Merge pull request galaxyproject#16954 from common-workflow-lab/pytho…

…n3.8

Python 3.8 as minimum

.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:

Makefile

@@ -52,6 +52,11 @@ format:  ## Format Python code base
 remove-unused-imports:  ## Remove unused imports in Python code base
 	$(IN_VENV) autoflake --in-place --remove-all-unused-imports --recursive --verbose lib/ test/
 
+pyupgrade:  ## Convert older code patterns to Python3.7/3.8 idiomatic ones
+	ack --type=python -f | grep -v '^lib/galaxy/schema/bco/\|^lib/galaxy/schema/drs/\|^lib/tool_shed_client/schema/trs\|^tools/\|^.venv/\|^.tox/\|^lib/galaxy/files/sources/\|^lib/galaxy/job_metrics/\|^lib/galaxy/objectstore/\|^lib/galaxy/tool_util/\|^lib/galaxy/util/\|^test/functional/tools/cwl_tools/' | xargs pyupgrade --py38-plus
+	ack --type=python -f | grep -v '^lib/galaxy/schema/bco/\|^lib/galaxy/schema/drs/\|^lib/tool_shed_client/schema/trs\|^tools/\|^.venv/\|^.tox/\|^lib/galaxy/files/sources/\|^lib/galaxy/job_metrics/\|^lib/galaxy/objectstore/\|^lib/galaxy/tool_util/\|^lib/galaxy/util/\|^test/functional/tools/cwl_tools/' | xargs auto-walrus
+	ack --type=python -f lib/galaxy/files/sources/ lib/galaxy/job_metrics/ lib/galaxy/objectstore/ lib/galaxy/tool_util/ lib/galaxy/util/ | xargs pyupgrade --py37-plus
+
 docs-slides-ready:
 	test -f plantuml.jar ||  wget http://jaist.dl.sourceforge.net/project/plantuml/plantuml.jar
 	java -jar plantuml.jar -c $(DOC_SOURCE_DIR)/slideshow/architecture/images/plantuml_options.txt -tsvg $(SLIDESHOW_DIR)/architecture/images/ *.plantuml.txt

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:
 

client/src/api/schema/schema.ts

@@ -2422,8 +2422,8 @@ export interface components {
             /**
              * Type
              * @description The digest method used to create the checksum.
-             * The value (e.g. `sha-256`) SHOULD be listed as `Hash Name String` in the https://www.iana.org/assignments/named-information/named-information.xhtml#hash-alg[IANA Named Information Hash Algorithm Registry]. Other values MAY be used, as long as implementors are aware of the issues discussed in https://tools.ietf.org/html/rfc6920#section-9.4[RFC6920].
-             * GA4GH may provide more explicit guidance for use of non-IANA-registered algorithms in the future. Until then, if implementors do choose such an algorithm (e.g. because it's implemented by their storage provider), they SHOULD use an existing standard `type` value such as `md5`, `etag`, `crc32c`, `trunc512`, or `sha1`.
+             * The value (e.g. `sha-256`) SHOULD be listed as `Hash Name String` in the https://www.iana.org/assignments/named-information/named-information.xhtml#hash-alg[IANA Named Information Hash Algorithm Registry]. Other values MAY be used, as long as implementers are aware of the issues discussed in https://tools.ietf.org/html/rfc6920#section-9.4[RFC6920].
+             * GA4GH may provide more explicit guidance for use of non-IANA-registered algorithms in the future. Until then, if implementers do choose such an algorithm (e.g. because it's implemented by their storage provider), they SHOULD use an existing standard `type` value such as `md5`, `etag`, `crc32c`, `trunc512`, or `sha1`.
              * @example sha-256
              */
             type: string;

doc/parse_gx_xsd.py

@@ -107,8 +107,7 @@ def _build_tag(tag, hide_attributes):
                     assertions_buffer.write(f"#### ``{element.attrib['name']}``:\n\n{doc}\n\n")
             text = text.replace(line, assertions_buffer.getvalue())
     tag_help.write(text)
-    best_practices = _get_bp_link(annotation_el)
-    if best_practices:
+    if best_practices := _get_bp_link(annotation_el):
         tag_help.write("\n\n### Best Practices\n")
         tag_help.write(
             """

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/actions/library.py

@@ -224,8 +224,7 @@ def _get_path_paste_uploaded_datasets(self, trans, params, library_bunch, respon
         return uploaded_datasets, 200, None
 
     def _get_path_files_and_folders(self, params, preserve_dirs):
-        problem_response = self._check_path_paste_params(params)
-        if problem_response:
+        if problem_response := self._check_path_paste_params(params):
             return problem_response
         files_and_folders = []
         for line, path in self._paths_list(params):

lib/galaxy/app.py

@@ -846,8 +846,7 @@ def to_str(self, **kwd):
 
 class ExecutionTimerFactory:
     def __init__(self, config):
-        statsd_host = getattr(config, "statsd_host", None)
-        if statsd_host:
+        if statsd_host := getattr(config, "statsd_host", None):
             from galaxy.web.statsd_client import GalaxyStatsdClient
 
             self.galaxy_statsd_client: Optional[GalaxyStatsdClient] = GalaxyStatsdClient(

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/auth/__init__.py

@@ -123,8 +123,7 @@ def active_authenticators(self, email, username, password):
 
 def _get_allow_register(d):
     s = d.get("allow-register", True)
-    lower_s = str(s).lower()
-    if lower_s == "challenge":
+    if (lower_s := str(s).lower()) == "challenge":
         return lower_s
     else:
         return string_as_bool(s)

lib/galaxy/celery/__init__.py

@@ -101,8 +101,7 @@ def get_galaxy_app():
 
 @lru_cache(maxsize=1)
 def build_app():
-    kwargs = get_app_properties()
-    if kwargs:
+    if kwargs := get_app_properties():
         kwargs["check_migrate_databases"] = False
         kwargs["use_display_applications"] = False
         kwargs["use_converters"] = False

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"