Support for Python 3.13

.github/CODEOWNERS

@@ -2,9 +2,7 @@
 # currently active dependency manager (DM) to trigger an automatic review
 # request from the DM upon changes. Please see AEP-002 for details:
 # https://github.com/aiidateam/AEP/tree/master/002_dependency_management
-setup.*                         @aiidateam/dependency-manager
-environment.yml                 @aiidateam/dependency-manager
-requirements*.txt               @aiidateam/dependency-manager
-pyproject.toml                  @aiidateam/dependency-manager
-utils/dependency_management.py  @aiidateam/dependency-manager
-.github/workflows/dm.yml        @aiidateam/dependency-manager
+environment.yml                 @unkcpz @agoscinski
+pyproject.toml                  @unkcpz @agoscinski
+uv.lock                         @unkcpz @agoscinski
+utils/dependency_management.py  @unkcpz @agoscinski

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

@@ -12,8 +12,8 @@ inputs:
     required: false
   # NOTE: Hard-learned lesson: we cannot use type=boolean here, apparently :-(
   # https://stackoverflow.com/a/76294014
-  from-requirements:
-    description: Install aiida-core dependencies from pre-compiled requirements.txt file
+  from-lock:
+    description: Install aiida-core dependencies from a uv lock file
     default: 'true'
     required: false
 
@@ -25,26 +25,18 @@ runs:
     with:
       python-version: ${{ inputs.python-version }}
 
-  - name: Install uv installer
-    run: curl --proto '=https' --tlsv1.2 -LsSf https://${{ env.UV_URL }} | sh
-    env:
-      UV_VERSION: 0.2.9
-      UV_URL: github.com/astral-sh/uv/releases/download/$UV_VERSION/uv-installer.sh
-    shell: bash
+  - name: Set up uv
+    uses: astral-sh/setup-uv@v4
+    with:
+      version: 0.5.5
 
-  - name: Install dependencies from requirements-py-*.txt
-    if: ${{ inputs.from-requirements == 'true' }}
-    run: uv pip install --system -r requirements/requirements-py-${{ inputs.python-version }}.txt
+  - name: Install dependencies from uv lock
+    # NOTE: We're also asserting that the lockfile is up to date
+    if: ${{ inputs.from-lock == 'true' }}
+    run: uv sync --locked --extra pre-commit
     shell: bash
 
   - name: Install aiida-core
-    run: uv pip install --system ${{ env.NO_DEPS }} -e .${{ inputs.extras }}
-    env:
-        # Don't install dependencies if they were installed through requirements file AND
-        # if no extras are required.
-        #
-        # If this syntax looks weird to you, dear reader, know that this is
-        # GHA's way to do ternary operator. :-/
-        # https://docs.github.com/en/actions/learn-github-actions/expressions#example
-      NO_DEPS: ${{ (inputs.from-requirements == 'true' && inputs.extras == '')  && '--no-deps' || '' }}
+    if: ${{ inputs.from-lock != 'true' }}
+    run: uv pip install --system -e .${{ inputs.extras }}
     shell: bash

.github/workflows/ci-code.yml

@@ -18,47 +18,15 @@ env:
 
 jobs:
 
-  check-requirements:
-
-    runs-on: ubuntu-latest
-    timeout-minutes: 5
-
-    steps:
-    - uses: actions/checkout@v4
-
-    - name: Set up Python 3.12
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.12'
-
-    - name: Install utils/ dependencies
-      run: pip install -r utils/requirements.txt
-
-    - name: Check requirements files
-      id: check_reqs
-      run: python ./utils/dependency_management.py check-requirements DEFAULT
-
-    - name: Create commit comment
-      if: failure() && steps.check_reqs.outputs.error
-      uses: peter-evans/commit-comment@v3
-      with:
-        path: pyproject.toml
-        body: |
-          ${{ steps.check_reqs.outputs.error }}
-
-          Click [here](https://github.com/aiidateam/aiida-core/wiki/AiiDA-Dependency-Management) for more information on dependency management.
-
   tests:
 
-    needs: [check-requirements]
-
     runs-on: ubuntu-latest
     timeout-minutes: 45
 
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.12']
+        python-version: ['3.9', '3.13']
 
     services:
       postgres:
@@ -96,15 +64,15 @@ jobs:
         python-version: ${{ matrix.python-version }}
 
     - name: Setup environment
-      run: .github/workflows/setup.sh
+      run: source .venv/bin/activate && .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
       # so run code coverage only for python 3.9.
-      run: pytest -n auto --db-backend psql -m 'not nightly' tests/ ${{ matrix.python-version == '3.9' && '--cov aiida' || '' }}
+      run: uv run 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'
@@ -118,7 +86,6 @@ jobs:
 
   tests-presto:
 
-    needs: [check-requirements]
     runs-on: ubuntu-latest
     timeout-minutes: 20
 
@@ -139,12 +106,11 @@ jobs:
     - name: Run test suite
       env:
         AIIDA_WARN_v3: 0
-      run: pytest -n auto -m 'presto' tests/
+      run: uv run pytest -n auto -m 'presto' tests/
 
 
   verdi:
 
-    needs: [check-requirements]
     runs-on: ubuntu-latest
     timeout-minutes: 10
 
@@ -154,8 +120,8 @@ jobs:
     - name: Install aiida-core
       uses: ./.github/actions/install-aiida-core
       with:
-        python-version: '3.12'
-        from-requirements: 'false'
+        python-version: '3.13'
+        from-lock: 'false'
 
     - name: Run verdi tests
       run: |

.github/workflows/docs-build.yml

@@ -25,7 +25,7 @@ jobs:
       with:
         python-version: '3.9'
         extras: '[docs,tests,rest,atomic_tools]'
-        from-requirements: 'false'
+        from-lock: 'false'
 
     - name: Build HTML docs
       id: linkcheck

.github/workflows/release.yml

@@ -42,7 +42,7 @@ jobs:
       with:
         python-version: '3.11'
         extras: '[pre-commit]'
-        from-requirements: 'false'
+        from-lock: 'false'
 
     - name: Run pre-commit
       run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )

.github/workflows/test-install.yml

@@ -4,7 +4,6 @@ on:
   pull_request:
     paths:
     - environment.yml
-    - '**/requirements*.txt'
     - pyproject.toml
     - util/dependency_management.py
     - .github/workflows/test-install.yml
@@ -14,7 +13,7 @@ on:
 
 # 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
+  # only cancel in-progress jobs or runs for the current workflow - matches against branch & tags
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
@@ -30,44 +29,24 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
-    - name: Set up Python 3.9
+    - name: Set up Python 3.11
       uses: actions/setup-python@v5
       with:
         python-version: '3.9'
 
-    - name: Install utils/ dependencies
-      run: pip install -r utils/requirements.txt
-
-    - name: Validate
-      run: |
-        python ./utils/dependency_management.py check-requirements
-        python ./utils/dependency_management.py validate-all
-
-  resolve-pip-dependencies:
-    # Check whether the environments defined in the requirements/* files are
-    # resolvable.
-
-    needs: [validate-dependency-specification]
-    if: github.repository == 'aiidateam/aiida-core'
-    runs-on: ubuntu-latest
-    timeout-minutes: 5
-
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v4
+      with:
+        version: 0.5.5
 
-    steps:
-    - uses: actions/checkout@v4
+    - name: Install utils/ dependencies
+      run: uv pip install --system -r utils/requirements.txt
 
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
+    - name: Validate uv lockfile
+      run: uv lock --locked
 
-    - name: Resolve dependencies from requirements file.
-      run: |
-        pip install --dry-run --ignore-installed -r requirements/requirements-py-${{ matrix.python-version }}.txt
+    - name: Validate conda environment file
+      run: python ./utils/dependency_management.py validate-environment-yml
 
   create-conda-environment:
     # Verify that we can create a valid conda environment from the environment.yml file.
@@ -132,7 +111,7 @@ jobs:
       fail-fast: false
       matrix:
 
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
 
         # Not being able to install with conda on a specific Python version is
         # not sufficient to fail the run, but something we want to be aware of.
@@ -183,7 +162,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
 
     services:
       postgres:
@@ -220,7 +199,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
         extras: '[atomic_tools,docs,notebook,rest,tests,tui]'
-        from-requirements: 'false'
+        from-lock: 'false'
 
     - name: Setup AiiDA environment
       run: .github/workflows/setup.sh
@@ -230,112 +209,3 @@ jobs:
         AIIDA_TEST_PROFILE: test_aiida
         AIIDA_WARN_v3: 1
       run: pytest -n auto --db-backend psql tests -m 'not nightly' tests/
-
-    - name: Freeze test environment
-      run: pip freeze | sed '1d' | tee requirements-py-${{ matrix.python-version }}.txt
-
-    # Add python-version specific requirements/ file to the requirements.txt artifact.
-    # This artifact can be used in the next step to automatically create a pull request
-    # updating the requirements (in case they are  inconsistent with the pyproject.toml file).
-    - uses: actions/upload-artifact@v4
-      with:
-        name: requirements-py-${{ matrix.python-version }}.txt
-        path: requirements-py-${{ matrix.python-version }}.txt
-
-# Check whether the requirements/ files are consistent with the dependency specification in the pyproject.toml file.
-# If the check fails, warn the user via a comment and try to automatically create a pull request to update the files
-# (does not work on pull requests from forks).
-
-  check-requirements:
-
-    needs: tests
-
-    runs-on: ubuntu-latest
-    timeout-minutes: 5
-
-    steps:
-    - uses: actions/checkout@v4
-
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v5
-      with:
-        python-version: 3.9
-
-    - name: Install utils/ dependencies
-      run: pip install -r utils/requirements.txt
-
-    - name: Check consistency of requirements/ files
-      id: check_reqs
-      continue-on-error: true
-      run: python ./utils/dependency_management.py check-requirements DEFAULT --no-github-annotate
-
-#
-# The following steps are only executed if the consistency check failed.
-#
-    - name: Create commit comment
-      if: steps.check_reqs.outcome == 'Failure'  # only run if requirements/ are inconsistent
-      uses: peter-evans/commit-comment@v3
-      with:
-        token: ${{ secrets.GITHUB_TOKEN }}
-        path: pyproject.toml
-        body: |
-          The requirements/ files are inconsistent!
-
-    # Check out the base branch so that we can prepare the pull request.
-    - name: Checkout base branch
-      if: steps.check_reqs.outcome == 'Failure'  # only run if requirements/ are inconsistent
-      uses: actions/checkout@v4
-      with:
-        ref: ${{ github.head_ref }}
-        clean: true
-
-    - name: Download requirements.txt files
-      if: steps.check_reqs.outcome == 'Failure'  # only run if requirements/ are inconsistent
-      uses: actions/download-artifact@v4
-      with:
-        pattern: requirements-py-*
-        merge-multiple: true
-        path: requirements
-
-    - name: Commit requirements files
-      if: steps.check_reqs.outcome == 'Failure'  # only run if requirements/ are inconsistent
-      run: |
-        git add requirements/*
-
-    - name: Create pull request for updated requirements files
-      if: steps.check_reqs.outcome == 'Failure'  # only run if requirements/ are inconsistent
-      id: create_update_requirements_pr
-      continue-on-error: true
-      uses: peter-evans/create-pull-request@v7
-      with:
-        branch: update-requirements
-        commit-message: Automated update of requirements/ files.
-        title: Update requirements/ files.
-        body: |
-          Update requirements files to ensure that they are consistent
-          with the dependencies specified in the 'pyproject.toml' file.
-
-          Please note, that this pull request was likely created to
-          resolve the inconsistency for a specific dependency, however
-          other versions that have changed since the last update will
-          be included as part of this commit as well.
-
-          Click [here](https://github.com/aiidateam/aiida-core/wiki/AiiDA-Dependency-Management) for more information.
-
-    - name: Create PR comment on success
-      if: steps.create_update_requirements_pr.outcome == 'Success'
-      uses: peter-evans/create-or-update-comment@v4
-      with:
-        issue-number: ${{ github.event.number }}
-        body: |
-          I automatically created a pull request (#${{ steps.create_update_requirements_pr.outputs.pr_number }}) that adapts the
-          requirements/ files according to the dependencies specified in the 'pyproject.toml' file.
-
-    - name: Create PR comment on failure
-      if: steps.create_update_requirements_pr.outcome == 'Failure'
-      uses: peter-evans/create-or-update-comment@v4
-      with:
-        issue-number: ${{ github.event.number }}
-        body: |
-          Please update the requirements/ files to ensure that they
-          are consistent with the dependencies specified in the 'pyproject.toml' file.