chore(deps): update repository maintenance

.github/workflows/create_github_release.yaml

@@ -18,7 +18,7 @@ jobs:
       tag_version: ${{ steps.create_release.outputs.tag_version }}
     steps:
       - name: Checkout
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           fetch-depth: 0
       - name: Create Release
@@ -38,7 +38,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
       - name: Update system repositories
         run: sudo apt-get update
       - name: Install system dependencies
@@ -48,13 +48,13 @@ jobs:
           libharfbuzz-dev libfribidi-dev \
           pandoc
       - name: Setup R
-        uses: r-lib/actions/setup-r@6f6e5bc62fba3a704f74e7ad7ef7676c5c6a2590 # v2.11.4
+        uses: r-lib/actions/setup-r@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2.12.0
         with:
           r-version: ${{ matrix.r_version }}
           use-public-rspm: true
         id: r
       - name: Install dependencies
-        uses: r-lib/actions/setup-renv@6f6e5bc62fba3a704f74e7ad7ef7676c5c6a2590 # v2.11.4
+        uses: r-lib/actions/setup-renv@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2.12.0
       - name: Build Package
         run: R CMD build .
       - name: Rename Package

.github/workflows/draft-paper.yaml

@@ -11,9 +11,9 @@ jobs:
     name: Paper Draft
     steps:
       - name: Checkout
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
       - name: Build draft PDF
-        uses: openjournals/openjournals-draft-action@master
+        uses: openjournals/openjournals-draft-action@85a18372e48f551d8af9ddb7a747de685fbbb01c # master
         with:
           journal: joss
           # This should be the path to the paper within your repo.

.github/workflows/github_release.yml

@@ -19,7 +19,7 @@ jobs:
       tag_version: ${{ steps.create_release.outputs.tag_version }}
     steps:
       - name: Checkout
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           fetch-depth: 0
       - name: Get most recent tag
@@ -46,7 +46,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
       - name: Install system dependencies
         run: |
           sudo apt-get update && \
@@ -56,20 +56,20 @@ jobs:
           libudunits2-dev libharfbuzz-dev libfribidi-dev \
           pandoc
       - name: Setup R
-        uses: r-lib/actions/setup-r@6f6e5bc62fba3a704f74e7ad7ef7676c5c6a2590 # v2.11.4
+        uses: r-lib/actions/setup-r@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2.12.0
         with:
           r-version: ${{ matrix.r_version }}
           use-public-rspm: true
         id: r
       - name: Install dependencies
-        uses: r-lib/actions/setup-renv@6f6e5bc62fba3a704f74e7ad7ef7676c5c6a2590 # v2.11.4
+        uses: r-lib/actions/setup-renv@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2.12.0
       - name: Build Package
         run: R CMD build .
       - name: Rename Package
         run: echo "NEWNAME=$(./utilities/rename-package.R *.tar.gz)" >> "$GITHUB_ENV"
       - name: Attest builds
         id: attest_build
-        uses: actions/attest-build-provenance@00014ed6ed5efc5b1ab7f7f34a39eb55d41aa4f8 # v3.1.0
+        uses: actions/attest-build-provenance@96278af6caaf10aea03fd8d33a09a777ca52d62f # v3.2.0
         with:
           subject-path: ${{ env.NEWNAME }}
       - name: debug

.github/workflows/pkgdown.yml

@@ -19,9 +19,9 @@ jobs:
       id-token: write
     steps:
       - name: Checkout
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
       - name: Setup R
-        uses: r-lib/actions/setup-r@6f6e5bc62fba3a704f74e7ad7ef7676c5c6a2590 # v2.11.4
+        uses: r-lib/actions/setup-r@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2.12.0
         with:
           r-version: renv
       - name: Install system dependencies
@@ -33,7 +33,7 @@ jobs:
           libudunits2-dev libharfbuzz-dev libfribidi-dev \
           pandoc
       - name: Install dependencies
-        uses: r-lib/actions/setup-renv@6f6e5bc62fba3a704f74e7ad7ef7676c5c6a2590 # v2.11.4
+        uses: r-lib/actions/setup-renv@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2.12.0
       - name: Build pkgdown site
         run: Rscript -e 'pkgdown::build_site_github_pages(install = TRUE)'
       - name: Deploy pkgdown site

.github/workflows/rworkflows.yml

@@ -39,7 +39,7 @@ jobs:
           bioc: devel
           r: auto
     steps:
-    - uses: neurogenomics/rworkflows@master
+    - uses: neurogenomics/rworkflows@6aaf49348859a96eea744b1907b1fe850e3ead5e # master
       with:
         run_bioccheck: ${{ true }}
         run_rcmdcheck: ${{ true }}

.github/workflows/test-coverage.yaml

@@ -15,13 +15,13 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
 
-      - uses: r-lib/actions/setup-r@6f6e5bc62fba3a704f74e7ad7ef7676c5c6a2590 # v2
+      - uses: r-lib/actions/setup-r@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@6f6e5bc62fba3a704f74e7ad7ef7676c5c6a2590 # v2
+      - uses: r-lib/actions/setup-r-dependencies@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2
         with:
           extra-packages: any::covr
           needs: coverage

.github/workflows/test-coverage.yml

@@ -21,13 +21,13 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
 
-      - uses: r-lib/actions/setup-r@6f6e5bc62fba3a704f74e7ad7ef7676c5c6a2590 # v2.11.4
+      - uses: r-lib/actions/setup-r@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2.12.0
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@6f6e5bc62fba3a704f74e7ad7ef7676c5c6a2590 # v2.11.4
+      - uses: r-lib/actions/setup-r-dependencies@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2.12.0
         with:
           extra-packages: any::covr
           needs: coverage

.pre-commit-config.yaml

@@ -67,7 +67,7 @@ repos:
           - --branch
           - RELEASE.*
   - repo: https://github.com/compilerla/conventional-pre-commit
-    rev: v4.3.0
+    rev: v4.4.0
     hooks:
       - args:
           - build
@@ -86,7 +86,7 @@ repos:
         stages:
           - commit-msg
   - repo: https://github.com/Lucas-C/pre-commit-hooks
-    rev: v1.5.5
+    rev: v1.5.6
     hooks:
       - id: forbid-crlf
       - id: remove-crlf