Merge pull request galaxyproject#16639 from nsoranzo/dependencies_wf_…

…py3.8

Fix dependency update GitHub workflow

.github/workflows/dependencies.yaml

@@ -9,17 +9,17 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8']  # poetry requires Python >=3.8
+        python-version: ['3.7']
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python-version }}
-      - name: Cache pip dir
-        uses: actions/cache@v3
-        with:
-          path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
+          # 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
       - name: Update dependencies
         run: | 
           python -m venv .venv

Makefile

@@ -139,7 +139,7 @@ release-bootstrap-history: ## bootstrap history for a new release
 update-lint-requirements:
 	./lib/galaxy/dependencies/update_lint_requirements.sh
 
-update-dependencies: update-lint-requirements ## update pinned and dev dependencies
+update-dependencies: update-lint-requirements ## update pinned, dev and typecheck dependencies
 	$(IN_VENV) ./lib/galaxy/dependencies/update.sh
 
 $(CWL_TARGETS):

lib/galaxy/dependencies/update.sh

@@ -50,6 +50,7 @@ PINNED_REQUIREMENTS_FILE=$this_directory/pinned-requirements.txt
 PINNED_DEV_REQUIREMENTS_FILE=$this_directory/dev-requirements.txt
 poetry export -f requirements.txt --without-hashes --output "$PINNED_REQUIREMENTS_FILE"
 poetry export --only dev -f requirements.txt --without-hashes --output "$PINNED_DEV_REQUIREMENTS_FILE"
+poetry export --only typecheck -f requirements.txt --without-hashes --output "$this_directory/pinned-typecheck-requirements.txt"
 
 # Fix requirements
 

lib/galaxy/dependencies/update_lint_requirements.sh

@@ -2,12 +2,10 @@
 
 set -e
 
-# This script updates the pinned requirements for both linting and typechecking.
-# The requirements are split into two parts due to incompatible dependencies:
-# flake8 requires importlib-metadata 4.2; typecheck requirements do not
-# depende on importlib-metadata; however, they must be installed into the same
-# virtual environment as Galaxy's core dependencies, which depend on
-# importlib-metadata 4.13.
+# This script updates the pinned requirements for linting.
+# The lint requirements are split from the the other ones due to incompatible
+# dependencies: flake8 requires importlib-metadata 4.2, while the Galaxy's core
+# dependencies depend on importlib-metadata 4.13.
 
 THIS_DIRECTORY="$(cd "$(dirname "$0")" > /dev/null && pwd)"
 
@@ -23,4 +21,3 @@ update_pinned_reqs() {
 }
 
 update_pinned_reqs lint
-update_pinned_reqs typecheck

pyproject.toml

@@ -22,9 +22,14 @@ homepage = "https://galaxyproject.org/"
 repository = "https://github.com/galaxyproject/galaxy/"
 documentation = "https://docs.galaxyproject.org/"
 
+[[tool.poetry.source]]
+name = "PyPI"
+priority = "default"
+
 [[tool.poetry.source]]
 name = "galaxyproject"
 url = "https://wheels.galaxyproject.org/simple"
+priority = "primary"
 
 [tool.poetry.dependencies]
 a2wsgi = "*"
@@ -152,6 +157,22 @@ tuspy = "*"
 twill = "*"
 watchdog = "*"
 
+[tool.poetry.group.typecheck.dependencies]
+mypy = "*"
+pydantic = "<2"  # for pydantic.mypy plugin
+types-bleach = "*"
+types-boto = "*"
+types-contextvars = "*"
+types-dataclasses = "*"
+types-docutils = "*"
+types-Markdown = "*"
+types-paramiko = "*"
+types-pkg-resources = "*"
+types-python-dateutil = "*"
+types-PyYAML = "*"
+types-requests = "*"
+types-six = "*"
+
 [tool.ruff]
 select = ["E", "F", "B", "UP"]
 target-version = "py37"