mirror of
https://github.com/chanzuckerberg/cellxgene.git
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Github Actions Workflow updates compatibility matrix: - Added MacOS Catalina and Big Sur to test compat matrix - Added Python 3.9 to test compat matrix, but avoid running 3.9 for matrix jobs that do not have `tables` pypi build available for the given env - Maintains running tests on both cellxgene main branch and latest pypi release. - Add explicit matrix exclusions for matrix combinations that will never pass (see comments). - Numerous refactorings to the workflow config to simplify matrix. Basically a rewrite. - The anndata pkg is now tested at a pinned release and at latest release, but no longer using `master` branch version. To limit cross-product explosion of matrix jobs, the pinned anndata version is only tested on py3.8 and cellxgene latest release. - Run unit and smoke tests in a single job, to improve speed, reduce workflow complexity and the number of jobs. Also fixes the redundant testing of unit tests. Within each job, the unit and smoke tests are run in separate steps for ease of troubleshooting. - Fixed termination of backend server to allow both smoke tests to run within a single job (both attempt to use 5005 port, sequentially, but first server was not being terminated). - Replaced `continue-on-error: true` with `fail-fast: false`, which allows all matrix jobs to run independently, while also ensuring the that entire workflow is flagged as failed if any matrix job fails - The `smoke-test-annotations` fail intermittently and have been disabled. Fix will be addressed in story: https://app.zenhub.com/workspaces/single-cell-5e2a191dad828d52cc78b028/issues/chanzuckerberg/cellxgene/2433
This commit is contained in:
Andrew Tolopko
173
.github/workflows/compatibility_tests.yml
vendored
173
.github/workflows/compatibility_tests.yml
vendored
@@ -1,11 +1,19 @@
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name: Compatibility Tests
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# TODO: Reinstate before merge to main
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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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# TEMPORARY
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# TODO: Remove before merge to main
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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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- atolopko/2410-update-compatibility-test-matrix
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env:
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JEST_ENV: prod
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@@ -22,85 +30,102 @@ jobs:
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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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matrix-compatibility-test:
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name: cxg:${{ matrix.cellxgene_build }} os:${{ matrix.os }} py:${{ matrix.python-version }} anndata:${{ matrix.anndata_version || 'latest' }}
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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python-version: [3.6, 3.7, 3.8]
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anndata-version: [0.7.6]
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test-suite: [smoke-test, smoke-test-annotations]
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# note: The `macos-latest` is latest Catalina version, and not Big Sur. So we explicitly ask for Big Sur (`macos-11`)
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os: [ubuntu-latest, macos-latest, macos-11]
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python-version: [3.6, 3.7, 3.8, 3.9]
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cellxgene_build: [main, latest]
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exclude:
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# 3.6 no longer avail on Big Sur (`macos-11`)
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- os: macos-11
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python-version: 3.6
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# no pypi build exists for macos+py3.9 and source install fails to
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# install `tables` py pkg (a `scanpy` dependency), so we test py3.9
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# only on ubuntu
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- os: macos-11
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python-version: 3.9
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- os: macos-latest
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python-version: 3.9
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# add anndata pinned version test for subset of matrix configurations,
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# in order to reduce matrix cross-product explosion
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include:
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- python-version: 3.8
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cellxgene_build: latest
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# TODO: dynamically use the literal version in requirements.txt,
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# to avoid having to update this in manually in the future
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# TODO: Do not bother running this if anndata latest version
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# matches this pinned version, to avoid a redundant test
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anndata_version: '==0.7.6'
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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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- name: Cache env vars
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run: echo "PIP_CACHE=`python -m pip cache dir`" >> $GITHUB_ENV
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- name: Cache env vars (MacOS)
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if: startsWith(matrix.os, 'macos')
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run: echo "BREW_CACHE=`brew --cache`" >> $GITHUB_ENV
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# FIXME: Only working for Linux
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- name: Python cache
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uses: actions/cache@v1
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with:
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path: ${{ env.PIP_CACHE }}
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key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
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restore-keys: |
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${{ runner.os }}-pip-
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- name: Node cache
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uses: actions/cache@v1
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with:
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path: ~/.npm
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key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
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restore-keys: |
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${{ runner.os }}-node-
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- name: Brew cache (MacOS)
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if: startsWith(matrix.os, 'macos')
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uses: actions/cache@v1
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with:
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path: ${{ env.BREW_CACHE }}
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key: ${{ runner.os }}-brew-
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- name: Install dependencies (Ubuntu Linux)
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if: startsWith(matrix.os, 'ubuntu')
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run: |
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sudo apt-get update
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sudo apt-get install -y libhdf5-serial-dev
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- name: Install dependencies (MacOS)
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if: startsWith(matrix.os, 'macos')
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run: brew install hdf5
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- name: Install cellxgene from `main` branch
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if: matrix.cellxgene_build == 'main'
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run: |
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# 1. only install the dev requirements on top of what is in the cellxgene pip package
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sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev
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sed -i 's/-r requirements.txt//' server/requirements-dev.txt
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pip install -r server/requirements-dev.txt
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# 2. install cellxgene
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make pydist install-dist
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# 3. install anndata
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pip install anndata==${{ matrix.anndata-version }}
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- 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//' server/requirements-dev.txt
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pip install -r 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' 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 ${{ matrix.test-suite }}
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- name: Install cellxgene from latest release (pypi.org)
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if: matrix.cellxgene_build == 'latest'
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run: |
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pip install --upgrade cellxgene
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# install the additional dev requirements on top of what is in the
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# cellxgene pip package, which are needed for testing, but otherwise
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# keep same pip pkg versions as in the cxg release
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sed -i'' -e 's/-r requirements.txt//' server/requirements-dev.txt
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pip install -r server/requirements-dev.txt
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- name: Install anndata version per matrix variable
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run: pip install anndata${{ matrix.anndata_version }}
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- name: Install node
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run: make dev-env-client
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# Run different types of test separately, to facilitate troubleshooting
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- name: Unit Tests - client
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run: make unit-test-client
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- name: Unit Tests - server
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run: make unit-test-server
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- name: Smoke Tests
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run: make smoke-test
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# FIXME: Fails intermittently. See https://app.zenhub.com/workspaces/single-cell-5e2a191dad828d52cc78b028/issues/chanzuckerberg/cellxgene/2415
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# - name: Smoke Tests with Annotations
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# run: make smoke-test-annotations
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