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Tests linux

Converting to mamba #34

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Converting to mamba

Converting to mamba #34

Workflow file for this run

.github/workflows/tests-linux.yml at 401a284
name: Tests linux
on:
workflow_dispatch:
pull_request:
branches:
- dev
- master
push:
branches:
- dev
- master
jobs:
build-linux:
runs-on: ubuntu-latest
strategy:
max-parallel: 5
matrix:
python-version: ["3.8", "3.9", "3.10"]
timeout-minutes: 60 # add a timeout
steps:
- uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Display Python version
run: python -c "import sys; print(sys.version)"
- name: Install dependencies
shell: bash -l {0}
run: |
sudo apt-get update
sudo apt-get install openslide-tools
sudo apt-get install pandoc
- name: Setup Micromamba
uses: mamba-org/setup-micromamba@v1
with:
micromamba-version: '1.5.6-0'
environment-name: pathml
environment-file: requirements/environment_test.yml
init-shell: >-
bash
create-args: >-
python=${{ matrix.python-version }}
- name: Debugging
run: |
echo "Printing the environment.yml file..."
cat requirements/environment_test.yml
echo "Checking the status of micro mamba..."
micromamba config
echo "Checking the available disk space..."
df -h
# - name: Install dependencies with micromamba
# shell: bash -l {0}
# run: micromamba env update --file requirements/environment_test.yml --name pathml
- name: Micromamba info
shell: bash -l {0}
run: |
micromamba info
micromamba config
micromamba list
- name: Set default Temurin JDK 17
run: |
sudo update-java-alternatives --set temurin-17-jdk-amd64 || true
java -version
- name: Install PathML
shell: bash -l {0}
run: pip install -e .
- name: Install torchvision
shell: bash -l {0}
run: pip install torchvision==0.14.1
- name: disk usage
shell: bash -l {0}
run: |
sudo df -h
sudo du -h
- name: free disk space
run: |
sudo swapoff -a
sudo rm -f /swapfile
sudo apt clean
docker rmi $(docker image ls -aq)
sudo df -h
sudo du -h
# - name: Check Coverage Command
# run: |
# which coverage
# coverage --version
# - name: Test with pytest for tile_stitcher
# run: |
# java -version
# python -m pytest tests/preprocessing_tests/test_tilestitcher.py
# - name: Test with pytest and generate coverage report
# shell: bash -l {0}
# run: |
# coverage run -m pytest -m "not slow and not exclude"
# coverage xml
# - name: Upload coverage to Codecov
# uses: codecov/codecov-action@v2
# with:
# token: ${{ secrets.CODECOV_TOKEN }}
# env_vars: OS,PYTHON
# fail_ci_if_error: true
# files: ./coverage.xml
# name: codecov-umbrella
# verbose: true
- name: Test other modules with pytest and generate coverage
shell: bash -l {0}
run: |
COVERAGE_FILE=.coverage_others coverage run -m pytest -m "not slow and not exclude"
- name: Test tile_stitcher with pytest and generate coverage
shell: bash -l {0}
run: |
COVERAGE_FILE=.coverage_tilestitcher coverage run -m pytest tests/preprocessing_tests/test_tilestitcher.py
- name: List Files in Directory
shell: bash -l {0}
run: |
ls -la
- name: Combine Coverage Data
shell: bash -l {0}
run: |
coverage combine .coverage_tilestitcher .coverage_others
- name: Generate Combined Coverage Report
shell: bash -l {0}
run: |
coverage xml -o combined_coverage.xml
# - name: Combine coverage data
# shell: bash -l {0}
# run: |
# coverage combine coverage_tilestitcher.xml coverage_others.xml
# coverage xml -o coverage_combined.xml
- name: Upload combined coverage to Codecov
uses: codecov/codecov-action@v2
with:
token: ${{ secrets.CODECOV_TOKEN }}
env_vars: OS,PYTHON
fail_ci_if_error: true
files: ./combined_coverage.xml
name: codecov-umbrella
verbose: true
- name: Compile docs
shell: bash -l {0}
run: |
cd docs
pip install -r readthedocs-requirements.txt
make html