ci-install.yml

# Lingfei Wang, 2022, 2023. 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
    branches:
      - master
      - dev
  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@v4
      with:
        ref: ${{ steps.version.outputs.version }}
    - name: Set up Python 3.8
      uses: actions/setup-python@v5
      with:
        python-version: 3.8
    - name: Obtain install script
      id: runscript
      run: |
        # Install command in README.rst (indented in Installation section)
        # Get first code-block in section Installation
        linestart=$(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@v5
      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@v4
      with:
        ref: ${{ steps.version.outputs.version }}
    - name: Set up Python 3.8
      uses: actions/setup-python@v5
      with:
        python-version: 3.8
    - name: Obtain install script
      id: run0
      run: |
        # Install command in README.rst (indented in Installation section)
        # Get first code-block in section Installation
        linestart=$(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" >> $GITHUB_ENV
    - id: runscript
      uses: actions/github-script@v7
      with:
        script: |
          core.setOutput("run", `${{ env.run }}`);
    
  install-linux-conda:
    runs-on: ubuntu-latest
    needs: install-script-conda
    steps:
    - name: Set up Python 3.8
      uses: actions/setup-python@v5
      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: ["11.7",""]
    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@v4
      with:
        ref: ${{ steps.version.outputs.version }}
    - name: Install
      uses: ./.github/actions/install-bash
      with:
        python-version: ${{ matrix.python-version }}
        cuda-version: ${{ matrix.cuda-version }}