try sharing whole environment #42
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| name: download occurrence cube | ||
| on: | ||
| workflow_dispatch: # Manual | ||
| push: | ||
| branches: # Changes to GRIIS Checklist | ||
| - "uat" | ||
| paths: | ||
| - "data/output/UAT_processing/data_input_checklist_indicators.tsv" | ||
| schedule: | ||
| - cron: '0 0 1 1-12 *' # 1st of the month 00:00 between january & december | ||
| env: | ||
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | ||
| GITHUB_TOKEN: ${{ secrets.AUTOMATISATION }} | ||
| amiabot: ${{ secrets.AMIABOT }} | ||
| jobs: | ||
| setup-environment: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| fetch-depth: 0 | ||
| token: ${{ secrets.AUTOMATISATION }} | ||
| - name: Set up environment | ||
| run: | | ||
| echo "R_LIBS_USER=$HOME/.local/share/R" >> $GITHUB_ENV | ||
| echo "GITHUB_TOKEN=${{ secrets.AUTOMATISATION }}" >> $GITHUB_ENV | ||
| echo "amiabot=${{ secrets.AMIABOT }}" >> $GITHUB_ENV | ||
| - name: Setup R | ||
| uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| r-version: 'release' | ||
| - name: Setup pandoc | ||
| uses: r-lib/actions/setup-pandoc@v2 | ||
| - name: Install linux libraries | ||
| run: | | ||
| sudo apt update | ||
| sudo apt install -y libsodium-dev libcurl4-openssl-dev libgdal-dev libproj-dev libudunits2-dev libharfbuzz-dev libfribidi-dev | ||
| - name: Install R packages | ||
| run: | | ||
| source("src/get_cubes/install_packages_cube_base.R") | ||
| source("src/get_cubes/install_packages_cube_extra.R") | ||
| shell: Rscript {0} | ||
| - name: Save environment | ||
| run: | | ||
| mkdir -p $HOME/environment | ||
| env > $HOME/environment/env_vars.txt | ||
| dpkg -l > $HOME/environment/installed_packages.txt | ||
| R -e "installed.packages()" > $HOME/environment/r_packages.txt | ||
| - name: Upload environment | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: environment | ||
| path: $HOME/environment | ||
| build-queries: | ||
| needs: setup-environment | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| with: | ||
| fetch-depth: 0 | ||
| token: ${{ secrets.AUTOMATISATION }} | ||
| - name: Download environment | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| name: environment | ||
| path: $HOME/environment | ||
| - name: Restore environment | ||
| run: | | ||
| set -a | ||
| source $HOME/environment/env_vars.txt | ||
| set +a | ||
| - name: create queries | ||
| run: source("src/get_cubes/run_build_queries.R") | ||
| shell: Rscript {0} | ||
| - name: upload queries | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| path: ./data/interim/cube_queries/* | ||
| download-cubes: | ||
| needs: build-queries | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| gbif_user: ${{ secrets.GBIF_USER }} | ||
| email: ${{ secrets.GBIF_EMAIL }} | ||
| gbif_pwd: ${{ secrets.GBIF_PWD }} | ||
| strategy: | ||
| matrix: | ||
| param_value: ["FAMILY", "GENUS", "SPECIES", "SUBSPECIES_FORM_VARIETY", "CLASS"] | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| with: | ||
| fetch-depth: 0 | ||
| token: ${{ secrets.AUTOMATISATION }} | ||
| - name: Download environment | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| name: environment | ||
| path: $HOME/environment | ||
| - name: Restore environment | ||
| run: | | ||
| set -a | ||
| source $HOME/environment/env_vars.txt | ||
| set +a | ||
| - name: download queries | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| path: ./data/interim/cube_queries/* | ||
| - name: download cubes | ||
| run: | | ||
| Rscript -e "rmarkdown::render('src/get_cubes/download_cubes.Rmd', params = list(rank = '${{ matrix.param_value }}'), knit_root_dir = '../../')" | ||
| - name: Upload cube artifact | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: ${{ matrix.param_value == 'CLASS' && 'be_classes_cube_raw' || format('be_alientaxa_cube_{0}', matrix.param_value) }}.csv | ||
| path: ./cube_data/ | ||
| compile-cubes: | ||
| needs: download-cubes | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| with: | ||
| fetch-depth: 0 | ||
| token: ${{ secrets.AUTOMATISATION }} | ||
| - name: Download environment | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| name: environment | ||
| path: $HOME/environment | ||
| - name: Restore environment | ||
| run: | | ||
| set -a | ||
| source $HOME/environment/env_vars.txt | ||
| set +a | ||
| - name: download rank cubes artifacts | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| pattern: be_alientaxa_cube_* | ||
| merge-multiple: true | ||
| path: ./cube_data/ | ||
| - name: compile cubes | ||
| run: source("src/get_cubes/run_compile_cubes.R") | ||
| shell: Rscript {0} | ||
| - name: upload occ cube | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: be_alientaxa_cube.csv | ||
| path: ./cube_data/be_alientaxa_cube.csv | ||
| compile-class-cube: | ||
| needs: download-cubes | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| with: | ||
| fetch-depth: 0 | ||
| token: ${{ secrets.AUTOMATISATION }} | ||
| - name: Download environment | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| name: environment | ||
| path: $HOME/environment | ||
| - name: Restore environment | ||
| run: | | ||
| set -a | ||
| source $HOME/environment/env_vars.txt | ||
| set +a | ||
| - name: download class cube artifact | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| pattern: be_classes_cube_raw | ||
| merge-multiple: true | ||
| path: ./cube_data/ | ||
| - name: compile class cube | ||
| run: source("src/get_cubes/run_compile_class_cube.R") | ||
| shell: Rscript {0} | ||
| - name: upload class cube | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: be_classes_cube.csv | ||
| path: ./cube_data/be_classes_cube.csv | ||
