targets #3396
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
| # MIT License | |
| # Copyright (c) 2021 Eli Lilly and Company | |
| # Author: William Michael Landau (will.landau at gmail) | |
| # Edited by Adam Wilson (adamw at buffalo) | |
| # 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 | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| schedule: | |
| # - cron: '1 0 * * 0' # runs every Sunday at 00:01 | |
| - cron: '0 0 * * *' # runs every day at midnight | |
| # - cron: '0 */6 * * *' # run every 6th hour | |
| name: targets | |
| jobs: | |
| targets: | |
| runs-on: ubuntu-latest | |
| container: adamwilsonlab/emma:latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| RENV_PATHS_ROOT: ~/.local/share/renv | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| lfs: 'true' | |
| - name: Whitelist directory | |
| run: git config --global --add safe.directory /__w/emma_envdata/emma_envdata | |
| - name: Checkout LFS objects | |
| run: git lfs checkout | |
| continue-on-error: true | |
| # # - name: Install Linux system dependencies | |
| # # if: runner.os == 'Linux' | |
| # # run: | | |
| # # sudo apt-get update | |
| # - name: DECRYPT rgee SECRETS | |
| # run: ./.github/decrypt_secret.sh | |
| # env: | |
| # RGEE_SECRET: ${{ secrets.RGEE_SECRET }} | |
| # continue-on-error: true | |
| # - name: Check git settings | |
| # run: | |
| # git config --get http.postBuffer | |
| # continue-on-error: true | |
| - name: Install R Package Dependencies | |
| run: |- | |
| Rscript -e "questionr::qscan(list.files(pattern='*.R',recursive=T), load = TRUE, detail = FALSE)" # this scans all scripts and installs any needed packages | |
| Rscript -e "remotes::install_github('ROpenSci/bibtex')" | |
| - 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 targets-runs | |
| continue-on-error: true | |
| - name: Checkout previous run | |
| if: steps.runs-exist.outcome == 'success' | |
| uses: actions/checkout@v2 | |
| with: | |
| ref: targets-runs | |
| fetch-depth: 1 | |
| path: .targets-runs | |
| lfs: 'true' #attempting to fix issue with target-committed lfs files not being treated as lfs | |
| - name: Restore output files from the previous run | |
| if: steps.runs-exist.outcome == 'success' | |
| run: | | |
| for (dest in scan(".targets-runs/.targets-files", what = character())) { | |
| source <- file.path(".targets-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: | | |
| # Sys.setenv(HOME="/home/rstudio") | |
| # cmdstanr::set_cmdstan_path("/home/rstudio/.cmdstanr/cmdstan-2.28.1") | |
| # cmdstanr::check_cmdstan_toolchain() | |
| # #cmdstanr::install_cmdstan() | |
| # targets::tar_make() | |
| # shell: Rscript {0} | |
| - 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: | | |
| ./.github/decrypt_secret.sh | |
| ls ~/.config/earthengine | |
| earthengine -h | |
| echo " main dir" | |
| ls | |
| echo "scratch dir" | |
| ls scratch_code | |
| echo "secrets dir" | |
| ls secrets | |
| env: | |
| RGEE_SECRET: ${{ secrets.RGEE_SECRET }} | |
| GD_SECRET: ${{ secrets.GD_SECRET }} | |
| continue-on-error: true | |
| - name: Install custom rgee | |
| run: | | |
| devtools::install_github(repo = "bmaitner/rgee", | |
| ref = "noninteractive_auth") | |
| shell: Rscript {0} | |
| - name: Run targets pt 2 | |
| run: | | |
| #targets::tar_destroy(destroy = "all",ask = FALSE) #uncomment to reset | |
| targets::tar_make() | |
| shell: Rscript {0} | |
| - name: Identify files that the targets pipeline produced | |
| run: git ls-files -mo --exclude=renv > .targets-files | |
| - name: Create the runs branch if it does not already exist | |
| if: steps.runs-exist.outcome != 'success' | |
| run: git checkout --orphan targets-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 .targets-runs/.git . | |
| rm -r .targets-runs | |
| - name: update md | |
| run: | | |
| webshot::install_phantomjs() | |
| knitr::knit("README.Rmd") | |
| shell: Rscript {0} | |
| - name: Upload latest run | |
| run: | | |
| git config --local user.name "GitHub Actions" | |
| git config --local user.email "actions@github.com" | |
| rm -r .gitignore .github/workflows | |
| git lfs track _targets/objects/* #use git LFS to track the targets output (larger files) | |
| git lfs track data/raw_data/* | |
| git lfs track data/* #use git LFS to track the data output (larger files) | |
| git lfs track "raw_data/**" #use git LFS to track raw_data output (larger files) | |
| git lfs track "data/**" | |
| git lfs track _targets/metadata/* #track metadata | |
| git lfs track *.tif | |
| git add .gitattributes | |
| git add --all -- ':!renv' ':!*json' | |
| for file in $(git ls-files ':!*.json' -mo --exclude=renv) | |
| do | |
| git add -f $file | |
| done | |
| git commit -am "Run pipeline" | |
| git push origin targets-runs | |
| # Move the loop below up two lines (after git add) to commit large files. | |
| - name: Prepare failure artifact | |
| if: failure() | |
| run: rm -rf .git .github .targets-files .targets-runs | |
| - name: Post failure artifact | |
| if: failure() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
| path: . |