Merge branch 'main' into pre-commit-ci-update-config

.github/actions/install-aiida-core/action.yml

@@ -7,16 +7,18 @@ inputs:
     default: '3.9'              # Lowest supported version
     required: false
   extras:
-    description: aiida-core extras (including brackets)
-    default: ''
+    description: list of optional dependencies
+    # NOTE: The default 'pre-commit' extra recursively contains
+    # other extras needed to run the tests.
+    default: pre-commit
     required: false
   # NOTE: Hard-learned lesson: we cannot use type=boolean here, apparently :-(
   # https://stackoverflow.com/a/76294014
   # NOTE2: When installing from lockfile, aiida-core and its dependencies
   # are installed in a virtual environment located in .venv directory.
   # Subsuquent jobs steps must either activate the environment or use `uv run`
   from-lock:
-    description: Install aiida-core dependencies from a uv lock file
+    description: Install aiida-core dependencies from uv lock file
     default: 'true'
     required: false
 
@@ -29,19 +31,18 @@ runs:
       python-version: ${{ inputs.python-version }}
 
   - name: Set up uv
-    uses: astral-sh/setup-uv@v4
+    uses: astral-sh/setup-uv@v5
     with:
-      version: 0.5.6
+      version: 0.5.x
+      python-version: ${{ inputs.python-version }}
 
   - name: Install dependencies from uv lock
     if: ${{ inputs.from-lock == 'true' }}
     # NOTE: We're asserting that the lockfile is up to date
-    # NOTE2: 'pre-commit' extra recursively contains other extras
-    # needed to run the tests.
-    run: uv sync --locked --extra pre-commit
+    run: uv sync --locked ${{ inputs.extras && format('--extra {0}', inputs.extras) || '' }}
     shell: bash
 
   - name: Install aiida-core
     if: ${{ inputs.from-lock != 'true' }}
-    run: uv pip install --system -e .${{ inputs.extras }}
+    run: uv pip install -e .${{ inputs.extras }}
     shell: bash

.github/workflows/ci-code.yml

@@ -64,16 +64,22 @@ jobs:
         python-version: ${{ matrix.python-version }}
 
     - name: Setup environment
-      # Note: The virtual environment in .venv was created by uv in previous step
-      run: source .venv/bin/activate && .github/workflows/setup.sh
+      run: .github/workflows/setup.sh
 
     - name: Run test suite
       env:
         AIIDA_TEST_PROFILE: test_aiida
         AIIDA_WARN_v3: 1
-      # Python 3.12 has a performance regression when running with code coverage
+      # NOTE1: Python 3.12 has a performance regression when running with code coverage
       # so run code coverage only for python 3.9.
-      run: uv run pytest -n auto --db-backend psql -m 'not nightly' tests/ ${{ matrix.python-version == '3.9' && '--cov aiida' || '' }}
+      # NOTE2: Unset CI envvar to workaround a pymatgen issue for Python 3.9
+      # https://github.com/materialsproject/pymatgen/issues/4243
+      # TODO: Remove a workaround for VIRTUAL_ENV once the setup-uv action is updated
+      # https://github.com/astral-sh/setup-uv/issues/219
+      run: |
+        ${{ matrix.python-version == '3.9' && 'unset CI' || '' }}
+        ${{ matrix.python-version == '3.9' && 'VIRTUAL_ENV=$PWD/.venv' || '' }}
+        pytest -n auto --db-backend psql -m 'not nightly' tests/ ${{ matrix.python-version == '3.9' && '--cov aiida' || '' }}
 
     - name: Upload coverage report
       if: matrix.python-version == 3.9 && github.repository == 'aiidateam/aiida-core'
@@ -122,7 +128,10 @@ jobs:
       uses: ./.github/actions/install-aiida-core
       with:
         python-version: '3.12'
-        from-lock: 'false'
+        from-lock: 'true'
+        # NOTE: The `verdi devel check-undesired-imports` fails if
+        # the 'tui' extra is installed.
+        extras: ''
 
     - name: Run verdi tests
       run: |

.github/workflows/test-install.yml

@@ -11,6 +11,9 @@ on:
   schedule:
   - cron: 30 02 * * *      # nightly build
 
+env:
+  FORCE_COLOR: 1
+
 # https://docs.github.com/en/actions/using-jobs/using-concurrency
 concurrency:
   # only cancel in-progress jobs or runs for the current workflow - matches against branch & tags
@@ -32,18 +35,18 @@ jobs:
     - name: Set up Python 3.11
       uses: actions/setup-python@v5
       with:
-        python-version: '3.9'
+        python-version: '3.11'
 
     - name: Set up uv
-      uses: astral-sh/setup-uv@v4
+      uses: astral-sh/setup-uv@v5
       with:
-        version: 0.5.6
+        version: 0.5.x
 
     - name: Install utils/ dependencies
       run: uv pip install --system -r utils/requirements.txt
 
     - name: Validate uv lockfile
-      run: uv lock --locked
+      run: uv lock --check
 
     - name: Validate conda environment file
       run: python ./utils/dependency_management.py validate-environment-yml
@@ -208,4 +211,11 @@ jobs:
       env:
         AIIDA_TEST_PROFILE: test_aiida
         AIIDA_WARN_v3: 1
-      run: pytest -n auto --db-backend psql tests -m 'not nightly' tests/
+      # Unset CI envvar to workaround a pymatgen issue for Python 3.9
+      # https://github.com/materialsproject/pymatgen/issues/4243
+      # TODO: Remove a workaround for VIRTUAL_ENV once the setup-uv action is updated
+      # https://github.com/astral-sh/setup-uv/issues/219
+      run: |
+        ${{ matrix.python-version == '3.9' && 'unset CI' || '' }}
+        ${{ matrix.python-version == '3.9' && 'VIRTUAL_ENV=$PWD/.venv' || '' }}
+        pytest -n auto --db-backend psql tests -m 'not nightly' tests/

.pre-commit-config.yaml

@@ -191,12 +191,13 @@ repos:
   - id: check-uv-lock
     name: Check uv lockfile up to date
     # NOTE: This will not automatically update the lockfile
-    entry: uv lock --locked
+    entry: uv lock --check
     language: system
     pass_filenames: false
     files: >-
       (?x)^(
         pyproject.toml|
+        uv.lock|
       )$
 
   - id: generate-conda-environment