ensembl_tui/.github/workflows/testing_develop.yml at fb9353d2ba65eb6f16c5ee44dfbe5013b60d08ee · cogent3/ensembl_tui · GitHub

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name: CI

on:
  push:
    branches-ignore:
      - master
  pull_request:
    branches-ignore:
      - master

jobs:
  ci-not-internet:
    name: "Python ${{ matrix.python-version }} (${{ matrix.os }})"
    runs-on: ${{ matrix.os }}

    strategy:
      matrix:
        os: [ubuntu-latest, macos-latest, windows-latest]
        python-version: ["3.11", "3.13"]

    steps:
      - uses: "actions/checkout@v4"
        with:
          fetch-depth: 0

      - name: Set up small cache
        id: cache-small-data
        uses: actions/cache@v3
        with:
          path: tests/data
          key: ${{ runner.os }}-small-v3-${{ hashFiles('tests/data/small-115.zip') }}
          restore-keys: |
            ${{ runner.os }}-small-v3-

      - name: Check cache status
        run: |
          echo "Cache hit: ${{ steps.cache-small-data.outputs.cache-hit }} ***"

      - name: Download small data file
        if: steps.cache-small-data.outputs.cache-hit != 'true'
        run: |
          curl -L -o tests/data/small-115.zip "https://www.dropbox.com/scl/fi/cknsuhd6k8t6fjn1odzog/small-115.zip?rlkey=zkacmbhx4ssf4v80d78dd9uql&dl=1"

      - name: Set up apes installed cache
        id: cache-apes-data
        uses: actions/cache@v3
        with:
          path: tests/data
          key: ${{ runner.os }}-apes-v3-${{ hashFiles('tests/data/apes-115.zip') }}
          restore-keys: |
            ${{ runner.os }}-apes-v3-

      - name: Check apes data cache status
        run: |
          echo "Cache hit: ${{ steps.cache-apes-data.outputs.cache-hit }} ***"

      - name: Download apes installation data file
        if: steps.cache-apes-data.outputs.cache-hit != 'true'
        run: |
          curl -L -o tests/data/apes-115.zip "https://www.dropbox.com/scl/fi/h6kd0rlntvyzcb6d485fa/apes-115.zip?rlkey=4hza000j7btue6qwnxvnid5gb&dl=1"

      - name: Set up apes maf cache
        id: cache-apes-data-maf
        uses: actions/cache@v3
        with:
          path: tests/data
          key: ${{ runner.os }}-apes-maf-v3-${{ hashFiles('tests/data/apes-115-maf.zip') }}
          restore-keys: |
            ${{ runner.os }}-apes-maf-v3-

      - name: Check apes maf cache status
        run: |
          echo "Cache hit: ${{ steps.cache-apes-data-maf.outputs.cache-hit }} ***"

      - name: Download apes maf data file
        if: steps.cache-apes-data-maf.outputs.cache-hit != 'true'
        run: |
          curl -L -o tests/data/apes-115-maf.zip "https://www.dropbox.com/scl/fi/2wmle5kzjdqralppvddsr/apes-115-maf.zip?rlkey=u1hbfo0jqwhfkfukntgx5tbfn&dl=1"

      - name: Unzip data files
        run: |
          cd tests/data
          unzip -o -q small-115.zip
          unzip -o -q apes-115.zip
          unzip -o -q apes-115-maf.zip

      - uses: "actions/setup-python@v5"
        with:
            python-version: "${{ matrix.python-version }}"

      - name: Install uv
        uses: astral-sh/setup-uv@v6
        with:
          enable-cache: true
          cache-dependency-glob: "pyproject.toml"

      - name: "Installs for ${{ matrix.python-version }}"
        run: |
          uv venv venv -p python${{ matrix.python-version }}
          uv tool install -p venv nox

      - name: "Run nox for ${{ matrix.python-version }}"
        run: |
          nox -db uv --force-python python -s test -- -m 'not internet' --durations=10 --cov-report lcov:lcov-${{matrix.os}}-${{matrix.python-version}}.lcov --cov-report term --cov-append --cov ensembl_tui

      - name: Coveralls Parallel
        uses: coverallsapp/github-action@v2
        with:
          parallel: true
          github-token: ${{ secrets.github_token }}
          flag-name: run-${{matrix.python-version}}-${{matrix.os}}
          file: "tests/lcov-${{matrix.os}}-${{matrix.python-version}}.lcov"

  ci-internet:
    name: "Python ${{ matrix.python-version }} (${{ matrix.os }})"
    runs-on: ${{ matrix.os }}

    strategy:
      matrix:
        os: [ubuntu-latest]
        python-version: ["3.13"]

    steps:
      - uses: "actions/checkout@v4"
        with:
          fetch-depth: 0

      - name: Install uv
        uses: astral-sh/setup-uv@v3
        with:
          enable-cache: true
          cache-dependency-glob: "pyproject.toml"

      - name: "Installs for ${{ matrix.python-version }}"
        run: |
          uv venv venv -p python${{ matrix.python-version }}
          uv tool install -p venv nox

      - name: "Run nox for ${{ matrix.python-version }}"
        run: |
          nox -db uv -s test-${{ matrix.python-version }} -- -m 'internet' --durations=10 --cov-report lcov:lcov-${{matrix.os}}-${{matrix.python-version}}-internet.lcov --cov-report term --cov-append --cov ensembl_tui

      - name: Coveralls Parallel
        uses: coverallsapp/github-action@v2
        with:
          parallel: true
          github-token: ${{ secrets.github_token }}
          flag-name: run-${{matrix.python-version}}-${{matrix.os}}
          file: "tests/lcov-${{matrix.os}}-${{matrix.python-version}}-internet.lcov"

  finish:
    name: "Finish Coveralls"
    needs: [ci-not-internet, ci-internet]
    runs-on: ubuntu-latest
    steps:
    - name: Coveralls Finished
      uses: coverallsapp/github-action@v2
      with:
        github-token: ${{ secrets.github_token }}
        parallel-finished: true