deployblog #182
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| #........................................................................................................................... | |
| # References: | |
| # - https://github.com/orchid00/actions_sandbox/issues/41#issuecomment-816970613 | |
| # - https://github.com/murraycadzow/test_blogdown/blob/master/.github/workflows/deploy_blogdown.yml | |
| # - https://blog--simonpcouch.netlify.app/blog/r-github-actions-commit/ | |
| # - https://github.com/simonpcouch/scheduled-commit-action/blob/master/.github/workflows/schedule-commit.yaml | |
| # - https://github.community/t/github-actions-bot-email-address/17204 | |
| # - https://www.etiennebacher.com/posts/2021-03-19-use-github-actions-with-r-markdown-and-distill/ | |
| # - https://github.com/pbatey/flexdashboard-example | |
| # - https://ramikrispin.github.io/2020/09/deploying-flexdashboard-on-github-pages/ | |
| # | |
| # It is also possible to create a "single" (not a multi-page) Github Pages by including | |
| # - a 'docs' directory in the root of the repository | |
| # - by converting the .Rmd to .html then rename the .html file to 'index.html' and adding the 'index.html' to 'docs' | |
| # - by including a '.nojekyll' file inside the 'docs' directory | |
| # then just push to github. Reference: | |
| # https://jupyterbook.org/publish/gh-pages.html#option-1-copy-and-paste-your-books-build-contents-into-a-new-folder | |
| #........................................................................................................................... | |
| #................................................................................................ | |
| # run a cron-job every week (say, on Sunday at 23:00 pm | |
| # The time difference between UTC and EEST - my current time zone - is 3 hours: | |
| # | |
| # https://crontab.guru/examples.html | |
| # https://docs.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events# | |
| # https://upptime.js.org/blog/2021/01/22/github-actions-schedule-not-working/ | |
| #................................................................................................ | |
| on: | |
| schedule: | |
| - cron: "0 23 * * SUN" | |
| push: | |
| branches: master | |
| #............................................................................................................................................. | |
| # Create every week an updated .Rmd file (including the .Rds data) and push these files to a separate directory of the "/content/post" folder | |
| # Before building the 'hugo' website use "build_rmd = TRUE" otherwise the index of website won't be built, see: | |
| # https://github.com/rstudio/blogdown/blob/master/NEWS.md#new-features-3 | |
| # since blogdown version==0.21 the blogdown::build_site() no longer recompiles R Markdown files by default | |
| # For major Changes in Blogdown (especially from version >=0.21), see: https://github.com/rstudio/blogdown/blob/master/NEWS.md | |
| # | |
| # To commit and push the changes I use the default setting of the github actions repo | |
| # Because I received an error I've added "${{ github.event.pull_request.head.ref }}" | |
| # | |
| # The "asc_desc_linestring" parameter must be one of the following: | |
| # - an empty string ( "" ). In this case a sinle color Linestring will be plotted | |
| # - a boolean in form of a character ('TRUE' or 'FALSE'). If TRUE split in peak of the data | |
| # - a lubridate::hms('17:05:00') object in form of a character string, i.e. "17H 5M 0S" | |
| # The GPS data will be split based on the input lubridate time point | |
| # | |
| # As mentioned in | |
| # https://github.com/aws-actions/configure-aws-credentials/issues/9#issuecomment-569370732 | |
| # the "awscli" is available when using "aws-actions/configure-aws-credentials@v1" | |
| # | |
| # Switch to environment variables for the input parameters as discussed in the next weblinks and make sure that these are character strings: | |
| # https://github.blog/changelog/2019-10-01-github-actions-new-workflow-syntax-features/#env-at-the-workflow-and-job-level | |
| # https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#env | |
| # https://docs.github.com/en/actions/reference/context-and-expression-syntax-for-github-actions#env-context | |
| # https://github.com/actions/starter-workflows/issues/68#issuecomment-538026112 | |
| # https://github.com/actions/starter-workflows/issues/68#issuecomment-524661275 | |
| # | |
| # Using the "working-directory" keyword, I can specify the working directory of where to run the command of a specific step | |
| # It seems that the default path of the working directory was changed before running the step "Fitbit Parameter Setting and Script" | |
| # | |
| # I solved the issue related with the issue ‘No such file or directory’, see: | |
| # https://github.community/t/no-such-file-or-directory-error-when-running-scheduled-github-action/184570 | |
| # | |
| # Regarding the 'DATE' parameter, I had to create an additional step, see also: | |
| # https://github.community/t/how-can-i-set-an-expression-as-an-environment-variable-at-workflow-level/16516/7 | |
| # https://stackoverflow.com/a/64649397/8302386 | |
| #............................................................................................................................................. | |
| name: deployblog | |
| jobs: | |
| blogdown: | |
| name: Render-Blog | |
| runs-on: macOS-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| if: github.event_name == 'pull_request' | |
| with: | |
| fetch-depth: 0 | |
| ref: ${{ github.event.pull_request.head.ref }} | |
| - uses: actions/checkout@v2 | |
| if: github.event_name != 'pull_request' | |
| with: | |
| fetch-depth: 0 | |
| - uses: r-lib/actions/setup-r@v1 | |
| - uses: r-lib/actions/setup-pandoc@v1 | |
| - name: Install XQuartz | |
| run: brew install xquartz | |
| - name: Configure AWS Credentials | |
| uses: aws-actions/configure-aws-credentials@v1 | |
| with: | |
| aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| aws-region: eu-central-1 | |
| # - name: test if awscli is available | |
| # run: aws s3 ls | |
| - name: Install ImageMagick | |
| run: brew install imagemagick | |
| - name: Install udunits | |
| run: brew install udunits | |
| - name: "Install spatial libraries (copied from https://github.com/r-spatial/sf/blob/master/.github/workflows/tic-db.yml#L99)" | |
| run: | | |
| # conflicts with gfortran from r-lib/actions when linking gcc | |
| rm '/usr/local/bin/gfortran' | |
| brew install pkg-config gdal proj geos | |
| - name: Install required packages | |
| run: | | |
| Rscript -e 'install.packages(c("DT", "magick", "glue", "rmarkdown", "remotes"))' | |
| Rscript -e "Sys.setenv(GITHUB_PAT = '${{ secrets.GH_PAT }}'); remotes::install_github(c('rstudio/blogdown'), upgrade = 'always', dependencies = TRUE, repos = 'https://cloud.r-project.org/')" | |
| - name: "Install the Github version of 'rayshader'" | |
| run: Rscript -e "Sys.setenv(GITHUB_PAT = '${{ secrets.GH_PAT }}'); remotes::install_github(c('tylermorganwall/rayshader'), upgrade = 'always', dependencies = TRUE, repos = 'https://cloud.r-project.org/')" | |
| - name: "Install the Github versions of 'CopernicusDEM' and 'fitbitViz'" | |
| run: Rscript -e "Sys.setenv(GITHUB_PAT = '${{ secrets.GH_PAT }}'); remotes::install_github(c('mlampros/CopernicusDEM', 'mlampros/fitbitViz'), upgrade = 'always', dependencies = TRUE, repos = 'https://cloud.r-project.org/')" | |
| - name: install hugo | |
| run: Rscript -e 'blogdown::install_hugo()' | |
| - name: Fitbit DATE parameter (this has to be a separate step) | |
| # run: echo "DATE='2022-02-27'">> $GITHUB_ENV | |
| run: echo "DATE=$(date +'%Y-%m-%d')" >> $GITHUB_ENV | |
| - name: Fitbit Parameter Setting and Script | |
| working-directory: ${{ github.workspace }} | |
| env: | |
| previous_n_days: "6" | |
| sleep_time_begins: "00H 40M 0S" | |
| sleep_time_ends: "08H 00M 0S" | |
| asc_desc_linestring: "" | |
| time_zone: "Europe/Athens" | |
| buffer_meters: "1500" | |
| resolution_dem: "30" | |
| verbose_Rmd: "FALSE" | |
| run: Rscript R_templates/data_template.R ${{ secrets.USER_ID }} ${{ secrets.FITBIT_TOKEN }} ${previous_n_days} ${{ env.DATE }} "${sleep_time_begins}" "${sleep_time_ends}" "${asc_desc_linestring}" ${time_zone} ${buffer_meters} ${resolution_dem} ${verbose_Rmd} | |
| - name: Commit files | |
| run: | | |
| git config --local user.email "actions@github.com" | |
| git config --local user.name "GitHub Actions" | |
| git add --all | |
| git commit -am "add data and .Rmd file" | |
| git push | |
| - name: Render blog | |
| run: Rscript -e 'blogdown::build_site(build_rmd = TRUE)' | |
| - uses: actions/upload-artifact@v1 | |
| with: | |
| name: public | |
| path: public/ | |
| #............................................................................. | |
| # Need to first create an empty gh-pages branch see | |
| # https://pkgdown.r-lib.org/reference/deploy_site_github.html | |
| # and also add secrets for a GH_PAT and EMAIL to the repository gh-action from | |
| # Cecilapp/GitHub-Pages-deploy | |
| #............................................................................. | |
| checkout-and-deploy: | |
| runs-on: ubuntu-latest | |
| needs: blogdown | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@master | |
| - name: Download artifact | |
| uses: actions/download-artifact@v1.0.0 | |
| with: | |
| name: public # Artifact name (optional) | |
| path: public # Destination path (optional) | |
| - name: Deploy to GitHub Pages | |
| uses: Cecilapp/GitHub-Pages-deploy@v3 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GH_PAT }} # https://github.com/settings/tokens | |
| with: | |
| email: ${{ secrets.EMAIL }} | |
| build_dir: public/ # "_site/" by default | |