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Code Issues Packages Projects Releases Wiki Activity

Further refine compatibility tests (#1215)

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* Make sure apt is up to date before pulling hdf5

* Only install py dev reqs in cxg release vs anndata master test

* Don't need bu flag when using sed on ubuntu

* Don't re-install package reqs in python x anndata ver tests

* Minor documentation fix
This commit is contained in:
Matt Weiden
2020-03-11 14:16:05 -07:00
committed by GitHub
parent 3bf72829c2
commit a862f2b2a4
1 changed files with 15 additions and 4 deletions
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.github/workflows/compatibility_tests.yml
+15 -4
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@@ -38,8 +38,13 @@ jobs:
python-version: ${{ matrix.python-version }} python-version: ${{ matrix.python-version }}
- name: Install dependencies - name: Install dependencies
run: | run: |
sudo apt-get install libhdf5-serial-dev # 1. only install the dev requirements on top of what is in the cellxgene pip package
make pydist install-dist dev-env sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev
sed -i 's/-r requirements.txt//' server/requirements-dev.txt
pip install -r server/requirements-dev.txt
# 2. install cellxgene
make pydist install-dist
# 3. install anndata
pip install anndata==${{ matrix.anndata-version }} pip install anndata==${{ matrix.anndata-version }}
# workaround for anndata 0.6.22.post1 bug # workaround for anndata 0.6.22.post1 bug
[[ "0.6.22.post1" = "${{ matrix.anndata-version }}" ]] && pip install h5py==2.9.0 || true [[ "0.6.22.post1" = "${{ matrix.anndata-version }}" ]] && pip install h5py==2.9.0 || true
@@ -69,8 +74,14 @@ jobs:
path: anndata path: anndata
- name: Install dependencies - name: Install dependencies
run: | run: |
cd cellxgene
# 1. only install the dev requirements on top of what is in the cellxgene pip package
make dev-env-client
sed -i 's/-r requirements.txt//' server/requirements-dev.txt
pip install -r server/requirements-dev.txt
# 2. install cellxgene
pip install --upgrade cellxgene pip install --upgrade cellxgene
cd cellxgene && make dev-env # 3. install anndata
cd ../anndata && pip install -e . cd ../anndata && pip install -e .
- name: Tests - name: Tests
run: cd cellxgene && make unit-test ${{ matrix.test-suite }} run: cd cellxgene && make unit-test ${{ matrix.test-suite }}
@@ -99,7 +110,7 @@ jobs:
- name: Install dependencies - name: Install dependencies
run: | run: |
cd cellxgene cd cellxgene
sed -i.bu -E 's/^anndata[>=]=[0-9]+.[0-9]+.[0-9]+$/anndata/g' server/requirements.txt sed -i -E 's/^anndata[>=]=[0-9]+.[0-9]+.[0-9]+$/anndata/g' server/requirements.txt
make pydist install-dist dev-env make pydist install-dist dev-env
cd ../anndata cd ../anndata
pip install -e . pip install -e .