diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index 93f3d279..aae66c1d 100644 --- a/.github/workflows/gh-ci-cron.yaml +++ b/.github/workflows/gh-ci-cron.yaml @@ -20,16 +20,16 @@ defaults: jobs: gen_matrix: - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest outputs: matrix: ${{ steps.get-mdakits.outputs.matrix }} steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - id: get-python - uses: actions/setup-python@v4 + uses: actions/setup-python@v6 with: - python-version: "3.12" + python-version: "3.13" - id: get-mdakits run: | @@ -43,9 +43,9 @@ jobs: python-min: ${{ steps.get-compatible-python.outputs.oldest-python }} steps: - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v6 with: - python-version: "3.12" + python-version: "3.13" - id: get-compatible-python uses: MDAnalysis/mdanalysis-compatible-python@main @@ -54,14 +54,14 @@ jobs: mdakit-ci: needs: [gen_matrix, env_config] - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest strategy: fail-fast: false matrix: mdakit: ${{fromJSON(needs.gen_matrix.outputs.matrix)}} jobstep: ['latest', 'develop'] steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - id: get-base-python-deps name: get-base-python-deps @@ -79,11 +79,10 @@ jobs: - id: install-conda-env name: install-conda-env - uses: conda-incubator/setup-miniconda@v3 + uses: conda-incubator/setup-miniconda@v4 with: python-version: ${{ env.PYVER }} add-pip-as-python-dependency: true - architecture: x64 use-mamba: true miniforge-version: latest channels: conda-forge @@ -153,7 +152,7 @@ jobs: - id: upload-artifacts name: upload-artifacts - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@v7 with: name: cron-statuses-${{ matrix.mdakit }}-${{ matrix.jobstep }} path: ${{ matrix.mdakit }}-${{ matrix.jobstep }}-statuses.json @@ -163,16 +162,16 @@ jobs: process_results: if: ${{ always() }} needs: mdakit-ci - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest permissions: contents: write pull-requests: write packages: none issues: write steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - - uses: actions/download-artifact@v4 + - uses: actions/download-artifact@v8 with: path: json-statuses/ @@ -191,7 +190,7 @@ jobs: env: GITHUB_TOKEN: ${{ github.token }} - - uses: stefanzweifel/git-auto-commit-action@v4 + - uses: stefanzweifel/git-auto-commit-action@v7 with: commit_message: commit changes to status files skip_dirty_check: false @@ -200,22 +199,22 @@ jobs: deploy_docs: if: ${{ always() }} needs: process_results - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: setup_micromamba - uses: mamba-org/setup-micromamba@v1 + uses: mamba-org/setup-micromamba@v3 with: environment-file: docs/requirements.yaml environment-name: MDAKitRegistry-docs create-args: >- - python=3.9 + python=3.12 pip - name: build_docs run: | cd docs && sphinx-build -b html source build - name: deploy docs - uses: peaceiris/actions-gh-pages@v3 + uses: peaceiris/actions-gh-pages@v4 with: github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: ./docs/build diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index e7a92342..439a2441 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -16,20 +16,20 @@ defaults: jobs: gen_matrix: - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest outputs: matrix: ${{ steps.get-changed-mdakits.outputs.matrix }} steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - id: get-python - uses: actions/setup-python@v4 + uses: actions/setup-python@v6 with: - python-version: 3.9 + python-version: 3.13 - id: files name: get changed filed - uses: masesgroup/retrieve-changed-files@v3 + uses: masesgroup/retrieve-changed-files@v4 with: format: 'json' - id: get-changed-mdakits @@ -46,9 +46,9 @@ jobs: python-stable: ${{ steps.get-compatible-python.outputs.stable-python }} python-min: ${{ steps.get-compatible-python.outputs.oldest-python }} steps: - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v6 with: - python-version: "3.12" + python-version: "3.13" - id: get-compatible-python uses: MDAnalysis/mdanalysis-compatible-python@main @@ -57,19 +57,19 @@ jobs: mdakit-ci: needs: [gen_matrix, env_config] - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest strategy: fail-fast: false matrix: mdakit: ${{fromJSON(needs.gen_matrix.outputs.matrix)}} jobstep: ['latest', 'develop'] steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - id: get-base-python-deps name: get-base-python-deps run: | - pip install requests setuptools packaging pyyaml pydantic PyGithub + python -m pip install requests setuptools packaging pyyaml pydantic PyGithub - id: check-set-python-bounds name: check-set-python-bounds @@ -82,11 +82,10 @@ jobs: - id: install-conda-env name: install-conda-env - uses: conda-incubator/setup-miniconda@v3 + uses: conda-incubator/setup-miniconda@v4 with: python-version: ${{ env.PYVER }} add-pip-as-python-dependency: true - architecture: x64 use-mamba: true miniforge-version: latest channels: conda-forge @@ -98,7 +97,7 @@ jobs: name: install-conda-base-deps run: | mamba install requests setuptools packaging pyyaml pydantic - pip install PyGithub + python -m pip install PyGithub - id: install-mdakit name: install-mdakit @@ -119,8 +118,8 @@ jobs: continue-on-error: false run: | install=$(python utils/get_testdeps.py --mdakit ${{matrix.mdakit}}) - echo "install tests:${install}" - eval ${install} + echo "test installs: ${install}" + eval "${install}" - id: install-mdanalysis name: install-mdanalysis diff --git a/utils/get_install.py b/utils/get_install.py index 6f4b3983..bead02d7 100644 --- a/utils/get_install.py +++ b/utils/get_install.py @@ -53,4 +53,4 @@ args = parser.parse_args() kit = MDAKit(f"mdakits/{args.mdakit}") instructions = kit.get_install(f"{args.itype}") - print(instructions) + print(instructions.lower()) diff --git a/utils/get_testdeps.py b/utils/get_testdeps.py index bd878075..1558b7b3 100644 --- a/utils/get_testdeps.py +++ b/utils/get_testdeps.py @@ -46,4 +46,4 @@ args = parser.parse_args() kit = MDAKit(f"mdakits/{args.mdakit}") instructions = kit.get_test_deps() - print(instructions) + print(instructions.lower())