Merge pull request #96 from inbo/automatic-update-2024-11-18T08-15-54Z #26
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| on: | |
| push: | |
| branches: | |
| - main | |
| paths: | |
| - output/** | |
| workflow_dispatch: | |
| name: dwc-mapping | |
| jobs: | |
| fetch-data: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: ubuntu-latest, r: 'release'} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| GITHUB_TOKEN: ${{ secrets.AUTOMATISATION }} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| token: ${{ secrets.AUTOMATISATION }} | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| - name: Setup pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install linux libraries | |
| run: | | |
| sudo apt install libsodium-dev | |
| sudo apt-get install libcurl4-openssl-dev | |
| sudo apt-get install libgdal-dev libproj-dev | |
| sudo apt install libudunits2-dev | |
| - name: Install R packages | |
| run: | | |
| source("script/install_packages_dwc.R") | |
| shell: Rscript {0} | |
| - name: DWC mapping | |
| run: | | |
| source("script/run_dwc_mapping.R") | |
| shell: Rscript {0} | |
| - name: Commit and push changes | |
| uses: devops-infra/action-commit-push@master | |
| with: | |
| github_token: ${{ secrets.AUTOMATISATION }} | |
| commit_prefix: "[AUTO]" | |
| commit_message: "dwc mapping" | |
| target_branch: automatic-dwc-mapping | |
| - name: DWC mapping bycatch | |
| run: | | |
| source("script/run_dwc_mapping_bycatch.R") | |
| shell: Rscript {0} | |
| - name: Commit and push changes | |
| uses: devops-infra/action-commit-push@master | |
| with: | |
| github_token: ${{ secrets.AUTOMATISATION }} | |
| commit_prefix: "[AUTO]" | |
| commit_message: "dwc mapping bycatch" | |
| - name: DWC join bycatch with catch | |
| run: | | |
| source("script/run_dwc_joinbycatch_catch.R") | |
| shell: Rscript {0} | |
| - name: Commit and push changes | |
| uses: devops-infra/action-commit-push@master | |
| with: | |
| github_token: ${{ secrets.AUTOMATISATION }} | |
| commit_prefix: "[AUTO]" | |
| commit_message: "dwc join bycatch with catch" | |
| - name: Get branch name | |
| run: | | |
| git branch --show-current | |
| - name: Create pull request | |
| uses: devops-infra/[email protected] | |
| with: | |
| github_token: ${{ secrets.AUTOMATISATION }} | |
| target_branch: main | |
| title: "[AUTO] dwc mapping" | |
| template: .github/PR_dwc_mapping.md | |
| reviewer: SanderDevisscher | |
| label: automated workflow | |
| get_diff: false |