Minor updates. #146
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| # Lingfei Wang, 2022. All rights reserved. | |
| name: Installation script test | |
| on: | |
| schedule: | |
| - cron: '20 7 * * 1' | |
| push: | |
| paths: | |
| - '.github/workflows/ci-install.yml' | |
| - '.github/actions/install-bash/**' | |
| - README.rst | |
| workflow_dispatch: | |
| inputs: | |
| ref: | |
| description: 'Commit or branch to run action on' | |
| required: true | |
| default: 'dev' | |
| jobs: | |
| install-script-bash: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| run: ${{ steps.runscript.outputs.run }} | |
| steps: | |
| - name: Show version | |
| id: version | |
| run: | | |
| if [ "a${{ inputs.ref }}" != "a" ]; then | |
| v="${{ inputs.ref }}" | |
| elif [ "a${GITHUB_REF}" != "a" ]; then | |
| v="${GITHUB_REF}" | |
| elif [ "a${{ github.event.repository.default_branch }}" != "a" ]; then | |
| v="${{ github.event.repository.default_branch }}" | |
| else | |
| exit 1 | |
| fi | |
| echo "$v" | |
| echo "version=$v" >> $GITHUB_OUTPUT | |
| - uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ steps.version.outputs.version }} | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 | |
| - name: Obtain install script | |
| id: runscript | |
| run: | | |
| # Install command in README.rst (indented in Installation section) | |
| # Get first code-block in section Installation | |
| linestart=$(grep -n '^Installation' README.rst | awk -F: '{print $1}' | head -n 1) | |
| lineend=$(tail -n +$(( linestart + 2 )) README.rst | grep -n '^==' | awk -F: '{print $1}' | head -n 1) | |
| linestart2=$(tail -n +$linestart README.rst | head -n $lineend | grep -n '^Option [0-9]: with .*bash script' | awk -F: '{print $1}' | head -n 1) | |
| echo "Step 1" | |
| tail -n +$linestart README.rst | head -n $lineend | |
| linestart=$(( linestart + linestart2 )) | |
| lineend=$(tail -n +$(( linestart + 2 )) README.rst | head -n $lineend | grep -n '^--' | awk -F: '{print $1}' | head -n 1) | |
| echo "Step 2" | |
| tail -n +$(( linestart + 2 )) README.rst | head -n $lineend | |
| linestart2=$(tail -n +$linestart README.rst | head -n $lineend | grep -n '^.. code-block::' | awk -F: '{print $1}' | head -n 1) | |
| echo "Step 3" | |
| tail -n +$linestart README.rst | head -n $lineend | |
| lineend2=$(tail -n +$linestart README.rst | head -n $lineend | tail -n +$(( linestart2 + 1 )) | grep -n '^.. code-block::' | awk -F: '{print $1}' | head -n 1) | |
| echo "Step 4" | |
| tail -n +$linestart README.rst | head -n $lineend | |
| echo "Step 5" | |
| tail -n +$linestart README.rst | head -n $lineend | tail -n +$(( linestart2 + 1 )) | |
| s1="$(tail -n +$linestart README.rst | head -n $lineend | tail -n +$linestart2 | head -n $lineend2 | grep '^[[:blank:]]' | sed 's/^[[:space:]]*//g')" | |
| echo "Step 6" | |
| tail -n +$linestart README.rst | head -n $lineend | |
| echo "Step 7" | |
| tail -n +$linestart README.rst | head -n $lineend | tail -n +$linestart2 | head -n $lineend2 | |
| echo "Step 8" | |
| echo "$s1" | |
| #If failed here: update this line and the same line in /.github/actions/install-bash/action.yml to match the lines in /README.rst | |
| cmp <(echo "$s1") <(echo "wget https://tinyurl.com/dictys -O - | bash") || exit 1 | |
| echo "run=$s1" >> $GITHUB_OUTPUT | |
| install-linux-bash: | |
| runs-on: ubuntu-latest | |
| needs: install-script-bash | |
| steps: | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 | |
| - name: Add conda to system path | |
| run: | | |
| # $CONDA is an environment variable pointing to the root of the miniconda directory | |
| echo $CONDA/bin >> $GITHUB_PATH | |
| - name: Test install | |
| run: | | |
| echo '::group::Test install output' | |
| ${{ needs.install-script-bash.outputs.run }} | |
| echo '::endgroup::' | |
| install-script-conda: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| run: ${{ steps.runscript.outputs.run }} | |
| steps: | |
| - name: Show version | |
| id: version | |
| run: | | |
| if [ "a${{ inputs.ref }}" != "a" ]; then | |
| v="${{ inputs.ref }}" | |
| elif [ "a${GITHUB_REF}" != "a" ]; then | |
| v="${GITHUB_REF}" | |
| elif [ "a${{ github.event.repository.default_branch }}" != "a" ]; then | |
| v="${{ github.event.repository.default_branch }}" | |
| else | |
| exit 1 | |
| fi | |
| echo "$v" | |
| echo "version=$v" >> $GITHUB_OUTPUT | |
| - uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ steps.version.outputs.version }} | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 | |
| - name: Obtain install script | |
| id: run0 | |
| run: | | |
| # Install command in README.rst (indented in Installation section) | |
| # Get first code-block in section Installation | |
| linestart=$(grep -n '^Installation' README.rst | awk -F: '{print $1}' | head -n 1) | |
| lineend=$(tail -n +$(( linestart + 2 )) README.rst | grep -n '^==' | awk -F: '{print $1}' | head -n 1) | |
| echo "Step 1" | |
| tail -n +$linestart README.rst | head -n $lineend | |
| linestart2=$(tail -n +$linestart README.rst | head -n $lineend | grep -n '^Option [0-9]: with .*conda$' | awk -F: '{print $1}' | head -n 1) | |
| linestart=$(( linestart + linestart2 )) | |
| echo "Step 2" | |
| tail -n +$(( linestart + 2 )) README.rst | head -n $lineend | |
| lineend=$(tail -n +$(( linestart + 2 )) README.rst | head -n $lineend | grep -n '^--' | awk -F: '{print $1}' | head -n 1) | |
| linestart2=$(tail -n +$linestart README.rst | head -n $lineend | grep -n '^.. code-block::' | awk -F: '{print $1}' | head -n 1) | |
| echo "Step 3" | |
| tail -n +$linestart README.rst | head -n $lineend | tail -n +$(( linestart2 + 1 )) | |
| lineend2=$(tail -n +$linestart README.rst | head -n $lineend | tail -n +$(( linestart2 + 1 )) | grep -n '^.. code-block::' | awk -F: '{print $1}' | head -n 1) | |
| echo "Step 4" | |
| echo "$linestart" | |
| echo "$lineend" | |
| tail -n +$linestart README.rst | head -n $lineend | |
| echo "Step 5" | |
| echo "$linestart2" | |
| echo "$lineend2" | |
| tail -n +$linestart README.rst | head -n $lineend | tail -n +$linestart2 | head -n $lineend2 | |
| s1="$(tail -n +$linestart README.rst | head -n $lineend | tail -n +$linestart2 | head -n $lineend2 | grep '^[[:blank:]]' | sed 's/^[[:space:]]*//g')" | |
| #If failed here: update this line and the same line in /.github/actions/install-conda/action.yml to match the lines in /README.rst | |
| cmp <(echo "$s1") <(echo "conda create -y -n dictys -c conda-forge python=3.9 mamba"; echo ". activate dictys"; echo "mamba install -y -c lingfeiwang -c bioconda -c conda-forge -c pytorch dictys pytorch torchvision torchaudio cpuonly") || exit 1 | |
| echo "run<<EOF" >> $GITHUB_ENV | |
| echo "$s1" >> $GITHUB_ENV | |
| echo "EOF" >> $GITHUB_ENV | |
| - id: runscript | |
| uses: actions/github-script@v6 | |
| with: | |
| script: | | |
| core.setOutput("run", `${{ env.run }}`); | |
| install-linux-conda: | |
| runs-on: ubuntu-latest | |
| needs: install-script-conda | |
| steps: | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 | |
| - name: Add conda to system path | |
| run: | | |
| # $CONDA is an environment variable pointing to the root of the miniconda directory | |
| echo $CONDA/bin >> $GITHUB_PATH | |
| - name: Test install | |
| run: | | |
| echo '::group::Test install output' | |
| ${{ needs.install-script-conda.outputs.run }} | |
| echo '::endgroup::' | |
| install-linux: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.9","3.10",""] | |
| cuda-version: ["11.3",""] | |
| steps: | |
| - name: Show version | |
| id: version | |
| run: | | |
| if [ "a${{ inputs.ref }}" != "a" ]; then | |
| v="${{ inputs.ref }}" | |
| elif [ "a${GITHUB_REF}" != "a" ]; then | |
| v="${GITHUB_REF}" | |
| elif [ "a${{ github.event.repository.default_branch }}" != "a" ]; then | |
| v="${{ github.event.repository.default_branch }}" | |
| else | |
| exit 1 | |
| fi | |
| echo "$v" | |
| echo "version=$v" >> $GITHUB_OUTPUT | |
| - uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ steps.version.outputs.version }} | |
| - name: Install | |
| uses: ./.github/actions/install-bash | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cuda-version: ${{ matrix.cuda-version }} |