Adding functions and scripts for downloading, extracting, and processing observations, initial conditions, land cover types, ERA5 drivers for anchor sites within NA. #1342
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| on: | |
| issue_comment: | |
| types: [created] | |
| name: Commands | |
| jobs: | |
| style: | |
| if: startsWith(github.event.comment.body, '/style') | |
| name: style | |
| runs-on: macOS-latest | |
| steps: | |
| - id: file_changes | |
| uses: trilom/file-changes-action@v1.2.4 | |
| - name: list changed files | |
| run: echo '${{ steps.file_changes.outputs.files_modified }}' | |
| - name: work around https://github.com/actions/checkout/issues/766 | |
| run: git config --global --add safe.directory "$GITHUB_WORKSPACE" | |
| - uses: actions/checkout@v4 | |
| with: | |
| set-safe-directory: false | |
| - uses: r-lib/actions/pr-fetch@master | |
| with: | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| - uses: r-lib/actions/setup-r@master | |
| - name: Install styler | |
| run: | | |
| Rscript -e 'install.packages("styler")' | |
| - name: run styler | |
| shell: bash | |
| env: | |
| FILES: ${{ join(fromJSON(steps.file_changes.outputs.files_modified), ' ') }} | |
| run: | | |
| for f in ${FILES}; do | |
| if [[ "$f" == *.R || "$f" == *.Rmd ]] | |
| then Rscript -e 'styler::style_file("'${f}'")' | |
| fi | |
| done | |
| - name: commit | |
| run: | | |
| git add \*.R | |
| git add \*.Rmd | |
| if [ "$(git diff --name-only --cached)" != "" ]; then git commit -m 'automated syle update' ; fi | |
| - uses: r-lib/actions/pr-push@master | |
| with: | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| document: | |
| if: (startsWith(github.event.comment.body, '/style') || startsWith(github.event.comment.body, '/document')) | |
| runs-on: ubuntu-latest | |
| container: pecan/depends:develop | |
| steps: | |
| - name: work around https://github.com/actions/checkout/issues/766 | |
| run: git config --global --add safe.directory "$GITHUB_WORKSPACE" | |
| - uses: actions/checkout@v4 | |
| with: | |
| set-safe-directory: false | |
| - uses: r-lib/actions/pr-fetch@v1 | |
| with: | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: update dependency lists | |
| run: Rscript scripts/generate_dependencies.R | |
| - name: install any new dependencies | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| working-directory: docker/depends | |
| run: Rscript pecan.depends.R | |
| - id: file_changes | |
| uses: trilom/file-changes-action@v1.2.4 | |
| - name : make | |
| shell: bash | |
| env: | |
| FILES: ${{ join(fromJSON(steps.file_changes.outputs.files_modified), ' ') }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| echo ${FILES} \ | |
| | tr ' ' '\n' \ | |
| | grep -e base -e models -e modules \ | |
| | cut -d / -f 1-2 \ | |
| | sort \ | |
| | uniq \ | |
| | xargs -n1 -I{} make .doc/{} | |
| - name: commit | |
| run: | | |
| git config --global user.email "pecan_bot@example.com" | |
| git config --global user.name "PEcAn stylebot" | |
| git add \*.Rd \*NAMESPACE Makefile.depends docker/depends/pecan_package_dependencies.R docker/depends/pecan_deps_from_github.txt | |
| if [ "$(git diff --name-only --cached)" != "" ]; then git commit -m 'automated documentation update' ; fi | |
| - uses: r-lib/actions/pr-push@master | |
| with: | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} |