Merge pull request #132 from saeyslab/SC_19_github-actions

Sc 19 GitHub actions

.github/workflows/run_tests.yml

@@ -0,0 +1,83 @@
+name: Run tests
+
+on:
+ workflow_dispatch:
+
+ push:
+ branches:
+ - main
+
+ pull_request:
+ branches:
+ - main
+
+ paths:
+ - 'src/napari_sparrow/**'
+ - '.github/workflows/run_tests.yml'
+
+env:
+ CACHE_NUMBER: 1 # increase to reset cache manually
+
+jobs:
+ test:
+
+ strategy:
+ matrix:
+ os: [ ubuntu-latest ] #[ubuntu-latest, macos-latest]
+ python-version: ['3.10']
+ runs-on: ${{ matrix.os }}
+
+ steps:
+ - uses: actions/checkout@v2
+
+ # these libraries enable testing on Qt on linux
+ - uses: tlambert03/setup-qt-libs@v1
+
+ - name: Setup Mambaforge
+ uses: conda-incubator/setup-miniconda@v2
+ with:
+ miniforge-variant: Mambaforge
+ miniforge-version: latest
+ activate-environment: napari-sparrow
+ use-mamba: true
+ python-version: ${{ matrix.python-version }}
+
+ - name: Set cache environment variables
+ shell: bash -l {0}
+ run: |
+ CONDA_PREFIX=$(python -c "import sys; print(sys.prefix)")
+ echo "$CONDA_PREFIX"
+ echo "CONDA_PREFIX=$CONDA_PREFIX" >> $GITHUB_ENV
+
+ #- name: Set cache date
+ # run: echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV
+
+ - uses: actions/cache@v3
+ with:
+ path: ${{ env.CONDA_PREFIX }}
+ key: conda-env-${{ runner.os }}-${{ matrix.python-version }}-${{ hashFiles('environment.yml') }}-${{ env.CACHE_NUMBER }}
+ id: cache
+
+ - name: Update environment
+ run: mamba env update -n napari-sparrow -f environment.yml
+ if: steps.cache.outputs.cache-hit != 'true'
+
+
+ # this runs the platform-specific tests declared in tox.ini
+ - name: Test with tox
+ shell: bash -l {0}
+ run: |
+ conda activate napari-sparrow
+ pip install -e '.[testing]'
+ pip install tox tox-gh-actions
+ tox
+ env:
+ PLATFORM: ${{ matrix.os }}
+
+
+ - name: Upload coverage.xml
+ uses: actions/upload-artifact@v2
+ with:
+ name: coverage-report
+ path: coverage.xml
+

.gitignore

@@ -19,6 +19,7 @@ notebooks
 src/napari_sparrow/_tests/test_data/*
 !src/napari_sparrow/_tests/test_data/20272_slide1_A1-1_DAPI_4288_2144.tiff
 !src/napari_sparrow/_tests/test_data/20272_slide1_A1-1_results_4288_2144.txt
+!src/napari_sparrow/_tests/test_data/dummy_markers.csv
 
 # Add exection for example configs for resolve and vizgen
 !configs/allocate/resolve_liver.yaml

environment.yml

@@ -2,54 +2,33 @@ name: napari-sparrow
 channels:
  - pytorch
  - conda-forge
- - defaults
 dependencies:
- - python=3.10
- - ipykernel=6.9.1
- - pytorch=1.12
- # disable for non-CUDA GPUs
- - cudatoolkit=11.3
+ - geopandas=0.12.2
+ - leidenalg=0.9.1
+ - matplotlib=3.5.2
  - napari=0.4.16
- - pandas==1.4.2
- - numpy==1.21.6
- - scikit-image==0.19.2
- - seaborn==0.11.2
- - matplotlib==3.5.2
- - scipy==1.8.0
- - jupyterlab==3.4.0
- - ipywidgets==7.7.0
- - anndata==0.9.1
- - tqdm==4.64.0
- - opencv==4.5.5
- - modestimage==0.2
- - widgetsnbextension==3.6.0
- # polygons
- - geopandas==0.12.2
- - rasterio==1.3.2
- # scanpy
- - scanpy==1.9.1
- - python-igraph
- # dev tools
- - pre-commit
- - pytest
- - tox
- - mypy
- - pip
+ - numpy=1.24.4
+ - opencv=4.5.5
+ - pip=22.2.2
+ - python=3.10.8
+ - pytorch=1.12.1
+ - rasterio=1.3.2
+ - scanpy=1.9.1
+ - scipy=1.8.0
+ - seaborn=0.11.2
  - pip:
- - squidpy==1.2.0
- - cellpose==2.0.5
+ - anndata==0.9.1
  - basicpy==1.0.0
- - nbmake==1.3.4
- - pytest-xdist==2.5.0
- - pytest-qt==4.2.0
- - spatialdata==0.0.9
- - napari-spatialdata==0.2.4
- - aicsimageio==4.9.4
- - multiscale-spatial-image==0.11.2
- - voronoi-diagram-for-polygons==0.1.6 # https://github.com/longavailable/voronoi-diagram-for-polygons/issues/6
- - black==23.1.0
- - hydra-core==1.2.0
- - leidenalg==0.9.1
+ - cellpose==2.0.5
+ - jax==0.4.6
+ - jaxlib==0.4.6
  - shapely==2.0.1
- - submitit==1.4.5
-
+ - spatialdata==0.0.9
+ - squidpy==1.2.0
+ - voronoi-diagram-for-polygons==0.1.6
+ - xarray==2022.12.0
+ - xarray-dataclasses==1.5.0
+ - xarray-datatree==0.0.12
+ - xarray-schema==0.0.3
+ - xarray-spatial==0.3.5
+ - pandas==1.4.2

pyproject.toml

@@ -0,0 +1,7 @@
+[build-system]
+requires = ["setuptools>=42.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+# pyproject.toml file content
+[tool.coverage.run]
+omit = ["src/napari_sparrow/_tests/*", "experiments/*"]

setup.cfg

@@ -30,13 +30,21 @@ project_urls =
 [options]
 packages = find:
 install_requires =
- hydra-colorlog==1.2.0
- hydra-core==1.2.0
- hydra-optuna-sweeper==1.2.0
+ pandas==1.4.2
+ spatialdata==0.0.9
+ cellpose==2.0.5
+ squidpy==1.2.0
+ matplotlib<3.7 # scanpy not compatible with matplotlib>=3.7
+ scanpy==1.9.1
+ jax==0.4.6
+ jaxlib==0.4.6
+ basicpy==1.0.0
+ voronoi-diagram-for-polygons==0.1.6
+ rasterio==1.3.2
+ seaborn==0.11.2
+ leidenalg==0.9.1
  magicgui
- numpy
  pyrootutils
- qtpy
 python_requires = >=3.8
 include_package_data = True
 package_dir =
@@ -53,14 +61,28 @@ napari.manifest =
  napari-sparrow = napari_sparrow:napari.yaml
 
 [options.extras_require]
+plugin =
+ napari==0.4.16
+ hydra-core==1.2.0
+ hydra-colorlog==1.2.0
+ napari-spatialdata==0.2.4
+
 testing =
- napari
- pyqt5
+ napari==0.4.16
+ hydra-core==1.2.0
+ hydra-colorlog==1.2.0
  pytest
  pytest-cov
  pytest-qt
  tox
 
+cli =
+ hydra-core==1.2.0
+ hydra-colorlog==1.2.0
+ submitit==1.4.5 
+ hydra-submitit-launcher==1.2.0
+
+
 [options.package_data]
 * = *.yaml
 

src/napari_sparrow/_tests/conftest.py

@@ -23,7 +23,7 @@ def cfg_pipeline_global() -> DictConfig:
  "dataset.data_dir=${paths.data_dir}",
  "dataset.image=${dataset.data_dir}/20272_slide1_A1-1_DAPI_4288_2144.tiff",
  "dataset.coords=${dataset.data_dir}/20272_slide1_A1-1_results_4288_2144.txt",
- #"dataset.markers=${dataset.data_dir}/markerGeneListMartinNoLow.csv",
+ "dataset.markers=${dataset.data_dir}/dummy_markers.csv",
  "allocate.delimiter='\t'",
  "allocate.column_x=0",
  "allocate.column_y=1",