Fix sampling in NuthKaab and set better default values for other classes
#1059
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 | |
| name: build | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| test: | |
| name: ${{ matrix.os }}, python ${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ["ubuntu-latest", "macos-latest", "windows-latest"] | |
| python-version: ["3.8", "3.9", "3.10"] | |
| # Run all shells using bash (including Windows) | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| # We initiate the environment empty, and check if a key for this environment doesn't already exist in the cache | |
| - name: Initiate empty environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| auto-update-conda: true | |
| use-mamba: true | |
| channel-priority: strict | |
| activate-environment: xdem-dev | |
| - name: Get month for resetting cache | |
| id: get-date | |
| run: echo "cache_date=$(/bin/date -u '+%Y%m')" >> $GITHUB_ENV | |
| shell: bash | |
| - name: Cache conda env | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: conda-${{ matrix.os }}-${{ matrix.python-version }}-${{ env.cache_date }}-${{ hashFiles('dev-environment.yml') }}-${{ env.CACHE_NUMBER }} | |
| env: | |
| CACHE_NUMBER: 0 # Increase this value to reset cache if environment.yml has not changed | |
| id: cache | |
| # The trick below is necessary because the generic environment file does not specify a Python version, and only | |
| # "conda env update" can be used to update with an environment file, which upgrades the Python version | |
| # (we add "graphviz" from dev-environment to solve all dependencies at once, at graphviz relies on image | |
| # processing packages very much like geo-packages; not a problem for docs, dev installs where all is done at once) | |
| - name: Install base environment with a fixed Python version | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: | | |
| mamba install pyyaml python=${{ matrix.python-version }} | |
| pkgs_conda_base=`python .github/scripts/get_yml_env_nopy.py "environment.yml" --p "conda"` | |
| pkgs_pip_base=`python .github/scripts/get_yml_env_nopy.py "environment.yml" --p "pip"` | |
| mamba install python=${{ matrix.python-version }} $pkgs_conda_base graphviz opencv | |
| if [[ "$pkgs_pip_base" != "None" ]]; then | |
| pip install $pkgs_pip_base | |
| fi | |
| - name: Install project | |
| run: pip install -e . --no-dependencies | |
| # This steps allows us to check the "import xdem" with the base environment provided to users, before adding | |
| # development-specific dependencies by differencing the env and dev-env yml files | |
| - name: Check import works with base environment | |
| run: | | |
| # We unset the PROJ_DATA environment variable to make PROJ work on Windows | |
| unset PROJ_DATA | |
| python -c "import xdem" | |
| # This time, the trick below is necessary because: 1/ "conda update" does not support a file -f as argument | |
| # and also 2/ "conda env update" does not support --freeze-installed or --no-update-deps | |
| - name: Update environment with development packages if cache does not exist | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: | | |
| # We unset the PROJ_DATA environment variable to make PROJ work on Windows | |
| unset PROJ_DATA | |
| pkgs_conda_dev=`python -c "import xdem.misc; xdem.misc.diff_environment_yml('environment.yml', 'dev-environment.yml', 'conda')"` | |
| pkgs_pip_dev=`python -c "import xdem.misc; xdem.misc.diff_environment_yml('environment.yml', 'dev-environment.yml', 'pip')"` | |
| mamba install $pkgs_conda_dev --freeze-installed | |
| if [[ "$pkgs_pip_dev" != "None" ]]; then | |
| pip install $pkgs_pip_dev | |
| fi | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --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 | |
| - name: Setup pip dependencies | |
| run: pip install pytest-cov coveralls coveragepy-lcov | |
| - name: Test with pytest | |
| run: | | |
| # We unset the PROJ_DATA environment variable to make PROJ work on Windows | |
| unset PROJ_DATA | |
| pytest -ra --cov=xdem/ | |
| # We can skip the conversion step once this PR of pytest is merged: https://github.com/pytest-dev/pytest-cov/pull/536 | |
| # and replace pytest argument by --cov-report=lcov | |
| - name: Converting coverage to LCOV format | |
| run: coveragepy-lcov --data_file_path .coverage --output_file_path coverage.info | |
| - name: Upload coverage to Coveralls | |
| uses: coverallsapp/github-action@master | |
| with: | |
| github-token: ${{ secrets.github_token }} | |
| flag-name: run-${{ matrix.test_number }} | |
| path-to-lcov: coverage.info | |
| parallel: true | |
| finish: | |
| needs: test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Upload to Coveralls finished | |
| uses: coverallsapp/github-action@master | |
| with: | |
| github-token: ${{ secrets.github_token }} | |
| parallel-finished: true |