Add LesionCountWeightedByAssignment, RefLesionsCount, PredLesionsCount #11
Workflow file for this run
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| # This file will define what the workflow consists of, that is what operations we want to perform and when. The first | |
| # part names the action, the second states when the action is triggered (on push or on pull request) and on what | |
| # branches (main and dev in our case). | |
| name: Unit Tests | |
| on: | |
| push: | |
| branches: [ main ] # run when anything is pushed to these branches | |
| pull_request: | |
| branches: [ main ] # run for the code submitted as a PR to these branches | |
| # jobs are a series of steps which run commands in the chosen virtualized environment to perform some action | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest # run in Ubuntu VM, so assuming a Unix-like environment for our commands | |
| steps: | |
| # first step checks out the code into | |
| - uses: actions/checkout@v2 | |
| # Setup Python using a existing action "actions/setup-python@v2" from Github's library of actions | |
| # Arguments are provided to this action using the key-values under "with" | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.9 | |
| # Install the requirements for this library plus those for running out tests (flake8 and coverage) | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| pip install -r requirements-dev.txt | |
| # Run flake8 to do basic code quality checks, the output will appear in the action log | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --exit-zero --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics \ | |
| --per-file-ignores="__init__.py:F401" | |
| # Run the unit tests using the coverage program and create the XML output file | |
| - name: Test with pytest | |
| run: | | |
| pytest --cov --cov-config=.coveragerc --cov-report=xml -vv | |
| # Using Codecov's action, upload the coverage report for the triggering commit/PR | |
| - name: Upload coverage | |
| uses: codecov/codecov-action@v2 | |
| with: | |
| file: ./coverage.xml | |
| fail_ci_if_error: true | |
| verbose: true | |
| version: "v0.1.15" | |
| build_docs: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.9 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements-docs.txt | |
| - name: Install Metrics Reloaded | |
| run: | | |
| python -m pip install . | |
| - name: Build docs | |
| run: | | |
| cd docs && make html |