Update vegmap shapefile download and metadata; add new functions and … #4200
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| # MIT License | |
| # Copyright (c) 2021 Eli Lilly and Company | |
| # Author: William Michael Landau (will.landau at gmail) | |
| # Edited by Adam Wilson (adamw at buffalo) | |
| # Written with help from public domain (CC0 1.0 Universal) workflow files by Jim Hester: | |
| # * https://github.com/r-lib/actions/blob/master/examples/check-full.yaml | |
| # * https://github.com/r-lib/actions/blob/master/examples/blogdown.yaml | |
| # | |
| # Permission is hereby granted, free of charge, to any person obtaining a copy | |
| # of this software and associated documentation files (the "Software"), to deal | |
| # in the Software without restriction, including without limitation the rights | |
| # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
| # copies of the Software, and to permit persons to whom the Software is | |
| # furnished to do so, subject to the following conditions: | |
| # | |
| # The above copyright notice and this permission notice shall be included in all | |
| # copies or substantial portions of the Software. | |
| # | |
| # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
| # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
| # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
| # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
| # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
| # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE | |
| # SOFTWARE. | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - master | |
| - dev-adam-appeears | |
| - dev-jiyeon | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| schedule: | |
| - cron: '0 0 * * 0' # runs every Sunday at midnight UTC | |
| # - cron: '0 0 * * *' # runs every day at midnight | |
| # - cron: '0 */6 * * *' # run every 6th hour | |
| name: targets | |
| jobs: | |
| targets: | |
| runs-on: ubuntu-latest | |
| container: adamwilsonlab/emma:latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| EARTHDATA_PASSWORD: ${{ secrets.EARTHDATA_PASSWORD }} | |
| EARTHDATA_USER: ${{ secrets.EARTHDATA_USER }} | |
| RENV_PATHS_ROOT: ~/.local/share/renv | |
| ACTIONS_RUNNER_DEBUG: true | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| ref: dev-adam-appeears | |
| lfs: true | |
| - name: Whitelist directory | |
| run: git config --global --add safe.directory /__w/emma_envdata/emma_envdata | |
| - name: Install system deps for keyring | |
| run: | | |
| apt-get update | |
| apt-get install -y libsecret-1-0 libsecret-1-dev | |
| - name: Install R Package Dependencies | |
| run: |- | |
| Rscript -e "questionr::qscan(list.files(pattern='*.R',recursive=T), load = TRUE, detail = TRUE)" # this scans all scripts and installs any needed packages | |
| - name: Parse _targets.R | |
| run: Rscript -e "parse('_targets.R')" | |
| - name: Cache packages | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.RENV_PATHS_ROOT }} | |
| key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }} | |
| restore-keys: ${{ runner.os }}-renv- | |
| - name: Cache targets store | |
| uses: actions/cache@v3 | |
| with: | |
| path: _targets/ | |
| key: targets-${{ hashFiles('_targets.R', 'R/**') }} | |
| restore-keys: targets- | |
| - name: Run targets pipeline | |
| run: | | |
| Rscript -e "targets::tar_make()" 2>&1 | tee targets-output.log || echo "tar_make failed, see log above" | |
| shell: bash | |
| continue-on-error: true | |
| - name: Export final data products to releases | |
| if: github.ref == 'refs/heads/main' | |
| run: | | |
| # Load final targets and export to data/releases/ | |
| targets::tar_load_everything() | |
| # Create releases directory | |
| dir.create("data/releases", recursive = TRUE, showWarnings = FALSE) | |
| # Export domain as gpkg (example - adjust to your actual target names) | |
| if (exists("domain")) { | |
| sf::st_write( | |
| sf::st_as_sf(domain), | |
| "data/releases/domain.gpkg", | |
| delete_dsn = TRUE | |
| ) | |
| } | |
| # Add other final outputs here as needed | |
| # Example: write.csv(final_data, "data/releases/final_data.csv") | |
| shell: Rscript {0} | |
| continue-on-error: true | |
| - name: Upload to GitHub Releases | |
| if: github.ref == 'refs/heads/main' | |
| uses: softprops/action-gh-release@v1 | |
| with: | |
| tag_name: latest | |
| files: | | |
| data/releases/* | |
| body: | | |
| Latest data products from targets pipeline | |
| Updated: ${{ github.event.head_commit.timestamp }} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Prepare failure artifact | |
| if: failure() | |
| run: rm -rf .git .github | |
| - name: Post failure artifact | |
| if: failure() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: ${{ runner.os }}-results | |
| path: . | |
| - name: Create review PR on failure | |
| if: failure() && github.event_name == 'push' | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| # Create error log if it doesn't exist | |
| if [ ! -f targets-output.log ]; then | |
| echo "No targets-output.log file found. Pipeline may have failed during execution." > targets-output.log | |
| fi | |
| # Get last 100 lines of error | |
| tail -100 targets-output.log > error-summary.txt | |
| # Create branch | |
| BRANCH="auto-fix-$(date +%s)" | |
| git config user.name "github-actions[bot]" | |
| git config user.email "github-actions[bot]@users.noreply.github.com" | |
| git checkout -b "$BRANCH" | |
| # Add error log | |
| mkdir -p .github/workflow-logs | |
| cp targets-output.log .github/workflow-logs/failure-$(date +%Y%m%d-%H%M%S).log | |
| git add .github/workflow-logs/ | |
| git commit -m "Add workflow failure log for review" || true | |
| git push origin "$BRANCH" | |
| # Create PR (Copilot will auto-review it) | |
| gh pr create \ | |
| --title "🚨 Targets workflow failed - Review needed" \ | |
| --body "## Workflow Failure | |
| The targets pipeline failed. GitHub Copilot will review this PR. | |
| ### Error Summary | |
| \`\`\` | |
| $(cat error-summary.txt) | |
| \`\`\` | |
| ### Full Log | |
| See \`.github/workflow-logs/\` for complete output. | |
| **Next steps:** | |
| 1. Review Copilot's suggestions in the PR | |
| 2. Apply fixes | |
| 3. Close this PR once resolved" \ | |
| --base main \ | |
| --head "$BRANCH" \ | |
| --label "bug,auto-generated" | |
| - name: Comment on existing PR with status | |
| if: always() && github.event_name == 'pull_request' | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| STATUS="${{ steps.targets.outcome }}" | |
| if [ "$STATUS" = "success" ]; then | |
| EMOJI="✅" | |
| MESSAGE="Targets workflow completed successfully!" | |
| else | |
| EMOJI="❌" | |
| MESSAGE="Targets workflow failed. See logs below." | |
| fi | |
| if [ ! -f targets-output.log ]; then | |
| echo "No targets-output.log file found. Pipeline completed without explicit log output." > targets-output.log | |
| fi | |
| gh pr comment ${{ github.event.pull_request.number }} --body "## $EMOJI Targets Workflow Result | |
| $MESSAGE | |
| <details> | |
| <summary>Show last 50 lines of output</summary> | |
| \`\`\` | |
| $(tail -50 targets-output.log) | |
| \`\`\` | |
| </details>" |