Adding a few comments about custom schisto code #31
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| name: Run Tests and Build | |
| on: [push, pull_request] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| concurrency: | |
| # make sure only one run of this workflow for a given PR or a given branch | |
| # can happen at one time. previous queued or started runs will be cancelled. | |
| # github.workflow is the workflow name | |
| # github.ref is the ref that triggered the workflow run | |
| # on push, this is refs/heads/<branch name> | |
| # on pull request, this is refs/pull/<pull request number>/merge | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| # build: dependency of make install | |
| # nomkl: make sure numpy w/out mkl | |
| # setuptools_scm: needed for versioning to work | |
| CONDA_DEFAULT_DEPENDENCIES: python-build nomkl setuptools_scm | |
| LATEST_SUPPORTED_PYTHON_VERSION: "3.12" | |
| jobs: | |
| check-syntax-errors: | |
| name: Check for syntax errors | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.LATEST_SUPPORTED_PYTHON_VERSION }} | |
| # this is fast enough that it's not worth caching | |
| - name: Set up environment | |
| run: pip install flake8 | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| python -m flake8 src --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| python -m flake8 src --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| check-rst-syntax: | |
| name: Check RST syntax | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| name: Set up python | |
| with: | |
| python-version: ${{ env.LATEST_SUPPORTED_PYTHON_VERSION }} | |
| - name: Set up environment | |
| run: pip install doc8 | |
| - name: Lint with doc8 | |
| run: | | |
| # Skip line-too-long errors (D001) | |
| python -m doc8 --ignore D001 HISTORY.rst README_PYTHON.rst | |
| run-model-tests: | |
| name: Run model tests | |
| runs-on: ${{ matrix.os }} | |
| needs: check-syntax-errors | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [3.8, 3.9, "3.10", "3.11", "3.12"] | |
| os: [windows-latest, macos-13] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Fetch complete history for accurate versioning | |
| # NOTE: It takes twice as long to save the sample data cache | |
| # as it does to do a fresh clone (almost 5 minutes vs. 2.5 minutes) | |
| # Test data is way, way faster by contrast (on the order of a few | |
| # seconds to archive). | |
| - name: Restore git-LFS test data cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: data/invest-test-data | |
| key: git-lfs-testdata-${{ hashfiles('Makefile') }} | |
| - name: Set up python environment | |
| uses: ./.github/actions/setup_env | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| requirements-files: requirements.txt requirements-dev.txt constraints_tests.txt | |
| requirements: ${{ env.CONDA_DEFAULT_DEPENDENCIES }} | |
| - name: Download previous conda environment.yml | |
| continue-on-error: true | |
| # Using 'dawidd6' since 'download-artifact' GH action doesn't | |
| # support downloading artifacts from prior workflow runs | |
| uses: dawidd6/action-download-artifact@v2 | |
| with: | |
| workflow: build-and-test.yml | |
| # Get frozen conda env artifact from last successful workflow | |
| workflow_conclusion: success | |
| name: Conda Env for ${{ matrix.os }} ${{ matrix.python-version }} | |
| path: ./conda-env-artifact | |
| - name: Compare conda environments | |
| run: | | |
| micromamba list > conda-env.txt | |
| # make sure that the exit code is always 0 | |
| # otherwise, an error appears in the action annotations | |
| diff ./conda-env.txt ./conda-env-artifact/conda-env.txt || true | |
| - name: Build and install wheel | |
| run: | | |
| # uninstall InVEST if it was already in the restored cache | |
| python -m pip uninstall -y natcap.invest | |
| python -m build --wheel | |
| ls -la dist | |
| pip install $(find dist -name "natcap.invest*.whl") | |
| - name: Run model tests | |
| run: make test | |
| - name: Upload wheel artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: Wheel for ${{ matrix.os }} ${{ matrix.python-version }} | |
| path: dist | |
| - name: Upload conda env artifact | |
| uses: actions/upload-artifact@v4 | |
| continue-on-error: true | |
| with: | |
| name: Conda Env for ${{ matrix.os }} ${{ matrix.python-version }} | |
| path: conda-env.txt | |
| - name: Authenticate GCP | |
| if: github.event_name != 'pull_request' | |
| uses: google-github-actions/auth@v2 | |
| with: | |
| credentials_json: ${{ secrets.GOOGLE_SERVICE_ACC_KEY }} | |
| - name: Set up GCP | |
| if: github.event_name != 'pull_request' | |
| uses: google-github-actions/setup-gcloud@v2 | |
| - name: Deploy artifacts to GCS | |
| if: github.event_name != 'pull_request' | |
| run: make deploy | |
| test-source-distribution: | |
| name: Check sdist | |
| runs-on: ${{ matrix.os }} | |
| needs: check-syntax-errors | |
| strategy: | |
| matrix: | |
| python-version: [3.8, 3.9, "3.10", "3.11", "3.12"] | |
| os: [windows-latest, macos-13] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Fetch complete history for accurate versioning | |
| - uses: ./.github/actions/setup_env | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| requirements-files: requirements.txt | |
| requirements: ${{ env.CONDA_DEFAULT_DEPENDENCIES }} twine | |
| - name: Build source distribution | |
| run: | | |
| # Because we're using PEP518 build requirements, the user's | |
| # computer is guaranteed to have cython available at build | |
| # time. Thus, it is no longer necessary to distribute the | |
| # .cpp files in addition to the .pyx files. | |
| # | |
| # Elevating any python warnings to errors to catch build issues ASAP. | |
| python -W error -m build --sdist | |
| - name: Install from source distribution | |
| run : | | |
| # Install natcap.invest from the sdist in dist/ | |
| pip install $(find dist -name "natcap[._-]invest*") | |
| # Model tests should cover model functionality, we just want | |
| # to be sure that we can import `natcap.invest` here. | |
| # The point here is to make sure that we can build | |
| # natcap.invest from source and that it imports. | |
| python -c "from natcap.invest import *" | |
| - name: Check long description with twine | |
| run: twine check $(find dist -name "natcap[._-]invest*") | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: Source distribution ${{ matrix.os }} ${{ matrix.python-version }} | |
| path: dist | |
| # Secrets not available in PR so don't use GCP. | |
| # Only upload sdist in one of the matrix cases so we don't | |
| # overwrite artifacts or have duplicates (mac/windows sdists have | |
| # different extensions) | |
| - name: Authenticate GCP | |
| if: github.event_name != 'pull_request' && matrix.os == 'macos-13' && matrix.python-version == env.LATEST_SUPPORTED_PYTHON_VERSION | |
| uses: google-github-actions/auth@v2 | |
| with: | |
| credentials_json: ${{ secrets.GOOGLE_SERVICE_ACC_KEY }} | |
| - name: Set up GCP | |
| if: github.event_name != 'pull_request' && matrix.os == 'macos-13' && matrix.python-version == env.LATEST_SUPPORTED_PYTHON_VERSION | |
| uses: google-github-actions/setup-gcloud@v2 | |
| - name: Deploy artifacts to GCS | |
| if: github.event_name != 'pull_request' && matrix.os == 'macos-13' && matrix.python-version == env.LATEST_SUPPORTED_PYTHON_VERSION | |
| run: make deploy | |
| validate-resources: | |
| name: Validate Sampledata & User Guide | |
| runs-on: windows-latest | |
| needs: check-syntax-errors | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Fetch complete history for accurate versioning | |
| - uses: ./.github/actions/setup_env | |
| with: | |
| python-version: ${{ env.LATEST_SUPPORTED_PYTHON_VERSION }} | |
| requirements-files: requirements.txt | |
| requirements: ${{ env.CONDA_DEFAULT_DEPENDENCIES }} pytest | |
| - name: Make install | |
| run: make install | |
| - name: Validate sample data | |
| run: make validate_sampledata | |
| - name: Validate user guide links | |
| run: make validate_userguide_filenames | |
| run-workbench-tests: | |
| name: Run Workbench Tests | |
| runs-on: ${{ matrix.os }} | |
| needs: check-syntax-errors | |
| strategy: | |
| fail-fast: false | |
| max-parallel: 4 | |
| matrix: | |
| os: [windows-latest, macos-13] | |
| steps: | |
| - name: Check out repo | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Fetch complete history for accurate versioning | |
| - name: Set up python environment | |
| uses: ./.github/actions/setup_env | |
| with: | |
| python-version: ${{ env.LATEST_SUPPORTED_PYTHON_VERSION }} | |
| requirements-files: requirements.txt requirements-dev.txt | |
| requirements: ${{ env.CONDA_DEFAULT_DEPENDENCIES }} | |
| - name: Make install | |
| run: make install | |
| - name: Set up node | |
| uses: actions/setup-node@v3 | |
| with: | |
| node-version: 20 | |
| - name: Restore node_modules cache | |
| id: nodemodules-cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: workbench/node_modules | |
| key: ${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('workbench/yarn.lock') }} | |
| - name: Install workbench dependencies | |
| if: steps.nodemodules-cache.outputs.cache-hit != 'true' | |
| working-directory: workbench | |
| run: | | |
| yarn config set network-timeout 600000 -g | |
| yarn install | |
| - name: Run workbench tests | |
| working-directory: workbench | |
| env: | |
| CI: true | |
| run: yarn test | |
| build-binaries: | |
| name: Build binaries | |
| needs: check-syntax-errors | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [macos-13, windows-latest] | |
| include: | |
| - os: macos-13 | |
| puppeteer-log: ~/Library/Logs/invest-workbench/ | |
| workspace-path: InVEST-failed-mac-workspace.tar | |
| binary-extension: dmg | |
| - os: windows-latest | |
| puppeteer-log: ~/AppData/Roaming/invest-workbench/logs/ | |
| workspace-path: ${{ github.workspace }} | |
| binary-extension: exe | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Fetch complete history for accurate versioning | |
| - name: Set up conda environment | |
| uses: ./.github/actions/setup_env | |
| with: | |
| python-version: ${{ env.LATEST_SUPPORTED_PYTHON_VERSION }} | |
| requirements-files: | | |
| requirements.txt | |
| requirements-dev.txt | |
| requirements-docs.txt | |
| constraints_tests.txt | |
| requirements: ${{ env.CONDA_DEFAULT_DEPENDENCIES }} pandoc | |
| - name: Make install | |
| run: make install | |
| # Not caching chocolatey packages because the cache may not be reliable | |
| # https://github.com/chocolatey/choco/issues/2134 | |
| # and this step only takes about 30 seconds. | |
| - name: Install build dependencies (Windows) | |
| if: matrix.os == 'windows-latest' | |
| shell: powershell | |
| run: | | |
| choco install zip unzip | |
| $env:PATH += ";C:\ProgramData\chocolatey\bin" | |
| Import-Module $env:ChocolateyInstall\helpers\chocolateyProfile.psm1 | |
| refreshenv # Choco-provided command to reload environment variables | |
| - name: Build userguide | |
| run: make userguide | |
| - name: Build binaries | |
| run: make CONDA="$MAMBA_EXE" binaries | |
| - name: Install Node.js | |
| uses: actions/setup-node@v3 | |
| with: | |
| node-version: 18 | |
| - name: Restore node_modules cache | |
| id: nodemodules-cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: workbench/node_modules | |
| key: ${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('workbench/yarn.lock') }} | |
| - name: Install Workbench Dependencies | |
| if: steps.nodemodules-cache.outputs.cache-hit != 'true' | |
| working-directory: workbench | |
| run: | | |
| yarn config set network-timeout 600000 -g | |
| yarn install | |
| - name: Download mamba installer for distribution (MacOS) | |
| if: matrix.os == 'macos-13' | |
| run: curl -fsSLo Miniforge-pypy3-MacOSX-x86_64.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge-pypy3-MacOSX-x86_64.sh" | |
| - name: Install mamba for MacOS | |
| if: matrix.os == 'macos-13' | |
| run: bash Miniforge-pypy3-MacOSX-x86_64.sh -b -p dist/miniforge3 | |
| - name: Download mamba installer for distribution (Windows) | |
| if: matrix.os == 'windows-latest' | |
| run: curl -fsSLo Miniforge-pypy3-Windows-x86_64.exe "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge-pypy3-Windows-x86_64.exe" | |
| - name: Install mamba for Windows | |
| if: matrix.os == 'windows-latest' | |
| shell: cmd | |
| run: Miniforge-pypy3-Windows-x86_64.exe /InstallationType=JustMe /RegisterPython=0 /S /D=%cd%\dist\miniforge3 | |
| - name: Authenticate GCP | |
| if: github.event_name != 'pull_request' | |
| uses: google-github-actions/auth@v2 | |
| with: | |
| credentials_json: ${{ secrets.GOOGLE_SERVICE_ACC_KEY }} | |
| - name: Set up GCP | |
| if: github.event_name != 'pull_request' | |
| uses: google-github-actions/setup-gcloud@v2 | |
| - name: Build Workbench (PRs) | |
| if: github.event_name == 'pull_request' | |
| working-directory: workbench | |
| env: | |
| GH_TOKEN: env.GITHUB_TOKEN | |
| DEBUG: electron-builder | |
| CSC_IDENTITY_AUTO_DISCOVERY: false # disable electron-builder code signing | |
| run: | | |
| yarn run build | |
| yarn run dist | |
| - name: Build Workbench (macOS) | |
| if: github.event_name != 'pull_request' && matrix.os == 'macos-13' # secrets not available in PR | |
| working-directory: workbench | |
| env: | |
| GH_TOKEN: env.GITHUB_TOKEN | |
| DEBUG: electron-builder | |
| CSC_LINK: 2025-01-16-Expiry-AppStore-App.p12 | |
| CSC_KEY_PASSWORD: ${{ secrets.MACOS_CODESIGN_CERT_PASS }} | |
| run: | | |
| gsutil cp gs://stanford_cert/$CSC_LINK $CSC_LINK | |
| yarn run build | |
| yarn run dist | |
| - name: Build Workbench (Windows) | |
| if: github.event_name != 'pull_request' && matrix.os == 'windows-latest' # secrets not available in PR | |
| working-directory: workbench | |
| env: | |
| GH_TOKEN: env.GITHUB_TOKEN | |
| DEBUG: electron-builder | |
| #CSC_LINK: Stanford-natcap-code-signing-cert-expires-2024-01-26.p12 | |
| #CSC_KEY_PASSWORD: ${{ secrets.WINDOWS_CODESIGN_CERT_PASS }} | |
| run: | | |
| #gsutil cp gs://stanford_cert/$CSC_LINK $CSC_LINK | |
| yarn run build | |
| yarn run dist | |
| - name: Test electron app with puppeteer | |
| working-directory: workbench | |
| run: npx cross-env CI=true yarn run test-electron-app | |
| - name: Sign binaries (macOS) | |
| if: github.event_name != 'pull_request' && matrix.os == 'macos-13' # secrets not available in PR | |
| env: | |
| CERT_FILE: 2025-01-16-Expiry-AppStore-App.p12 | |
| CERT_PASS: ${{ secrets.MACOS_CODESIGN_CERT_PASS }} | |
| run: | | |
| WORKBENCH_BINARY=$(find "$(pwd)/workbench/dist" -type f -name 'invest_*.dmg' | head -n 1) | |
| make WORKBENCH_BIN_TO_SIGN="$WORKBENCH_BINARY" codesign_mac | |
| #- name: Sign binaries (Windows) | |
| # if: github.event_name != 'pull_request' && matrix.os == 'windows-latest' # secrets not available in PR | |
| # env: | |
| # CERT_FILE: Stanford-natcap-code-signing-cert-expires-2024-01-26.p12 | |
| # CERT_PASS: ${{ secrets.WINDOWS_CODESIGN_CERT_PASS }} | |
| # run: | | |
| # # figure out the path to signtool.exe (it keeps changing with SDK updates) | |
| # SIGNTOOL_PATH=$(find 'C:\\Program Files (x86)\\Windows Kits\\10' -type f -name 'signtool.exe*' | head -n 1) | |
| # WORKBENCH_BINARY=$(find "$(pwd)/workbench/dist" -type f -name 'invest_*.exe' | head -n 1) | |
| # make WORKBENCH_BIN_TO_SIGN="$WORKBENCH_BINARY" SIGNTOOL="$SIGNTOOL_PATH" codesign_windows | |
| - name: Deploy artifacts to GCS | |
| if: github.event_name != 'pull_request' | |
| run: make deploy | |
| - name: Upload workbench binary artifact | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: Workbench-${{ runner.os }}-binary | |
| path: workbench/dist/*.${{ matrix.binary-extension }} | |
| - name: Upload user's guide artifact (Windows) | |
| if: matrix.os == 'windows-latest' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: InVEST-user-guide | |
| path: dist/InVEST_*_userguide.zip | |
| - name: Upload workbench logging from puppeteer | |
| uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: ${{ runner.os }}_puppeteer_log.zip' | |
| path: ${{ matrix.puppeteer-log }} | |
| - name: Run invest-autotest with binaries | |
| if : | | |
| (github.event_name == 'push' && | |
| (startsWith(github.ref, 'refs/heads/release') || github.ref == 'refs/heads/main')) || | |
| (github.event_name == 'pull_request' && startsWith(github.head_ref, 'autorelease')) | |
| run: make invest_autotest | |
| - name: Tar the workspace to preserve permissions (macOS) | |
| if: failure() && matrix.os == 'macos-13' | |
| run: tar -cvf ${{ matrix.workspace-path}} ${{ github.workspace }} | |
| - name: Upload workspace on failure | |
| if: ${{ failure() }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: InVEST-failed-${{ runner.os }}-workspace | |
| path: ${{ matrix.workspace-path}} | |
| build-sampledata: | |
| name: Build sampledata archives | |
| needs: check-syntax-errors | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Fetch complete history for accurate versioning | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.LATEST_SUPPORTED_PYTHON_VERSION }} | |
| - name: Install dependencies | |
| # dependencies of setup.py, needed to get the version string | |
| run: pip install babel cython numpy setuptools setuptools_scm wheel | |
| - run: make sampledata sampledata_single | |
| - name: Upload sample data artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: InVEST-sample-data | |
| path: dist/*.zip | |
| - name: Authenticate GCP | |
| if: github.event_name != 'pull_request' | |
| uses: google-github-actions/auth@v2 | |
| with: | |
| credentials_json: ${{ secrets.GOOGLE_SERVICE_ACC_KEY }} | |
| - name: Set up GCP | |
| if: github.event_name != 'pull_request' | |
| uses: google-github-actions/setup-gcloud@v2 | |
| - name: Deploy artifacts to GCS | |
| if: github.event_name != 'pull_request' | |
| run: make deploy |