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chore: upgrade backend dependencies (#2641)

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chore: upgrade backend dependencies (#2641)
This commit is contained in:
atarashansky
2023-11-29 14:16:39 -08:00
committed by GitHub
parent 4bb9a2b834
commit 6505f6cbf5
36 changed files with 161 additions and 315 deletions
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.github/workflows/compatibility_tests.yml
+68 -79
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@@ -2,7 +2,7 @@ name: Compatibility Tests
on:
schedule:
- cron: '0 8 7 * 2'
- cron: "0 8 7 * 2"
push:
branches:
- main
@@ -30,94 +30,83 @@ jobs:
matrix:
# note: The `macos-latest` is latest Catalina version, and not Big Sur. So we explicitly ask for Big Sur (`macos-11`)
os: [ubuntu-latest, macos-latest, macos-11]
python-version: [3.6, 3.7, 3.8, 3.9]
python-version: [3.8, 3.9, 3.10, 3.11]
cellxgene_build: [main, latest]
exclude:
# 3.6 no longer avail on Big Sur (`macos-11`)
- os: macos-11
python-version: 3.6
# no pypi build exists for macos+py3.9 and source install fails to
# install `tables` py pkg (a `scanpy` dependency), so we test py3.9
# only on ubuntu
- os: macos-11
python-version: 3.9
- os: macos-latest
python-version: 3.9
# add anndata pinned version test for subset of matrix configurations,
# in order to reduce matrix cross-product explosion
include:
- python-version: 3.8
- python-version: 3.9
cellxgene_build: latest
# TODO: dynamically use the literal version in requirements.txt,
# to avoid having to update this in manually in the future
# TODO: Do not bother running this if anndata latest version
# matches this pinned version, to avoid a redundant test
anndata_version: '==0.7.6'
anndata_version: "==0.10.3"
steps:
- uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Cache env vars
run: echo "PIP_CACHE=`python -m pip cache dir`" >> $GITHUB_ENV
- name: Cache env vars (MacOS)
if: startsWith(matrix.os, 'macos')
run: echo "BREW_CACHE=`brew --cache`" >> $GITHUB_ENV
# FIXME: Only working for Linux
- name: Python cache
uses: actions/cache@v1
with:
path: ${{ env.PIP_CACHE }}
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: Brew cache (MacOS)
if: startsWith(matrix.os, 'macos')
uses: actions/cache@v1
with:
path: ${{ env.BREW_CACHE }}
key: ${{ runner.os }}-brew-
- name: Install dependencies (Ubuntu Linux)
if: startsWith(matrix.os, 'ubuntu')
run: |
sudo apt-get update
sudo apt-get install -y libhdf5-serial-dev
- name: Install dependencies (MacOS)
if: startsWith(matrix.os, 'macos')
run: brew install hdf5
- name: Install cellxgene from `main` branch
if: matrix.cellxgene_build == 'main'
run: |
pip install -r server/requirements-dev.txt
make pydist install-dist
- name: Install cellxgene from latest release (pypi.org)
if: matrix.cellxgene_build == 'latest'
run: |
pip install --upgrade cellxgene
# install the additional dev requirements on top of what is in the
# cellxgene pip package, which are needed for testing, but otherwise
# keep same pip pkg versions as in the cxg release
sed -i'' -e 's/-r requirements.txt//' server/requirements-dev.txt
pip install -r server/requirements-dev.txt
- name: Install anndata version per matrix variable
run: pip install anndata${{ matrix.anndata_version }}
- name: Install node
run: make dev-env-client
# Run different types of test separately, to facilitate troubleshooting
- name: Unit Tests - client
run: make unit-test-client
- name: Unit Tests - server
run: make unit-test-server
- name: Smoke Tests
run: make smoke-test
- uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Cache env vars
run: echo "PIP_CACHE=`python -m pip cache dir`" >> $GITHUB_ENV
- name: Cache env vars (MacOS)
if: startsWith(matrix.os, 'macos')
run: echo "BREW_CACHE=`brew --cache`" >> $GITHUB_ENV
# FIXME: Only working for Linux
- name: Python cache
uses: actions/cache@v1
with:
path: ${{ env.PIP_CACHE }}
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: Brew cache (MacOS)
if: startsWith(matrix.os, 'macos')
uses: actions/cache@v1
with:
path: ${{ env.BREW_CACHE }}
key: ${{ runner.os }}-brew-
- name: Install dependencies (Ubuntu Linux)
if: startsWith(matrix.os, 'ubuntu')
run: |
sudo apt-get update
sudo apt-get install -y libhdf5-serial-dev
- name: Install dependencies (MacOS)
if: startsWith(matrix.os, 'macos')
run: brew install hdf5
- name: Install cellxgene from `main` branch
if: matrix.cellxgene_build == 'main'
run: |
pip install -r server/requirements-dev.txt
make pydist install-dist
- name: Install cellxgene from latest release (pypi.org)
if: matrix.cellxgene_build == 'latest'
run: |
pip install --upgrade cellxgene
# install the additional dev requirements on top of what is in the
# cellxgene pip package, which are needed for testing, but otherwise
# keep same pip pkg versions as in the cxg release
sed -i'' -e 's/-r requirements.txt//' server/requirements-dev.txt
pip install -r server/requirements-dev.txt
- name: Install anndata version per matrix variable
run: pip install anndata${{ matrix.anndata_version }}
- name: Install node
run: make dev-env-client
# Run different types of test separately, to facilitate troubleshooting
- name: Unit Tests - client
run: make unit-test-client
- name: Unit Tests - server
run: make unit-test-server
- name: Smoke Tests
run: make smoke-test
# FIXME: Fails intermittently. See https://app.zenhub.com/workspaces/single-cell-5e2a191dad828d52cc78b028/issues/chanzuckerberg/cellxgene/2415
# - name: Smoke Tests with Annotations
# run: make smoke-test-annotations
.github/workflows/push_tests.yml
+10 -10
View File
@@ -17,10 +17,10 @@ jobs:
- uses: actions/checkout@v2
- run: |
git fetch --depth=1 origin +${{github.base_ref}}
- name: Set up Python 3.7
- name: Set up Python 3.9
uses: actions/setup-python@v4
with:
python-version: 3.7
python-version: 3.9
- name: Node cache
uses: actions/cache@v1
with:
@@ -46,12 +46,12 @@ jobs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.7 (pyenv) # pyenv needed for mlflow in cli annotate tests
- name: Set up Python 3.9 (pyenv) # pyenv needed for mlflow in cli annotate tests
uses: gabrielfalcao/pyenv-action@v9
with:
default: 3.7
command: pip install -U pip # upgrade pip after installing python
- run: pip install virtualenv # virtualenv needed for mlflow in cli annotate tests
default: 3.9
command: pip install -U pip # upgrade pip after installing python
- run: pip install virtualenv # virtualenv needed for mlflow in cli annotate tests
- name: Python cache
uses: actions/cache@v1
with:
@@ -79,10 +79,10 @@ jobs:
timeout-minutes: 20
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.7
- name: Set up Python 3.9
uses: actions/setup-python@v4
with:
python-version: 3.7
python-version: 3.9
- name: Python cache
uses: actions/cache@v1
with:
@@ -110,10 +110,10 @@ jobs:
# timeout-minutes: 20
# steps:
# - uses: actions/checkout@v2
# - name: Set up Python 3.7
# - name: Set up Python 3.9
# uses: actions/setup-python@v4
# with:
# python-version: 3.7
# python-version: 3.9
# - name: Python cache
# uses: actions/cache@v1
# with: