Merge pull request #676 from JGCRI/v3_dev

Hector V3

.Rbuildignore

@@ -3,7 +3,7 @@
 ^hector.Rproj$
 ^\.Rproj\.user$
 
-## Github config, license, CI, etc.
+## GitHub config, license, CI, etc.
 ^CONTRIBUTING.md$
 ^LICENSE.md$
 ^changelog.txt$
@@ -18,18 +18,19 @@
 ^project_files$
 ^output$
 ^scripts$
+^scripts/
 ^logs$
 ^test_hector.sh$
 ^src/hector$
 ^src/.*\.txt$
 ^src/.*\.a$
 ^src/.*\.d$
+^.*\.o$
 ^src/main.*$
 ^src/makefile.standalone$
 ^src/testing$
 ^misc$
 ^data-raw$
-^analysis$
 ^.vscode$
 
 # pkgdown config and output
@@ -39,3 +40,11 @@ _pkgdown.yml
 
 # lintr config
 .lintr
+^doc$
+^Meta$
+^vignettes/articles$
+
+# README and similar files
+^CITATION\.cff$
+^CODE_OF_CONDUCT\.md$
+^README\.Rmd$

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,60 @@
+name: R-CMD-check
+# Controls when the action will run.
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - '**' # matches every branch
+
+  schedule:
+    # * is a special character in YAML so you have to quote this string
+    # Launch run at 6am the 1st of every month.
+    - cron:  '0 6 1 * *'
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          args: 'c("--no-manual", "--as-cran")'
+          error-on: '"error"'
+          check-dir: '"check"'

.github/workflows/codecov.yaml

@@ -4,9 +4,9 @@ on:
       - master
   pull_request:
     branches:
-      - master
+      - '**' # matches every branch
   schedule:
-   # * is a special character in YAML so you have to quote this string, it is set up to run at 6am 
+   # * is a special character in YAML so you have to quote this string, it is set up to run at 6am
    # on the first day of the month, this is helpful for periods of time when PRs are not being merged.
     - cron:  '0 6 1 * *'
   # Allows you to run this workflow manually from the Actions tab
@@ -16,15 +16,15 @@ name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: 'release'
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -40,6 +40,9 @@ jobs:
           key: macOS-r-4.0-2-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: macOS-r-4.0-2-
 
+      - name: Install libcurl
+        run: sudo apt-get install libcurl4-openssl-dev
+
       - name: Install dependencies
         run: |
           install.packages(c("remotes"))

.github/workflows/command-line.yaml

@@ -8,12 +8,13 @@ on:
   push:
     branches:
       - master
-      - github_actions
   pull_request:
-    branches: master
+    branches:
+      - '**' # matches every branch
+
   schedule:
     # * is a special character in YAML so you have to quote this string
-    # Launch run at 6am the 1st of every month.	
+    # Launch run at 6am the 1st of every month.
     - cron:  '0 6 1 * *'
 
   # Allows you to run this workflow manually from the Actions tab
@@ -32,9 +33,7 @@ jobs:
       - uses: actions/checkout@v2
       - name: build and run
         run: |
-          sudo apt install libboost-filesystem-dev libboost-system-dev
-
-          ver=`awk '/define.*BOOST_LIB_VERSION/ {print $3}' /usr/include/boost/version.hpp`
-          echo Boost version $ver
-          BOOSTLIB=/usr/local/lib BOOSTVERSION=$ver BOOSTROOT=/usr/include/boost make hector
+          sudo apt-get update
+          sudo apt install libboost-dev
+          make hector
           bash ./test_hector.sh ./src/hector

.github/workflows/leeyabot.yml

@@ -0,0 +1,55 @@
+name: leeyabot
+on:
+  pull_request:
+    branches:
+      - '**' # matches every branch
+
+jobs:
+  run:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: iterative/setup-cml@v1
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+
+      - name: Install libcurl
+        run: sudo apt-get install libcurl4-openssl-dev
+
+      - name: Install dependencies
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          install.packages(c("ggplot2", "rmarkdown", "dplyr", "remotes", "here"))
+          remotes::install_github("hadley/emo")
+          remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Generate report
+        run: |
+          rmarkdown::render("./scripts/OutputDifferences.Rmd", run_pandoc = FALSE)
+        shell: Rscript {0}
+
+      - name: Post comment
+        env:
+          REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+            # Post reports as comments in GitHub PRs
+            cd scripts/
+            if [ -f "diff_plot.png" ]
+            then
+                cat OutputDifferences.knit.md >> report.md
+                echo "![](./diff_plot.png)" >> report.md
+                echo "![](./comp_plot.png)" >> report.md
+            elif [ -f "same_plot.png" ]
+            then
+                cat OutputDifferences.knit.md >> report.md
+            else
+                cat OutputDifferences.knit.md >> report.md
+                echo "leeyabot down :(" > report.md
+            fi
+            cml comment create report.md

.github/workflows/pkgdown.yaml

@@ -1,53 +1,47 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
+    branches: [master]
+  pull_request:
     branches:
-      - main
-      - master
-  schedule:
-    # * is a special character in YAML so you have to quote this string
-    # Launch run at 6am the 1st of every month.
-    - cron:  '0 6 1 * *'
-
-  # Allows you to run this workflow manually from the Actions tab
+      - '**' # matches every branch
+  release:
+    types: [published]
   workflow_dispatch:
 
 name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@v1
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown", type = "binary")
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
-      - name: Install package
-        run: R CMD INSTALL .
-
-      - name: Deploy package
-        run: |
-          git config --local user.email "[email protected]"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs