Adjust nilearn calls for bleeding-edge #20
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| --- | |
| # Workflow to build the documentation. | |
| name: Build documentation | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - '*' | |
| jobs: | |
| # Steps to build the documentation. | |
| build_docs: | |
| # This prevents this workflow from running on a fork. | |
| if: github.repository == 'parietal-INRIA/fmralign' | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 360 | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - name: Source caching | |
| uses: actions/cache@v3 | |
| with: | |
| path: .git | |
| key: source-cache-${{ runner.os }}-${{ github.run_id }} | |
| restore-keys: | | |
| source-cache-${{ runner.os }} | |
| - name: Checkout fmralign | |
| uses: actions/checkout@v3 | |
| with: | |
| # If pull request, checkout HEAD commit with all commit history | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| fetch-depth: 0 | |
| - name: Complete checkout | |
| run: | | |
| set -x | |
| if ! git remote -v | grep upstream; then | |
| git remote add upstream https://github.com/parietal-INRIA/fmralign.git | |
| fi | |
| git fetch upstream | |
| - name: Merge with upstream | |
| run: | | |
| set -x | |
| echo $(git log -1 --pretty=%B) | tee gitlog.txt | |
| echo "gitlog.txt = $(cat gitlog.txt)" | |
| echo $GITHUB_REF_NAME | tee merge.txt | |
| if [ "$GITHUB_REF_NAME" != "main" ]; then | |
| echo "Merging $(cat merge.txt)"; | |
| git pull --ff-only upstream "refs/pull/$(cat merge.txt)"; | |
| fi | |
| # Set up environment | |
| - name: Install apt packages | |
| run: | | |
| sudo -E apt-get -yq update | |
| sudo -E apt-get -yq --no-install-suggests --no-install-recommends install \ | |
| dvipng texlive-latex-base texlive-latex-extra | |
| - name: Setup conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-activate-base: true | |
| activate-environment: '' | |
| miniconda-version: latest | |
| channels: conda-forge | |
| - name: Install packages in conda env | |
| run: | | |
| conda init bash | |
| echo "conda version = $(conda --version)" | |
| conda create -n testenv | |
| conda install -n testenv -yq python=3.9 | |
| source activate testenv | |
| python -m pip install --user --upgrade --progress-bar off pip | |
| # See pyproject.toml for dependency group options | |
| python -m pip install .[jax,test,doc] | |
| # Run the doc build. | |
| - name: Build docs | |
| run: | | |
| source activate testenv | |
| echo "Conda active env = $CONDA_DEFAULT_ENV"; | |
| cd doc; | |
| set -o pipefail; | |
| make html | tee log.txt; | |
| - name: Upload documentation | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: doc | |
| path: doc/_build/html |