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VarunUllanatVarunUllanat
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Merge pull request #429 from Dana-Farber-AIOS/dev
PathML 3.0.0: New Features and User Experience Improvements
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‎.gitattributes

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tests/testdata/tilestitching_testdata/*.tif filter=lfs diff=lfs merge=lfs -text

‎.github/workflows/precommit-hooks.yaml

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on: [pull_request]
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jobs:
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build:
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lint:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python 3.8
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uses: actions/setup-python@v1
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with:
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python-version: 3.8
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- name: Linting
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run: |
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pip install pre-commit
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pre-commit run --all-files
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- uses: actions/checkout@v3
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- uses: psf/black@stable
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pre-commit:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-python@v3
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- uses: pre-commit/action@v3.0.0
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with:
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extra_args: flake8 --all-files

‎.github/workflows/publish-to-docker-hub.yml

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password: ${{ secrets.DOCKERHUB_TOKEN }}
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- name: Build and push
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id: docker_build
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uses: docker/build-push-action@v2.7.0
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uses: docker/build-push-action@v4
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with:
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context: .
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platforms: linux/amd64,linux/arm64
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push: true
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tags: |
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pathml/pathml:latest

‎.github/workflows/tests-conda.yml

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‎.github/workflows/tests-linux.yml

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name: Tests linux
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on:
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workflow_dispatch:
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pull_request:
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branches:
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- dev
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- master
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push:
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branches:
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- dev
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- master
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jobs:
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build-linux:
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runs-on: ubuntu-latest
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strategy:
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max-parallel: 5
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matrix:
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python-version: ["3.8", "3.9", "3.10"]
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timeout-minutes: 60 # add a timeout
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Install dependencies
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shell: bash -l {0}
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run: |
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sudo apt-get update
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sudo apt-get install openslide-tools
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sudo apt-get install pandoc
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- name: Setup Micromamba
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uses: mamba-org/setup-micromamba@v1
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with:
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micromamba-version: '1.5.6-0'
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environment-name: pathml
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environment-file: requirements/environment_test.yml
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init-shell: >-
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bash
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create-args: >-
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python=${{ matrix.python-version }}
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- name: Debugging
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run: |
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echo "Printing the environment.yml file..."
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cat requirements/environment_test.yml
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echo "Checking the status of micro mamba..."
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micromamba config
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echo "Checking the available disk space..."
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df -h
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# - name: Install dependencies with micromamba
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# shell: bash -l {0}
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# run: micromamba env update --file requirements/environment_test.yml --name pathml
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- name: Micromamba info
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shell: bash -l {0}
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run: |
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micromamba info
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micromamba config
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micromamba list
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- name: Set default Temurin JDK 17
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run: |
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sudo update-java-alternatives --set temurin-17-jdk-amd64 || true
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java -version
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- name: Install PathML
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shell: bash -l {0}
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run: pip install -e .
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- name: Install torchvision
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shell: bash -l {0}
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run: pip install torchvision==0.14.1
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- name: disk usage
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shell: bash -l {0}
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run: |
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sudo df -h
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sudo du -h
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- name: free disk space
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run: |
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sudo swapoff -a
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sudo rm -f /swapfile
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sudo apt clean
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docker rmi $(docker image ls -aq)
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sudo df -h
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sudo du -h
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# - name: Check Coverage Command
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# run: |
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# which coverage
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# coverage --version
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# - name: Test with pytest for tile_stitcher
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# run: |
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# java -version
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# python -m pytest tests/preprocessing_tests/test_tilestitcher.py
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# - name: Test with pytest and generate coverage report
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# shell: bash -l {0}
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# run: |
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# coverage run -m pytest -m "not slow and not exclude"
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# coverage xml
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# - name: Upload coverage to Codecov
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# uses: codecov/codecov-action@v2
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# with:
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# token: ${{ secrets.CODECOV_TOKEN }}
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# env_vars: OS,PYTHON
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# fail_ci_if_error: true
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# files: ./coverage.xml
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# name: codecov-umbrella
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# verbose: true
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- name: Test other modules with pytest and generate coverage
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shell: bash -l {0}
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run: |
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COVERAGE_FILE=.coverage_others coverage run -m pytest -m "not slow and not exclude"
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- name: Test tile_stitcher with pytest and generate coverage
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shell: bash -l {0}
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run: |
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COVERAGE_FILE=.coverage_tilestitcher coverage run -m pytest tests/preprocessing_tests/test_tilestitcher.py
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- name: List Files in Directory
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shell: bash -l {0}
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run: |
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ls -la
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- name: Combine Coverage Data
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shell: bash -l {0}
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run: |
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coverage combine .coverage_tilestitcher .coverage_others
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- name: Generate Combined Coverage Report
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shell: bash -l {0}
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run: |
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coverage xml -o combined_coverage.xml
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# - name: Combine coverage data
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# shell: bash -l {0}
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# run: |
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# coverage combine coverage_tilestitcher.xml coverage_others.xml
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# coverage xml -o coverage_combined.xml
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- name: Upload combined coverage to Codecov
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uses: codecov/codecov-action@v2
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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env_vars: OS,PYTHON
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fail_ci_if_error: true
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files: ./combined_coverage.xml
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name: codecov-umbrella
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verbose: true
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- name: Compile docs
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shell: bash -l {0}
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run: |
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cd docs
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pip install -r readthedocs-requirements.txt
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make html

‎.github/workflows/tests-macos.yml

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name: Tests MacOS
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on:
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workflow_dispatch:
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pull_request:
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branches:
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- dev_graph
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push:
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branches:
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- dev_graph
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jobs:
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build:
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name: Build (${{ matrix.os }}, Python ${{ matrix.python-version }})
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [macos-latest]
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python-version: ["3.8", "3.9", "3.10"]
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steps:
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- uses: actions/checkout@v2
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- name: Install openslide
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shell: bash -l {0}
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run: brew install openslide
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- name: Setup Micromamba
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uses: mamba-org/setup-micromamba@v1
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with:
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micromamba-version: '1.5.6-0'
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environment-name: pathml
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environment-file: requirements/environment_mac.yml
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init-shell: >-
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bash
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create-args: >-
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python=${{ matrix.python-version }}
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- name: Micromamba info
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shell: bash -l {0}
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run: |
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micromamba info
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micromamba config
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micromamba list
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- name: Set default Temurin JDK 17
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run: |
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sudo update-java-alternatives --set temurin-17-jdk-amd64 || true
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java -version
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- name: Install PathML
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shell: bash -l {0}
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run: pip install -e .
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- name: Install torchvision
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shell: bash -l {0}
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run: pip install torchvision==0.14.1
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- name: Test other modules with pytest and generate coverage
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shell: bash -l {0}
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run: |
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COVERAGE_FILE=.coverage_others coverage run -m pytest -m "not slow and not exclude"
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- name: Test tile_stitcher with pytest and generate coverage
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shell: bash -l {0}
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run: |
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COVERAGE_FILE=.coverage_tilestitcher coverage run -m pytest tests/preprocessing_tests/test_tilestitcher.py

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