ci: move every workflow to the org reusable templates

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

@@ -1,57 +1,39 @@
+## Thin caller -- the matrix, system dependencies, caching and the check itself
+## live in PredictiveEcology/actions. Pinned @main deliberately: tags freeze and
+## rot (this repo's revdeps workflow sat on install-spatial-deps@v0.3, whose
+## ubuntugis PPA installs a GDAL that is ABI-incompatible with Posit's noble
+## cache). The actions repo gates merges with its own self-test CI.
+##
+## Triggers were [master, development]. There is no `master` branch here and the
+## default branch is `main`, so this workflow had never run on main at all.
+
+name: R-CMD-check
+
 on:
   push:
-    branches:
-      - master
-      - development
+    branches: [main, development]
   pull_request:
-    branches:
-      - master
-      - development
+    branches: [main, development]
 
-name: R-CMD-check
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.event_name == 'pull_request' }}
 
 jobs:
   R-CMD-check:
-    if: "!contains(github.event.commits[0].message, '[skip-ci]')"
-    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: 'devel'}
-          - {os: windows-latest, r: 'release'}
-          - {os: windows-latest, r: 'oldrel-1'}
-          - {os: windows-latest, r: 'oldrel-2'}
-          - {os: ubuntu-latest,   r: 'devel'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
-          - {os: ubuntu-latest,   r: 'oldrel-2'}
-
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      OMP_THREAD_LIMIT: 4
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          Ncpus: 4
-          r-version: ${{ matrix.config.r }}
-          use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: |
-            any::rcmdcheck
-
-      - uses: r-lib/actions/check-r-package@v2
-        with:
-          upload-snapshots: true
+    uses: PredictiveEcology/actions/.github/workflows/R-CMD-check.yaml@main
+    secrets: inherit
+    with:
+      ## The org default matrix covers macOS release, windows devel/release/
+      ## oldrel-1, ubuntu devel/release/oldrel-1 and a nosuggests leg (a gain --
+      ## there was no _R_CHECK_DEPENDS_ONLY_ leg before).
+      ##
+      ## The extra legs exist to cover the declared floor. DESCRIPTION says
+      ## `R (>= 4.3)`, and with release at 4.6 that floor is oldrel-3 -- which
+      ## the hand-rolled matrix never tested: it stopped at oldrel-2, so the
+      ## DESCRIPTION claim was unverified. ubuntu oldrel-3 tests it. The
+      ## oldrel-2 legs are carried over from the previous matrix.
+      extra-config: |
+        [{"config": {"os": "ubuntu-latest",  "nosuggests": false, "r": "oldrel-2"}},
+         {"config": {"os": "windows-latest", "nosuggests": false, "r": "oldrel-2"}},
+         {"config": {"os": "ubuntu-latest",  "nosuggests": false, "r": "oldrel-3"}}]

.github/workflows/pkgdown.yaml

@@ -1,48 +1,19 @@
-# 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
+## Thin caller -- the pkgdown build and the gh-pages deploy live in
+## PredictiveEcology/actions. The hand-rolled version was already identical to
+## the shared one step for step, so nothing is customised here.
+
+name: pkgdown
+
 on:
   push:
-    branches: [main, master]
+    branches: [main]
   pull_request:
-    branches: [main, master]
+    branches: [main]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
-
 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 }}
-    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/github-pages-deploy-action@v4
-        with:
-          clean: false
-          branch: gh-pages
-          folder: docs
+    uses: PredictiveEcology/actions/.github/workflows/pkgdown.yaml@main
+    secrets: inherit

.github/workflows/revdeps.yaml

@@ -1,57 +1,25 @@
-## Workflow derived from https://github.com/r-lib/actions/tree/v2/examples and
-##   https://github.com/yihui/crandalf/blob/main/.github/workflows/rev-check.yaml
+## Thin caller -- the job harness (checkout, geospatial system libraries, R,
+## dependency install) and the revdeps-check action live in
+## PredictiveEcology/actions.
 ##
-## Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+## Was: pull_request + weekly across a THREE-OS matrix, calling the composite
+## action directly. The shared action's own README warns revdep checks are too
+## resource intensive for standard runners, and each revdep gets a full
+## R CMD check with its dependency closure installed first -- hours of runner
+## time per PR, for a signal almost no PR changes. Now dispatch plus the same
+## weekly schedule, on the shared single-leg default.
+##
+## This also drops the stale install-spatial-deps@v0.3 pin; the shared workflow
+## uses @main, which is what PR #43 was opened to fix.
+
+name: revdeps
+
 on:
-  pull_request:
-    branches: [main, master, development]
-  schedule:
-    - cron: '23 23 * * 0 '
   workflow_dispatch:
-
-name: revdeps-check
+  schedule:
+    - cron: '23 23 * * 0'
 
 jobs:
-  revdeps-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: 'release'}
-
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      OMP_THREAD_LIMIT: 4
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - uses: PredictiveEcology/actions/install-spatial-deps@v0.3
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          extra-repositories: https://predictiveecology.r-universe.dev
-          Ncpus: 4
-          r-version: ${{ matrix.config.r }}
-          use-public-rspm: false
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: |
-            any::rcmdcheck
-            any::systemfonts
-          needs: check
-
-      - uses: PredictiveEcology/actions/revdeps-check@main
-        with:
-          quiet: false
-          timeout: 30
+  revdeps:
+    uses: PredictiveEcology/actions/.github/workflows/revdeps.yaml@main
+    secrets: inherit

.github/workflows/test-coverage.yaml

@@ -1,36 +1,29 @@
+## Thin caller -- covr, the codecov upload and the trace-file handling live in
+## PredictiveEcology/actions.
+##
+## Two behaviour changes worth knowing, both improvements:
+##   * runs on ubuntu-latest, not macOS-latest (the shared default);
+##   * the shared workflow sets NOT_CRAN=true, so skip_on_cran() tests now run
+##     under coverage. That raises the measured figure and can surface tests
+##     that had never executed in CI. Require hit exactly that on migration.
+##
+## Triggers were [master, development]; there is no `master` branch here.
+
+name: test-coverage
+
 on:
   push:
-    branches:
-      - master
-      - development
+    branches: [main, development]
   pull_request:
-    branches:
-      - master
-      - development
+    branches: [main, development]
 
-name: test-coverage
+## Never cancel a push/merge coverage run -- covr is slow and merges land close
+## together, so cancelling one reads as spurious red. PRs are fair game.
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.event_name == 'pull_request' }}
 
 jobs:
   test-coverage:
-    if: "!contains(github.event.commits[0].message, '[skip-ci]')"
-    runs-on: macOS-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
-    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::covr
-
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
+    uses: PredictiveEcology/actions/.github/workflows/test-coverage.yaml@main
+    secrets: inherit