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Code Issues Packages Projects Releases Wiki Activity

Simplify CI checks on git push, add nightly checks on cron (#1158)

Browse Source 
* Switch push tests to Github Actions

* Add nightly tests

* Add anndata check

* Add test status badges

* Add anndata 0.6.22.post1 workaround

* Rename Nightly tests to Compatibility Tests

* Fix to anndata fix

* Turn on cron schedule

* Fix badge mardown in README.md

* Fix cron schedule
This commit is contained in:
Matt Weiden
2020-02-18 11:57:19 -08:00
committed by GitHub
parent d30087ca63
commit c630be33df
6 changed files with 216 additions and 33 deletions
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101
.github/workflows/compatibility_tests.yml vendored Normal file
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name: Compatability Tests
on:
schedule:
- cron: '0 8 7 * 2'
env:
JEST_ENV: prod
jobs:
docker-build:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v1
with:
python-version: ${{ matrix.python-version }}
- name: Build docker image
run: docker build .
cellxgene-master-with-python-and-anndata-versions:
name: python versions x anndata versions
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [3.6, 3.7, 3.8]
anndata-version: [0.6.22.post1, 0.7.1]
test-suite: [smoke-test, smoke-test-annotations]
steps:
- uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v1
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: |
sudo apt-get install libhdf5-serial-dev
make pydist install-dist dev-env
pip install anndata==${{ matrix.anndata-version }}
# workaround for anndata 0.6.22.post1 bug
[[ "0.6.22.post1" = "${{ matrix.anndata-version }}" ]] && pip install h5py==2.9.0 || true
- name: Tests
run: make unit-test ${{ matrix.test-suite }}
cellxgene-release-with-anndata-master:
name: cellxgene release with anndata master
runs-on: ubuntu-latest
strategy:
matrix:
test-suite: [smoke-test, smoke-test-annotations]
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.7
uses: actions/setup-python@v1
with:
python-version: 3.7
- name: Checkout
uses: actions/checkout@v2
with:
path: cellxgene
- name: Checkout tools repo
uses: actions/checkout@v2
with:
repository: theislab/anndata
path: anndata
- name: Install dependencies
run: |
pip install --upgrade cellxgene
cd cellxgene && make dev-env
cd ../anndata && pip install -e .
- name: Tests
run: cd cellxgene && make unit-test ${{ matrix.test-suite }}
cellxgene-master-with-anndata-master:
name: cellxgene master with anndata master
runs-on: ubuntu-latest
strategy:
matrix:
test-suite: [smoke-test, smoke-test-annotations]
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.7
uses: actions/setup-python@v1
with:
python-version: 3.7
- name: Checkout
uses: actions/checkout@v2
with:
path: cellxgene
- name: Checkout tools repo
uses: actions/checkout@v2
with:
repository: theislab/anndata
path: anndata
- name: Install dependencies
run: |
cd cellxgene && make pydist install-dist dev-env
cd ../anndata && pip install -e .
- name: Tests
run: cd cellxgene && make unit-test ${{ matrix.test-suite }}

101
.github/workflows/push_tests.yml vendored Normal file
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name: Push Tests
on: [push]
env:
JEST_ENV: prod
jobs:
lint:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.7
uses: actions/setup-python@v1
with:
python-version: 3.7
- name: Lint with flake8
run: |
pip install flake8
make lint
unit-test:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.7
uses: actions/setup-python@v1
with:
python-version: 3.7
- name: Python cache
uses: actions/cache@v1
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
restore-keys: |
${{ runner.os }}-pip-
- name: Node cache
uses: actions/cache@v1
with:
path: ~/.npm
key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
restore-keys: |
${{ runner.os }}-node-
- name: Install dependencies
run: make pydist install-dist dev-env-server
- name: Unit tests
run: make unit-test
smoke-tests:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.7
uses: actions/setup-python@v1
with:
python-version: 3.7
- name: Python cache
uses: actions/cache@v1
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
restore-keys: |
${{ runner.os }}-pip-
- name: Node cache
uses: actions/cache@v1
with:
path: ~/.npm
key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
restore-keys: |
${{ runner.os }}-node-
- name: Install dependencies
run: make pydist install-dist
- name: Smoke tests (without annotations feature)
run: cd client && make smoke-test
smoke-tests-annotations:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.7
uses: actions/setup-python@v1
with:
python-version: 3.7
- name: Python cache
uses: actions/cache@v1
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
restore-keys: |
${{ runner.os }}-pip-
- name: Node cache
uses: actions/cache@v1
with:
path: ~/.npm
key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
restore-keys: |
${{ runner.os }}-node-
- name: Install dependencies
run: make pydist install-dist
- name: Smoke tests (with annotations feature)
run: cd client && make smoke-test-annotations