Merge pull request #41 from poissonconsulting/update-actions

Update actions and links; increase R dependency version; remove runbisonpic and shinybisonpic from suggests
poissonconsulting · Nov 15, 2024 · f16a312 · f16a312
2 parents 27372dc + 18da1b7
commit f16a312
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Showing 9 changed files with 135 additions and 28 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -6,7 +6,9 @@ on:
   pull_request:
     branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -25,18 +27,14 @@ jobs:
           - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      GITHUB_PAT: ${{ secrets.PRIVATE_ACTIONS_PAT }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
       - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
-
-      - uses: r-lib/actions/setup-tinytex@v2
-      - run: tlmgr --version
-
+
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,50 @@
+# 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: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+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@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.github/workflows/render-readme.yaml b/.github/workflows/render-readme.yaml
@@ -0,0 +1,38 @@
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: render-readme
+
+jobs:
+  render-readme:
+    if: "contains(github.event.head_commit.message, 'render rmd')"
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: devtools
+
+      - name: Build package
+        run: |
+          devtools::install()
+        shell: Rscript {0}
+
+      - name: Render readme
+        run: |
+          rmarkdown::render("README.Rmd")
+        shell: Rscript {0}
+
+      - name: Commit README.md
+        run: |
+          git add README.md
+          git commit -m 'Re-build README.Rmd' || echo "Render README"
+          git push origin || echo "Render README"
diff --git a/.github/workflows/test-coverage-private.yaml → .github/workflows/test-coverage.yaml b/.github/workflows/test-coverage-private.yaml → .github/workflows/test-coverage.yaml
@@ -6,16 +6,16 @@ on:
   pull_request:
     branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
-      GITHUB_PAT: ${{ secrets.PRIVATE_ACTIONS_PAT }}
-      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} 
-
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
     steps:
       - uses: actions/checkout@v4
 
@@ -25,28 +25,37 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -16,8 +16,11 @@ Authors@R: c(
 Description: This package facilitates the manipulation, exploration, and
     analysis of wood bison camera trap data.
 License: Apache License (>= 2)
+URL: https://github.com/poissonconsulting/bisonpictools,
+    https://poissonconsulting.github.io/bisonpictools/
+BugReports: https://github.com/poissonconsulting/bisonpictools/issues
 Depends: 
-    R (>= 3.5.0)
+    R (>= 4.1)
 Imports: 
     BH,
     chk,
@@ -41,8 +44,6 @@ Suggests:
     RcppEigen,
     readxl,
     rmarkdown,
-    runbisonpic,
-    shinybisonpic,
     testthat (>= 3.0.0),
     withr
 VignetteBuilder: 
@@ -51,11 +52,9 @@ Remotes:
     poissonconsulting/chktemplate,
     poissonconsulting/embr,
     poissonconsulting/newdata,
-    poissonconsulting/runbisonpic,
-    poissonconsulting/shinybisonpic,
     poissonconsulting/smbr
 Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
diff --git a/README.Rmd b/README.Rmd
@@ -20,15 +20,15 @@ library(bisonpictools)
 <!-- badges: start -->
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![R-CMD-check](https://github.com/poissonconsulting/bisonpictools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/poissonconsulting/bisonpictools/actions/workflows/R-CMD-check.yaml)
-[![codecov](https://codecov.io/gh/poissonconsulting/bisonpictools/graph/badge.svg?token=znqSXiltZo)](https://codecov.io/gh/poissonconsulting/bisonpictools)
+[![Codecov test coverage](https://codecov.io/gh/poissonconsulting/bisonpictools/graph/badge.svg)](https://app.codecov.io/gh/poissonconsulting/bisonpictools)
 <!-- badges: end -->
 
 The goal of `bisonpictools` is to facilitate the visualization and analysis of camera trap data for wood bison herds.
 The package includes functions to check the correct formatting of data, visualize the data, manipulate and analyse the data using a complex custom-built Bayesian model, and generate predictions of abundances, survival and fecundity rates, and population ratios.
 
 ## bisonpic Suite
 
-`bisonpictools` is one of three packages in the **bisonpic** suite of tools:
+`bisonpictools` is one of three packages in the [bisonpic suite](https://github.com/poissonconsulting/bisonpicsuite) of tools.
 
 - [`bisonpictools`](https://github.com/poissonconsulting/bisonpictools)
 - [`shinybisonpic`](https://github.com/poissonconsulting/shinybisonpic)

diff --git a/README.md b/README.md
@@ -8,7 +8,8 @@
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![R-CMD-check](https://github.com/poissonconsulting/bisonpictools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/poissonconsulting/bisonpictools/actions/workflows/R-CMD-check.yaml)
-[![codecov](https://codecov.io/gh/poissonconsulting/bisonpictools/graph/badge.svg?token=znqSXiltZo)](https://codecov.io/gh/poissonconsulting/bisonpictools)
+[![Codecov test
+coverage](https://codecov.io/gh/poissonconsulting/bisonpictools/graph/badge.svg)](https://app.codecov.io/gh/poissonconsulting/bisonpictools)
 <!-- badges: end -->
 
 The goal of `bisonpictools` is to facilitate the visualization and
@@ -20,8 +21,8 @@ rates, and population ratios.
 
 ## bisonpic Suite
 
-`bisonpictools` is one of three packages in the **bisonpic** suite of
-tools:
+`bisonpictools` is one of three packages in the [bisonpic
+suite](https://github.com/poissonconsulting/bisonpicsuite) of tools.
 
 - [`bisonpictools`](https://github.com/poissonconsulting/bisonpictools)
 - [`shinybisonpic`](https://github.com/poissonconsulting/shinybisonpic)

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -0,0 +1,3 @@
+url: https://poissonconsulting.github.io/bisonpictools/
+template:
+  bootstrap: 5
diff --git a/man/bisonpictools-package.Rd b/man/bisonpictools-package.Rd