targets #1405
This file contains hidden or 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
| # classic | |
| # MIT License | |
| # Copyright (c) 2021 Eli Lilly and Company | |
| # Author: William Michael Landau (will.landau at gmail) | |
| # 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 | |
| - 2025_website | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| schedule: | |
| # - cron: '1 0 * * 0' #every sunday just after midnight | |
| - cron: '0 0 * * *' #daily at midnight | |
| name: targets | |
| jobs: | |
| targets: | |
| runs-on: ubuntu-latest | |
| container: adamwilsonlab/emma:latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GH_PAT_BSM }} | |
| # RENV_PATHS_ROOT: ~/.local/share/renv | |
| steps: | |
| - name: Extract branch name | |
| shell: bash | |
| run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})" | |
| id: extract_branch | |
| # - name: Maximize build space | |
| # uses: easimon/maximize-build-space@master # https://github.com/easimon/maximize-build-space | |
| # with: | |
| # # root-reserve-mb: 512 | |
| # # swap-size-mb: 1024 | |
| # remove-dotnet: 'true' | |
| # remove-android: 'true' | |
| # remove-haskell: 'true' | |
| - uses: actions/checkout@v4 | |
| with: | |
| lfs: 'true' | |
| fetch-depth: 0 # added | |
| - name: Whitelist directory | |
| run: git config --global --add safe.directory /__w/emma_report/emma_report | |
| - name: Checkout LFS objects | |
| run: git lfs checkout | |
| continue-on-error: true | |
| - name: Install R Package Dependencies | |
| run: |- | |
| Rscript -e "update.packages(ask = FALSE)" | |
| Rscript -e "install.packages('geotargets', repos = c('https://ropensci.r-universe.dev', 'https://cran.r-project.org'))" | |
| Rscript -e "questionr::qscan(list.files(pattern='*.R',recursive=T), load = TRUE, detail = TRUE)" # this scans all scripts and installs any needed packages | |
| #- name: Authorize Github for R | |
| # run: |- | |
| # - name: Cache packages | |
| # uses: actions/cache@v1 | |
| # with: | |
| # path: ${{ env.RENV_PATHS_ROOT }} | |
| # key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }} | |
| # restore-keys: ${{ runner.os }}-renv- | |
| # - name: Restore packages | |
| # shell: Rscript {0} | |
| # run: | | |
| # if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv") | |
| # renv::restore() | |
| - name: Check if previous runs exists | |
| id: runs-exist | |
| run: git ls-remote --exit-code --heads origin ${{ steps.extract_branch.outputs.branch }}-runs | |
| continue-on-error: true | |
| - name: Checkout previous run | |
| if: steps.runs-exist.outcome == 'success' | |
| uses: actions/checkout@v2 | |
| with: | |
| ref: ${{ steps.extract_branch.outputs.branch }}-runs | |
| fetch-depth: 1 | |
| path: .${{ steps.extract_branch.outputs.branch }}-runs | |
| ## This restore output is temporarily uncommented while debugging runs | |
| # - name: Restore output files from the previous run | |
| # if: steps.runs-exist.outcome == 'success' | |
| # run: | | |
| # for (dest in scan(".${{ steps.extract_branch.outputs.branch }}-runs/.targets-files", what = character())) { | |
| # source <- file.path(".${{ steps.extract_branch.outputs.branch }}-runs", dest) | |
| # if (!file.exists(dirname(dest))) dir.create(dirname(dest), recursive = TRUE) | |
| # if (file.exists(source)) file.rename(source, dest) | |
| # } | |
| # shell: Rscript {0} | |
| # - name: Run targets pipeline | |
| # run: targets::tar_make(callr_function = NULL) | |
| # shell: Rscript {0} | |
| # - name: Identify files that the targets pipeline produced | |
| # run: git ls-files -mo --exclude=renv > .targets-files | |
| - name: Run targets pt 1 | |
| run: | | |
| Sys.setenv(HOME="/home/rstudio") | |
| cmdstanr::set_cmdstan_path("/home/rstudio/.cmdstanr/cmdstan-2.28.1") | |
| cmdstanr::check_cmdstan_toolchain() | |
| #cmdstanr::install_cmdstan() | |
| shell: Rscript {0} | |
| - name: Verify credentials | |
| run: | | |
| pwd | |
| ls | |
| ./.github/decrypt_secret.sh | |
| ls ~/.config/earthengine | |
| earthengine -h | |
| env: | |
| RGEE_SECRET: ${{ secrets.RGEE_SECRET }} | |
| continue-on-error: true | |
| # - name: check on files | |
| # run: | | |
| # file data/raw_data/ndvi_modis/2021_12_19.tif | |
| # file data/raw_data/ndvi_modis/2022_01_01.tif | |
| # continue-on-error: true | |
| - name: Run targets pt 2 | |
| run: | | |
| targets::tar_destroy(destroy = "all",ask = FALSE) | |
| targets::tar_make() | |
| shell: Rscript {0} | |
| - name: Create the runs branch if it does not already exist | |
| if: steps.runs-exist.outcome != 'success' | |
| run: git checkout --orphan ${{ steps.extract_branch.outputs.branch }}-runs | |
| - name: Put the worktree in the runs branch if the latter already exists | |
| if: steps.runs-exist.outcome == 'success' | |
| run: | | |
| rm -r .git | |
| mv .${{ steps.extract_branch.outputs.branch }}-runs/.git . | |
| rm -r .${{ steps.extract_branch.outputs.branch }}-runs | |
| - name: Upload latest run | |
| run: | | |
| git config --local user.name "GitHub Actions" | |
| git config --local user.email "[email protected]" | |
| rm -r .github/workflows # .gitignore | |
| git lfs track _targets/objects/* #use git LFS to track the targets output (larger files) | |
| # git lfs track "data/**" | |
| git add --all -- ':!renv' | |
| for file in $(git ls-files -mo --exclude=renv) | |
| do | |
| git add -f $file | |
| done | |
| git commit -am "Run pipeline" | |
| git push origin ${{ steps.extract_branch.outputs.branch }}-runs | |
| # - name: Upload latest run (commit & push to <branch>-runs) | |
| # run: | | |
| # git config --local user.name "GitHub Actions" | |
| # git config --local user.email "[email protected]" | |
| # rm -r .github/workflows | |
| # if [ -f .gitattributes ]; then | |
| # git add .gitattributes | |
| # git add --renormalize . | |
| # fi | |
| # git add --all -- ':!renv' | |
| # # for file in $(git ls-files -mo --exclude-standard -- ':!:renv/*'); do | |
| # # git add -f "$file" || true | |
| # # done | |
| # for file in $(git ls-files -moi --exclude-standard -- _targets/ data/ ':!:renv/*'); do | |
| # git add -f "$file" || true | |
| # done | |
| # git commit -m "Run pipeline" || echo "Nothing to commit" | |
| # git push origin ${{ steps.extract_branch.outputs.branch }}-runs | |
| - name: Prepare failure artifact | |
| if: failure() | |
| run: rm -rf .git .github .targets-files .${{ steps.extract_branch.outputs.branch }}-runs | |
| - name: Post failure artifact | |
| if: failure() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
| path: . |