Clang-tidy linter tool

Author: gregorgorjanc

.pre-commit-config.yaml

@@ -17,11 +17,13 @@ repos:
       - id: check-yaml
       - id: check-added-large-files
       - id: check-merge-conflict
-  - repo: https://github.com/benjeffery/pre-commit-clang-format
-    rev: "1.0"
-    hooks:
-      - id: clang-format
-        verbose: true
+
+  # - repo: https://github.com/benjeffery/pre-commit-clang-format
+  #   rev: "1.0"
+  #   hooks:
+  #     - id: clang-format
+  #       verbose: true
+
   - repo: local
     hooks:
       - id: air-format
@@ -37,3 +39,15 @@ repos:
         language: system
         pass_filenames: false
         files: '\.(R|Rmd|rmd|qmd|Qmd)$'
+
+      - id: clang-format
+        name: clang-format
+        entry: clang-format -i --style=file
+        language: system
+        files: '\.(c|cc|cpp|cxx|h|hh|hpp|hxx)$'
+
+      - id: clang-tidy
+        name: clang-tidy for RcppTskit
+        entry: python RcppTskit/tools/clang-tidy.py
+        language: python
+        files: '\.(c|cc|cpp|cxx|h|hh|hpp|hxx)$'

README.md

@@ -92,8 +92,9 @@ git clone https://github.com/HighlanderLab/RcppTskit.git
 
 We use [pre-commit](https://pre-commit.com) hooks to ensure code quality. Specifically, we use:
 * [air](https://github.com/posit-dev/air) to format R code,
-* [jarl](https://github.com/etiennebacher/jarl) to lint R code, and
-* [clang-format](https://clang.llvm.org/docs/ClangFormat.html) to format C/C++ code.
+* [jarl](https://github.com/etiennebacher/jarl) to lint R code,
+* [clang-format](https://clang.llvm.org/docs/ClangFormat.html) to format C/C++ code, and
+* [clang-tidy](https://clang.llvm.org/extra/clang-tidy/) to lint C/C++ code.
 
 To install the hooks, run:
 
@@ -109,37 +110,37 @@ If you plan to update `tskit`, follow instructions in `extern/README.md`.
 
 Then open `RcppTskit` package directory in your favourite R IDE (Positron, RStudio, text-editor-of-your-choice, etc.) and implement your changes.
 
-You should routinely check the status of the package (in R):
+You should routinely check your changes (in R):
 
 ```
 # Note that the RcppTskit R package is in the RcppTskit sub-directory
 setwd("path/to/RcppTskit/RcppTskit")
 
-# Run checks of your changes, documentation, tests, etc.
+# Check
 devtools::check()
 
-# Install the package
+# Install
 devtools::install()
 
-# Run just tests
+# Test
 devtools::test()
 
-# Check code test coverage
+# Test coverage
 cov <- covr::package_coverage(clean = TRUE)
 covr::report(cov)
 ```
 
-Alternatively you can check from the command line:
+Alternatively check your changes from the command line:
 
 ```
 # Note that the RcppTskit package is in the RcppTskit sub-directory
 cd path/to/RcppTskit/RcppTskit
 
-# Run checks of your changes, documentation, tests, etc.
+# Check
 R CMD build RcppTskit
 R CMD check RcppTskit_*.tar.gz
 
-# Install the package
+# Install
 R CMD INSTALL RcppTskit_*.tar.gz
 ```
 

RcppTskit/notes_pkg_dev.Rmd

@@ -2,6 +2,8 @@
 
 ## Next TODOs
 
+* Hide pointer functions and organise docs!?
+
  Missing link(s) in Rd file 'TreeSequence.Rd':
      ‘ts_dump’ ‘ts_summary’
 
@@ -119,19 +121,82 @@ To ignore multiple lines use `# nocov start/stop`.
 
 In `Rcpp` code use `// # nocov ...`.
 
-## Air formatter
+## Air formatter of R code
 
 https://usethis.r-lib.org/reference/use_air.html
 ```
 usethis::use_air()
 ```
 
-## Jarl linter and fixer (buil on Air)
+Setup editor and `air.toml`.
+
+In comand line, run:
+
+```
+air format .
+air format --check .
+```
+
+## Jarl linter of R code
 
 https://jarl.etiennebacher.com
 
-* Add jarl.toml to ~/.config/jarl and to the package folder
-* TODO
+Setup editor and `jarl.toml`. Can also do `~/.config/jarl`.
+
+```
+jarl check .
+jarl check --fix .
+```
+
+## clang-format of C/C++ code
+
+```
+# All files (run from the RcppTskit directory)
+find src -type f \( -name '*.c' -o -name '*.cpp' -o -name '*.h' -o -name '*.hpp' \) \
+  ! -path 'inst/include/tskit/*' \
+  ! -path 'src/tskit/*' \
+  ! -path 'src/RcppExports.cpp' \
+  -exec clang-format -i {} +
+
+# All files (run from the repo root)
+find . -type f \( -name '*.c' -o -name '*.cpp' -o -name '*.h' -o -name '*.hpp' \) \
+  ! -path './extern/*' \
+  ! -path './RcppTskit/inst/include/tskit/*' \
+  ! -path './RcppTskit/src/tskit/*' \
+  ! -path './RcppTskit/src/RcppExports.cpp' \
+  -exec clang-format -i {} +
+
+# Single file
+clang-format -i --style=file src/RcppTskit_minimal.cpp
+
+# Only changes
+git diff --name-only main | grep -E '\.(c|cpp|h|hpp)$' | xargs clang-format -i
+```
+
+or
+
+```
+pre-commit run clang-format src/RcppTskit.cpp
+pre-commit run clang-format --all-files
+```
+
+## clang-tidy linter of C/C++ code
+
+```
+echo $(brew --prefix llvm)/bin/clang-tidy
+# /opt/homebrew/opt/llvm/bin/clang-tidy
+export CLANG_TIDY="$(brew --prefix llvm)/bin/clang-tidy"
+./tools/clang-tidy.py src/RcppTskit.cpp
+./RcppTskit/tools/clang-tidy.py RcppTskit/src/test_tsk_abort_stderr.cpp -- -system-headers '-header-filter=.*'   -extra-arg=-Wno-unknown-warning-option
+./tools/clang-tidy.py src/test_tsk_abort_stderr.cpp -- -system-headers '-header-filter=.*'   -extra-arg=-Wno-unknown-warning-option
+```
+
+or
+
+```
+pre-commit run clang-tidy src/RcppTskit.cpp
+pre-commit run clang-tidy --all-files
+```
 
 ## GitHub actions
 
@@ -144,7 +209,7 @@ usethis::use_github_action("check-standard")
 # Code testing coverage with covr
 usethis::use_github_action("test-coverage")
 
-# Air formatting
+# Air formatting --> moved to pre-commit
 usethis::use_github_action(url = "https://github.com/posit-dev/setup-air/blob/main/examples/format-suggest.yaml")
 usethis::use_github_action(url = "https://github.com/posit-dev/setup-air/blob/main/examples/format-check.yaml")
 ```