Set up formatting for R, check formatting in CI (#295)

* Set up formatting for R, automatic formatting in CI

* Run formatters

* Update doc

* More dev docs

* Update python metadata

* use install-juliaup for consistency

Author: WardBrian

.github/workflows/main.yaml

@@ -16,6 +16,29 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  check-formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out github
+        uses: actions/checkout@v5
+        with:
+          submodules: recursive
+
+      - name: Set up Julia
+        uses: julia-actions/install-juliaup@v2
+        with:
+          channel: lts
+
+      - name: Install Formatters
+        run: |
+          sudo apt install -y clang-format black isort
+          curl --proto '=https' --tlsv1.2 -LsSf https://github.com/posit-dev/air/releases/download/0.8.0/air-installer.sh | sh
+          julia --project=julia -e 'import Pkg; Pkg.add("JuliaFormatter")'
+
+      - name: Run formatting checks
+        run: |
+          make format-check || (echo "::error title=Formatting::Formatting check failed, run \`make format\` locally" && exit 1)
+
   build:
     runs-on: ${{matrix.os}}
     strategy:
@@ -37,14 +60,12 @@ jobs:
           path: ./stan/
           key: ${{ runner.os }}-stan-${{ hashFiles('stan/src/stan/version.hpp') }}-v${{ env.CACHE_VERSION }}
 
-
       - name: Set up PATH for C example
         if: matrix.os == 'windows-latest'
         run: |
           Add-Content $env:GITHUB_PATH "$(pwd)/stan/lib/stan_math/lib/tbb"
           Add-Content $env:GITHUB_PATH "$(pwd)/test_models/full"
 
-
       - name: Build C example (Windows)
         if: matrix.os == 'windows-latest'
         run: |
@@ -91,7 +112,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.9", "3.12"]
+        python-version: ["3.9", "3.14"]
       fail-fast: false
     steps:
       - name: Check out github
@@ -298,7 +319,6 @@ jobs:
         timeout-minutes: 60
         run: |
           cargo clippy
-          cargo fmt --check
           cargo run --example=example
 
           # run all tests with feature download-bridgestan-src

CONTRIBUTING.md

@@ -26,6 +26,8 @@ We follow standard open source and GitHub practices:
 
 * We add unit tests when changing or adding code.
 
+* We keep our code formatted using automatic tools (`make format` can run all of them for you).
+
 * We keep the main branch in a release-ready state at all times.
 
 * We propose updates through [GitHub Pull Requests](https://github.com/roualdes/bridgestan/pulls) so that we can do code review.  We do not push directly to the main branch.

Makefile

@@ -114,18 +114,24 @@ stan-update-remote:
 compile_info:
 	@echo '$(LINK.cpp) $(BRIDGE_O) $(LDLIBS) $(SUNDIALS_TARGETS) $(MPI_TARGETS) $(TBB_TARGETS)'
 
-# set to false if you want to fail on formatting errors
-# e.g., in continuous integration
-BS_FORMAT_IGNOREABLE ?= true
 
-.PHONY: format
+
+.PHONY: format format-check
 format:
-	clang-format -i src/*.cpp src/*.hpp src/*.h || $(BS_FORMAT_IGNOREABLE)
-	isort python || $(BS_FORMAT_IGNOREABLE)
-	black python || $(BS_FORMAT_IGNOREABLE)
-	julia --project=julia -e 'using JuliaFormatter; format("julia/")' || $(BS_FORMAT_IGNOREABLE)
-#    R seems to have no good formatter that doesn't choke on doc comments
-#    Rscript -e 'formatR::tidy_dir("R/", recursive=TRUE)' || $(BS_FORMAT_IGNOREABLE)
+	clang-format -i src/*.cpp src/*.hpp src/*.h || true
+	isort python || true
+	black python || true
+	julia --project=julia -e 'using JuliaFormatter; format("julia/")' || true
+	air format R || true
+	cd rust && cargo fmt || true
+
+format-check:
+	clang-format --dry-run --Werror src/*.cpp src/*.hpp src/*.h
+	isort python --check
+	black python --check
+	julia --project=julia -e 'using JuliaFormatter; if !format("julia/", overwrite=false) exit(1) end'
+	air format R --check
+	cd rust && cargo fmt --check
 
 # print value of makefile variable (e.g., make print-TBB_TARGETS)
 .PHONY: print-%