mirror of
https://github.com/chanzuckerberg/cellxgene.git
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78c9d24ed4
* move local_server -> backend/server server-> backend/czi_hosted, pull common code into backend/common update imports, tests and make commands
109 lines
3.5 KiB
YAML
109 lines
3.5 KiB
YAML
name: Compatibility Tests
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on:
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schedule:
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- cron: '0 8 7 * 2'
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push:
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branches:
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- main
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env:
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JEST_ENV: prod
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jobs:
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docker-build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Build docker image
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run: docker build .
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cellxgene-main-with-python-and-anndata-versions:
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name: python versions x anndata versions
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runs-on: ubuntu-latest
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continue-on-error: true
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strategy:
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matrix:
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python-version: [3.6, 3.7] # As of Oct 2020 Anndata is not compatible with 3.8
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anndata-version: [0.7.0, 0.7.1, 0.7.2, 0.7.3, 0.7.4, 0.7.5]
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test-suite: [smoke-test, smoke-test-annotations]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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# 1. only install the dev requirements on top of what is in the cellxgene pip package
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sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev
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sed -i 's/-r requirements.txt//' backend/server/requirements-dev.txt
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pip install -r backend/server/requirements-dev.txt
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# 2. install cellxgene
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make pydist install-dist
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# 3. install anndata
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pip install anndata==${{ matrix.anndata-version }}
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# workaround for anndata 0.6.22.post1 bug
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[[ "0.6.22.post1" = "${{ matrix.anndata-version }}" ]] && pip install h5py==2.9.0 || true
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- name: Tests
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run: make unit-test ${{ matrix.test-suite }}
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cellxgene-release-with-anndata-master:
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name: cellxgene release with anndata master
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runs-on: ubuntu-latest
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strategy:
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matrix:
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test-suite: [smoke-test, smoke-test-annotations]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python 3.7
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uses: actions/setup-python@v1
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with:
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python-version: 3.7
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- name: Checkout
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uses: actions/checkout@v2
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with:
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path: cellxgene
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- name: Install dependencies
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run: |
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cd cellxgene
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# 1. only install the dev requirements on top of what is in the cellxgene pip package
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make dev-env-client
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sed -i 's/-r requirements.txt//' backend/server/requirements-dev.txt
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pip install -r backend/server/requirements-dev.txt
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# 2. install cellxgene
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pip install --upgrade cellxgene
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# 3. install anndata
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pip install git+https://github.com/theislab/anndata
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- name: Tests
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run: cd cellxgene && make unit-test ${{ matrix.test-suite }}
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cellxgene-main-with-anndata-master:
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name: cellxgene main with anndata master
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runs-on: ubuntu-latest
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strategy:
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matrix:
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test-suite: [smoke-test, smoke-test-annotations]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python 3.7
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uses: actions/setup-python@v1
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with:
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python-version: 3.7
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- name: Checkout
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uses: actions/checkout@v2
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with:
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path: cellxgene
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- name: Install dependencies
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run: |
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cd cellxgene
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sed -i -E 's/^anndata[>=]=[0-9]+.[0-9]+.[0-9]+$/anndata/g' backend/server/requirements.txt
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make pydist install-dist dev-env
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pip install git+https://github.com/theislab/anndata
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- name: Tests
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run: cd cellxgene && make unit-test ${{ matrix.test-suite }}
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