enforce formatting of C++ code (#76)

* add clang format

* add github action check

* indent

* move around

* run make format-cpp

* pin clang-format version?

* try 18

* pin version

* Revert "run make format-cpp"

This reverts commit 576f925.

* run `make format-cpp`

* remove a few pragma messages

* run format

* add includes

.clang-format

@@ -0,0 +1,6 @@
+BasedOnStyle: Google
+IndentWidth: 2
+UseTab: Never
+ColumnLimit: 100
+IndentPPDirectives: AfterHash
+AlignAfterOpenBracket: BlockIndent

.github/workflows/test-linux.yml

@@ -88,6 +88,11 @@ jobs:
       - name: Install dependencies
         run: |
           source ./tools/linux_ci_setup.sh
+      - name: Run clang-format
+        run: |
+          pip install clang-format==19.1.3
+          make format-cpp
+          git diff --exit-code --compact-summary || { echo "Code formatting failed; run 'make format-cpp'"; exit 1; }
       - name: Build bmdscore
         run: |
           source ./tools/linux_ci_env.sh

Makefile

@@ -1,4 +1,4 @@
-.PHONY: clean lint format test coverage build dist docs docs-docx docs-serve docs-clean loc
+.PHONY: clean lint format format-cpp test coverage build dist docs docs-docx docs-serve docs-clean loc
 .DEFAULT_GOAL := help
 
 define PRINT_HELP_PYSCRIPT
@@ -24,6 +24,9 @@ lint:  ## Check for python formatting issues
 format:  ## Modify python code where possible
 	@ruff format . && ruff check . --fix --show-fixes
 
+format-cpp: ## Format C++ code
+	@find src -name "*.cpp" -o -name "*.h" | xargs clang-format -i
+
 test: ## Run unit tests
 	@py.test
 

docs/source/development.md

@@ -62,6 +62,15 @@ make coverage
 make run_tests_with_coverage
 ```
 
+Code formatting is also enforced in the C++ codebase. To run the formatter, use the following command:
+
+```bash
+pip install clang-format==19.1.3
+make format-cpp
+```
+
+A specific version of clang-format is pinned for reproducibility on all platforms.
+
 ## Build and testing `bmds-ui` (BMDS Desktop)
 
 See [documentation](https://github.com/USEPA/BMDS-UI/blob/main/docs/development.md) in the BMDS-UI repository.

src/bmdscore/DichGammaBMD_NC.cpp

@@ -1,56 +1,56 @@
 #include "DichGammaBMD_NC.h"
 
 #ifdef R_COMPILATION
-        //necessary things to run in R
-        #include <RcppGSL.h>
-        #include <RcppEigen.h>
+// necessary things to run in R
+#  include <RcppEigen.h>
+#  include <RcppGSL.h>
 #else
-        #include <Eigen/Dense>
+#  include <Eigen/Dense>
 #endif
 
+#include <gsl/gsl_blas.h>
+#include <gsl/gsl_cdf.h>
+#include <gsl/gsl_ieee_utils.h>
+#include <gsl/gsl_integration.h>
+#include <gsl/gsl_linalg.h>
 #include <gsl/gsl_math.h>
+#include <gsl/gsl_matrix.h>
 #include <gsl/gsl_randist.h>
 #include <gsl/gsl_rng.h>
 #include <gsl/gsl_test.h>
-#include <gsl/gsl_ieee_utils.h>
-#include <gsl/gsl_integration.h>
 #include <gsl/gsl_vector.h>
-#include <gsl/gsl_matrix.h>
-#include <gsl/gsl_blas.h>
-#include <gsl/gsl_linalg.h>
-#include <gsl/gsl_cdf.h>
 
-double GAMMA_BMD_EXTRA_NC_INEQUALITY(Eigen::MatrixXd theta, void* data){
-	log_gamma_inequality *M = (log_gamma_inequality*)data;
-	double inequality = M->inequality;
-	double BMD = M->BMD;
-	double BMR = M->BMR;
-	bool   geq = M->geq;
-
-	double g = GAMMA_G(theta(0, 0));
-	double a = GAMMA_A(theta(1, 0));
-	double Z = GAMMA_EXTRA_Z(g, a, BMR); //note BMD is a placeholder
-	Z = Z/BMD;
-	double rV = 0.0;
-	rV = (geq) ? inequality - Z : Z - inequality;
-	return rV;
+double GAMMA_BMD_EXTRA_NC_INEQUALITY(Eigen::MatrixXd theta, void* data) {
+  log_gamma_inequality* M = (log_gamma_inequality*)data;
+  double inequality = M->inequality;
+  double BMD = M->BMD;
+  double BMR = M->BMR;
+  bool geq = M->geq;
+
+  double g = GAMMA_G(theta(0, 0));
+  double a = GAMMA_A(theta(1, 0));
+  double Z = GAMMA_EXTRA_Z(g, a, BMR);  // note BMD is a placeholder
+  Z = Z / BMD;
+  double rV = 0.0;
+  rV = (geq) ? inequality - Z : Z - inequality;
+  return rV;
 }
 
 double GAMMA_BMD_ADDED_NC_INEQUALITY(Eigen::MatrixXd theta, void* data) {
-	log_gamma_inequality *M = (log_gamma_inequality*)data;
-	double inequality = M->inequality;
-	double BMD = M->BMD;
-	double BMR = M->BMR;
-	bool   geq = M->geq;
+  log_gamma_inequality* M = (log_gamma_inequality*)data;
+  double inequality = M->inequality;
+  double BMD = M->BMD;
+  double BMR = M->BMR;
+  bool geq = M->geq;
 
-	double g = GAMMA_G(theta(0, 0));
-	double a = GAMMA_A(theta(1, 0));
+  double g = GAMMA_G(theta(0, 0));
+  double a = GAMMA_A(theta(1, 0));
 
-	double Z = GAMMA_ADDED_Z(g, a, BMR);
-	Z = Z / BMD;
-	double rV = 0.0;
+  double Z = GAMMA_ADDED_Z(g, a, BMR);
+  Z = Z / BMD;
+  double rV = 0.0;
 
-	rV = (geq)? inequality - Z: Z - inequality;
+  rV = (geq) ? inequality - Z : Z - inequality;
 
-	return rV;
+  return rV;
 }

src/bmdscore/DichLogProbitBMD_NC.cpp

@@ -1,51 +1,49 @@
 #define STRICT_R_HEADERS
 
+#include "DichLogProbitBMD_NC.h"
 
 #include <gsl/gsl_cdf.h>
 #include <gsl/gsl_randist.h>
-#include "DichLogProbitBMD_NC.h"
 
 #ifdef R_COMPILATION
-        //necessary things to run in R
-        #include <RcppGSL.h>
-        #include <RcppEigen.h>
+// necessary things to run in R
+#  include <RcppEigen.h>
+#  include <RcppGSL.h>
 #else
-        #include <Eigen/Dense>
+#  include <Eigen/Dense>
 #endif
 
-
-double logProbit_BMD_EXTRA_NC_INEQUALITY(Eigen::MatrixXd theta, void* data){
-	log_probit_inequality *M = (log_probit_inequality*)data;
-	double inequality = M->inequality;
-	double BMD = M->BMD;
-	double BMR = M->BMR;
-	bool   geq = M->geq;
-
-	double g = LOGPROBIT_G(theta(0, 0));
-	double a = LOGPROBIT_A(theta(1, 0));
-	double Z = LOGPROBIT_EXTRA_Z(g, a, BMR); //note BMD is a placeholder
-	Z = Z / log(BMD);
-	double rV = 0.0;
-	rV = (geq) ? inequality - Z : Z - inequality;
-	return rV;
+double logProbit_BMD_EXTRA_NC_INEQUALITY(Eigen::MatrixXd theta, void* data) {
+  log_probit_inequality* M = (log_probit_inequality*)data;
+  double inequality = M->inequality;
+  double BMD = M->BMD;
+  double BMR = M->BMR;
+  bool geq = M->geq;
+
+  double g = LOGPROBIT_G(theta(0, 0));
+  double a = LOGPROBIT_A(theta(1, 0));
+  double Z = LOGPROBIT_EXTRA_Z(g, a, BMR);  // note BMD is a placeholder
+  Z = Z / log(BMD);
+  double rV = 0.0;
+  rV = (geq) ? inequality - Z : Z - inequality;
+  return rV;
 }
 
 double logProbit_BMD_ADDED_NC_INEQUALITY(Eigen::MatrixXd theta, void* data) {
-	log_probit_inequality *M = (log_probit_inequality*)data;
-	double inequality = M->inequality;
-	double BMD = M->BMD;
-	double BMR = M->BMR;
-	bool   geq = M->geq;
-
-	double g = LOGPROBIT_G(theta(0, 0));
-	double a = LOGPROBIT_A(theta(1, 0));
+  log_probit_inequality* M = (log_probit_inequality*)data;
+  double inequality = M->inequality;
+  double BMD = M->BMD;
+  double BMR = M->BMR;
+  bool geq = M->geq;
 
+  double g = LOGPROBIT_G(theta(0, 0));
+  double a = LOGPROBIT_A(theta(1, 0));
 
-	double Z = LOGPROBIT_ADDED_Z(g, a, BMR);
-	Z = Z / log(BMD);
-	double rV = 0.0;
+  double Z = LOGPROBIT_ADDED_Z(g, a, BMR);
+  Z = Z / log(BMD);
+  double rV = 0.0;
 
-	rV = (geq)? inequality - Z: Z - inequality;
+  rV = (geq) ? inequality - Z : Z - inequality;
 
-	return rV;
+  return rV;
 }

src/bmdscore/DichLogisticBMD_NC.cpp

@@ -1,42 +1,41 @@
 #include "DichLogisticBMD_NC.h"
 
 #ifdef R_COMPILATION
-        //necessary things to run in R
-        #include <RcppGSL.h>
-        #include <RcppEigen.h>
+// necessary things to run in R
+#  include <RcppEigen.h>
+#  include <RcppGSL.h>
 #else
-        #include <Eigen/Dense>
+#  include <Eigen/Dense>
 #endif
 
 double LOGISTIC_BMD_EXTRA_NC_INEQUALITY(Eigen::MatrixXd theta, void* data) {
-	logistic_inequality *M = (logistic_inequality*)data;
-	double inequality = M->inequality;
-	double BMD = M->BMD;
-	double BMR = M->BMR;
-	bool   geq = M->geq;
-
-	double a = LOGISTIC_A(theta(0, 0));
-	double Z = LOGISTIC_EXTRA_Z(a, BMR); //note BMD is a placeholder
-	Z = Z / BMD;
-	double rV = 0.0;
-	rV = (geq) ? inequality - Z : Z - inequality;
-	return rV;
+  logistic_inequality* M = (logistic_inequality*)data;
+  double inequality = M->inequality;
+  double BMD = M->BMD;
+  double BMR = M->BMR;
+  bool geq = M->geq;
+
+  double a = LOGISTIC_A(theta(0, 0));
+  double Z = LOGISTIC_EXTRA_Z(a, BMR);  // note BMD is a placeholder
+  Z = Z / BMD;
+  double rV = 0.0;
+  rV = (geq) ? inequality - Z : Z - inequality;
+  return rV;
 }
 
 double LOGISTIC_BMD_ADDED_NC_INEQUALITY(Eigen::MatrixXd theta, void* data) {
-	logistic_inequality *M = (logistic_inequality*)data;
-	double inequality = M->inequality;
-	double BMD = M->BMD;
-	double BMR = M->BMR;
-	bool   geq = M->geq;
+  logistic_inequality* M = (logistic_inequality*)data;
+  double inequality = M->inequality;
+  double BMD = M->BMD;
+  double BMR = M->BMR;
+  bool geq = M->geq;
 
-	double a = LOGISTIC_A(theta(0, 0));
-	double Z = LOGISTIC_ADDED_Z(a, BMR);
-	Z = pow(Z, a) / pow(BMD, a);
-	double rV = 0.0;
+  double a = LOGISTIC_A(theta(0, 0));
+  double Z = LOGISTIC_ADDED_Z(a, BMR);
+  Z = pow(Z, a) / pow(BMD, a);
+  double rV = 0.0;
 
-	rV = (geq) ? inequality - Z : Z - inequality;
+  rV = (geq) ? inequality - Z : Z - inequality;
 
-	return rV;
+  return rV;
 }
-

src/bmdscore/DichProbitBMD_NC.cpp

@@ -1,44 +1,44 @@
 #include "DichProbitBMD_NC.h"
 
 #ifdef R_COMPILATION
-        //necessary things to run in R
-        #include <RcppGSL.h>
-        #include <RcppEigen.h>
+// necessary things to run in R
+#  include <RcppEigen.h>
+#  include <RcppGSL.h>
 #else
-        #include <Eigen/Dense>
+#  include <Eigen/Dense>
 #endif
 
 #include <gsl/gsl_cdf.h>
 #include <gsl/gsl_randist.h>
 
 double PROBIT_BMD_EXTRA_NC_INEQUALITY(Eigen::MatrixXd theta, void* data) {
-	probit_inequality *M = (probit_inequality*)data;
-	double inequality = M->inequality;
-	double BMD = M->BMD;
-	double BMR = M->BMR;
-	bool   geq = M->geq;
-
-	double a = PROBIT_A(theta(0, 0));
-	double Z = PROBIT_EXTRA_Z(a, BMR); //note BMD is a placeholder
-	Z = Z / BMD;
-	double rV = 0.0;
-	rV = (geq) ? inequality - Z : Z - inequality;
-	return rV;
+  probit_inequality* M = (probit_inequality*)data;
+  double inequality = M->inequality;
+  double BMD = M->BMD;
+  double BMR = M->BMR;
+  bool geq = M->geq;
+
+  double a = PROBIT_A(theta(0, 0));
+  double Z = PROBIT_EXTRA_Z(a, BMR);  // note BMD is a placeholder
+  Z = Z / BMD;
+  double rV = 0.0;
+  rV = (geq) ? inequality - Z : Z - inequality;
+  return rV;
 }
 
 double PROBIT_BMD_ADDED_NC_INEQUALITY(Eigen::MatrixXd theta, void* data) {
-    probit_inequality *M = (probit_inequality*)data;
-	double inequality = M->inequality;
-	double BMD = M->BMD;
-	double BMR = M->BMR;
-	bool   geq = M->geq;
+  probit_inequality* M = (probit_inequality*)data;
+  double inequality = M->inequality;
+  double BMD = M->BMD;
+  double BMR = M->BMR;
+  bool geq = M->geq;
 
-	double a = PROBIT_A(theta(0, 0));
-	double Z = PROBIT_ADDED_Z(a, BMR);
-	Z = pow(Z, a) / pow(BMD, a);
-	double rV = 0.0;
+  double a = PROBIT_A(theta(0, 0));
+  double Z = PROBIT_ADDED_Z(a, BMR);
+  Z = pow(Z, a) / pow(BMD, a);
+  double rV = 0.0;
 
-	rV = (geq) ? inequality - Z : Z - inequality;
+  rV = (geq) ? inequality - Z : Z - inequality;
 
-	return rV;
+  return rV;
 }