Merge branch 'main' into issue-#111/replace-popt-in-rbdock

.github/workflows/build_matrix.yml

@@ -8,13 +8,13 @@ on:
 
 jobs:
   check-lint:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
     - uses: actions/checkout@v4
     - name: setup-lint
       run: |
         sudo apt-get update
-        sudo apt-get install -y --no-install-recommends clang-format make
+        sudo apt-get install -y --no-install-recommends clang-format=1:14.0-55~exp2 make
     - name: check-lint
       run: make lint-check
 

Makefile

@@ -58,6 +58,15 @@ CONFIG                      ?= RELEASE
 RBT_VERSION                 ?= v$(shell date +%y.%m-alpha)
 CXX                         ?= g++
 
+# OS-specific settings
+LIB_PATH_VAR := LD_LIBRARY_PATH
+ifeq ($(shell uname),Darwin)
+    BREW_PREFIX := /opt/homebrew
+    CXX_BASE_FLAGS += -I$(BREW_PREFIX)/include
+    LINK_FLAGS += -L$(BREW_PREFIX)/lib
+    LIB_PATH_VAR := DYLD_LIBRARY_PATH
+endif
+
 CXX_BASE_FLAGS              += -Wall
 CXX_STD                     ?= c++17
 EXE_FOLDER				    = src/exe
@@ -87,6 +96,12 @@ DEFINES                     += -DRBT_VERSION=\"$(RBT_VERSION)\"
 CXX_FLAGS                   := $(CXX_BASE_FLAGS) $(CXX_CONFIG_FLAGS) $(CXX_WARNING_FLAGS) $(CXX_EXTRA_FLAGS) $(DEFINES)
 LINK_FLAGS                  := -shared
 LIB_DEPENDENCIES            += -lm
+
+# Modify library dependencies for macOS
+ifeq ($(shell uname),Darwin)
+    LIB_DEPENDENCIES = -L$(BREW_PREFIX)/lib -lm
+endif
+
 LIBS                        += $(LIB_DEPENDENCIES) -lRbt
 INCLUDE                     := $(addprefix -I./, $(shell find include/ -type d )) $(addprefix -I./, $(shell find import/ -type d ))
 TESTS_INCLUDE				:= $(INCLUDE) $(addprefix -I./, $(shell find tests/include/ -type d ))
@@ -161,15 +176,15 @@ test: build ## run the tests suite
 
 test_dock_run: build tests/data/1YET_test.as
 	mkdir -p tests/results
-	cd tests/data ; RBT_ROOT=../.. LD_LIBRARY_PATH=../../lib:$(LD_LIBRARY_PATH) ../../bin/rbdock -r1YET_test.prm -i 1YET_c.sd -p dock.prm -n 1 -s 48151623 -o ../results/1YET_test_out > ../results/1YET_test_out.log
+	cd tests/data ; RBT_ROOT=../.. $(LIB_PATH_VAR)=../../lib:$($(LIB_PATH_VAR)) ../../bin/rbdock -r1YET_test.prm -i 1YET_c.sd -p dock.prm -n 1 -s 48151623 -o ../results/1YET_test_out > ../results/1YET_test_out.log
 
 	@tests/scripts/check_results.sh ./tests/data/1YET_reference_out.sd ./tests/results/1YET_test_out.sd
 
 test_rbcavity: tests/data/1koc.as tests/data/1YET.as tests/data/1YET_test.as
 	diff -q tests/data/1YET_test.as tests/data/1YET_reference_out.as
 
 test_suite: build_tests
-	LD_LIBRARY_PATH=./lib tests/bin/test_suite
+	$(LIB_PATH_VAR)=./lib tests/bin/test_suite
 
 clean: ## removes the object files and folder
 	@rm -rf obj
@@ -220,13 +235,13 @@ scripts: build_directories
 lib: lib/libRbt.so
 
 lib/libRbt.so: $(objects)
-	$(CXX) $(CXX_FLAGS) -shared -L$(LIBRARY) $^ -o lib/libRbt.so $(LIB_DEPENDENCIES)
+	$(CXX) $(CXX_FLAGS) $(LINK_FLAGS) -shared $^ -o lib/libRbt.so $(LIB_DEPENDENCIES)
 
 bin/%: src/exe/%.cxx lib/libRbt.so
 	$(CXX) $(CXX_FLAGS) $(INCLUDE) -L$(LIBRARY) -o $@ $< $(LIBS)
 
 tests/data/%.as: tests/data/%.prm bin/rbcavity
-	cd tests/data ; RBT_ROOT=../.. LD_LIBRARY_PATH=../../lib:$(LD_LIBRARY_PATH) ../../bin/rbcavity -r$(notdir $<) -was
+	cd tests/data ; RBT_ROOT=../.. $(LIB_PATH_VAR)=../../lib:$($(LIB_PATH_VAR)) ../../bin/rbcavity -r$(notdir $<) -was
 
 tests_directories:
 	@mkdir -p tests/obj tests/bin

README.md

@@ -1,13 +1,14 @@
 # rDock
+
 [![.github/workflows/build_matrix.yml](https://github.com/CBDD/rDock/actions/workflows/build_matrix.yml/badge.svg?branch=main)](https://github.com/CBDD/rDock/actions/workflows/build_matrix.yml)
 
-* [Quick start guide](#quick-start-guide)
-    + [Requirements](#requirements)
-    + [Compilation](#compilation)
-    + [Testing](#testing)
-    + [Installation](#installation)
-    + [Next steps](#next-steps)
-* [rDock legacy version](#rdock-legacy-version)
+- [Quick start guide](#quick-start-guide)
+  - [Requirements](#requirements)
+  - [Compilation](#compilation)
+  - [Testing](#testing)
+  - [Installation](#installation)
+  - [Next steps](#next-steps)
+- [rDock legacy version](#rdock-legacy-version)
 
 ## Quick start guide
 
@@ -19,16 +20,22 @@ In order to install precompiled binaries, you can follow the same steps as the [
 
 make sure the following requirements are installed and available:
 
-* make
-* a c++ compiler (g++ by default)
-* git (optional if you download the code directly)
+- make
+- a c++ compiler (g++ by default)
+- git (optional if you download the code directly)
 
 if you're running ubuntu, you can get all of them by running
 
 ```
 sudo apt update && sudo apt install -y make git g++
 ```
 
+if you're running `macOS`, make sure to use gcc instead of clang. You can install gcc and popt using homebrew
+
+```
+brew install gcc popt
+```
+
 you can also check requirements for other officially supported distributions in the [Dockerfiles](https://github.com/CBDD/rDock/blob/main/.github/docker) used for CI
 
 ### Compilation
@@ -41,7 +48,14 @@ cd rDock
 make
 ```
 
-if you have multiple cores available, you may want to speed up the build process running make like this (replace 4 with the number of parallel processes you'd like to run)  
+on `macOS`, you may need to run `export CXX=g++` before running make in order to use gcc instead of clang. Here is an example for gcc-14 installed with homebrew:
+
+```
+export CXX=/opt/homebrew/Cellar/gcc/14.2.0_1/bin/g++-14
+```
+
+if you have multiple cores available, you may want to speed up the build process running make like this (replace 4 with the number of parallel processes you'd like to run)
+
 ```
 make -j 4
 ```
@@ -62,7 +76,6 @@ select the location for rDock binaries, library and development headers to be in
 
 then set the PREFIX environment variable to point to this folder, for example ~/.local
 
-
 ```
 PREFIX=~/.local make install
 ```
@@ -81,6 +94,8 @@ export LD_LIBRARY_PATH=~/.local/lib:$LD_LIBRARY_PATH
 export RBT_ROOT=~/.local/rDock
 ```
 
+on `macOS`, LD_LIBRARY_PATH needs to be replaced by `DYLD_LIBRARY_PATH`
+
 you may want to add these lines to your profile/configuration files like ~/.bashrc
 
 ### Next steps

import/simplex/include/NMObjective.h

@@ -6,7 +6,7 @@
 #if !defined _userfile_
 #define _userfile_
 
-#include <malloc.h>
+#include <stdlib.h>
 #include <vector>
 
 double getInitialStep();