Skip to content
ci

[STYLE] use ruff in lieu of black/flake8/isort + add pre-commit (#219) #366

Sign in to view logs

[STYLE] use ruff in lieu of black/flake8/isort + add pre-commit (#219)

[STYLE] use ruff in lieu of black/flake8/isort + add pre-commit (#219) #366

Workflow file for this run

.github/workflows/ci.yml at eebff66
name: ci
on:
push:
branches: [ main ]
pull_request:
branches: [ main ]
jobs:
test:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
steps:
- uses: actions/checkout@v3
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install the package
run: |
sudo apt update
sudo apt install -y libopenslide0
python -m pip install --upgrade pip setuptools wheel
python -m pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cpu openslide-python tiffslide
python -m pip install --editable .[dev]
- name: Run tests
run: python -m pytest --verbose tests/
test-pytorch-nightly:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python 3.10
uses: actions/setup-python@v4
with:
python-version: "3.10"
- name: Install the package
run: |
sudo apt update
sudo apt install -y libopenslide0
python -m pip install --upgrade pip setuptools wheel
python -m pip install --pre torch torchvision --extra-index-url https://download.pytorch.org/whl/nightly/cpu openslide-python tiffslide
python -m pip install --editable .[dev]
- name: Run tests
run: python -m pytest --verbose tests/
test-docker:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Build Docker image
run: docker build -t wsinferimage .
- name: Run pytest in Docker image
run: |
docker run --rm --shm-size=512m --workdir /opt/wsinfer/ --entrypoint bash wsinferimage \
-c "python -m pip install -e /opt/wsinfer[dev] && python -m pytest -vx /opt/wsinfer/tests/test_all.py"
- name: Run wsinfer on a sample image in Docker
run: |
mkdir slides
cd slides
wget -q https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/JP2K-33003-1.svs
cd ..
docker run --rm --shm-size=512m --volume $HOME:$HOME --volume $(pwd):/work --workdir /work wsinferimage run \
--wsi-dir slides/ --results-dir results/ --model breast-tumor-resnet34.tcga-brca
test -f results/run_metadata_*.json
test -f results/patches/JP2K-33003-1.h5
test -f results/model-outputs-csv/JP2K-33003-1.csv
test $(wc -l < results/model-outputs-csv/JP2K-33003-1.csv) -eq 675
test-package:
strategy:
matrix:
os: [ubuntu-latest, windows-latest, macos-latest]
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v3
- name: Set up Python 3.10
uses: actions/setup-python@v4
with:
python-version: "3.10"
- name: Install OpenSlide on Ubuntu
if: matrix.os == 'ubuntu-latest'
run: sudo apt update && sudo apt install -y libopenslide0
- name: Install OpenSlide on macOS
if: matrix.os == 'macos-latest'
run: brew install openslide
- name: Install the wsinfer python package
run: |
python -m pip install --upgrade pip setuptools wheel
python -m pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cpu openslide-python tiffslide
python -m pip install .
- name: Run 'wsinfer run' on Unix
if: matrix.os != 'windows-latest'
run: |
mkdir newdir && cd newdir
mkdir slides && cd slides
wget -q https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/JP2K-33003-1.svs
cd ..
WSINFER_FORCE_CPU=1 wsinfer run --wsi-dir slides/ --results-dir results/ --model breast-tumor-resnet34.tcga-brca
test -f results/run_metadata_*.json
test -f results/patches/JP2K-33003-1.h5
test -f results/model-outputs-csv/JP2K-33003-1.csv
test $(wc -l < results/model-outputs-csv/JP2K-33003-1.csv) -eq 675
# FIXME: tissue segmentation has different outputs on Windows. The patch sizes
# are the same but the coordinates found are different.
- name: Run 'wsinfer run' on Windows
if: matrix.os == 'windows-latest'
run: |
mkdir newdir && cd newdir
mkdir slides && cd slides
Invoke-WebRequest -URI https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/JP2K-33003-1.svs -OutFile JP2K-33003-1.svs
cd ..
wsinfer run --wsi-dir slides/ --results-dir results/ --model breast-tumor-resnet34.tcga-brca
Test-Path -Path results/run_metadata_*.json -PathType Leaf
Test-Path -Path results/patches/JP2K-33003-1.h5 -PathType Leaf
Test-Path -Path results/model-outputs-csv/JP2K-33003-1.csv -PathType Leaf
# test $(python -c "print(sum(1 for _ in open('results/model-outputs/JP2K-33003-1.csv')))") -eq 675
mypy:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python 3.10
uses: actions/setup-python@v4
with:
python-version: "3.10"
- name: Install the package
run: |
sudo apt update
sudo apt install -y libopenslide0
python -m pip install --upgrade pip setuptools wheel
python -m pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cpu openslide-python tiffslide
python -m pip install -e .[all]
- name: Check types
run: python -m mypy --install-types --non-interactive wsinfer/ tests/
docs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: "3.10"
- name: Install the package
run: |
sudo apt update
sudo apt install -y libopenslide0
python -m pip install --upgrade pip setuptools wheel
python -m pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cpu openslide-python tiffslide
python -m pip install .[docs]
- name: Build docs
run: |
cd docs
make html