Cpp code organization (#72)

* Reorganize C++ sources into subdirectories

- Move bgm- and bgmCompare-specific C++ code into src/bgm/ and src/bgmCompare/
- Update build system to support C++ sources in subdirectories
- Generate src/sources.mk at configure time to list all .cpp files
- Include sources.mk from Makevars.in using portable (CRAN-compliant) rules

* Finalize C++ refactor: path-qualified headers and single include root

- Reorganize remaining C++ files into src/ subdirectories
- Include headers relative to src/ and drop per-module -I flags

* Use ARMA_MY_LOG instead of arma::log in compute_Vn_mfm_sbm()

* Cleanup Makevars.in

* Final commit

Author: MaartenMarsman

.Rbuildignore

@@ -1,15 +1,35 @@
-^renv$
-^renv\.lock$
+# RStudio / IDE
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^\.vscode$
 
-^Readme.Rmd$
-^\.github$
-^_pkgdown\.yml$
+# renv
+^renv$
+^renv\.lock$
+
+# pkgdown / docs
 ^docs$
 ^pkgdown$
-^vignettes/introduction_cache
+^_pkgdown\.yml$
+^Readme\.Rmd$
+^vignettes/introduction_cache$
+
+# GitHub / CI
+^\.github$
+
+# R CMD build artifacts
 ^doc$
 ^Meta$
-^\.vscode$
-^dev/
+
+# Development helpers
+^dev$
+
+# ---- C/C++ build artifacts (REQUIRED) ----
+^src/.*\.o$
+^src/.*\.so$
+^src/.*\.dll$
+
+# ---- Generated build files ----
+^src/Makevars$
+^src/Makevars\.win$
+^src/sources\.mk$

.gitignore

@@ -5,6 +5,9 @@
 src/*.o
 src/*.so
 src/*.dll
+src/**/*.o
+src/**/*.so
+src/**/*.dll
 .DS_Store
 /doc/
 /Meta/

R/RcppExports.R

@@ -9,18 +9,6 @@ run_bgm_parallel <- function(observations, num_categories, pairwise_scale, edge_
     .Call(`_bgms_run_bgm_parallel`, observations, num_categories, pairwise_scale, edge_prior, inclusion_probability, beta_bernoulli_alpha, beta_bernoulli_beta, beta_bernoulli_alpha_between, beta_bernoulli_beta_between, dirichlet_alpha, lambda, interaction_index_matrix, iter, warmup, counts_per_category, blume_capel_stats, main_alpha, main_beta, na_impute, missing_index, is_ordinal_variable, baseline_category, edge_selection, update_method, pairwise_effect_indices, target_accept, pairwise_stats, hmc_num_leapfrogs, nuts_max_depth, learn_mass_matrix, num_chains, nThreads, seed, progress_type)
 }
 
-get_explog_switch <- function() {
-    .Call(`_bgms_get_explog_switch`)
-}
-
-rcpp_ieee754_exp <- function(x) {
-    .Call(`_bgms_rcpp_ieee754_exp`, x)
-}
-
-rcpp_ieee754_log <- function(x) {
-    .Call(`_bgms_rcpp_ieee754_log`, x)
-}
-
 sample_omrf_gibbs <- function(no_states, no_variables, no_categories, interactions, thresholds, iter) {
     .Call(`_bgms_sample_omrf_gibbs`, no_states, no_variables, no_categories, interactions, thresholds, iter)
 }

R/generate_makevars_sources.R

@@ -0,0 +1,26 @@
+cpp <- list.files(
+  "src",
+  pattern = "\\.cpp$",
+  recursive = TRUE,
+  full.names = TRUE
+)
+
+# strip leading "src/"
+cpp <- sub("^src/", "", cpp)
+
+con <- file("src/sources.mk", open = "w")
+
+writeLines(c(
+  "# ------------------------------------------------------------------",
+  "# THIS FILE IS AUTO-GENERATED - DO NOT EDIT",
+  "# Generated by configure",
+  "# To add C++ code, place .cpp files anywhere under src/",
+  "# ------------------------------------------------------------------",
+  "SOURCES = \\"
+), con)
+
+writeLines(paste0("  ", cpp, " \\"), con)
+writeLines("", con)
+
+close(con)
+

configure

@@ -1,9 +1,12 @@
 #!/bin/sh
 
-# Get flags from RcppParallel
+# RcppParallel flags
 RCPP_PARALLEL_CPPFLAGS=`"${R_HOME}/bin/Rscript" -e "cat(RcppParallel::CxxFlags())"`
 RCPP_PARALLEL_LIBS=`"${R_HOME}/bin/Rscript" -e "cat(RcppParallel::LdFlags())"`
 
+# Generate sources.mk using R
+"${R_HOME}/bin/Rscript" R/generate_makevars_sources.R > src/sources.mk
+
 # Substitute into Makevars
 sed -e "s|@RCPP_PARALLEL_CPPFLAGS@|${RCPP_PARALLEL_CPPFLAGS}|" \
     -e "s|@RCPP_PARALLEL_LIBS@|${RCPP_PARALLEL_LIBS}|" \

configure.win

@@ -1,8 +1,12 @@
 #!/bin/sh
 
+# RcppParallel flags
 RCPP_PARALLEL_CPPFLAGS=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "cat(RcppParallel::CxxFlags())"`
 RCPP_PARALLEL_LIBS=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "cat(RcppParallel::LdFlags())"`
 
+# Generate sources.mk using R
+"${R_HOME}/bin/Rscript" R/generate_makevars_sources.R > src/sources.mk
+
 # Substitute into Makevars.win
 sed -e "s|@RCPP_PARALLEL_CPPFLAGS@|${RCPP_PARALLEL_CPPFLAGS}|" \
     -e "s|@RCPP_PARALLEL_LIBS@|${RCPP_PARALLEL_LIBS}|" \

src/Makevars.in

@@ -1,5 +1,9 @@
 CXX_STD = CXX20
 
-PKG_CPPFLAGS = @RCPP_PARALLEL_CPPFLAGS@ -DARMA_NO_DEBUG
+include sources.mk
+
+OBJECTS = $(SOURCES:.cpp=.o)
+
+PKG_CPPFLAGS = @RCPP_PARALLEL_CPPFLAGS@ -DARMA_NO_DEBUG -I.
 
 PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) @RCPP_PARALLEL_LIBS@

src/RcppExports.cpp

@@ -101,38 +101,6 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
-// get_explog_switch
-Rcpp::String get_explog_switch();
-RcppExport SEXP _bgms_get_explog_switch() {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    rcpp_result_gen = Rcpp::wrap(get_explog_switch());
-    return rcpp_result_gen;
-END_RCPP
-}
-// rcpp_ieee754_exp
-Rcpp::NumericVector rcpp_ieee754_exp(Rcpp::NumericVector x);
-RcppExport SEXP _bgms_rcpp_ieee754_exp(SEXP xSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::NumericVector >::type x(xSEXP);
-    rcpp_result_gen = Rcpp::wrap(rcpp_ieee754_exp(x));
-    return rcpp_result_gen;
-END_RCPP
-}
-// rcpp_ieee754_log
-Rcpp::NumericVector rcpp_ieee754_log(Rcpp::NumericVector x);
-RcppExport SEXP _bgms_rcpp_ieee754_log(SEXP xSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Rcpp::NumericVector >::type x(xSEXP);
-    rcpp_result_gen = Rcpp::wrap(rcpp_ieee754_log(x));
-    return rcpp_result_gen;
-END_RCPP
-}
 // sample_omrf_gibbs
 IntegerMatrix sample_omrf_gibbs(int no_states, int no_variables, IntegerVector no_categories, NumericMatrix interactions, NumericMatrix thresholds, int iter);
 RcppExport SEXP _bgms_sample_omrf_gibbs(SEXP no_statesSEXP, SEXP no_variablesSEXP, SEXP no_categoriesSEXP, SEXP interactionsSEXP, SEXP thresholdsSEXP, SEXP iterSEXP) {
@@ -185,9 +153,6 @@ END_RCPP
 static const R_CallMethodDef CallEntries[] = {
     {"_bgms_run_bgmCompare_parallel", (DL_FUNC) &_bgms_run_bgmCompare_parallel, 36},
     {"_bgms_run_bgm_parallel", (DL_FUNC) &_bgms_run_bgm_parallel, 34},
-    {"_bgms_get_explog_switch", (DL_FUNC) &_bgms_get_explog_switch, 0},
-    {"_bgms_rcpp_ieee754_exp", (DL_FUNC) &_bgms_rcpp_ieee754_exp, 1},
-    {"_bgms_rcpp_ieee754_log", (DL_FUNC) &_bgms_rcpp_ieee754_log, 1},
     {"_bgms_sample_omrf_gibbs", (DL_FUNC) &_bgms_sample_omrf_gibbs, 6},
     {"_bgms_sample_bcomrf_gibbs", (DL_FUNC) &_bgms_sample_bcomrf_gibbs, 8},
     {"_bgms_compute_Vn_mfm_sbm", (DL_FUNC) &_bgms_compute_Vn_mfm_sbm, 4},

src/bgm_helper.cpp src/bgm/bgm_helper.cppsrc/bgm_helper.cpp renamed to src/bgm/bgm_helper.cpp

@@ -1,6 +1,6 @@
 #include <RcppArmadillo.h>
-#include "bgm_helper.h"
-#include "common_helpers.h"
+#include "bgm/bgm_helper.h"
+#include "utils/common_helpers.h"
 
 
 

src/bgm_helper.h src/bgm/bgm_helper.hsrc/bgm_helper.h renamed to src/bgm/bgm_helper.h

@@ -1,7 +1,7 @@
 #pragma once
 
 #include <RcppArmadillo.h>
-#include "rng_utils.h"
+#include "rng/rng_utils.h"
 
 // Vectorize main_effect matrix
 arma::vec vectorize_main_effects_bgm(