Update uv.lock + CI tweaks + fix pymatgen issue (#6676)

Recreate the uv lockfile (`uv.lock`) with a newer uv version that uses an updated resolution strategy.

Previously, it tried to find a version of the package that would be compatible with all supported Python versions, which in turn meant that if a package dropped support for 3.9 for example, we'd be stuck on an old version.
In the new uv version, this is not the case, and uv will try to find the newest version of a package for a given python version.

Incidentally, this also help partly resolve the pymatgen issue, see #6680. The issue has been fixed in a new version of monty package, which however does not support Python 3.9. So in the updated lockfile, the issue is fixed for Python >=3.10.

For Python 3.9, a workaround suggested in materialsproject/pymatgen#4243, and unset the CI environmental variable.
Since this workaround is quite targeted (only in two specific job steps, and only for Python 3.9), I believe this is acceptable, and we will be dropping Python 3.9 support sometimes this year anyway.

.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