CI update in github workflows

.github/workflows/ci.yml

@@ -7,7 +7,7 @@ on:
   push:
     branches:
       - master
-    tags: '*'
+    tags: ['*']
 
 concurrency:
   # Skip intermediate builds: always.
@@ -23,55 +23,46 @@ jobs:
       fail-fast: false
       matrix:
         julia-version:
-          - '1' # will expand to the latest stable 1.x release of Julia.
+          - '1'
         os:
           - ubuntu-latest
           - macos-latest
           - windows-latest
         R-version:
           - 'release'
-        arch:
-          - x64
     steps:
       - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+      - uses: julia-actions/cache@v2
       - name: Install R
-        if: matrix.os == 'macOS-latest'
         uses: r-lib/actions/setup-r@v2
         with:
+          use-public-rspm: true
           r-version: ${{ matrix.R-version }}
       - name: set R lib path to be found by julia RCall
         if: matrix.os == 'ubuntu-latest'
-        run: echo "LD_LIBRARY_PATH=$(R RHOME)/lib" >> $GITHUB_ENV
-      - uses: julia-actions/setup-julia@v1
-        with:
-          version: ${{ matrix.julia-version }}
-          arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
+        run: echo "LD_LIBRARY_PATH=$(R RHOME)/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         with:
           file: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+
   docs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
       - uses: r-lib/actions/setup-r@v2
-      - run: echo "LD_LIBRARY_PATH=$(R RHOME)/lib" >> $GITHUB_ENV
-      - uses: julia-actions/setup-julia@v1
+      - run: echo "LD_LIBRARY_PATH=$(R RHOME)/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
+      - uses: julia-actions/setup-julia@v2
         with:
           version: '1'
+      - uses: julia-actions/cache@v2
       - name: install dependencies
         run: |
           julia --project=docs -e '

.github/workflows/doccleanup.yml

@@ -1,28 +1,34 @@
-name: Doc Preview Cleanup
+# remove PR previews once they're merged
+name: doc preview cleanup
 
 on:
   pull_request:
     types: [closed]
 
+# ensure that only one "doc preview cleanup" workflow is force-pushing at a time
+concurrency:
+  group: doc-preview-cleanup
+  cancel-in-progress: false
+
 jobs:
   doc-preview-cleanup:
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
     steps:
-      - name: Checkout gh-pages branch
-        uses: actions/checkout@v2
+      - name: checkout gh-pages branch
+        uses: actions/checkout@v4
         with:
           ref: gh-pages
-
-      - name: Delete preview and history
+      - name: delete preview and history + push changes
         run: |
-            git config user.name "Documenter.jl"
-            git config user.email "[email protected]"
-            git rm -rf "previews/PR$PRNUM"
-            git commit -m "delete preview"
-            git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+          if [ -d "${preview_dir}" ]; then
+              git config user.name "Documenter.jl"
+              git config user.email "[email protected]"
+              git rm -rf "${preview_dir}"
+              git commit -m "delete preview"
+              git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+              git push --force origin gh-pages-new:gh-pages
+          fi
         env:
-            PRNUM: ${{ github.event.number }}
-
-      - name: Push changes
-        run: |
-            git push --force origin gh-pages-new:gh-pages
+          preview_dir: previews/PR${{ github.event.number }}

README.md

@@ -3,7 +3,10 @@
 [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://cecileane.github.io/PhyloPlots.jl/stable)
 [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://cecileane.github.io/PhyloPlots.jl/dev)
 [![Build status](https://github.com/cecileane/PhyloPlots.jl/workflows/CI/badge.svg?branch=master)](https://github.com/cecileane/PhyloPlots.jl/actions/workflows/ci.yml)
-[![codecov.io](http://codecov.io/github/cecileane/PhyloPlots.jl/coverage.svg?branch=master)](http://codecov.io/github/cecileane/PhyloPlots.jl?branch=master)
+[![Coverage](https://codecov.io/gh/cecileane/PhyloPlots.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/cecileane/PhyloPlots.jl)
+[![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle)
+[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
+[![PkgEval](https://JuliaCI.github.io/NanosoldierReports/pkgeval_badges/P/PhyloPlots.svg)](https://JuliaCI.github.io/NanosoldierReports/pkgeval_badges/report.html)
 
 ## overview
 

docs/Project.toml

@@ -6,4 +6,4 @@ PhyloPlots = "c0d5b6db-e3fc-52bc-a87d-1d050989ed3b"
 RCall = "6f49c342-dc21-5d91-9882-a32aef131414"
 
 [compat]
-Documenter = "~1"
+Documenter = "1"