Python 3.8 as new minimum version

Fixes: #16394

Also upgrade code to Python 3.8 syntax with:

```
ack --type=python -f | grep -v '^lib/galaxy/schema/bco/\|^lib/galaxy/schema/drs/\|lib/tool_shed_client/schema/trs.*.py\|^tools/\|^.venv/\|^.tox/' | grep -v '^lib/galaxy/files/sources/\|^lib/galaxy/job_metrics/\|^lib/galaxy/objectstore/\|^lib/galaxy/tool_util/\|^lib/galaxy/util/' | xargs pyupgrade --py38-plus
```

.circleci/config.yml

@@ -15,7 +15,7 @@ variables:
 jobs:
   get_code:
     docker:
-      - image: cimg/python:3.7
+      - image: cimg/python:3.8
     <<: *set_workdir
     steps:
       # Replace standard code checkout with shallow clone to speed things up.
@@ -73,7 +73,7 @@ jobs:
             - ~/repo
   validate_test_tools:
     docker:
-      - image: cimg/python:3.7
+      - image: cimg/python:3.8
     <<: *set_workdir
     steps:
       - *restore_repo_cache

.github/workflows/api.yaml

@@ -28,7 +28,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
         chunk: [0, 1]
     services:
       postgres:

.github/workflows/check_test_class_names.yaml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4

.github/workflows/converter_tests.yaml

@@ -22,7 +22,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
     steps:
       - if: github.event_name == 'schedule'
         run: |

.github/workflows/cwl_conformance.yaml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
         marker: ['green', 'red and required', 'red and not required']
         conformance-version: ['cwl_conformance_v1_0'] #, 'cwl_conformance_v1_1', 'cwl_conformance_v1_2']
     services:

.github/workflows/db_indexes.yaml

@@ -24,11 +24,11 @@ jobs:
       matrix:
         db: ['postgresql', 'sqlite']
         postgresql-version: ['13']
-        python-version: ['3.7']
+        python-version: ['3.8']
         include:
           - db: postgresql
             postgresql-version: '9.6'
-            python-version: '3.7'
+            python-version: '3.8'
     services:
       postgres:
         image: postgres:${{ matrix.postgresql-version }}

.github/workflows/dependencies.yaml

@@ -9,17 +9,12 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          # poetry requires Python >=3.8, but lint requirements currently need
-          # to be generated with `pip freeze`` on the oldest Python version
-          # supported by Galaxy.
-          python-version: |
-            ${{ matrix.python-version }}
-            3.8
+          python-version: ${{ matrix.python-version }}
       - name: Update dependencies
         run: | 
           python -m venv .venv

.github/workflows/deployment.yaml

@@ -33,7 +33,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
     steps:
       - uses: actions/checkout@v3
         with:

.github/workflows/docs.yaml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
     steps:
       - name: Get target branch name (push)
         if: github.event_name == 'push'

.github/workflows/first_startup.yaml

@@ -21,7 +21,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7', '3.11']
+        python-version: ['3.8', '3.11']
     defaults:
       run:
         shell: bash -l {0}

.github/workflows/framework.yaml

@@ -25,7 +25,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
     services:
       postgres:
         image: postgres:13

.github/workflows/integration.yaml

@@ -29,7 +29,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
         chunk: ['0', '1', '2', '3']
     services:
       postgres:

.github/workflows/integration_selenium.yaml

@@ -29,7 +29,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
     services:
       postgres:
         image: postgres:13

.github/workflows/lint.yaml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7', '3.11']
+        python-version: ['3.8', '3.11']
     env:
       LINT_PATH: 'lib/galaxy/dependencies/pinned-lint-requirements.txt'
       TYPE_PATH: 'lib/galaxy/dependencies/pinned-typecheck-requirements.txt'

.github/workflows/lint_openapi_schema.yml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7', '3.11']
+        python-version: ['3.8', '3.11']
     steps:
       - uses: actions/checkout@v3
         with:

.github/workflows/mulled.yaml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
     steps:
       - uses: actions/checkout@v3
         with:

.github/workflows/osx_startup.yaml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7', '3.11']
+        python-version: ['3.8', '3.11']
     defaults:
       run:
         shell: bash -l {0}

.github/workflows/performance.yaml

@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
     services:
       postgres:
         image: postgres:13

.github/workflows/publish_artifacts.yaml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
         matrix:
-            python-version: ['3.7']
+            python-version: ['3.8']
     steps:
       - uses: actions/setup-python@v4
         with:

.github/workflows/reports_startup.yaml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7', '3.11']
+        python-version: ['3.8', '3.11']
     defaults:
       run:
         shell: bash -l {0}

.github/workflows/selenium.yaml

@@ -30,7 +30,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
         chunk: [0, 1, 2]
     services:
       postgres:

.github/workflows/test_galaxy_packages.yaml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7', '3.11']
+        python-version: ['3.8', '3.11']
     steps:
       - uses: actions/checkout@v3
         with:

.github/workflows/test_galaxy_packages_for_pulsar.yaml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.7']  # don't upgrade, see https://github.com/galaxyproject/galaxy/pull/16649
     steps:
       - uses: actions/checkout@v3
         with:

.github/workflows/toolshed.yaml

@@ -21,7 +21,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7', '3.11']
+        python-version: ['3.8', '3.11']
         shed-api: ['v1', 'v2']
         test-install-client: ['galaxy_api', 'standalone']
     services:

.github/workflows/unit-postgres.yaml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
     services:
       postgres:
         image: postgres:13

.github/workflows/unit.yaml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7', '3.11']
+        python-version: ['3.8', '3.11']
     steps:
       - uses: actions/checkout@v3
         with:

README.rst

@@ -24,12 +24,12 @@ Community support is available at `Galaxy Help <https://help.galaxyproject.org/>
 Galaxy Quickstart
 =================
 
-Galaxy requires Python 3.7 . To check your Python version, run:
+Galaxy requires Python 3.8 . To check your Python version, run:
 
 .. code:: console
 
     $ python -V
-    Python 3.7.6
+    Python 3.8.18
 
 Start Galaxy:
 

doc/source/admin/python.md

@@ -1,6 +1,6 @@
 # Supported Python versions
 
-Galaxy's core functionality is currently supported on Python **>=3.7** .
+Galaxy's core functionality is currently supported on Python **>=3.8** .
 
 If Galaxy complains about the version of Python you are using:
 

doc/source/dev/debugging_tests.md

@@ -52,7 +52,7 @@ index 6647588dfb..c8d82957a1 100644
 @@ -14,7 +14,7 @@ jobs:
        fail-fast: false
        matrix:
-         python-version: ['3.7']
+         python-version: ['3.8']
 -        subset: ['upload_datatype', 'extended_metadata', 'kubernetes', 'not (upload_datatype or extended_metadata or kubernetes)']
 +        subset: ['not (upload_datatype or extended_metadata or kubernetes)']
      services:

lib/galaxy/app_unittest_utils/tools_support.py

@@ -123,7 +123,7 @@ class MockContext:
     def __init__(self, model_objects=None):
         self.expunged_all = False
         self.flushed = False
-        self.model_objects = model_objects or defaultdict(lambda: {})
+        self.model_objects = model_objects or defaultdict(dict)
         self.created_objects = []
         self.current = self
 

lib/galaxy/celery/tasks.py

@@ -68,12 +68,12 @@
 log = get_logger(__name__)
 
 
-@lru_cache()
+@lru_cache
 def setup_data_table_manager(app):
     app._configure_tool_data_tables(from_shed_config=False)
 
 
-@lru_cache()
+@lru_cache
 def cached_create_tool_from_representation(app, raw_tool_source):
     return create_tool_from_representation(
         app=app, raw_tool_source=raw_tool_source, tool_dir="", tool_source_class="XmlToolSource"

lib/galaxy/datatypes/text.py

@@ -6,6 +6,7 @@
 import logging
 import os
 import re
+import shlex
 import subprocess
 import tempfile
 from typing import (
@@ -38,7 +39,6 @@
 )
 from galaxy.util import (
     nice_size,
-    shlex_join,
     string_as_bool,
     unicodify,
 )
@@ -242,7 +242,7 @@ def _display_data_trusted(
                 ofilename = dataset.get_file_name()
                 log.exception(
                     'Command "%s" failed. Could not convert the Jupyter Notebook to HTML, defaulting to plain text.',
-                    shlex_join(cmd),
+                    shlex.join(cmd),
                 )
             return open(ofilename, mode="rb"), headers
 

lib/galaxy/datatypes/util/maf_utilities.py

@@ -658,9 +658,6 @@ def get_starts_ends_fields_from_gene_bed(line):
     if len(fields) < 12:
         raise Exception(f"Not a proper 12 column BED line ({line}).")
     tx_start = int(fields[1])
-    strand = fields[5]
-    if strand != "-":
-        strand = "+"  # Default strand is +
     cds_start = int(fields[6])
     cds_end = int(fields[7])
 

lib/galaxy/dependencies/update.sh

@@ -6,7 +6,7 @@
 
 set -e
 
-SUPPORTED_PYTHON_VERSIONS="3.7 3.8 3.9 3.10 3.11"
+SUPPORTED_PYTHON_VERSIONS="3.8 3.9 3.10 3.11"
 NOT_SUPPORTED_NEXT_PYTHON_VERSION="3.12"
 
 this_directory="$(cd "$(dirname "$0")" > /dev/null && pwd)"

lib/galaxy/dependencies/update_lint_requirements.sh

@@ -11,7 +11,7 @@ THIS_DIRECTORY="$(cd "$(dirname "$0")" > /dev/null && pwd)"
 
 update_pinned_reqs() {
     VENV=$(mktemp -d "${TMPDIR:-/tmp}/$1_venv.XXXXXXXXXX")
-    python3.7 -m venv "${VENV}"
+    python3.8 -m venv "${VENV}"
     . "${VENV}/bin/activate"
     pip install --upgrade pip setuptools
     pip install -r "${THIS_DIRECTORY}/$1-requirements.txt"

lib/galaxy/managers/notification.py

@@ -409,7 +409,7 @@ def resolve_users(self, recipients: NotificationRecipients) -> List[User]:
         user_ids_from_roles_stmt = self._get_all_user_ids_from_roles_query(all_role_ids)
 
         union_stmt = union(user_ids_from_groups_stmt, user_ids_from_roles_stmt)
-        user_ids_from_groups_and_roles = set([id for id, in self.sa_session.execute(union_stmt)])
+        user_ids_from_groups_and_roles = {id for id, in self.sa_session.execute(union_stmt)}
         unique_user_ids.update(user_ids_from_groups_and_roles)
 
         stmt = select(User).where(User.id.in_(unique_user_ids))
@@ -448,7 +448,7 @@ def _expand_group_and_roles_ids(self, group_ids: Set[int], role_ids: Set[int]) -
                 .where(GroupRoleAssociation.role_id.in_(role_ids))
                 .distinct()
             )
-            group_ids_from_roles = set([id for id, in self.sa_session.execute(stmt) if id is not None])
+            group_ids_from_roles = {id for id, in self.sa_session.execute(stmt) if id is not None}
             new_group_ids = group_ids_from_roles - processed_group_ids
 
             # Get role IDs associated with any of the given group IDs
@@ -458,7 +458,7 @@ def _expand_group_and_roles_ids(self, group_ids: Set[int], role_ids: Set[int]) -
                 .where(GroupRoleAssociation.group_id.in_(group_ids))
                 .distinct()
             )
-            role_ids_from_groups = set([id for id, in self.sa_session.execute(stmt) if id is not None])
+            role_ids_from_groups = {id for id, in self.sa_session.execute(stmt) if id is not None}
             new_role_ids = role_ids_from_groups - processed_role_ids
 
             # Stop if there are no new group or role IDs to process