Merge branch 'master' into ipa_stub

.github/styler.R

@@ -0,0 +1,36 @@
+#!/usr/bin/env Rscript
+
+library("argparse")
+library("styler")
+
+parser <- ArgumentParser(description = "Call styler")
+parser$add_argument("dir",
+    metavar = "DIR", type = "character",
+    help = "File to parse"
+)
+parser$add_argument("--dry",
+    choices = c("off", "on"), default = "on"
+)
+args <- parser$parse_args()
+
+file_info <- file.info(args$dir)
+is_directory <- file_info$isdir
+
+if (is_directory) {
+    captured_output <- capture.output({
+        result <- style_dir(args$dir, indent_by = 4, dry = args$dry, recursive = TRUE)
+    })
+} else {
+    captured_output <- capture.output({
+        result <- style_file(args$dir, indent_by = 4, dry = args$dry)
+    })
+}
+
+n <- nrow(subset(result, changed == TRUE))
+if (n > 0) {
+    if (args$dry == "off") {
+        print(paste("Changed", n, "files"))
+    } else {
+        stop(paste("Linting failed for", n, "files"))
+    }
+}

.github/workflows/add_issue_to_project.yml

@@ -8,7 +8,7 @@ jobs:
     name: Add issue to project
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/add-to-project@v0.5.0
+      - uses: actions/add-to-project@v0.6.1
         with:
           # You can target a project in a different organization
           # to the issue

.github/workflows/ci.yaml

@@ -8,7 +8,7 @@ on:
     types: [run-all-tool-tests-command]
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_23.1
+  GALAXY_BRANCH: release_24.0
   MAX_CHUNKS: 40
 jobs:
   setup:
@@ -24,11 +24,11 @@ jobs:
       chunk-list: ${{ steps.discover.outputs.chunk-list }}
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
     - name: Add reaction
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
-      uses: peter-evans/create-or-update-comment@v2
+      uses: peter-evans/create-or-update-comment@v4
       with:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
@@ -44,11 +44,11 @@ jobs:
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
       run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)" >> $GITHUB_OUTPUT
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -57,7 +57,7 @@ jobs:
     # are not available as wheels, pip will build a wheel for them, which can be cached.
     - name: Install wheel
       run: pip install wheel
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
@@ -83,16 +83,16 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -105,11 +105,11 @@ jobs:
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
         additional-planemo-options: --biocontainers -s tests,output,inputs,help,general,command,citations,tool_xsd
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'Tool linting output'
-        path: lint_report.txt
+        path: lint_report.txt1
 
   test:
     name: Test tools
@@ -121,7 +121,7 @@ jobs:
       fail-fast: false
       matrix:
         chunk: ${{ fromJson(needs.setup.outputs.chunk-list) }}
-        python-version: ['3.7']
+        python-version: ['3.11']
     services:
       postgres:
         image: postgres:11
@@ -134,20 +134,20 @@ jobs:
     steps:
     # checkout the repository
     # and use it as the current working directory
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
     - name: Get number of CPU cores
-      uses: SimenB/github-actions-cpu-cores@v1
+      uses: SimenB/github-actions-cpu-cores@v2
       id: cpu-cores
     - name: Clean dotnet folder for space
       run: rm -Rf /usr/share/dotnet
@@ -164,7 +164,7 @@ jobs:
         galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
         # Limit each test to 15 minutes
         test_timeout: 900
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
@@ -179,18 +179,18 @@ jobs:
     needs: [setup, test]
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.11']
     # This job runs on Linux
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
       with:
         path: artifacts
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -201,7 +201,7 @@ jobs:
       with:
         mode: combine
         html-report: true
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'All tool test results'
         path: upload
@@ -212,7 +212,7 @@ jobs:
 
     - name: Create comment
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
-      uses: peter-evans/create-or-update-comment@v2
+      uses: peter-evans/create-or-update-comment@v4
       with:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}