BLD: fix the build (pin ubuntu version to 20.04)? #35
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| # Based on | |
| # https://github.com/fedarko/strainFlye/blob/main/.github/workflows/main.yml | |
| # (which was based on EMPress' workflow); some of the Node.js stuff based on | |
| # MetagenomeScope's JS workflow | |
| name: QIIME 2 CI | |
| on: [push, pull_request] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| # Test on multiple QIIME 2 versions. This is a nice way of making sure | |
| # that Qurro works on all of the QIIME 2 versions it actually, you | |
| # know, supports. As of writing, this includes QIIME 2 versions | |
| # | |
| # 1. 2020.11 | |
| # 2. 2021.2 | |
| # 3. 2021.4 | |
| # 4. 2021.8 | |
| # 5. 2021.11 | |
| # 6. 2022.2 | |
| # 7. 2022.8 | |
| # | |
| # We currently test just a subset of these versions, because each of | |
| # these builds takes a while (and testing each of these would probs be | |
| # overkill). | |
| # | |
| # We could use a matrix of just QIIME 2 version strings (e.g. | |
| # "2020.11", ...), but other stuff about the URLs change across QIIME 2 | |
| # versions (e.g. the "-py36-" or "-py38-" thing). It ends up being | |
| # easier just have the variable here be the URLs to the YAMLs. That | |
| # sentence has too many acronyms. Look, you get the point. | |
| # | |
| # Worth noting: the final of these URLs (with qiime2-latest) will | |
| # always be set to the latest version of QIIME 2. Thanks @thermokarst | |
| # for the heads up about this :) | |
| q2-yaml: [ | |
| "https://raw.githubusercontent.com/qiime2/environment-files/master/2020.11/release/qiime2-2020.11-py36-linux-conda.yml", | |
| "https://raw.githubusercontent.com/qiime2/environment-files/master/2021.8/release/qiime2-2021.8-py38-linux-conda.yml", | |
| "https://raw.githubusercontent.com/qiime2/environment-files/master/2022.2/release/qiime2-2022.2-py38-linux-conda.yml", | |
| "https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-linux-conda.yml" | |
| ] | |
| steps: | |
| # Updating from v2 to v3 to match, as of writing, | |
| # https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | |
| - name: Check out code | |
| uses: actions/checkout@v3 | |
| - name: Download the QIIME 2 conda environment YAML | |
| run: wget -O q2-env.yml ${{ matrix.q2-yaml }} | |
| # https://github.com/conda-incubator/setup-miniconda#example-3-other-options | |
| - name: Hit the yoinky sploinky (install QIIME 2) | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: qiime2-dev | |
| environment-file: q2-env.yml | |
| - name: Install Qurro (and its pip dependencies) | |
| run: conda run -n qiime2-dev pip install -e .[dev] | |
| - name: Set up Node.js | |
| uses: actions/setup-node@v1 | |
| - name: Install Qurro's Node.js development dependencies | |
| run: npm install -g mocha-headless-chrome nyc prettier@2.0.5 jshint | |
| - name: Run tests | |
| run: conda run -n qiime2-dev make test | |
| - name: Lint and stylecheck (not using Black to check Python code) | |
| run: conda run -n qiime2-dev make stylecheck_not_black | |
| # It's possible to install packages that break QIIME 2's CLI (e.g. | |
| # installing Click >= 8 into a Q2 2022.2 environment seems to break it -- | |
| # this is discussed in the developer documentation, CONTRIBUTING.md). | |
| # Verify that, by installing Qurro, we have not "broken" QIIME 2 in this | |
| # way. | |
| - name: Test that QIIME 2's CLI works | |
| run: conda run -n qiime2-dev qiime info | |
| - name: Upload code coverage information to Codecov | |
| uses: codecov/codecov-action@v2 |