conda-build.yml

name: Conda Build

on: [push, pull_request]

jobs:
  build:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Check version number consistency
        shell: python {0}
        run: |
          "Compare the version numers from the package and the conda recipe."

          # collect the package version
          import sys
          sys.path.append("/home/runner/work/sdrf-pipelines/sdrf-pipelines")
          import sdrf_pipelines
          package_version = sdrf_pipelines.__version__

          # collect the version from the conda recipe
          with open("./recipe/meta.yaml", encoding="utf-8") as f:
              for line in f.readlines():
                  if line.startswith("  version: "):
                      recipe_version = line.lstrip("  version:").strip().strip('"')
                      break

          if package_version == recipe_version:
              print(f"The package and recipe versions are consistent: {package_version}")
          else:
              raise ValueError(
                  "ERROR: The versions are inconsistent."
                  f"\nVersion in ./sdrf_pipelines/__init__.py: {package_version}"
                  f"\nVersion in ./recipe/meta.yaml:           {recipe_version}"
                  )

      - name: Set up Miniconda
        uses: conda-incubator/setup-miniconda@v3
        with:
          activate-environment: sdrf-pipelines
          environment-file: environment.yml
          auto-activate-base: false
          auto-update-conda: true
          python-version: '3.10'
          channels: conda-forge,bioconda,defaults

      - name: Install build dependencies
        run: |
          conda install conda-build conda-verify anaconda-client

      - name: Build the sdrf-pipelines package
        run: |
          conda build --package-format .tar.bz2 recipe

      - name: Install the package
        run: |
          PACKAGE_PATH=$(conda build --package-format .tar.bz2 --output recipe)
          conda install --offline "$PACKAGE_PATH"

      - name: Test install
        run: |
          parse_sdrf --help

      - name: Test validation of SDRF file
        run: |
          parse_sdrf validate-sdrf --sdrf_file tests/data/reference/PDC000126/PDC000126.sdrf.tsv

      - name: Test validation of SDRF file with cache only
        run: |
          parse_sdrf validate-sdrf --sdrf_file tests/data/reference/PDC000126/PDC000126.sdrf.tsv --use_ols_cache_only