Add pytest in GitHub Actions #9
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Add pytest with conda Allow workflow to run on pytest branch Fix script location Fix conda environment sourcing Add conda version script Add conda init Test setup miniconda Add conda creation Test Fix conda environment name Add execute permissions Fix pytest command Activate emcommon Fix footprint calculations Attempt to fix footprint test Attempt to fix footprint test Add MODE for footprint test Reset test footprint Sync with Jack
bin/run_pytest.sh
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there's no diff here so I'm guessing you just made it executable, which is good
.github/workflows/pytest.yml
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| on: | ||
| push: | ||
| branches: | ||
| - master | ||
| - pytest | ||
| - gis-based-mode-detection | ||
| pull_request: | ||
| branches: | ||
| - master | ||
| - pytest | ||
| - gis-based-mode-detection | ||
| schedule: | ||
| # * is a special character in YAML so you have to quote this string | ||
| - cron: '5 4 * * 0' |
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It can run on any push or PR to master. Don't need the other branches and don't need a schedule
.github/workflows/pytest.yml
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| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | ||
| jobs: | ||
| # This workflow contains a single job called "build" | ||
| build: |
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Ultimately I'd like to have 2 jobs that run in parallel, one for pytest and one for jest. Maybe this workflow can be named more generally
.github/workflows/pytest.yml
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| - uses: actions/checkout@v2 | ||
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| - name: Install and start MongoDB | ||
| uses: supercharge/[email protected] | ||
| with: | ||
| mongodb-version: 4.4.0 | ||
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| - uses: conda-incubator/setup-miniconda@v2 | ||
| with: | ||
| miniconda-version: "latest" | ||
| channels: bioconda, conda-forge, defaults | ||
| use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly! | ||
| auto-update-conda: true | ||
| auto-activate-base: true | ||
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| - name: Check existing version of miniconda | ||
| shell: bash -l {0} | ||
| run: conda info -a | ||
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| - name: Install emcommon conda environment | ||
| shell: bash -l {0} | ||
| run: | | ||
| # echo Test | ||
| conda env update -n emcommon -f bin/environment.yml | ||
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| - name: Show current conda environment | ||
| shell: bash -l {0} | ||
| run: | | ||
| conda activate emcommon && conda info --envs | ||
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| - name: Switch to emcommon and run the tests | ||
| shell: bash -l {0} | ||
| run: | | ||
| conda activate emcommon | ||
| PYTHONPATH=./src pytest test --asyncio-mode=auto |
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I don't think all of this is needed because setup.sh handles setting up the conda environment.
Can it just run setup.sh followed by run_pytest.sh?
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I have implemented all of the above. Thank you for your feedback. |
README.md
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| Anaconda is required. | ||
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It should not be necessary to install Anaconda manually, since the setup script automatically downloads miniconda and uses that.
Does this differ from what you've experienced?
README.md
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| @@ -21,7 +23,7 @@ Re-run this if you change the dependencies in `environment.yml` or `package.json | |||
| ## To contribute | |||
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| 1. Make your changes to Python code under the `src` directory. | |||
| 1. Run `bash bin/compile_to_js.sh` to build the JavaScript. This will produce output JS files in the `emcommon_js` directory. | |||
| 1. Run `bash bin/compile_to_js.sh` to build the JavaScript. This will produce output JS files in the `emcommon_js` directory. However, `pip install transcrypt` is required. | |||
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The setup script should automatically install transcrypt to the emcommon conda environment, so pip install transcrypt should not be necessary either
export_versions.sh is in the 'setup' folder of e-mission-server and will be downloaded dynamically via bin/setup.sh; does not need to be duplicated here We do not need babel to run the jest tests because Transcrypt outputs jest-compliant JS
This reverts commit a9fdffd.
This change adds an automated pytest using the conda environment.
The workflow is inspired from the one in e-mission-server: https://github.com/e-mission/e-mission-server/blob/master/.github/workflows/test-with-manual-install.yml