targets #4196
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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 | |
| - dev-jiyeon | |
| # 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-24.04 #ubuntu-22.04 | |
| container: adamwilsonlab/emma:latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| RENV_PATHS_ROOT: ~/.local/share/renv | |
| ACTIONS_RUNNER_DEBUG: true | |
| PYTHONPATH: /opt/conda/envs/r-reticulate/bin/python | |
| RETICULATE_PYTHON: /opt/conda/envs/r-reticulate/bin/python | |
| # GARGLE_AUTH_FILE: secrets/ee-wilsonlab-emma-ef416058504a.json | |
| GOOGLE_APPLICATION_CREDENTIALS: secrets/ee-wilsonlab-emma-ef416058504a.json | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| ref: main | |
| 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: List files in scratch_code | |
| # run: ls -lh scratch_code/ | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: '3.x' | |
| # - name: Install Python Dependencies | |
| # run: | | |
| # pip install earthengine-api | |
| # pip install -r requirements.txt # If you have other dependencies listed in a requirements file | |
| # - name: Verify Python Installation | |
| # run: | | |
| # python -m pip show earthengine-api | |
| # python -c "import ee; print(ee.__version__)" | |
| # # - name: Install Linux system dependencies | |
| # # if: runner.os == 'Linux' | |
| # # run: | | |
| # # sudo apt-get update | |
| - name: Install Google Cloud SDK in container | |
| run: | | |
| apt-get update | |
| apt-get install -y curl apt-transport-https ca-certificates gnupg | |
| echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] https://packages.cloud.google.com/apt cloud-sdk main" \ | |
| | tee /etc/apt/sources.list.d/google-cloud-sdk.list | |
| curl https://packages.cloud.google.com/apt/doc/apt-key.gpg \ | |
| | apt-key --keyring /usr/share/keyrings/cloud.google.gpg add - | |
| apt-get update | |
| apt-get install -y google-cloud-cli=492.0.0-0 | |
| - name: DECRYPT rgee SECRETS | |
| run: ./.github/decrypt_secret.sh | |
| env: | |
| RGEE_SECRET: ${{ secrets.RGEE_SECRET }} | |
| continue-on-error: true | |
| # - name: List files in secrets | |
| # run: ls -lh secrets/ | |
| # - name: Check git settings | |
| # run: | |
| # git config --get http.postBuffer | |
| # continue-on-error: true | |
| # - name: Display Service Account JSON | |
| # run: | | |
| # echo "=== Service Account JSON ===" | |
| # cat secrets/ee-wilsonlab-emma-ef416058504a.json | |
| # echo "============================" | |
| - name: Install Earth Engine API 1.5.4 in r-reticulate env | |
| run: | | |
| /opt/conda/envs/r-reticulate/bin/pip install --upgrade earthengine-api==0.1.370 #0.1.381 | |
| # conda install -n r-reticulate -y -c conda-forge earthengine-api=1.5.4 | |
| - name: Verify EE API version | |
| run: | | |
| /opt/conda/envs/r-reticulate/bin/pip show earthengine-api | |
| - name: Install R Package Dependencies | |
| run: |- | |
| Rscript -e "questionr::qscan(list.files(pattern='*.R',recursive=T), load = TRUE, detail = TRUE)" # this scans all scripts and installs any needed packages | |
| # - name: Upgrade rgee to latest from GitHub | |
| # run: | | |
| # Rscript -e "if (!requireNamespace('devtools', quietly = TRUE)) install.packages('devtools')" | |
| # Rscript -e 'devtools::install_github("r-spatial/rgee", ref="v.1.1.5")' | |
| # - name: Install rgee v1.1.5 from CRAN Archive | |
| # run: | | |
| # Rscript -e 'if (!requireNamespace("remotes", quietly=TRUE)) install.packages("remotes", repos="https://cloud.r-project.org")' | |
| # Rscript -e 'remotes::install_version("rgee", version="1.1.5", repos="https://cloud.r-project.org")' | |
| - name: Install rgee from bmaitner/rgee | |
| run: Rscript -e 'devtools::install_github(repo = "bmaitner/rgee", ref = "noninteractive_auth")' | |
| - name: Parse _targets.R | |
| run: Rscript -e "parse('_targets.R')" | |
| - name: Cache packages | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.RENV_PATHS_ROOT }} | |
| key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }} | |
| restore-keys: ${{ runner.os }}-renv- | |
| - name: Authenticate to GCP | |
| run: | | |
| # write the JSON secret to disk | |
| # activate the service account (no --scopes flag) | |
| gcloud auth activate-service-account \ | |
| --key-file="secrets/ee-wilsonlab-emma-ef416058504a.json" \ | |
| --project=ee-wilsonlab-emma \ | |
| --quiet | |
| - name: Add r-reticulate env to PATH | |
| run: echo "/opt/conda/envs/r-reticulate/bin" >> $GITHUB_PATH | |
| # - name: Authenticate Earth Engine | |
| # run: earthengine authenticate \ | |
| # --service_account \ | |
| # --quiet \ | |
| # #--key_file=${{ runner.temp }}/gee-key.json | |
| # - name: Authenticate to GCP (ADC with scopes) | |
| # run: | | |
| # gcloud auth application-default login \ | |
| # --project=ee-wilsonlab-emma \ | |
| # --scopes=https://www.googleapis.com/auth/cloud-platform \ | |
| # --quiet | |
| # - 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: Find credential JSON | |
| # run: | | |
| # echo "Searching for ee-wilsonlab-emma-ef416058504a.json ..." | |
| # find / -name 'ee-wilsonlab-emma-ef416058504a.json' 2>/dev/null || true | |
| # - 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 | |
| # /usr/bin/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: ${{ secrets.GD_SECRET }} | |
| continue-on-error: true | |
| # - name: Install custom rgee | |
| # run: | | |
| # # added below on april 9 from https://github.com/r-spatial/rgee/issues/353#issuecomment-1983765552 | |
| # library(reticulate) | |
| # py_config() # see the name of your conda (python) environment, in my case "r-reticulate" | |
| # reticulate::py_install('earthengine-api==0.1.370', envname='r-reticulate') | |
| # # Check the installation of "earthengine-api" with | |
| # py_list_packages() | |
| # pyl <- py_list_packages() | |
| # pyl[pyl$package == "earthengine-api", ] | |
| # # check python version with | |
| # py_run_string("import sys; print(sys.version)") | |
| # devtools::install_github(repo = "bmaitner/rgee", ref = "noninteractive_auth") | |
| # - name: Install custom rgee | |
| # run: | | |
| # Rscript -e "library(reticulate)" | |
| # Rscript -e "reticulate::py_install('earthengine-api==0.1.370', envname='r-reticulate')" | |
| # Rscript -e "pyl <- py_list_packages(); print(pyl[pyl$package == 'earthengine-api', ])" | |
| # Rscript -e "reticulate::py_run_string('import sys; print(sys.version)')" | |
| # Rscript -e "devtools::install_github(repo = 'bmaitner/rgee', ref = 'noninteractive_auth')" | |
| # shell: Rscript {0} | |
| # - name: Print environment | |
| # run: env | |
| # - name: Print R session info | |
| # run: Rscript -e 'sessionInfo()' | |
| # - name: “Set up gcloud CLI” | |
| # uses: google-github-actions/setup-gcloud@v1 | |
| # with: | |
| # project_id: ${{ secrets.GCP_PROJECT }} | |
| # service_account_key: ${{ secrets.GCP_SA_KEY }} | |
| - name: Run targets pt 2 | |
| run: | | |
| #reticulate::use_python('/usr/bin/python3') | |
| #rgee::ee_set_pyenv('/usr/bin/python3','r-reticulate', confirm = F) | |
| #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 "[email protected]" | |
| 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: . |