbd0..6ab395d0354b 100644
--- a/scripts/tool_shed/deprecate_repositories_without_metadata.py
+++ b/scripts/tool_shed/deprecate_repositories_without_metadata.py
@@ -68,7 +68,7 @@ def main():
     try:
         ini_file = args[0]
     except IndexError:
-        sys.exit("Usage: python %s <tool shed .ini file> [options]" % sys.argv[0])
+        sys.exit(f"Usage: python {sys.argv[0]} <tool shed .ini file> [options]")
     config_parser = configparser.ConfigParser({"here": os.getcwd()})
     config_parser.read(ini_file)
     config_dict = {}
@@ -103,7 +103,7 @@ def send_mail_to_owner(app, owner, email, repositories_deprecated, days=14):
     elif url is None:
         print("# Environment variable TOOL_SHED_CANONICAL_URL not set, not sending email to repository owner.")
         return
-    subject = "Regarding your tool shed repositories at %s" % url
+    subject = f"Regarding your tool shed repositories at {url}"
     message_body_template = (
         "The tool shed automated repository checker has discovered that one or more of your repositories hosted "
         + "at this tool shed url ${url} have remained empty for over ${days} days, so they have been marked as deprecated. If you have plans "
@@ -123,7 +123,7 @@ def send_mail_to_owner(app, owner, email, repositories_deprecated, days=14):
         )
         return True
     except Exception as e:
-        print("# An error occurred attempting to send email: %s" % e)
+        print(f"# An error occurred attempting to send email: {e}")
         return False
 
 
@@ -193,7 +193,7 @@ class DeprecateRepositoriesApplication:
 
     def __init__(self, config):
         if config.database_connection is False:
-            config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % config.database
+            config.database_connection = f"sqlite:///{config.database}?isolation_level=IMMEDIATE"
         # Setup the database engine and ORM
         self.model = tool_shed.webapp.model.mapping.init(
             config.file_path, config.database_connection, engine_options={}, create_tables=False
diff --git a/scripts/tools/re_escape_output.py b/scripts/tools/re_escape_output.py
index 9deab8c743cf..0ec3ee1e1edc 100644
--- a/scripts/tools/re_escape_output.py
+++ b/scripts/tools/re_escape_output.py
@@ -27,7 +27,7 @@ def __main__():
     if options.multiline:
         lines = [re.escape(input.read())]
     else:
-        lines = ["%s\n" % re.escape(line.rstrip("\n\r")) for line in input]
+        lines = ["{}\n".format(re.escape(line.rstrip("\n\r"))) for line in input]
     output.writelines(lines)
     output.close()
 
diff --git a/scripts/update_shed_config_path.py b/scripts/update_shed_config_path.py
index d3619a099704..a5bee3af9f63 100644
--- a/scripts/update_shed_config_path.py
+++ b/scripts/update_shed_config_path.py
@@ -40,7 +40,7 @@ def create_database(config_file):
     if database_connection is None:
         database_connection = parser.get("app:main", "database_connection")
     if database_connection is None:
-        database_connection = "sqlite:///%s" % parser.get("app:main", "database_file")
+        database_connection = "sqlite:///{}".format(parser.get("app:main", "database_file"))
     if database_connection is None:
         print("Unable to determine correct database connection.")
         exit(1)
@@ -78,7 +78,7 @@ def create_database(config_file):
     )
     opts = parser.parse_args()
     if not os.path.exists(opts.good_filename) and not opts.force:
-        print("The file %s does not exist, use the --force option to proceed." % opts.good_filename)
+        print(f"The file {opts.good_filename} does not exist, use the --force option to proceed.")
         exit(1)
     session, model = create_database(opts.config_file)
     exit(main(opts, session, model))
diff --git a/test/integration/chained_dyndest_rules/module2/rules.py b/test/integration/chained_dyndest_rules/module2/rules.py
index 1d7ea5c6eab3..b3b0c8048de6 100644
--- a/test/integration/chained_dyndest_rules/module2/rules.py
+++ b/test/integration/chained_dyndest_rules/module2/rules.py
@@ -15,7 +15,7 @@ def dyndest_chain_2(tmp_dir_prefix):
             "type": "python",
             "function": "dyndest_chain_3",
             "rules_module": "integration.chained_dyndest_rules.module3",
-            "tmp_dir_prefix_two": "%sand2" % tmp_dir_prefix,
+            "tmp_dir_prefix_two": f"{tmp_dir_prefix}and2",
         },
     )
 
diff --git a/test/integration/chained_dyndest_rules/module3/rules.py b/test/integration/chained_dyndest_rules/module3/rules.py
index f329428f24ef..add61a941ac0 100644
--- a/test/integration/chained_dyndest_rules/module3/rules.py
+++ b/test/integration/chained_dyndest_rules/module3/rules.py
@@ -14,5 +14,5 @@ def dyndest_chain_2():
 
 
 def dyndest_chain_3(tmp_dir_prefix_two):
-    tmp_dir = "$(mktemp -d -p $(pwd) %sand3XXXXXXXXXXXX)" % tmp_dir_prefix_two
+    tmp_dir = f"$(mktemp -d -p $(pwd) {tmp_dir_prefix_two}and3XXXXXXXXXXXX)"
     return JobDestination(runner="local", params={"tmp_dir": tmp_dir})
diff --git a/test/integration/test_repository_operations.py b/test/integration/test_repository_operations.py
index 551d3a24125d..510067db9660 100644
--- a/test/integration/test_repository_operations.py
+++ b/test/integration/test_repository_operations.py
@@ -66,7 +66,7 @@ def test_repository_update(self):
         response = self._install_repository(revision=REVISION_4, version="0.0.3", allow_upgraded=True)[0]
         assert int(response["ctx_rev"]) >= 4
         latest_revision = response["changeset_revision"]
-        repo_response = self._get("/api/tool_shed_repositories/%s" % response["id"]).json()
+        repo_response = self._get(f"/api/tool_shed_repositories/{response['id']}").json()
         assert repo_response["tool_shed_status"]["revision_update"] == "False"  # that should really be a boolean
         # now checkout revision 3 and attempt an update
         path_components = [
@@ -104,7 +104,7 @@ def test_repository_update(self):
             shed_config.write(shed_text)
         self._get("/api/tool_shed_repositories/check_for_updates", data={"id": response["id"]}, admin=True).json()
         # At this point things should look like there is minor update available
-        repo_response = self._get("/api/tool_shed_repositories/%s" % response["id"])
+        repo_response = self._get(f"/api/tool_shed_repositories/{response['id']}")
         repo_response.raise_for_status()
         repo_json = repo_response.json()
         assert repo_json["tool_shed_status"]["revision_update"] == "True"
diff --git a/test/integration/test_structured_dataset.py b/test/integration/test_structured_dataset.py
index ba81c3365cef..4f21261aaefa 100644
--- a/test/integration/test_structured_dataset.py
+++ b/test/integration/test_structured_dataset.py
@@ -25,7 +25,7 @@ def setUp(self):
 
     def test_fail_on_nonbinary(self):
         dataset = self.dataset_populator.new_dataset(
-            self.test_history_id, "file://%s/random-file" % TEST_DATA_DIRECTORY, file_type="txt", wait=True
+            self.test_history_id, f"file://{TEST_DATA_DIRECTORY}/random-file", file_type="txt", wait=True
         )
         dataset_id = dataset["dataset_id"]
         response = self._get(f"datasets/{dataset_id}/content/meta")
@@ -33,7 +33,7 @@ def test_fail_on_nonbinary(self):
 
     def test_api_meta(self):
         dataset = self.dataset_populator.new_dataset(
-            self.test_history_id, "file://%s/chopper.h5" % TEST_DATA_DIRECTORY, file_type="h5", wait=True
+            self.test_history_id, f"file://{TEST_DATA_DIRECTORY}/chopper.h5", file_type="h5", wait=True
         )
         dataset_id = dataset["dataset_id"]
         response = self._get(f"datasets/{dataset_id}/content/meta")
@@ -43,7 +43,7 @@ def test_api_meta(self):
 
     def test_api_attr(self):
         dataset = self.dataset_populator.new_dataset(
-            self.test_history_id, "file://%s/chopper.h5" % TEST_DATA_DIRECTORY, file_type="h5", wait=True
+            self.test_history_id, f"file://{TEST_DATA_DIRECTORY}/chopper.h5", file_type="h5", wait=True
         )
         dataset_id = dataset["dataset_id"]
         response = self._get(f"datasets/{dataset_id}/content/attr")
@@ -53,7 +53,7 @@ def test_api_attr(self):
 
     def test_api_stats(self):
         dataset = self.dataset_populator.new_dataset(
-            self.test_history_id, "file://%s/chopper.h5" % TEST_DATA_DIRECTORY, file_type="h5", wait=True
+            self.test_history_id, f"file://{TEST_DATA_DIRECTORY}/chopper.h5", file_type="h5", wait=True
         )
         dataset_id = dataset["dataset_id"]
         response = self._get(f"datasets/{dataset_id}/content/stats?path=%2Fentry%2Fdata%2Fdata")
@@ -63,7 +63,7 @@ def test_api_stats(self):
 
     def test_api_data(self):
         dataset = self.dataset_populator.new_dataset(
-            self.test_history_id, "file://%s/chopper.h5" % TEST_DATA_DIRECTORY, file_type="h5", wait=True
+            self.test_history_id, f"file://{TEST_DATA_DIRECTORY}/chopper.h5", file_type="h5", wait=True
         )
         dataset_id = dataset["dataset_id"]
         response = self._get(f"datasets/{dataset_id}/content/data?path=%2Fentry%2Fdata%2Fdata")
diff --git a/test/manual/gen_history_export_test_artifacts.py b/test/manual/gen_history_export_test_artifacts.py
index 1d971678e3a3..6840f2615676 100644
--- a/test/manual/gen_history_export_test_artifacts.py
+++ b/test/manual/gen_history_export_test_artifacts.py
@@ -49,7 +49,7 @@ def _gi(args):
     gi = galaxy.GalaxyInstance(args.host, key=args.api_key)
     name = "histexport-user-%d" % random.randint(0, 1000000)
 
-    user = gi.users.create_local_user(name, "%s@galaxytesting.dev" % name, "pass123")
+    user = gi.users.create_local_user(name, f"{name}@galaxytesting.dev", "pass123")
     user_id = user["id"]
     api_key = gi.users.create_user_apikey(user_id)
     user_gi = galaxy.GalaxyInstance(args.host, api_key)
diff --git a/test/manual/workflows_scaling.py b/test/manual/workflows_scaling.py
index f1b88332ba5f..2a1e39413342 100644
--- a/test/manual/workflows_scaling.py
+++ b/test/manual/workflows_scaling.py
@@ -90,10 +90,10 @@ def _run(args, gi, workflow_id, uuid):
         label_map = {}
 
     workflow_request = dict(
-        history="hist_id=%s" % history_id,
+        history=f"hist_id={history_id}",
     )
     workflow_request["inputs"] = json.dumps(label_map)
-    url = "workflows/%s/usage" % (workflow_id)
+    url = f"workflows/{workflow_id}/usage"
     invoke_response = dataset_populator._post(url, data=workflow_request).json()
     invocation_id = invoke_response["id"]
     workflow_populator = GiWorkflowPopulator(gi)
@@ -174,7 +174,7 @@ def _gi(args):
     gi = galaxy.GalaxyInstance(args.host, key=args.api_key)
     name = "wftest-user-%d" % random.randint(0, 1000000)
 
-    user = gi.users.create_local_user(name, "%s@galaxytesting.dev" % name, "pass123")
+    user = gi.users.create_local_user(name, f"{name}@galaxytesting.dev", "pass123")
     user_id = user["id"]
     api_key = gi.users.create_user_apikey(user_id)
     user_gi = galaxy.GalaxyInstance(args.host, api_key)
diff --git a/test/unit/app/queue_worker/conftest.py b/test/unit/app/queue_worker/conftest.py
index 4e8fa6b0be4f..728d91460237 100644
--- a/test/unit/app/queue_worker/conftest.py
+++ b/test/unit/app/queue_worker/conftest.py
@@ -20,7 +20,7 @@
 def create_base_test(connection, amqp_type: str, amqp_connection: Optional[str] = None):
     app = galaxy_mock.MockApp(database_connection=connection)
     app.config.database_connection = connection
-    app.config.amqp_internal_connection = amqp_connection or "sqlalchemy+%s" % app.config.database_connection
+    app.config.amqp_internal_connection = amqp_connection or f"sqlalchemy+{app.config.database_connection}"
     app.amqp_type = amqp_type
     return app
 
diff --git a/test/unit/app/test_markdown_validate.py b/test/unit/app/test_markdown_validate.py
index a1fbb0487112..0c99276ff915 100644
--- a/test/unit/app/test_markdown_validate.py
+++ b/test/unit/app/test_markdown_validate.py
@@ -13,7 +13,7 @@ def assert_markdown_invalid(markdown, at_line=None):
         failed = True
         if at_line is not None:
             assert "Invalid line %d" % (at_line + 1) in str(e)
-    assert failed, "Expected markdown [%s] to fail validation but it did not." % markdown
+    assert failed, f"Expected markdown [{markdown}] to fail validation but it did not."
 
 
 def test_markdown_validation():
diff --git a/test/unit/app/tools/conftest.py b/test/unit/app/tools/conftest.py
index ca09a3bc5514..f69d6ea70bff 100644
--- a/test/unit/app/tools/conftest.py
+++ b/test/unit/app/tools/conftest.py
@@ -56,7 +56,7 @@ def create_repo(session, changeset, installed_changeset, config_filename=None):
         "tools": [
             {
                 "add_to_tool_panel": False,  # to have repository.includes_tools_for_display_in_tool_panel=False in InstalledRepositoryManager.activate_repository()
-                "guid": "github.com/galaxyproject/example/test_tool/0.%s" % changeset,
+                "guid": f"github.com/galaxyproject/example/test_tool/0.{changeset}",
                 "tool_config": "tool.xml",
             }
         ],
diff --git a/test/unit/app/tools/test_wrappers.py b/test/unit/app/tools/test_wrappers.py
index a7be2e271d1b..746fef91f480 100644
--- a/test/unit/app/tools/test_wrappers.py
+++ b/test/unit/app/tools/test_wrappers.py
@@ -128,17 +128,17 @@ def valuewrapper(tool, value, paramtype, optional=False):
     parameter: ToolParameter
     if paramtype == "integer":
         optional = 'optional="true"' if optional else 'value="10"'
-        parameter = IntegerToolParameter(tool, XML('<param name="blah" type="integer" %s min="0" />' % optional))
+        parameter = IntegerToolParameter(tool, XML(f'<param name="blah" type="integer" {optional} min="0" />'))
     elif paramtype == "text":
         optional = 'optional="true"' if optional else 'value="foo"'
-        parameter = TextToolParameter(tool, XML('<param name="blah" type="text" %s/>' % optional))
+        parameter = TextToolParameter(tool, XML(f'<param name="blah" type="text" {optional}/>'))
     elif paramtype == "float":
         optional = 'optional="true"' if optional else 'value="10.0"'
-        parameter = FloatToolParameter(tool, XML('<param name="blah" type="float" %s/>' % optional))
+        parameter = FloatToolParameter(tool, XML(f'<param name="blah" type="float" {optional}/>'))
     elif paramtype == "boolean":
         optional = 'optional="true"' if optional else 'value=""'
         parameter = BooleanToolParameter(
-            tool, XML('<param name="blah" type="boolean" truevalue="truevalue" falsevalue="falsevalue" %s/>' % optional)
+            tool, XML(f'<param name="blah" type="boolean" truevalue="truevalue" falsevalue="falsevalue" {optional}/>')
         )
     return InputValueWrapper(parameter, value)
 
@@ -234,7 +234,7 @@ def input_extra_files_rewrite(self, dataset):
         return self.false_extra_files_path
 
     def unstructured_path_rewrite(self, path):
-        return "Rewrite<%s>" % path
+        return f"Rewrite<{path}>"
 
 
 def test_dataset_false_extra_files_path():
@@ -287,14 +287,13 @@ def _drilldown_parameter(tool):
 def _setup_blast_tool(tool, multiple=False):
     tool.app.write_test_tool_data("blastdb.loc", "val1\tname1\tpath1\nval2\tname2\tpath2\n")
     xml = XML(
-        """<param name="database" type="select" label="Nucleotide BLAST database" multiple="%s">
+        f"""<param name="database" type="select" label="Nucleotide BLAST database" multiple="{multiple}">
         <options from_file="blastdb.loc">
             <column name="value" index="0"/>
             <column name="name" index="1"/>
             <column name="path" index="2"/>
         </options>
     </param>"""
-        % multiple
     )
     parameter = SelectToolParameter(tool, xml)
     return parameter
diff --git a/test/unit/config/test_path_resolves_to.py b/test/unit/config/test_path_resolves_to.py
index d3252147dffb..97953b3d0787 100644
--- a/test/unit/config/test_path_resolves_to.py
+++ b/test/unit/config/test_path_resolves_to.py
@@ -157,7 +157,7 @@ def test_add_sample_file(mock_init, monkeypatch):
     # - has ".sample" suffix
     # Last value (sample file) resolved and listified; others dropped as files do not exist
     monkeypatch.setattr(BaseAppConfiguration, "add_sample_file_to_defaults", {"path1", "path4"})
-    monkeypatch.setattr(BaseAppConfiguration, "_in_sample_dir", lambda a, path: "/sample-dir/%s" % path)
+    monkeypatch.setattr(BaseAppConfiguration, "_in_sample_dir", lambda a, path: f"/sample-dir/{path}")
     config = BaseAppConfiguration()
 
     assert config._raw_config["path1"] == "my-config-files"
@@ -169,7 +169,7 @@ def test_add_sample_file(mock_init, monkeypatch):
 def test_select_one_path_from_list(mock_init, monkeypatch):
     # Expected: files do not exist, so use last file in list (would be sample file); value is not a list
     monkeypatch.setattr(BaseAppConfiguration, "add_sample_file_to_defaults", {"path1"})
-    monkeypatch.setattr(BaseAppConfiguration, "_in_sample_dir", lambda a, path: "/sample-dir/%s" % path)
+    monkeypatch.setattr(BaseAppConfiguration, "_in_sample_dir", lambda a, path: f"/sample-dir/{path}")
     config = BaseAppConfiguration()
 
     assert config._raw_config["path1"] == "my-config-files"
@@ -227,7 +227,7 @@ def path_exists(_, path):
         return True if path == "root/foo" else False
 
     monkeypatch.setattr(BaseAppConfiguration, "_path_exists", path_exists)
-    monkeypatch.setattr(BaseAppConfiguration, "_in_root_dir", lambda _, path: "root/%s" % path)
+    monkeypatch.setattr(BaseAppConfiguration, "_in_root_dir", lambda _, path: f"root/{path}")
     monkeypatch.setattr(BaseAppConfiguration, "paths_to_check_against_root", {"path1", "path4"})
 
 
diff --git a/test/unit/data/test_model_copy.py b/test/unit/data/test_model_copy.py
index 6487442f69ca..29416b552b83 100644
--- a/test/unit/data/test_model_copy.py
+++ b/test/unit/data/test_model_copy.py
@@ -53,7 +53,7 @@ def test_history_dataset_copy(num_datasets=NUM_DATASETS, include_metadata_file=I
         session.refresh(old_history)
         new_update_time = session.get(model.History, old_history.id).update_time
         assert original_update_time == new_update_time
-        print("history copied %s" % history_copy_timer)
+        print(f"history copied {history_copy_timer}")
         assert new_history.name == "new name"
         assert new_history.user == old_history.user
         for hda in new_history.active_datasets:
@@ -121,7 +121,7 @@ def test_history_collection_copy(list_size=NUM_DATASETS):
 
         history_copy_timer = ExecutionTimer()
         new_history = old_history.copy(target_user=old_history.user)
-        print("history copied %s" % history_copy_timer)
+        print(f"history copied {history_copy_timer}")
 
         for hda in new_history.active_datasets:
             assert hda.get_size() == 3
diff --git a/test/unit/data/test_quota.py b/test/unit/data/test_quota.py
index 96187045829d..5c34ea7cb056 100644
--- a/test/unit/data/test_quota.py
+++ b/test/unit/data/test_quota.py
@@ -67,7 +67,7 @@ def test_calculate_usage_per_source(self):
 class TestCalculateUsage(BaseModelTestCase):
     def setUp(self):
         model = self.model
-        u = model.User(email="calc_usage%s@example.com" % str(uuid.uuid1()), password="password")
+        u = model.User(email=f"calc_usage{uuid.uuid1()}@example.com", password="password")
         self.persist(u)
         h = model.History(name="History for Calculated Usage", user=u)
         self.persist(h)
diff --git a/test/unit/files/test_posix.py b/test/unit/files/test_posix.py
index 579b8ee1ca60..f64322db082b 100644
--- a/test/unit/files/test_posix.py
+++ b/test/unit/files/test_posix.py
@@ -480,7 +480,7 @@ def _configured_file_sources_with_root(
     if writable is not None:
         plugin["writable"] = writable
     if per_user and root:
-        plugin["root"] = "%s/${user.username}" % root
+        plugin["root"] = f"{root}/${{user.username}}"
         # setup files just for alice
         root = os.path.join(root, "alice")
         os.mkdir(root)
diff --git a/test/unit/objectstore/test_objectstore.py b/test/unit/objectstore/test_objectstore.py
index 4956ac970834..abcb6985a16c 100644
--- a/test/unit/objectstore/test_objectstore.py
+++ b/test/unit/objectstore/test_objectstore.py
@@ -182,7 +182,7 @@ def test_disk_store_by_uuid():
                 directory.temp_directory,
                 "files1",
                 output_dataset.rel_path_for_uuid_test(),
-                "dataset_%s.dat" % output_dataset.uuid,
+                f"dataset_{output_dataset.uuid}.dat",
             )
             assert not os.path.exists(output_real_path)
             output_working_path = directory.write("NEW CONTENTS", "job_working_directory1/example_output")
diff --git a/test/unit/tool_shed/test_shed_index.py b/test/unit/tool_shed/test_shed_index.py
index b589dc74fd83..ea5d5ef1bba4 100644
--- a/test/unit/tool_shed/test_shed_index.py
+++ b/test/unit/tool_shed/test_shed_index.py
@@ -40,7 +40,7 @@ def community_file_structure(community_file_dir):
     return community(
         file_path=os.path.join(community_file_dir, "database", "community_files"),
         hgweb_config_dir=community_file_dir,
-        dburi="sqlite:///%s" % os.path.join(community_file_dir, "database", "community.sqlite"),
+        dburi="sqlite:///{}".format(os.path.join(community_file_dir, "database", "community.sqlite")),
     )
 
 
diff --git a/test/unit/tool_util/mulled/test_mulled_list.py b/test/unit/tool_util/mulled/test_mulled_list.py
index 07e71905a310..1eb3e5fa084a 100644
--- a/test/unit/tool_util/mulled/test_mulled_list.py
+++ b/test/unit/tool_util/mulled/test_mulled_list.py
@@ -25,7 +25,7 @@ def test_get_singularity_containers():
 def test_get_missing_containers():
     test_dir = tempfile.mkdtemp()
     try:
-        exclude_list = "%s/blocklist.txt" % test_dir
+        exclude_list = f"{test_dir}/blocklist.txt"
         with open(exclude_list, "w") as f:
             f.write("a\n\nb\nc\nd")
         containers = get_missing_containers(
@@ -39,7 +39,7 @@ def test_get_missing_containers():
 def test_get_missing_envs():
     test_dir = tempfile.mkdtemp()
     try:
-        exclude_list = "%s/blocklist.txt" % test_dir
+        exclude_list = f"{test_dir}/blocklist.txt"
         with open(exclude_list, "w") as f:
             f.write("a\n\nb\nc\nd")
         envs = get_missing_envs(
diff --git a/test/unit/tool_util/test_tool_deps.py b/test/unit/tool_util/test_tool_deps.py
index 89eb6f8e5ad5..13d84e3bb16c 100644
--- a/test/unit/tool_util/test_tool_deps.py
+++ b/test/unit/tool_util/test_tool_deps.py
@@ -322,10 +322,9 @@ def _setup_module_command(temp_directory, contents):
     module_script = os.path.join(temp_directory, "modulecmd")
     __write_script(
         module_script,
-        """#!/bin/sh
-cat %s/example_output 1>&2;
-"""
-        % temp_directory,
+        f"""#!/bin/sh
+cat {temp_directory}/example_output 1>&2;
+""",
     )
     with open(os.path.join(temp_directory, "example_output"), "w") as f:
         # Subset of module avail from MSI cluster.
@@ -483,10 +482,9 @@ def _setup_lmod_command(temp_directory, contents):
     lmod_script = os.path.join(temp_directory, "lmod")
     __write_script(
         lmod_script,
-        """#!/bin/sh
-cat %s/lmod_example_output 1>&2;
-"""
-        % temp_directory,
+        f"""#!/bin/sh
+cat {temp_directory}/lmod_example_output 1>&2;
+""",
     )
     with open(os.path.join(temp_directory, "lmod_example_output"), "w") as f:
         # Subset of a "lmod -t avail" command of the LMOD environment module system.
@@ -544,7 +542,7 @@ def test_shell_commands_built():
 
 
 def __assert_foo_exported(commands):
-    command = ["bash", "-c", '%s; echo "$FOO"' % "".join(commands)]
+    command = ["bash", "-c", '{}; echo "$FOO"'.format("".join(commands))]
     process = Popen(command, stdout=PIPE)
     output = process.communicate()[0].strip()
     assert output == b"bar", f"Command {command} exports FOO as {unicodify(output)}, not bar"
diff --git a/test/unit/util/test_lazy_process.py b/test/unit/util/test_lazy_process.py
index bc113a33df6e..a301b23ba5ab 100644
--- a/test/unit/util/test_lazy_process.py
+++ b/test/unit/util/test_lazy_process.py
@@ -11,7 +11,7 @@ def test_lazy_process():
     """Create process, ensure start_process starts it and shutdown kills it."""
     t = tempfile.NamedTemporaryFile()
     os.remove(t.name)
-    lazy_process = LazyProcess(["bash", "-c", "touch %s; sleep 100" % t.name])
+    lazy_process = LazyProcess(["bash", "-c", f"touch {t.name}; sleep 100"])
     assert not os.path.exists(t.name)
     lazy_process.start_process()
     while not os.path.exists(t.name):
diff --git a/test/unit/util/test_rule_utils.py b/test/unit/util/test_rule_utils.py
index 99641d0f0084..c14cefb10e9a 100644
--- a/test/unit/util/test_rule_utils.py
+++ b/test/unit/util/test_rule_utils.py
@@ -25,6 +25,6 @@ def test_rules():
                     assert final_source == expected_final_source, msg
 
         elif "error" in test_case:
-            assert rule_set.has_errors, "rule [%s] does not contain errors" % test_case
+            assert rule_set.has_errors, f"rule [{test_case}] does not contain errors"
         else:
-            raise Exception("Problem with test case definition [%s]." % test_case)
+            raise Exception(f"Problem with test case definition [{test_case}].")
diff --git a/test/unit/util/test_sqlite_utils.py b/test/unit/util/test_sqlite_utils.py
index 758733579c5b..ef234f9b81f3 100644
--- a/test/unit/util/test_sqlite_utils.py
+++ b/test/unit/util/test_sqlite_utils.py
@@ -52,8 +52,8 @@ def __assert_query_errors(connection, query, match):
 
 
 def __assert_allowed(query):
-    assert sqlite.is_read_only_query(query), "Query [%s] fails allowlist." % query
+    assert sqlite.is_read_only_query(query), f"Query [{query}] fails allowlist."
 
 
 def __assert_not_allowed(query):
-    assert not sqlite.is_read_only_query(query), "Query [%s] incorrectly fails allowlist." % query
+    assert not sqlite.is_read_only_query(query), f"Query [{query}] incorrectly fails allowlist."

From 6492f07b1731ee1f75a3bb5ef6fd546e96059634 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 29 Apr 2024 00:15:51 +0100
Subject: [PATCH 19/21] Fix for mypy 1.10.0

---
 lib/galaxy/model/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 4cb9358961c9..93ee001aed73 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -6409,7 +6409,7 @@ def attribute_columns(column_collection, attributes, nesting_level=None):
         for entity in return_entities:
             q = q.add_columns(entity)
             if entity == DatasetCollectionElement:
-                q = q.filter(entity.id == dce.c.id)  # type:ignore[arg-type]
+                q = q.filter(entity.id == dce.c.id)
 
         q = q.order_by(*order_by_columns)
         return q

From 534010a8cb17cfb13f2e4574810eb41f5941b9cd Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 29 Apr 2024 12:29:15 +0100
Subject: [PATCH 20/21] Enable flake8-implicit-str-concat ruff rules

See https://docs.astral.sh/ruff/rules/#flake8-implicit-str-concat-isc
---
 client/src/api/schema/schema.ts                |  2 +-
 lib/galaxy/authnz/managers.py                  |  5 +++--
 lib/galaxy/celery/base_task.py                 |  2 +-
 lib/galaxy/datatypes/molecules.py              | 18 +++++++++---------
 lib/galaxy/datatypes/qiime2.py                 |  2 +-
 lib/galaxy/datatypes/tabular.py                |  3 ++-
 lib/galaxy/jobs/__init__.py                    |  4 ++--
 lib/galaxy/jobs/dynamic_tool_destination.py    | 12 +++++++-----
 lib/galaxy/jobs/runners/aws.py                 |  2 +-
 lib/galaxy/jobs/runners/chronos.py             |  2 +-
 lib/galaxy/model/__init__.py                   |  2 +-
 lib/galaxy/objectstore/pithos.py               |  6 +++---
 lib/galaxy/objectstore/rucio.py                |  2 +-
 lib/galaxy/schema/schema.py                    |  6 +++---
 lib/galaxy/tool_util/verify/test_data.py       |  4 ++--
 lib/galaxy/tools/data_fetch.py                 |  2 +-
 lib/galaxy/tools/search/__init__.py            |  2 +-
 lib/galaxy/util/custom_logging/fluent_log.py   |  2 +-
 lib/galaxy/webapps/galaxy/api/cloudauthz.py    |  4 ++--
 lib/galaxy/webapps/galaxy/api/job_tokens.py    |  2 +-
 lib/galaxy/webapps/galaxy/api/remote_files.py  |  4 ++--
 .../galaxy/controllers/visualization.py        |  6 ++----
 .../webapps/galaxy/services/library_folders.py |  2 +-
 pyproject.toml                                 |  5 +++--
 scripts/api/upload_to_history.py               |  4 ++--
 .../cleanup_datasets/admin_cleanup_datasets.py | 16 +++++++---------
 scripts/rst2html.py                            |  2 +-
 scripts/runtime_stats.py                       |  6 +++---
 .../deprecate_repositories_without_metadata.py |  4 ++--
 test/unit/app/managers/test_HDAManager.py      |  9 ++++-----
 test/unit/app/test_custom_templates.py         |  2 +-
 test/unit/data/datatypes/test_qiime2.py        |  6 +++---
 tools/data_export/send.py                      |  4 ++--
 tools/data_source/upload.py                    |  2 +-
 34 files changed, 78 insertions(+), 78 deletions(-)

diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
index a89d13317519..482ec3912ddb 100644
--- a/client/src/api/schema/schema.ts
+++ b/client/src/api/schema/schema.ts
@@ -19398,7 +19398,7 @@ export interface operations {
          * @description Allows remote job running mechanisms to get a fresh OIDC token that can be used on remote side to authorize user. It is not meant to represent part of Galaxy's stable, user facing API
          */
         parameters: {
-            /** @description A key used to authenticate this request as acting onbehalf or a job runner for the specified job */
+            /** @description A key used to authenticate this request as acting on behalf or a job runner for the specified job */
             /** @description OIDC provider name */
             query: {
                 job_key: string;
diff --git a/lib/galaxy/authnz/managers.py b/lib/galaxy/authnz/managers.py
index f7de71b2b201..edf13d19beb6 100644
--- a/lib/galaxy/authnz/managers.py
+++ b/lib/galaxy/authnz/managers.py
@@ -95,8 +95,9 @@ def _parse_oidc_config(self, config_file):
                         func = getattr(builtins, child.get("Type"))
                 except AttributeError:
                     log.error(
-                        "The value of attribute `Type`, `{}`, is not a valid built-in type;" " skipping this node"
-                    ).format(child.get("Type"))
+                        "The value of attribute `Type`, `%s`, is not a valid built-in type; skipping this node",
+                        child.get("Type"),
+                    )
                     continue
                 self.oidc_config[child.get("Property")] = func(child.get("Value"))
         except ImportError:
diff --git a/lib/galaxy/celery/base_task.py b/lib/galaxy/celery/base_task.py
index 6737aba0231c..94bb8d75956f 100644
--- a/lib/galaxy/celery/base_task.py
+++ b/lib/galaxy/celery/base_task.py
@@ -87,7 +87,7 @@ def calculate_task_start_time(  # type: ignore
             update_stmt = (
                 update(CeleryUserRateLimit)
                 .where(CeleryUserRateLimit.user_id == user_id)
-                .values(last_scheduled_time=text("greatest(last_scheduled_time + ':interval second', " ":now) "))
+                .values(last_scheduled_time=text("greatest(last_scheduled_time + ':interval second', :now)"))
                 .returning(CeleryUserRateLimit.last_scheduled_time)
             )
             result = sa_session.execute(update_stmt, {"interval": task_interval_secs, "now": now}).all()
diff --git a/lib/galaxy/datatypes/molecules.py b/lib/galaxy/datatypes/molecules.py
index a4cc26b549d2..193c32d65d6d 100644
--- a/lib/galaxy/datatypes/molecules.py
+++ b/lib/galaxy/datatypes/molecules.py
@@ -877,15 +877,15 @@ def get_matcher(self) -> re.Pattern:
         """
         pat = (
             r"(ATOM|HETATM)\s+"
-            + r"(\d+)\s+"
-            + r"([A-Z0-9]+)\s+"
-            + r"([A-Z0-9]+)\s+"
-            + r"(([A-Z]?)\s+)?"
-            + r"([-+]?\d*\.\d+|\d+)\s+"
-            + r"([-+]?\d*\.\d+|\d+)\s+"
-            + r"([-+]?\d*\.\d+|\d+)\s+"
-            + r"([-+]?\d*\.\d+|\d+)\s+"
-            + r"([-+]?\d*\.\d+|\d+)\s+"
+            r"(\d+)\s+"
+            r"([A-Z0-9]+)\s+"
+            r"([A-Z0-9]+)\s+"
+            r"(([A-Z]?)\s+)?"
+            r"([-+]?\d*\.\d+|\d+)\s+"
+            r"([-+]?\d*\.\d+|\d+)\s+"
+            r"([-+]?\d*\.\d+|\d+)\s+"
+            r"([-+]?\d*\.\d+|\d+)\s+"
+            r"([-+]?\d*\.\d+|\d+)\s+"
         )
         return re.compile(pat)
 
diff --git a/lib/galaxy/datatypes/qiime2.py b/lib/galaxy/datatypes/qiime2.py
index deaaf6a3da47..c9aa533ae8c2 100644
--- a/lib/galaxy/datatypes/qiime2.py
+++ b/lib/galaxy/datatypes/qiime2.py
@@ -275,7 +275,7 @@ def _get_versions(path, uuid):
         framework_version = framework_version_line.split(":")[1].strip()
         return version, framework_version
     except Exception:
-        raise ValueError("Archive does not contain a correctly formatted" " VERSION file.")
+        raise ValueError("Archive does not contain a correctly formatted VERSION file.")
 
 
 def _open_file_in_archive(zip_path, path, uuid):
diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index b9b79f046511..5b4e1d523e12 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -1223,7 +1223,8 @@ def __init__(self, **kwd):
             "DESC",
             "SRAS",
             "PRAS",
-            "PART_CHROM" "PART_CONTIG",
+            "PART_CHROM",
+            "PART_CONTIG",
             "PART_OFFSET",
             "PART_STRAND",
             "FILT",
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 8b0984886312..5e6f5d4be817 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1331,7 +1331,7 @@ def clear_working_directory(self):
         job = self.get_job()
         if not os.path.exists(self.working_directory):
             log.warning(
-                "(%s): Working directory clear requested but %s does " "not exist", self.job_id, self.working_directory
+                "(%s): Working directory clear requested but %s does not exist", self.job_id, self.working_directory
             )
             return
 
@@ -1535,7 +1535,7 @@ def change_state(self, state, info=False, flush=True, job=None):
 
         if job.state in model.Job.terminal_states:
             log.warning(
-                "(%s) Ignoring state change from '%s' to '%s' for job " "that is already terminal",
+                "(%s) Ignoring state change from '%s' to '%s' for job that is already terminal",
                 job.id,
                 job.state,
                 state,
diff --git a/lib/galaxy/jobs/dynamic_tool_destination.py b/lib/galaxy/jobs/dynamic_tool_destination.py
index 9e61e9adb88f..19a3d25776d7 100755
--- a/lib/galaxy/jobs/dynamic_tool_destination.py
+++ b/lib/galaxy/jobs/dynamic_tool_destination.py
@@ -1773,11 +1773,13 @@ def get_typo_correction(typo_str, word_set, max_dist):
         "--check-config",
         dest="check_config",
         nargs="?",
-        help="Use this option to validate tool_destinations.yml."
-        + " Optionally, provide the path to the tool_destinations.yml"
-        + " that you would like to check, and/or the path to the related"
-        + " job_conf.xml. Default: galaxy/config/tool_destinations.yml"
-        + "and galaxy/config/job_conf.xml",
+        help=(
+            "Use this option to validate tool_destinations.yml."
+            " Optionally, provide the path to the tool_destinations.yml"
+            " that you would like to check, and/or the path to the related"
+            " job_conf.xml. Default: galaxy/config/tool_destinations.yml"
+            "and galaxy/config/job_conf.xml"
+        ),
     )
 
     parser.add_argument("-j", "--job-config", dest="job_config")
diff --git a/lib/galaxy/jobs/runners/aws.py b/lib/galaxy/jobs/runners/aws.py
index 57b8dae427fa..9831cc42950e 100644
--- a/lib/galaxy/jobs/runners/aws.py
+++ b/lib/galaxy/jobs/runners/aws.py
@@ -399,7 +399,7 @@ def stop_job(self, job_wrapper):
         log.debug(msg.format(name=job_name))
 
     def recover(self, job, job_wrapper):
-        msg = "(name!r/runner!r) is still in {state!s} state, adding to" " the runner monitor queue"
+        msg = "(name!r/runner!r) is still in {state!s} state, adding to the runner monitor queue"
         job_id = job.get_job_runner_external_id()
         job_name = self.JOB_NAME_PREFIX + job_wrapper.get_id_tag()
         ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper)
diff --git a/lib/galaxy/jobs/runners/chronos.py b/lib/galaxy/jobs/runners/chronos.py
index 3bed4dc79a67..bb96c1b429dc 100644
--- a/lib/galaxy/jobs/runners/chronos.py
+++ b/lib/galaxy/jobs/runners/chronos.py
@@ -178,7 +178,7 @@ def stop_job(self, job_wrapper):
             LOGGER.error(msg.format(name=job_name))
 
     def recover(self, job, job_wrapper):
-        msg = "(name!r/runner!r) is still in {state!s} state, adding to" " the runner monitor queue"
+        msg = "(name!r/runner!r) is still in {state!s} state, adding to the runner monitor queue"
         job_id = job.get_job_runner_external_id()
         ajs = AsynchronousJobState(
             files_dir=job_wrapper.working_directory,
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 93ee001aed73..ded3c626d14d 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -3252,7 +3252,7 @@ def add_dataset(self, dataset, parent_id=None, genome_build=None, set_hid=True,
         elif not isinstance(dataset, (HistoryDatasetAssociation, HistoryDatasetCollectionAssociation)):
             raise TypeError(
                 "You can only add Dataset and HistoryDatasetAssociation instances to a history"
-                + f" ( you tried to add {str(dataset)} )."
+                f" ( you tried to add {str(dataset)} )."
             )
         is_dataset = is_hda(dataset)
         if parent_id:
diff --git a/lib/galaxy/objectstore/pithos.py b/lib/galaxy/objectstore/pithos.py
index 4d04b64246c3..60a710f1542d 100644
--- a/lib/galaxy/objectstore/pithos.py
+++ b/lib/galaxy/objectstore/pithos.py
@@ -83,7 +83,7 @@ def parse_config_xml(config_xml):
             log.error(msg)
             raise Exception(msg)
     except Exception:
-        log.exception("Malformed PithosObjectStore Configuration XML -- " "unable to continue")
+        log.exception("Malformed PithosObjectStore Configuration XML, unable to continue")
         raise
     return r
 
@@ -325,7 +325,7 @@ def _size(self, obj, **kwargs) -> int:
             try:
                 return os.path.getsize(self._get_cache_path(path))
             except OSError as ex:
-                log.warning(f"Could not get size of file {path} in local cache," f"will try Pithos. Error: {ex}")
+                log.warning("Could not get size of file %s in local cache, will try Pithos. Error: %s", path, ex)
         try:
             file = self.pithos.get_object_info(path)
         except ClientError as ce:
@@ -408,7 +408,7 @@ def _update_from_file(self, obj, **kwargs):
         if kwargs.get("create"):
             self._create(obj, **kwargs)
         if not self._exists(obj, **kwargs):
-            raise ObjectNotFound(f"objectstore.update_from_file, object does not exist: {obj}, " f"kwargs: {kwargs}")
+            raise ObjectNotFound(f"objectstore.update_from_file, object does not exist: {obj}, kwargs: {kwargs}")
 
         path = self._construct_path(obj, **kwargs)
         cache_path = self._get_cache_path(path)
diff --git a/lib/galaxy/objectstore/rucio.py b/lib/galaxy/objectstore/rucio.py
index ebc596903752..1d9c3d48b8d7 100644
--- a/lib/galaxy/objectstore/rucio.py
+++ b/lib/galaxy/objectstore/rucio.py
@@ -594,7 +594,7 @@ def _register_file(self, rel_path, file_name):
             file_name = self._get_cache_path(rel_path)
             if not os.path.islink(file_name):
                 raise ObjectInvalid(
-                    "rucio objectstore._register_file, rucio_register_only " "is set, but file in cache is not a link "
+                    "rucio objectstore._register_file, rucio_register_only is set, but file in cache is not a link "
                 )
         if os.path.islink(file_name):
             file_name = os.readlink(file_name)
diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index 5badff543962..95b6f125f0f5 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -1563,14 +1563,14 @@ class CreateHistoryPayload(Model):
         default=None,
         title="History ID",
         description=(
-            "The encoded ID of the history to copy. " "Provide this value only if you want to copy an existing history."
+            "The encoded ID of the history to copy. Provide this value only if you want to copy an existing history."
         ),
     )
     all_datasets: Optional[bool] = Field(
         default=True,
         title="All Datasets",
         description=(
-            "Whether to copy also deleted HDAs/HDCAs. Only applies when " "providing a `history_id` to copy from."
+            "Whether to copy also deleted HDAs/HDCAs. Only applies when providing a `history_id` to copy from."
         ),
     )
     archive_source: Optional[str] = Field(
@@ -3411,7 +3411,7 @@ class ShareWithPayload(Model):
         ...,
         title="User Identifiers",
         description=(
-            "A collection of encoded IDs (or email addresses) of users " "that this resource will be shared with."
+            "A collection of encoded IDs (or email addresses) of users that this resource will be shared with."
         ),
     )
     share_option: Optional[SharingOptions] = Field(
diff --git a/lib/galaxy/tool_util/verify/test_data.py b/lib/galaxy/tool_util/verify/test_data.py
index 68bf408543e1..5aa8f4763c16 100644
--- a/lib/galaxy/tool_util/verify/test_data.py
+++ b/lib/galaxy/tool_util/verify/test_data.py
@@ -11,11 +11,11 @@
 )
 
 UPDATE_TEMPLATE = Template(
-    "git --work-tree $dir --git-dir $dir/.git fetch && " "git --work-tree $dir --git-dir $dir/.git merge origin/master"
+    "git --work-tree $dir --git-dir $dir/.git fetch && git --work-tree $dir --git-dir $dir/.git merge origin/master"
 )
 
 UPDATE_FAILED_TEMPLATE = Template(
-    "Warning failed to update test repository $dir - " "update stdout was [$stdout] and stderr was [$stderr]."
+    "Warning failed to update test repository $dir - update stdout was [$stdout] and stderr was [$stderr]."
 )
 
 
diff --git a/lib/galaxy/tools/data_fetch.py b/lib/galaxy/tools/data_fetch.py
index 19e272ca4b6b..a6786c725dc9 100644
--- a/lib/galaxy/tools/data_fetch.py
+++ b/lib/galaxy/tools/data_fetch.py
@@ -305,7 +305,7 @@ def _resolve_item_with_primary(item):
                 if datatype.dataset_content_needs_grooming(path):
                     err_msg = (
                         "The uploaded files need grooming, so change your <b>Copy data into Galaxy?</b> selection to be "
-                        + "<b>Copy files into Galaxy</b> instead of <b>Link to files without copying into Galaxy</b> so grooming can be performed."
+                        "<b>Copy files into Galaxy</b> instead of <b>Link to files without copying into Galaxy</b> so grooming can be performed."
                     )
                     raise UploadProblemException(err_msg)
 
diff --git a/lib/galaxy/tools/search/__init__.py b/lib/galaxy/tools/search/__init__.py
index cc77ad0125a1..3fcce2caab42 100644
--- a/lib/galaxy/tools/search/__init__.py
+++ b/lib/galaxy/tools/search/__init__.py
@@ -233,7 +233,7 @@ def build_index(self, tool_cache, toolbox, index_help: bool = True) -> None:
                 # Add tool document to index (or overwrite if existing)
                 writer.update_document(**add_doc_kwds)
 
-        log.debug(f"Toolbox index of panel {self.panel_view_id}" f" finished {execution_timer}")
+        log.debug("Toolbox index of panel %s finished %s", self.panel_view_id, execution_timer)
 
     def _get_tools_to_remove(self, tool_cache) -> list:
         """Return list of tool IDs to be removed from index."""
diff --git a/lib/galaxy/util/custom_logging/fluent_log.py b/lib/galaxy/util/custom_logging/fluent_log.py
index ed9ede536e92..fde60ec00ae5 100644
--- a/lib/galaxy/util/custom_logging/fluent_log.py
+++ b/lib/galaxy/util/custom_logging/fluent_log.py
@@ -12,7 +12,7 @@
     FluentSender = None
 
 
-FLUENT_IMPORT_MESSAGE = "The Python fluent package is required to use this " "feature, please install it"
+FLUENT_IMPORT_MESSAGE = "The Python fluent package is required to use this feature, please install it"
 
 
 class FluentTraceLogger:
diff --git a/lib/galaxy/webapps/galaxy/api/cloudauthz.py b/lib/galaxy/webapps/galaxy/api/cloudauthz.py
index dc5a1ecf540a..e3e1ced53061 100644
--- a/lib/galaxy/webapps/galaxy/api/cloudauthz.py
+++ b/lib/galaxy/webapps/galaxy/api/cloudauthz.py
@@ -122,9 +122,9 @@ def create(self, trans, payload, **kwargs):
         description = payload.get("description", "")
 
         if not isinstance(config, dict):
-            log.debug(msg_template.format(f"invalid config type `{type(config)}`, expect `dict`"))
+            log.debug(msg_template.format(f"invalid config type `{type(config)}`, expected `dict`"))
             raise RequestParameterInvalidException(
-                "Invalid type for the required `config` variable; expect `dict` " f"but received `{type(config)}`."
+                f"Invalid type for the required `config` variable; expected `dict` but received `{type(config)}`."
             )
         if authn_id:
             try:
diff --git a/lib/galaxy/webapps/galaxy/api/job_tokens.py b/lib/galaxy/webapps/galaxy/api/job_tokens.py
index 8853f33d62bd..713e130a8a59 100644
--- a/lib/galaxy/webapps/galaxy/api/job_tokens.py
+++ b/lib/galaxy/webapps/galaxy/api/job_tokens.py
@@ -39,7 +39,7 @@ def get_token(
         job_id: EncodedDatabaseIdField,
         job_key: str = Query(
             description=(
-                "A key used to authenticate this request as acting on" "behalf or a job runner for the specified job"
+                "A key used to authenticate this request as acting on behalf or a job runner for the specified job"
             ),
         ),
         provider: str = Query(
diff --git a/lib/galaxy/webapps/galaxy/api/remote_files.py b/lib/galaxy/webapps/galaxy/api/remote_files.py
index 4edfe28cc6bc..5cc6d938b7d9 100644
--- a/lib/galaxy/webapps/galaxy/api/remote_files.py
+++ b/lib/galaxy/webapps/galaxy/api/remote_files.py
@@ -37,7 +37,7 @@
 TargetQueryParam: str = Query(
     default=RemoteFilesTarget.ftpdir,
     title="Target source",
-    description=("The source to load datasets from." " Possible values: ftpdir, userdir, importdir"),
+    description=("The source to load datasets from. Possible values: ftpdir, userdir, importdir"),
 )
 
 FormatQueryParam: Optional[RemoteFilesFormat] = Query(
@@ -54,7 +54,7 @@
     default=None,
     title="Recursive",
     description=(
-        "Whether to recursively lists all sub-directories." " This will be `True` by default depending on the `target`."
+        "Whether to recursively lists all sub-directories. This will be `True` by default depending on the `target`."
     ),
 )
 
diff --git a/lib/galaxy/webapps/galaxy/controllers/visualization.py b/lib/galaxy/webapps/galaxy/controllers/visualization.py
index 3928d2e6f02d..87a0c3947c55 100644
--- a/lib/galaxy/webapps/galaxy/controllers/visualization.py
+++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py
@@ -19,7 +19,6 @@
     UsesItemRatings,
 )
 from galaxy.structured_app import StructuredApp
-from galaxy.util import unicodify
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.visualization.genomes import GenomeRegion
 from galaxy.webapps.base.controller import (
@@ -263,9 +262,8 @@ def _handle_plugin_error(self, trans, visualization_name, exception):
             raise exception
         return trans.show_error_message(
             "There was an error rendering the visualization. "
-            + "Contact your Galaxy administrator if the problem persists."
-            + "<br/>Details: "
-            + unicodify(exception),
+            "Contact your Galaxy administrator if the problem persists."
+            f"<br/>Details: {exception}",
             use_panels=False,
         )
 
diff --git a/lib/galaxy/webapps/galaxy/services/library_folders.py b/lib/galaxy/webapps/galaxy/services/library_folders.py
index 36e74004210b..bc560c849238 100644
--- a/lib/galaxy/webapps/galaxy/services/library_folders.py
+++ b/lib/galaxy/webapps/galaxy/services/library_folders.py
@@ -218,7 +218,7 @@ def set_permissions(
             trans.app.security_agent.set_all_library_permissions(trans, folder, permissions)
         else:
             raise RequestParameterInvalidException(
-                'The mandatory parameter "action" has an invalid value.' 'Allowed values are: "set_permissions"'
+                'The mandatory parameter "action" has an invalid value. Allowed values are: "set_permissions"'
             )
         current_permissions = self.folder_manager.get_current_roles(trans, folder)
         return LibraryFolderCurrentPermissions(**current_permissions)
diff --git a/pyproject.toml b/pyproject.toml
index 0ebb92ddf93d..aaa26de5e38f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -191,8 +191,9 @@ exclude = [
 
 [tool.ruff.lint]
 # Enable: pycodestyle errors (E), Pyflakes (F), flake8-bugbear (B),
-# flake8-comprehensions (C4), flake8-logging-format (G) and pyupgrade (UP)
-select = ["E", "F", "B", "C4", "G", "UP"]
+# flake8-comprehensions (C4), flake8-logging-format (G),
+# flake8-implicit-str-concat (ISC) and pyupgrade (UP)
+select = ["E", "F", "B", "C4", "G", "ISC", "UP"]
 # Exceptions:
 # B008 Do not perform function calls in argument defaults (for FastAPI Depends and Body)
 # B9 flake8-bugbear opinionated warnings
diff --git a/scripts/api/upload_to_history.py b/scripts/api/upload_to_history.py
index e3c71e091444..5823143cf097 100755
--- a/scripts/api/upload_to_history.py
+++ b/scripts/api/upload_to_history.py
@@ -12,7 +12,7 @@
 except ImportError:
     print(
         "Could not import the requests module. See http://docs.python-requests.org/en/latest/"
-        + " or install with 'pip install requests'"
+        " or install with 'pip install requests'"
     )
     raise
 
@@ -46,7 +46,7 @@ def upload_file(base_url, api_key, history_id, filepath, **kwargs):
     if len(sys.argv) < 5:
         print(
             "history_upload.py <api key> <galaxy base url> <history id> <filepath to upload>\n"
-            + "  (where galaxy base url is just the root url where your Galaxy is served; e.g. 'localhost:8080')"
+            "  (where galaxy base url is just the root url where your Galaxy is served; e.g. 'localhost:8080')"
         )
         sys.exit(1)
 
diff --git a/scripts/cleanup_datasets/admin_cleanup_datasets.py b/scripts/cleanup_datasets/admin_cleanup_datasets.py
index 5c78ff0382b3..624fb3fac98d 100755
--- a/scripts/cleanup_datasets/admin_cleanup_datasets.py
+++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py
@@ -93,7 +93,7 @@ def main():
         help="config file (legacy, use --config instead)",
     )
     parser.add_argument("-d", "--days", dest="days", action="store", type=int, help="number of days (60)", default=60)
-    parser.add_argument("--tool_id", default=None, help="Text to match against tool_id" "Default: match all")
+    parser.add_argument("--tool_id", default=None, help="Text to match against tool_id. Default: match all")
     parser.add_argument(
         "--template",
         default=None,
@@ -121,10 +121,10 @@ def main():
         default=False,
     )
     parser.add_argument(
-        "--smtp", default=None, help="SMTP Server to use to send email. " "Default: [read from galaxy config file]"
+        "--smtp", default=None, help="SMTP Server to use to send email. Default: [read from galaxy config file]"
     )
     parser.add_argument(
-        "--fromaddr", default=None, help="From address to use to send email. " "Default: [read from galaxy config file]"
+        "--fromaddr", default=None, help="From address to use to send email. Default: [read from galaxy config file]"
     )
     populate_config_args(parser)
 
@@ -138,14 +138,12 @@ def main():
     if args.smtp is not None:
         app_properties["smtp_server"] = args.smtp
     if app_properties.get("smtp_server") is None:
-        parser.error("SMTP Server must be specified as an option (--smtp) " "or in the config file (smtp_server)")
+        parser.error("SMTP Server must be specified as an option (--smtp) or in the config file (smtp_server)")
 
     if args.fromaddr is not None:
         app_properties["email_from"] = args.fromaddr
     if app_properties.get("email_from") is None:
-        parser.error(
-            "From address must be specified as an option " "(--fromaddr) or in the config file " "(email_from)"
-        )
+        parser.error("From address must be specified as an option (--fromaddr) or in the config file (email_from)")
 
     scriptdir = os.path.dirname(os.path.abspath(__file__))
     template_file = args.template
@@ -262,7 +260,7 @@ def administrative_delete_datasets(
                     # Mark the HistoryDatasetAssociation as deleted
                     hda.deleted = True
                     app.sa_session.add(hda)
-                    print("Marked HistoryDatasetAssociation id %d as " "deleted" % hda.id)
+                    print("Marked HistoryDatasetAssociation id %d as deleted" % hda.id)
                 session = app.sa_session()
                 with transaction(session):
                     session.commit()
@@ -270,7 +268,7 @@ def administrative_delete_datasets(
     emailtemplate = Template(filename=template_file)
     for email, dataset_list in user_notifications.items():
         msgtext = emailtemplate.render(email=email, datasets=dataset_list, cutoff=cutoff_days)
-        subject = "Galaxy Server Cleanup " "- %d datasets DELETED" % len(dataset_list)
+        subject = "Galaxy Server Cleanup - %d datasets DELETED" % len(dataset_list)
         fromaddr = config.email_from
         print()
         print(f"From: {fromaddr}")
diff --git a/scripts/rst2html.py b/scripts/rst2html.py
index 5e825c5badd2..2b82025acc77 100755
--- a/scripts/rst2html.py
+++ b/scripts/rst2html.py
@@ -22,6 +22,6 @@
     publish_cmdline,
 )
 
-description = "Generates (X)HTML documents from standalone reStructuredText " "sources.  " + default_description
+description = "Generates (X)HTML documents from standalone reStructuredText sources.  " + default_description
 
 publish_cmdline(writer_name="html", description=description)
diff --git a/scripts/runtime_stats.py b/scripts/runtime_stats.py
index 9e6c9e5277aa..49a08a5d3e87 100755
--- a/scripts/runtime_stats.py
+++ b/scripts/runtime_stats.py
@@ -82,20 +82,20 @@ def parse_arguments():
         "--like",
         action="store_true",
         default=False,
-        help="Use SQL `LIKE` operator to find " "a shed-installed tool using the tool's " '"short" id',
+        help='Use SQL `LIKE` operator to find a shed-installed tool using the tool\'s "short" id',
     )
     populate_config_args(parser)
     parser.add_argument("-d", "--debug", action="store_true", default=False, help="Print extra info")
     parser.add_argument("-m", "--min", type=int, default=-1, help="Ignore runtimes less than MIN seconds")
     parser.add_argument("-M", "--max", type=int, default=-1, help="Ignore runtimes greater than MAX seconds")
-    parser.add_argument("-u", "--user", help="Return stats for only this user (id, email, " "or username)")
+    parser.add_argument("-u", "--user", help="Return stats for only this user (id, email, or username)")
     parser.add_argument(
         "-s", "--source", default="metrics", help="Runtime data source (SOURCES: {})".format(", ".join(DATA_SOURCES))
     )
     args = parser.parse_args()
 
     if args.like and "/" in args.tool_id:
-        print("ERROR: Do not use --like with a tool shed tool id (the tool " "id should not contain `/` characters)")
+        print("ERROR: Do not use --like with a tool shed tool id (the tool id should not contain `/` characters)")
         sys.exit(2)
 
     args.source = args.source.lower()
diff --git a/scripts/tool_shed/deprecate_repositories_without_metadata.py b/scripts/tool_shed/deprecate_repositories_without_metadata.py
index 6ab395d0354b..42a2e840886c 100644
--- a/scripts/tool_shed/deprecate_repositories_without_metadata.py
+++ b/scripts/tool_shed/deprecate_repositories_without_metadata.py
@@ -106,8 +106,8 @@ def send_mail_to_owner(app, owner, email, repositories_deprecated, days=14):
     subject = f"Regarding your tool shed repositories at {url}"
     message_body_template = (
         "The tool shed automated repository checker has discovered that one or more of your repositories hosted "
-        + "at this tool shed url ${url} have remained empty for over ${days} days, so they have been marked as deprecated. If you have plans "
-        + "for these repositories, you can mark them as un-deprecated at any time."
+        "at this tool shed url ${url} have remained empty for over ${days} days, so they have been marked as deprecated. If you have plans "
+        "for these repositories, you can mark them as un-deprecated at any time."
     )
     message_template = string.Template(message_body_template)
     body = "\n".join(textwrap.wrap(message_template.safe_substitute(days=days, url=url), width=95))
diff --git a/test/unit/app/managers/test_HDAManager.py b/test/unit/app/managers/test_HDAManager.py
index 226b1e8d70d9..a868c7ce5ca3 100644
--- a/test/unit/app/managers/test_HDAManager.py
+++ b/test/unit/app/managers/test_HDAManager.py
@@ -221,8 +221,7 @@ def test_accessible(self):
         assert accessible == item1
 
         self.log(
-            "after setting a dataset to private (one user) permissions, "
-            + "access should be not allowed for other users"
+            "after setting a dataset to private (one user) permissions, access should be not allowed for other users"
         )
         with self.assertRaises(exceptions.ItemAccessibilityException):
             self.hda_manager.get_accessible(
@@ -233,7 +232,7 @@ def test_accessible(self):
 
         self.log(
             "a copy of a restricted dataset in another users history should be inaccessible even to "
-            + "the histories owner"
+            "the histories owner"
         )
         history2 = self.history_manager.create(name="history2", user=non_owner)
         self.trans.set_history(history2)
@@ -300,7 +299,7 @@ def test_anon_accessibility(self):
 
         self.log(
             "anonymous users should not be able to access datasets within their own histories if "
-            + "permissions do not allow"
+            "permissions do not allow"
         )
         assert not self.hda_manager.is_accessible(item1, anon_user)
         with self.assertRaises(exceptions.ItemAccessibilityException):
@@ -308,7 +307,7 @@ def test_anon_accessibility(self):
 
         self.log(
             "those users with access permissions should still be allowed access to datasets "
-            + "within anon users' histories"
+            "within anon users' histories"
         )
         assert self.hda_manager.is_accessible(item1, dataset_owner)
 
diff --git a/test/unit/app/test_custom_templates.py b/test/unit/app/test_custom_templates.py
index e3a2f20136d4..2da4cfef8217 100644
--- a/test/unit/app/test_custom_templates.py
+++ b/test/unit/app/test_custom_templates.py
@@ -14,7 +14,7 @@
 """
 DEFAULT_TEMPLATE_HEADER_SUBSTRING = "The following variables are available"
 DEFAULT_TEMPLATE_OUTPUT_SUBSTRING = "<!DOCTYPE html>"
-CUSTOM_TEMPLATE_OUTPUT = "This is my custom template!\n" f"Name: {CONTEXT['name']}"
+CUSTOM_TEMPLATE_OUTPUT = f"This is my custom template!\nName: {CONTEXT['name']}"
 
 
 def test_it_can_render_a_default_template(tmp_path):
diff --git a/test/unit/data/datatypes/test_qiime2.py b/test/unit/data/datatypes/test_qiime2.py
index 8b57cf4431bc..9bfddc4e0037 100644
--- a/test/unit/data/datatypes/test_qiime2.py
+++ b/test/unit/data/datatypes/test_qiime2.py
@@ -147,7 +147,7 @@ def test_strip_properties_single():
 
 
 def test_strip_properties_double():
-    double_expression = 'FeatureData[Taxonomy % Properties("SILVIA"), ' 'DistanceMatrix % Axes("ASV", "ASV")]'
+    double_expression = 'FeatureData[Taxonomy % Properties("SILVIA"), DistanceMatrix % Axes("ASV", "ASV")]'
     stripped_expression = "FeatureData[Taxonomy, DistanceMatrix]"
 
     reconstructed_expression = _strip_properties(double_expression)
@@ -156,7 +156,7 @@ def test_strip_properties_double():
 
 
 def test_strip_properties_nested():
-    nested_expression = "Tuple[FeatureData[Taxonomy % " 'Properties("SILVIA")] % Axes("ASV", "ASV")]'
+    nested_expression = 'Tuple[FeatureData[Taxonomy % Properties("SILVIA")] % Axes("ASV", "ASV")]'
     stripped_expression = "Tuple[FeatureData[Taxonomy]]"
 
     reconstructed_expression = _strip_properties(nested_expression)
@@ -177,7 +177,7 @@ def test_strip_properties_complex():
 
 
 def test_strip_properties_keeps_different_binop():
-    expression_with_different_binop = 'FeatureData[Taxonomy % Properties("SILVIA"), ' "Taxonomy & Properties]"
+    expression_with_different_binop = 'FeatureData[Taxonomy % Properties("SILVIA"), Taxonomy & Properties]'
     stripped_expression = "FeatureData[Taxonomy, Taxonomy & Properties]"
 
     reconstructed_expression = _strip_properties(expression_with_different_binop)
diff --git a/tools/data_export/send.py b/tools/data_export/send.py
index fe4ce0348828..87270b1d8fad 100644
--- a/tools/data_export/send.py
+++ b/tools/data_export/send.py
@@ -102,7 +102,7 @@ def parse_args(args):
         "--object_label",
         type=str,
         required=True,
-        help="The label of the object created on the cloud-based storage for " "the data to be persisted.",
+        help="The label of the object created on the cloud-based storage for the data to be persisted.",
     )
 
     parser.add_argument(
@@ -110,7 +110,7 @@ def parse_args(args):
         "--filename",
         type=str,
         required=True,
-        help="The (absolute) filename of the data to be persisted on the " "cloud-based storage.",
+        help="The (absolute) filename of the data to be persisted on the cloud-based storage.",
     )
 
     parser.add_argument(
diff --git a/tools/data_source/upload.py b/tools/data_source/upload.py
index 823fee7cc9bf..d6c6b108650e 100644
--- a/tools/data_source/upload.py
+++ b/tools/data_source/upload.py
@@ -155,7 +155,7 @@ def add_file(dataset, registry, output_path: str) -> Dict[str, str]:
         if datatype.dataset_content_needs_grooming(dataset.path):
             err_msg = (
                 "The uploaded files need grooming, so change your <b>Copy data into Galaxy?</b> selection to be "
-                + "<b>Copy files into Galaxy</b> instead of <b>Link to files without copying into Galaxy</b> so grooming can be performed."
+                "<b>Copy files into Galaxy</b> instead of <b>Link to files without copying into Galaxy</b> so grooming can be performed."
             )
             raise UploadProblemException(err_msg)
     if not link_data_only:

From f01eaaef75f569bc896f150641f44147022389e8 Mon Sep 17 00:00:00 2001
From: Dannon <dannon.baker@gmail.com>
Date: Mon, 29 Apr 2024 15:15:36 -0400
Subject: [PATCH 21/21] Update client/src/components/Common/Heading.vue

Co-authored-by: Ahmed Hamid Awan <qe66653@umbc.edu>
---
 client/src/components/Common/Heading.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Common/Heading.vue b/client/src/components/Common/Heading.vue
index cb46df1b3c7c..dbbc5565ce63 100644
--- a/client/src/components/Common/Heading.vue
+++ b/client/src/components/Common/Heading.vue
@@ -48,8 +48,8 @@ const element = computed(() => {
 <template>
     <div v-if="props.separator" class="separator heading">
         <b-button v-if="collapsible" variant="link" size="sm" @click="$emit('click')">
-            <icon v-if="collapsed" fixed-width icon="angle-double-down" />
-            <icon v-else fixed-width icon="angle-double-up" />
+            <FontAwesomeIcon v-if="collapsed" fixed-width :icon="faAngleDoubleDown" />
+            <FontAwesomeIcon v-else fixed-width :icon="faAngleDoubleUp" />
         </b-button>
         <div v-else class="stripe"></div>
         <component