BUG: Fix the non-weighted DWI data serialization #301
Workflow file for this run
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| name: Unit and integration tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - maint/* | |
| pull_request: | |
| branches: | |
| - main | |
| - maint/* | |
| # Allow job to be triggered manually from GitHub interface | |
| workflow_dispatch: | |
| defaults: | |
| run: | |
| shell: bash | |
| # Force tox and pytest to use color | |
| env: | |
| FORCE_COLOR: true | |
| TEST_DATA_HOME: /home/runner/nifreeze-tests/ | |
| ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS: 4 | |
| ANTSPATH: /usr/share/miniconda/bin/ | |
| NIFREEZE_WERRORS: 1 | |
| TEST_DATA_REPO: https://gin.g-node.org/nipreps-data/tests-nifreeze | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| permissions: | |
| contents: read | |
| jobs: | |
| cache-test-data: | |
| runs-on: 'ubuntu-latest' | |
| outputs: | |
| SHA: ${{ steps.test-head.outputs.SHA }} | |
| steps: | |
| - name: Check remote HEAD | |
| id: test-head | |
| run: | | |
| SHA=$( git ls-remote $TEST_DATA_REPO HEAD | cut -f 1 ) | |
| echo SHA=$SHA >> $GITHUB_OUTPUT | |
| echo SHA7=${SHA:0:7} >> $GITHUB_OUTPUT | |
| - name: Check for data-v1-${{ steps.test-head.outputs.SHA }} | |
| uses: actions/cache@v4 | |
| id: test-data | |
| with: | |
| path: /home/runner/nifreeze-tests/ | |
| key: data-v1-${{ steps.test-head.outputs.SHA }} | |
| lookup-only: true | |
| - name: Create data-v1-${{ steps.test-head.outputs.SHA }} | |
| uses: actions/cache@v4 | |
| if: steps.test-data.outputs.cache-hit != 'true' | |
| with: | |
| path: /home/runner/nifreeze-tests/ | |
| key: data-v1-${{ steps.test-head.outputs.SHA }} | |
| restore-keys: | | |
| data-v1 | |
| data-v0 | |
| - name: Install the latest version of uv | |
| uses: astral-sh/setup-uv@v5 | |
| if: steps.test-data.outputs.cache-hit != 'true' | |
| - name: Install datalad | |
| if: steps.test-data.outputs.cache-hit != 'true' | |
| run: | | |
| uvx datalad-installer --sudo ok git-annex | |
| uv tool install --with=datalad-osf --with=datalad-next datalad | |
| uv tool install --with=datalad-next datalad-osf | |
| datalad wtf | |
| - name: Checkout commit ${{ steps.test-head.outputs.SHA7 }} | |
| if: steps.test-data.outputs.cache-hit != 'true' | |
| run: | | |
| if [[ ! -d "${TEST_DATA_HOME}" ]]; then | |
| datalad install -rg --source=${TEST_DATA_REPO} ${TEST_DATA_HOME} | |
| else | |
| cd ${TEST_DATA_HOME} | |
| datalad update --merge -r . | |
| datalad get -r -J4 * | |
| fi | |
| stable: | |
| # Unit tests only on Linux/Python 3.12 | |
| runs-on: 'ubuntu-latest' | |
| needs: ['cache-test-data'] | |
| strategy: | |
| matrix: | |
| python-version: ['3.10', '3.11', '3.12'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install the latest version of uv | |
| uses: astral-sh/setup-uv@v5 | |
| - name: Install ANTs | |
| run: | | |
| # Override libiconv pre-installed from anaconda channel | |
| # See https://github.com/conda-forge/libitk-feedstock/issues/98 | |
| # Since we're not creating a new environment, we must be explicit | |
| conda install -c conda-forge ants=2.5 libiconv | |
| - name: Verify antsRegistration path | |
| run: | | |
| export PATH=$ANTSPATH:$PATH | |
| which antsRegistration | |
| antsRegistration --version | |
| - uses: actions/cache/restore@v4 | |
| with: | |
| path: /home/runner/nifreeze-tests/ | |
| key: data-v1-${{ needs.cache-test-data.outputs.SHA }} | |
| - name: Install TeX Live | |
| run: | | |
| sudo apt-get update | |
| sudo apt install texlive texlive-latex-extra texlive-fonts-recommended cm-super dvipng | |
| - name: Install tox | |
| run: | | |
| uv tool install --with=tox-uv --with=tox-gh-actions tox | |
| - name: Show tox config | |
| run: tox c | |
| - name: Run tox | |
| run: | | |
| export PATH=$ANTSPATH:$PATH | |
| tox -v --exit-and-dump-after 1200 | |
| - uses: codecov/codecov-action@v4 | |
| if: ${{ always() }} | |
| with: | |
| files: cov.xml | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| checks: | |
| runs-on: 'ubuntu-latest' | |
| continue-on-error: true | |
| strategy: | |
| matrix: | |
| check: ['spellcheck', 'typecheck'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install the latest version of uv | |
| uses: astral-sh/setup-uv@v4 | |
| # Can remove this once there is a traits release that supports 3.13 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.12 | |
| - name: Install tox | |
| run: uv tool install tox --with=tox-uv | |
| - name: Show tox config | |
| run: tox c | |
| - name: Show tox config (this call) | |
| run: tox c -e ${{ matrix.check }} | |
| - name: Run check | |
| run: tox -e ${{ matrix.check }} |