Fix jarl complaints and adding pre-commit to GitHub Actions

Fixes #72

Author: gregorgorjanc

.github/workflows/pre-commit.yaml

@@ -0,0 +1,64 @@
+on:
+  push:
+    branches: [main, devel]
+  pull_request:
+
+name: pre-commit.yaml
+
+permissions: read-all
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install Rcpp
+        run: Rscript -e 'install.packages("Rcpp")'
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install --yes clang-format clang-tidy
+
+      - name: Install Air
+        uses: posit-dev/setup-air@v1
+
+      - name: Install Jarl
+        run: |
+          curl --proto '=https' --tlsv1.2 -LsSf \
+            https://github.com/etiennebacher/jarl/releases/latest/download/jarl-installer.sh | sh
+          echo "$HOME/.local/bin" >> "$GITHUB_PATH"
+
+      - name: Install pre-commit
+        run: python -m pip install --upgrade pre-commit
+
+      - name: Run pre-commit (pull request)
+        if: github.event_name == 'pull_request'
+        run: |
+          pre-commit run \
+            --from-ref "${{ github.event.pull_request.base.sha }}" \
+            --to-ref "${{ github.event.pull_request.head.sha }}" \
+            --show-diff-on-failure
+
+      - name: Run pre-commit (push)
+        if: github.event_name == 'push' && github.event.before != '0000000000000000000000000000000000000000'
+        run: |
+          pre-commit run \
+            --from-ref "${{ github.event.before }}" \
+            --to-ref "${{ github.sha }}" \
+            --show-diff-on-failure
+
+      - name: Run pre-commit (bootstrap)
+        if: github.event_name == 'push' && github.event.before == '0000000000000000000000000000000000000000'
+        run: pre-commit run --all-files --show-diff-on-failure

README.md

@@ -197,11 +197,13 @@ on each push and pull request.
 Specifically, we run:
 * [R CMD check](.github/workflows/R-CMD-check.yaml) on multiple platforms
   (see curent status [here](https://github.com/HighlanderLab/RcppTskit/actions/workflows/R-CMD-check.yaml)),
-* [covr test coverage](.github/workflows/covr.yaml)
-  (see current status [here](https://github.com/HighlanderLab/RcppTskit/actions/workflows/test-coverage.yaml)), and
-* [Roxygen documentation generation](.github/workflows/document.yaml)
-  (see current status [here](https://github.com/HighlanderLab/RcppTskit/actions/workflows/document.yaml)).
+* [documentation generation](.github/workflows/document.yaml)
+  (see current status [here](https://github.com/HighlanderLab/RcppTskit/actions/workflows/document.yaml)),
+* [pre-commit hooks](.github/workflows/pre-commit.yaml)
+  (see current status [here](https://github.com/HighlanderLab/RcppTskit/actions/workflows/pre-commit.yaml)), and
+* [test coverage](.github/workflows/test-coverage.yaml)
+  (see current status [here](https://github.com/HighlanderLab/RcppTskit/actions/workflows/test-coverage.yaml)).
 
 [R universe for RcppTskit](https://highlanderlab.r-universe.dev/RcppTskit)
 also provides another set of checks - see [here](https://highlanderlab.r-universe.dev/RcppTskit#checktable).
-These are provided once the code is merged into this repository.
+These are provided after new code is pushed or merged into this repository.