create full_timeseries.csv #28
Workflow file for this run
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| on: | |
| workflow_dispatch: | |
| push: | |
| branches: | |
| - 'uat' | |
| paths: | |
| - 'data/output/UAT_processing/data_input_checklist_indicators.tsv' | |
| name: create full_timeseries.csv | |
| 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 | |
| sudo apt install --yes libharfbuzz-dev libfribidi-dev | |
| R --no-save -e 'install.packages("devtools")' | |
| R --no-save -e 'devtools::install_github("inbo/INBOtheme@v0.5.9", force = TRUE)' | |
| R --no-save -e 'devtools::install_github("inbo/alien-species-portal@main", | |
| subdir = "alienSpecies", force = TRUE)' | |
| - name: install packages | |
| run: | | |
| source("src/install_packages_occ_indic.R") | |
| shell: Rscript {0} | |
| - name: occ_indic_preprocessing | |
| run: | | |
| source("src/run_occurrence_indicators_preprocessing.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: "update occ_indic_preprocessing" | |
| target_branch: automatic-update-occ_indic_preprocessing | |
| add_timestamp: true | |
| - name: Commit and push changes | |
| uses: devops-infra/action-commit-push@master | |
| with: | |
| github_token: ${{ secrets.AUTOMATISATION }} | |
| commit_prefix: "[AUTO]" | |
| commit_message: "update createTimeseries" | |
| target_branch: automatic-update-occ_indic_preprocessing | |
| add_timestamp: true | |
| - name: Get branch name | |
| run: | | |
| git branch --show-current | |
| - name: Create pull request | |
| uses: devops-infra/action-pull-request@v0.4.2 | |
| with: | |
| github_token: ${{ secrets.AUTOMATISATION }} | |
| target_branch: uat | |
| title: "[AUTO] update occ_indic_preprocessing" | |
| template: .github/PR_occ_indic_preprocessing.md | |
| reviewer: SanderDevisscher | |
| label: automated workflow | |
| get_diff: false |