conda-build.yml

name: Conda Build

on: [push, pull_request]

jobs:
  build:
    runs-on: ubuntu-latest

    steps:
    - name: Checkout repository
      uses: actions/checkout@v2

    - name: Set up Miniconda
      uses: conda-incubator/setup-miniconda@v2
      with:
        auto-update-conda: true
        python-version: 3.8
        channels: conda-forge,defaults,bioconda

    - name: Create conda environment
      run: conda env create -f environment.yml

    - name: Activate conda environment
      run: |
        source $CONDA/etc/profile.d/conda.sh
        conda activate sdrf-pipelines
      shell: bash

    - name: Install conda-build
      run: |
        source $CONDA/etc/profile.d/conda.sh
        conda activate sdrf-pipelines
        conda install -n sdrf-pipelines conda-build anaconda-client
      shell: bash -l {0}

    - name: Activate conda environment and build package
      run: |
        source $CONDA/etc/profile.d/conda.sh
        conda activate sdrf-pipelines
        conda build recipe
        PACKAGE_PATH=$(find /usr/share/miniconda/envs/sdrf-pipelines/conda-bld/noarch/ -name "sdrf-pipelines-*.tar.bz2" | head -n 1)
        conda install --offline "$PACKAGE_PATH"
      shell: bash -l {0}

    - name: Test the installed package
      run: |
        conda activate sdrf-pipelines
        parse_sdrf --help
      shell: bash -l {0}

    - name: Test validation of SDRF file
      run: |
        conda activate sdrf-pipelines
        parse_sdrf validate-sdrf --sdrf_file tests/data/reference/PDC000126/PDC000126.sdrf.tsv
      shell: bash -l {0}

    - name: Test validation of SDRF file with cache only
      run: |
        conda activate sdrf-pipelines
        parse_sdrf validate-sdrf --sdrf_file tests/data/reference/PDC000126/PDC000126.sdrf.tsv --use_ols_cache_only
      shell: bash -l {0}