update mains functions

epiverse-trace · Sep 10, 2023 · 91a460a · 91a460a
2 parents 9c7bc32 + eb55928
commit 91a460a
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Showing 210 changed files with 72,557 additions and 15,694 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/.github/workflows/.DS_Store b/.github/workflows/.DS_Store
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,13 +1,48 @@
 # 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
+#
+# Reproduce locally by running:
+# ```r
+# pak::pak(c("any::rcmdcheck", "."), dependencies = "Config/Needs/check")
+# rcmdcheck::rcmdcheck()
+# ```
 on:
   push:
     branches: [main, master]
+    paths:
+      - 'data/**'
+      - 'R/**'
+      - 'inst/**'
+      - 'man/**'
+      - 'src/**'
+      - 'tests/**'
+      - 'vignettes/**'
+      - 'DESCRIPTION'
+      - 'NAMESPACE'
+      - 'LICENSE'
+      - '.Rbuildignore'
+      - '.github/workflows/R-CMD-check.yaml'
   pull_request:
-    branches: [main, master]
+    paths:
+      - 'data/**'
+      - 'R/**'
+      - 'inst/**'
+      - 'man/**'
+      - 'src/**'
+      - 'tests/**'
+      - 'vignettes/**'
+      - 'DESCRIPTION'
+      - 'NAMESPACE'
+      - 'LICENSE'
+      - '.Rbuildignore'
+      - '.github/workflows/R-CMD-check.yaml'
 
 name: R-CMD-check
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -27,9 +62,11 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+      # Exists since R 4.3.0 but `false` by default
+      _R_CHECK_LENGTH_COLON_: true
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -45,5 +82,17 @@ jobs:
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
+        id: rcmdcheck
         with:
-          upload-snapshots: true
+<<<<<<< HEAD
+          upload-snapshots: true
+=======
+          upload-snapshots: true
+
+      # fail-fast but only if rcmdcheck step fails
+      - name: Manual fail-fast
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        if: always() && steps.rcmdcheck.outcome == 'failure'
+        run: gh run cancel ${{ github.run_id }}
+>>>>>>> review
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -1,26 +1,58 @@
 # 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
+#
+# Reproduce locally by running:
+# ```r
+# pak::pak(c("any::pkgdown", "."), dependencies = "Config/Needs/website")
+# pkgdown::build_site()
+# ```
 on:
   push:
     branches: [main, master]
+    paths:
+      - 'README.Rmd'
+      - 'README.md'
+      - 'index.Rmd'
+      - 'index.md'
+      - 'man/**'
+      - 'vignettes/**'
+      - '_pkgdown.yml'
+      - 'pkgdown/**'
+      - 'DESCRIPTION'
+      - '.Rbuildignore'
+      - '.github/**'
   pull_request:
-    branches: [main, master]
+    paths:
+      - 'README.Rmd'
+      - 'README.md'
+      - 'index.Rmd'
+      - 'index.md'
+      - 'man/**'
+      - 'vignettes/**'
+      - '_pkgdown.yml'
+      - 'pkgdown/**'
+      - 'DESCRIPTION'
+      - '.Rbuildignore'
+      - '.github/**'
   release:
     types: [published]
   workflow_dispatch:
 
 name: pkgdown
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   pkgdown:
     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 }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,6 +73,11 @@ jobs:
         if: github.event_name != 'pull_request'
         uses: JamesIves/[email protected]
         with:
-          clean: false
+          # We clean on releases because we want to remove old vignettes,
+          # figures, etc. that have been deleted from the `main` branch.
+          # But we clean ONLY on releases because we want to be able to keep
+          # both the 'stable' and 'dev' websites.
+          # Also discussed in https://github.com/r-lib/actions/issues/484
+          clean: ${{ github.event_name == 'release' }}
           branch: gh-pages
           folder: docs
diff --git a/.github/workflows/render_readme.yml b/.github/workflows/render_readme.yml
@@ -1,8 +1,25 @@
-# Name of the workflow
+# Reproduce locally by running:
+# ```r
+# pak::pak(c("any::rmarkdown", "any::usethis", "."))
+# writeLines(
+#   knitr::knit_expand(
+#     "README.Rmd",
+#     packagename = read.dcf("DESCRIPTION", "Package"),
+#     gh_repo = usethis:::github_remote_list()$repo_spec
+#   ),
+#   "README_expanded.Rmd"
+# )
+# rmarkdown::render(
+#   "README_expanded.Rmd",
+#   output_file = "README.md",
+#   output_dir = "."
+# )
+# unlink("README_expanded.Rmd")
+# ```
 name: render-readme
 
 # Controls when the action will run. Triggers include:
-# 
+#
 # - button trigger from github action page
 # - on changes to readme.Rmd
 
@@ -11,16 +28,25 @@ on:
   push:
     paths:
       - 'README.Rmd'
+      - '.github/workflows/render_readme.yml'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   render-readme:
-    runs-on: macos-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - name: Checkout repos
+<<<<<<< HEAD
         uses: actions/checkout@v2
+=======
+        uses: actions/checkout@v3
+>>>>>>> review
 
       - name: Setup R
         uses: r-lib/actions/setup-r@v2
@@ -29,11 +55,16 @@ jobs:
 
       - name: Setup pandoc
         uses: r-lib/actions/setup-pandoc@v2
+<<<<<<< HEAD
 
+=======
+
+>>>>>>> review
       - name: Install dependencies
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rmarkdown, local::.
+<<<<<<< HEAD
 
       - name: Compile the readme
         run: |
@@ -47,8 +78,26 @@ jobs:
             tf
           )
           rmarkdown::render(tf, output_file = "README.md", output_dir = ".")
+=======
+
+      - name: Compile the readme
+        run: |
+          writeLines(
+            knitr::knit_expand(
+              "README.Rmd",
+              packagename = read.dcf("DESCRIPTION", "Package"),
+              gh_repo     = Sys.getenv("GITHUB_REPOSITORY")
+            ),
+            "README_expanded.Rmd"
+          )
+          rmarkdown::render(
+            "README_expanded.Rmd",
+            output_file = "README.md",
+            output_dir  = "."
+          )
+>>>>>>> review
         shell: Rscript {0}
-        
+
       - name: Commit files
         run: |
           git config --local user.email "[email protected]"
@@ -60,4 +109,8 @@ jobs:
             git add man/figures/
           fi
           git diff-index --quiet HEAD || git commit -m "Automatic readme update"
-          git push origin || echo "No changes to push"
+<<<<<<< HEAD
+          git push origin || echo "No changes to push"
+=======
+          git push origin || echo "No changes to push"
+>>>>>>> review
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -1,10 +1,33 @@
 # 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
+#
+# Reproduce locally by running:
+# ```r
+# pak::pak("any::covr", dependencies = "Config/Needs/coverage")
+# covr::codecov(quiet = FALSE)
+# ```
 on:
   push:
     branches: [main, master]
+    paths:
+      - 'R/**'
+      - 'src/**'
+      - 'tests/**'
+      - 'inst/**'
+      - 'DESCRIPTION'
+      - '.github/workflows/test-coverage.yaml'
   pull_request:
-    branches: [main, master]
+    paths:
+      - 'R/**'
+      - 'src/**'
+      - 'tests/**'
+      - 'inst/**'
+      - 'DESCRIPTION'
+      - '.github/workflows/test-coverage.yaml'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 name: test-coverage
 
@@ -15,7 +38,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -28,4 +51,13 @@ jobs:
 
       - name: Test coverage
         run: covr::codecov(quiet = FALSE)
-        shell: Rscript {0}
+<<<<<<< HEAD
+        shell: Rscript {0}
+=======
+        shell: Rscript {0}
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+>>>>>>> review
diff --git a/.github/workflows/update-citation-cff.yaml b/.github/workflows/update-citation-cff.yaml
@@ -0,0 +1,55 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# The action runs when:
+# - A new release is published
+# - The DESCRIPTION or inst/CITATION are modified
+# - Can be run manually
+# For customizing the triggers, visit https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
+on:
+  release:
+    types: [published]
+  push:
+    paths:
+      - DESCRIPTION
+      - inst/CITATION
+      - .github/workflows/update-citation-cff.yaml
+  workflow_dispatch:
+
+name: Update CITATION.cff
+
+jobs:
+  update-citation-cff:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::cffr
+            any::V8
+
+      - name: Update CITATION.cff
+        run: |
+
+          library(cffr)
+
+          # Customize with your own code
+          # See https://docs.ropensci.org/cffr/articles/cffr.html
+
+          # Write your own keys
+          mykeys <- list()
+
+          # Create your CITATION.cff file
+          cff_write(keys = mykeys)
+
+        shell: Rscript {0}
+
+      - name: Commit results
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Action"
+          git add CITATION.cff
+          git commit -m 'Update CITATION.cff' || echo "No changes to commit"
+          git push origin || echo "No changes to commit"
diff --git a/.gitignore b/.gitignore
@@ -4,3 +4,7 @@ docs
 .Rproj.user
 /doc/
 /Meta/
+.DS_Store
+.Rhistory
+/..Rcheck/
+/Meta/