targets #3399
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| # 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: . |