diffexpr/.github/workflows/CI.yml at master · wckdouglas/diffexpr · GitHub

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# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: "CI"

env:
  REGISTRY: ghcr.io
  IMAGE_NAME: ${{ github.repository }}

on:
  push:
    branches: [ "*" ]
  pull_request:
    types: [opened, ready_for_review]

concurrency:
  group: ${{ github.ref }}
  cancel-in-progress: true


jobs:
  build-and-ci:
    name: miniconda build
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [3.6, 3.7, 3.8]
    env:
      SETUPTOOLS_USE_DISTUTILS: stdlib
    defaults:
      run:
        shell: bash -l {0}

    steps:
      - uses: actions/checkout@v2
      - uses: conda-incubator/setup-miniconda@v2
        with:
          activate-environment: test-environment
          python-version: ${{ matrix.python-version }}
          channels: bioconda,default,anaconda,r,conda-forge
          allow-softlinks: true
          channel-priority: 'flexible'
          show-channel-urls: true
          use-only-tar-bz2: true
          auto-update-conda: true

      - name: setup conda
        run: |
          conda config --set always_yes yes --set changeps1 no
          conda info -a
          conda list
          conda config --show-sources
          conda config --show

      - name: Install dependencies
        run: |
          conda install mamba
          mamba install pandas tzlocal rpy2 biopython ReportLab pytest-cov codecov  bioconductor-deseq2 gfortran_linux-64 bioconductor-apeglm

      - name: hack for missing sysconfigdata (py3.7 and py3.8, doing nothing really)
        if: matrix.python-version != '3.6'
        run: |
          ls $CONDA_PREFIX/lib/python${{ matrix.python-version }}/_sysconfigdata_x86_64_conda*.py

      - name: hack for missing sysconfigdata (py3.6)
        if: matrix.python-version == '3.6'
        run: |
          ls $CONDA_PREFIX/lib/python${{ matrix.python-version }}/_sysconfigdata_x86_64*.py
          cp $CONDA_PREFIX/lib/python${{ matrix.python-version }}/_sysconfigdata_x86_64_conda_cos6_linux_gnu.py  $CONDA_PREFIX/lib/python${{ matrix.python-version }}/_sysconfigdata_x86_64_conda_linux_gnu.py

      - name: install package
        run: |
          conda activate test-environment
          pip install .

      - name: install R packages
        run: |
          Rscript setup.R

      - name: Test with pytest
        run: |
          coverage run -m pytest -vvv

      - name: codecov
        run: |
          bash <(curl -s https://codecov.io/bash)

  build-and-push-image:
    runs-on: ubuntu-latest
    needs: build-and-ci
    permissions:
      contents: read
      packages: write

    steps:
      - name: Checkout repository
        uses: actions/checkout@v3

      - name: Log in to the Container registry
        uses: docker/login-action@v2
        with:
          registry: ${{ env.REGISTRY }}
          username: ${{ github.actor }}
          password: ${{ secrets.GITHUB_TOKEN }}

      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v2

      - name: Build and push Docker image
        if: github.ref_name  == 'master'
        uses: docker/build-push-action@v3
        with:
          context: .
          push: true
          target: diffexpr
          cache-from: type=gha
          cache-to: type=gha,mode=max
          tags: |
            ${{ env.REGISTRY }}/${{ github.repository }}/diffexpr:${{ github.ref_name }}
            ${{ env.REGISTRY }}/${{ github.repository }}/diffexpr:${{ github.sha }}

      - name: Build and push Dev Docker image
        uses: docker/build-push-action@v3
        with:
          context: .
          push: true
          target: diffexpr_dev
          cache-from: type=gha
          cache-to: type=gha,mode=max
          tags: |
            ${{ env.REGISTRY }}/${{ github.repository }}/diffexpr-dev:${{ github.ref_name }}
            ${{ env.REGISTRY }}/${{ github.repository }}/diffexpr-dev:${{ github.sha }}