ci-conda.yml

# Lingfei Wang, 2022. All rights reserved.
name: "Conda package"

on:
  push:
    branches:
      - master
      - dev
    paths:
      - 'setup.py'
      - 'src/**'
      - 'bin/**'
      - 'utils/conda/**'
      - '.github/actions/conda-build-publish/**'
      - '.github/actions/install-conda/**'
      - '.github/workflows/ci-conda.yml'
      - '.github/actions/zenodo-url-translate/**'
      - '.github/actions/inference-test-dataset/**'
      - '.github/scripts/inference-test-dataset.py'

jobs:
  build:
    name: Build and publish conda package with pretest suffix
    if: github.repository == 'pinellolab/dictys'
    runs-on: ubuntu-latest
    outputs:
      package: ${{ steps.publish-pretest.outputs.name }}
      version: ${{ steps.publish-pretest.outputs.version }}
      buildstr: ${{ steps.publish-pretest.outputs.buildstr }}
    steps:
      - name: Set up Python 3.8
        uses: actions/setup-python@v4
        with:
          python-version: 3.8
      - uses: actions/checkout@v3
        with:
          fetch-depth: 0
      - name: Mask token
        shell: bash
        run: echo "::add-mask::${{ secrets.ANACONDA_TOKEN }}"
      - name: Build and publish pretest version
        uses: ./.github/actions/conda-build-publish
        id: publish-pretest
        with:
          base-dir: utils/conda
          user: lingfeiwang
          token: ${{ secrets.ANACONDA_TOKEN }}
          preproc: "sed -i 's/  name: dictys/  name: dictys-pretest/' meta.yaml"
          options: "--force"
 
  test-blood1:
    name: Blood static network unit tests
    needs: build
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.9","3.10"]
    steps:
      - name: Set up Python 3.8
        uses: actions/setup-python@v4
        with:
          python-version: 3.8
      - name: Add conda to system path
        shell: bash
        run: |
          echo $CONDA/bin >> $GITHUB_PATH
      - uses: actions/checkout@v3
      - name: Install package
        uses: ./.github/actions/install-conda
        with:
          package: ${{ needs.build.outputs.package }}=${{ needs.build.outputs.version }}=${{ needs.build.outputs.buildstr }}
          python-version: ${{ matrix.python-version }}
      - name: Get dataset URL
        id: zenodo-url-translate
        uses: ./.github/actions/zenodo-url-translate
        with:
          url: https://zenodo.org/record/6858494/files/inference-blood1.tar.xz?download=1
      - name: Test dataset
        uses: ./.github/actions/inference-test-dataset
        with:
          url: ${{ steps.zenodo-url-translate.outputs.url }}
          test-path: ci_testspace
          makefile: test_static.mk
          expected-folder: test/tmp_static_expected
          actual-folder: test/tmp_static
          expected-h5: test/output/static_expected.h5
          actual-h5: test/output/static.h5
          makefile-params: '{"ENVMODE": "none", "NTH": "2", "DEVICE": "cpu", "GENOME_MACS2": "hs", "JOINT": "0", "KPARAMS-NETWORK-RECONSTRUCT+": " --nstep 10 --nstep_report 3"}'
          exclusions: 'reads.bam reads.bai net_weight.tsv.gz net_covfactor.tsv.gz net_meanvar.tsv.gz net_loss.tsv.gz net_stats.tsv.gz'
          
  build-publish:
    name: Build and publish conda package
    needs: [ build, test-blood1 ]
    if: ( github.ref_name == 'master' ) && ( github.repository == 'pinellolab/dictys' )
    runs-on: ubuntu-latest
    steps:
      - name: Set up Python 3.8
        uses: actions/setup-python@v4
        with:
          python-version: 3.8
      - uses: actions/checkout@v3
        with:
          fetch-depth: 0
      - name: Mask token
        shell: bash
        run: echo "::add-mask::${{ secrets.ANACONDA_TOKEN }}"
      - name: Get serial ID
        id: serialid
        shell: bash
        run: | 
          version='${{ needs.build.outputs.version }}'
          version="${version//./[.]}"
          serialid=$( (conda search -c lingfeiwang --override-channels -q dictys | grep '^dictys[[:blank:]]*'"$version"'[[:blank:]]' || true ) | wc -l)
          echo "serialid=$serialid" >> $GITHUB_OUTPUT
      - name: Build and publish release version
        uses: ./.github/actions/conda-build-publish
        id: publish
        with:
          base-dir: utils/conda
          user: lingfeiwang
          serialid: ${{ steps.serialid.outputs.serialid }}
          token: ${{ secrets.ANACONDA_TOKEN }}