update dependencies #39
Workflow file for this run
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| name: Download dataset | |
| on: | |
| push: | |
| branches: | |
| - nk/add-post-training-script-to-compute-csa | |
| # release: | |
| # types: [published] | |
| jobs: | |
| run_dataset_download: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.9.16' | |
| - name: Set up Conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| channels: conda-forge | |
| activate-environment: sct-env | |
| python-version: '3.9.16' | |
| - name: Install dependencies | |
| run: | | |
| conda install -y git-annex | |
| - name: Ensure git-annex is accessible via git | |
| run: | | |
| echo "$(conda info --base)/bin" >> $GITHUB_PATH | |
| export PATH="$(conda info --base)/bin:$PATH" | |
| which git-annex | |
| git-annex version | |
| - name: Configure Git identity | |
| run: | | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "GitHub Actions" | |
| - name: Install SCT | |
| shell: bash -l {0} | |
| run: | | |
| git clone https://github.com/spinalcordtoolbox/spinalcordtoolbox | |
| cd spinalcordtoolbox | |
| # Ensure Conda environment is properly activated | |
| eval "$(conda shell.bash hook)" | |
| conda activate sct-env | |
| ./install_sct -iy | |
| # # https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/master/.ci.sh | |
| # - name: Install SCT | |
| # shell: bash -l {0} | |
| # run: | | |
| # # source python/etc/profile.d/conda.sh >> $GITHUB_ENV | |
| # git clone https://github.com/spinalcordtoolbox/spinalcordtoolbox.git | |
| # cd spinalcordtoolbox | |
| # ./.ci.sh -i | |
| # # NB: install_sct edits ~/.bashrc, but those environment changes don't get passed to subsequent steps in GH Actions. | |
| # # So, we filter through the .bashrc and pass the values to $GITHUB_ENV and $GITHUB_PATH. | |
| # # Relevant documentation: https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#environment-files | |
| # cat ~/.bashrc | grep "export SCT_DIR" | cut -d " " -f 2 >> $GITHUB_ENV | |
| # cat ~/.bashrc | grep "export PATH" | grep -o "/.*" | cut -d ':' -f 1 >> $GITHUB_PATH | |
| # - name: Run dataset setup script | |
| # shell: bash -l {0} # Ensures the Conda environment is properly loaded | |
| # run: | | |
| # chmod +x scripts/compute_morphometrics_spine_generic.sh | |
| # source scripts/compute_morphometrics_spine_generic.sh | |
| # - name: Run model script | |
| # run: ./scripts/run_model.sh |