Merge pull request #2867 from robkooper/release/1.7.2

Release/1.7.2

.dockerignore

@@ -1,10 +1,18 @@
+# ignore git folder
 .git
 
+# ignore .install, need own version in docker
 .install
 
+# ignore packrat lib/src folders, others might be needed
+*/*/packrat/lib*/
+*/*/packrat/src/
+
+# ignore tests and contrib folder
 tests
 contrib
 
+# ignore compiled files from rtm
 modules/rtm/src/RTM/*.o
 modules/rtm/src/RTM/*/*.o
 modules/rtm/src/RTM/*/*/*.o

.github/ISSUE_TEMPLATE/Doc_changes.md

@@ -13,6 +13,6 @@ There is a broken URL link in the documentation. It is in the master version in
 
 ### Information for those wanting to make changes
 
-Please follow the instructions in the [Editing this Book](https://pecanproject.github.io/pecan-documentation/develop/bookediting.html) section of the documentation. 
+Please follow the instructions in the [Editing this Book](https://pecanproject.github.io/pecan-documentation/develop/about-the-pecan-book.html#bookediting) section of the documentation. 
 
-All R-markdown files related to documentation are located within the main directory `/pecan/book_source` except for the demos and vignettes which are in `pecan/documentation/tutorials`.
+All R-markdown files related to documentation are located within the main directory `/pecan/book_source` except for the demos and vignettes which are in `pecan/documentation/tutorials`.

.github/workflows/book.yml

@@ -0,0 +1,68 @@
+name: renderbook
+
+on:
+  push:
+    branches:
+      - master
+      - develop
+
+    tags:
+      - '*'
+
+  pull_request:
+
+jobs:
+  bookdown:
+    runs-on: ubuntu-latest  
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    container: 
+      image: pecan/depends:R4.0.3
+
+    steps:
+    # checkout source code
+    - uses: actions/checkout@v2
+    # install rmarkdown
+    - name: Install rmarkdown
+      run: |
+        Rscript -e 'install.packages(c("rmarkdown","bookdown"))'
+    # copy files
+    - name: copy extfiles
+      run: |
+        mkdir -p book_source/extfiles
+        cp -f documentation/tutorials/01_Demo_Basic_Run/extfiles/* book_source/extfiles
+    # compile PEcAn code
+    - name: build
+      run: make -j1
+    # render book
+    - name: Render Book
+      run: |
+        cd book_source
+        Rscript -e 'options(bookdown.render.file_scope=FALSE); bookdown::render_book("index.Rmd", "bookdown::gitbook")'
+    # save artifact
+    - uses: actions/upload-artifact@v2
+      with:
+        name: pecan-documentation
+        path: book_source/_book/
+    # download documentation repo
+    - name: Checkout documentation repo
+      if: github.event_name != 'pull_request'
+      uses: actions/checkout@v2
+      with:
+        repository: ${{ github.repository_owner }}/pecan-documentation
+        path: pecan-documentation
+        token: ${{ secrets.GH_PAT }}
+    # upload new documentation
+    - name: publish to github
+      if: github.event_name != 'pull_request'
+      run: |
+        git config --global user.email "[email protected]"
+        git config --global user.name "GitHub Documentation Robot"
+        export VERSION=${GITHUB_REF##*/}
+        cd pecan-documentation
+        mkdir -p $VERSION
+        rsync -a --delete ../book_source/_book/ ${VERSION}/
+        git add --all *
+        git commit -m "Build book from pecan revision ${GITHUB_SHA}" || true
+        git push -q origin master

.github/workflows/ci.yml

@@ -0,0 +1,223 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - master
+      - develop
+
+    tags:
+      - '*'
+
+  pull_request:
+
+  issue_comment:
+    types:
+      - created
+
+env:
+  R_LIBS_USER: /usr/local/lib/R/site-library
+  LC_ALL: en_US.UTF-8
+  NCPUS: 2
+  PGHOST: postgres
+  CI: true
+
+jobs:
+
+  # ----------------------------------------------------------------------
+  # R BUILD
+  # ----------------------------------------------------------------------
+  build:
+    if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build')
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        R:
+          - "4.0.3"
+          - "4.0.4"
+
+    container: 
+      image: pecan/depends:R${{ matrix.R }}
+
+    steps:
+    # checkout source code
+    - uses: actions/checkout@v2
+
+    # install additional tools needed
+    - name: install utils
+      run: apt-get update && apt-get install -y postgresql-client qpdf curl
+
+    # check dependencies
+    - name: update dependency lists
+      run: Rscript scripts/generate_dependencies.R
+    - name: check for out-of-date dependencies files
+      uses: infotroph/tree-is-clean@v1
+    - name: install newly-added dependencies
+      run: Rscript docker/depends/pecan.depends.R
+
+    # compile PEcAn code
+    - name: build
+      run: make -j1
+    - name: check for out-of-date files
+      uses: infotroph/tree-is-clean@v1
+
+  # ----------------------------------------------------------------------
+  # R TEST
+  # ----------------------------------------------------------------------
+  test:
+    if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build')
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        R:
+          - "4.0.3"
+          - "4.0.4"
+
+    services:
+      postgres:
+        image: mdillon/postgis:9.5
+        options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
+
+    container: 
+      image: pecan/depends:R${{ matrix.R }}
+
+    steps:
+    # checkout source code
+    - uses: actions/checkout@v2
+
+    # install additional tools needed
+    - name: install utils
+      run: apt-get update && apt-get install -y postgresql-client qpdf
+    - name: install new dependencies
+      run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R
+
+    # initialize database
+    - name: db setup
+      uses: docker://pecan/db:ci
+    - name: add models to db
+      run: ./scripts/add.models.sh
+
+    # run PEcAn tests
+    - name: test
+      run: make -j1 test
+    - name: check for out-of-date files
+      uses: infotroph/tree-is-clean@v1
+
+  # ----------------------------------------------------------------------
+  # R CHECK
+  # ----------------------------------------------------------------------
+  check:
+    if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build')
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        R:
+          - "4.0.3"
+          - "4.0.4"
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      _R_CHECK_LENGTH_1_CONDITION_: true
+      _R_CHECK_LENGTH_1_LOGIC2_: true
+      # Avoid compilation check warnings that come from the system Makevars
+      # See https://stat.ethz.ch/pipermail/r-package-devel/2019q2/003898.html
+      _R_CHECK_COMPILATION_FLAGS_KNOWN_: -Wformat -Werror=format-security -Wdate-time
+      # Keep R checks from trying to consult the very flaky worldclockapi.com
+      _R_CHECK_SYSTEM_CLOCK_: 0
+
+    container: 
+      image: pecan/depends:R${{ matrix.R }}
+
+    steps:
+    # checkout source code
+    - uses: actions/checkout@v2
+
+    # install additional tools needed
+    - name: install utils
+      run: apt-get update && apt-get install -y postgresql-client qpdf
+    - name: install new dependencies
+      run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R
+    # need processx > 3.5.2 to avoid cryptic errors from
+    # https://github.com/r-lib/rcmdcheck/issues/140
+    # Remove when https://github.com/r-lib/processx/pull/299 reaches CRAN
+    - name: update processx
+      run: Rscript -e 'devtools::install_github("r-lib/processx")'
+
+    # run PEcAn checks
+    - name: check
+      run: make -j1 check
+      env:
+        REBUILD_DOCS: "FALSE"
+        RUN_TESTS: "FALSE"
+    - name: check for out-of-date files
+      uses: infotroph/tree-is-clean@v1
+
+
+  # ----------------------------------------------------------------------
+  # SIPNET TESTS
+  # ----------------------------------------------------------------------
+  sipnet:
+    if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build')
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        R:
+          - "4.0.3"
+          - "4.0.4"
+
+    services:
+      postgres:
+        image: mdillon/postgis:9.5
+        options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
+
+    container: 
+      image: pecan/depends:R${{ matrix.R }}
+
+    steps:
+    # checkout source code
+    - uses: actions/checkout@v2
+
+    # install additional tools needed
+    - name: install utils
+      run: apt-get update && apt-get install -y postgresql-client qpdf
+    - name: install new dependencies
+      run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R
+
+    # initialize database
+    - name: db setup
+      uses: docker://pecan/db:ci
+    - name: add models to db
+      run: ./scripts/add.models.sh
+
+    # install sipnet
+    - name: Check out SIPNET
+      uses: actions/checkout@v2
+      with:
+        repository: PecanProject/sipnet
+        path: sipnet
+    - name: install sipnet
+      run: |
+        cd ${GITHUB_WORKSPACE}/sipnet
+        make
+
+    # compile PEcAn code
+    - name: build
+      run: make -j1
+
+    # run SIPNET test
+    - name: integration test
+      run: ./tests/integration.sh ghaction

.github/workflows/depends.yml

@@ -0,0 +1,76 @@
+name: Docker Depends Image
+
+on:
+  push:
+    branches:
+      - develop
+      - master
+
+  # this runs on the develop branch
+  schedule:
+    - cron: '0 0 * * *'
+
+env:
+  # official supported version of R
+  SUPPORTED: 4.0.3
+  DOCKERHUB_ORG: pecan
+
+jobs:
+  depends:
+    if: github.repository == 'PecanProject/pecan'
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        R:
+          - "4.0.3"
+          - "4.0.4"
+
+    steps:
+      - uses: actions/checkout@v2
+
+      # calculate some variables that are used later
+      - name: github branch
+        run: |
+          BRANCH=${GITHUB_REF##*/}
+          echo "GITHUB_BRANCH=${BRANCH}" >> $GITHUB_ENV
+
+          tags="R${{ matrix.R }}"
+          if [ "${{ matrix.R }}" == "${{ env.SUPPORTED }}" ]; then
+            if [ "$BRANCH" == "master" ]; then
+              tags="${tags},latest"
+            elif [ "$BRANCH" == "develop" ]; then
+              tags="${tags},develop"
+            fi
+          fi
+          echo "TAG=${tags}" >> $GITHUB_ENV
+
+      # this will publish to the actor (person) github packages
+      - name: Publish to GitHub
+        uses: elgohr/[email protected]
+        env:
+          R_VERSION: ${{ matrix.R  }}
+        with:
+          name: ${{ github.repository_owner }}/pecan/depends
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+          context: docker/depends
+          tags: "${{ env.TAG }}"
+          registry: docker.pkg.github.com
+          buildargs: R_VERSION
+
+      # this will publish to the clowder dockerhub repo
+      - name: Publish to Docker Hub
+        uses: elgohr/[email protected]
+        env:
+          R_VERSION: ${{ matrix.R  }}
+        with:
+          name: ${{ env.DOCKERHUB_ORG }}/depends
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+          context: docker/depends
+          tags: "${{ env.TAG }}"
+          buildargs: R_VERSION