Makefile

# Custom Makefile for direct compilation and installation of the rDock library and binaries
# 2023-03-31, Zaragoza, Spain
# 
# How to use this Makefile:
#
# set any environment variables you need to set before (or while) invoking make with the desired target, e.g.:
#   export CXX=g++-7; make -j 4
# or
#   CXX=g++-9 PREFIX=~/.local make -j 4
#
# the following targets are available for the user:
#   help: display this help
#   targets: display a list of all the targets available with a short description
#   build: build the library and binaries (default target)
#   build_lib: build the library
#   build_bin: build the binaries
#   test: run the tests suite
#   test_dock_run: run rbdock and compare results with a reference run
#   test_rbcavity: runs rbcavity on the test systems to generate the .as files
#   clean: removes the object files
#   clean_lib: removes the lib folder
#   clean_bin: removes the compiled binaries
#   clean_tests: removes the files generated by test execution
#   veryclean: removes all the above
#   install: install the library, binaries, and headers in PREFIX folder
#         and the data folder in RBT_ROOT (see below)
#   full: cleans everything and rebuilds the library and binaries from scratch,
#         then runs the tests and uses the install target to install everything
#   lint: format the code using clang-format. Requires clang-format to be installed
#         it is recommended to run this target before committing any changes to the code
#         as the CI will fail if the code is not properly formatted.
#
#
# the following variables can be configured by the user:
#   CONFIG: the configuration to build. Can be DEBUG or RELEASE. Default: RELEASE
#           if DEBUG is set, the library and binaries are built with debug symbols and
#           the -D_DEBUG macro is defined, making the code more verbose (but slower).
#
#   PREFIX: the folder where to install the library, binaries, and headers. Default: /usr
#			binaries are installed in $(PREFIX)/bin, library in $(PREFIX)/lib,
#			and headers in $(PREFIX)/include/rdock
#
#   RBT_ROOT: the folder where the rDock data folder is installed. Default: $(PREFIX)/share/rdock
#
#   CXX: the c++ compiler to use. Default: g++
#
#   CXX_EXTRA_FLAGS: extra flags to pass to the compiler. Default: empty
#
#   CXX_STD: the c++ standard to use. Default: c++17
#
#   RBT_VERSION: the version of the library. Default: vYY.MM-alpha
#           this is used by the CI/CD pipeline to set the version of the library and binaries
#           you can set it to any value you want for your local builds, for cosmetic purposes.

PREFIX                      ?= /usr
RBT_ROOT                    ?= $(PREFIX)/share/rdock
CONFIG                      ?= RELEASE
RBT_VERSION                 ?= v$(shell date +%y.%m-alpha)
CXX                         ?= g++

CXX_BASE_FLAGS              += -Wall
CXX_STD                     ?= c++17
EXE_FOLDER				    = src/exe

CXX_EXTRA_FLAGS             ?=
CXX_BASE_FLAGS              += -pipe -std=$(CXX_STD) -fPIC
CXX_DEBUG_CONFIG_FLAGS      += -O0 -g
CXX_RELEASE_CONFIG_FLAGS    += -O3 -ffast-math
CXX_WARNING_FLAGS           +=

DEBUG_DEFINES               := -D_DEBUG
RELEASE_DEFINES             := -D_NDEBUG

ifeq ($(LEGACY_BUILD),YES)
	_ := $(error This option has been removed. If you really need it, checkout the rdock-legacy branch and try again.)
endif

ifeq ($(CONFIG),DEBUG)
	CXX_CONFIG_FLAGS        += $(CXX_DEBUG_CONFIG_FLAGS)
	DEFINES                 += $(DEBUG_DEFINES)
else
	CXX_CONFIG_FLAGS        += $(CXX_RELEASE_CONFIG_FLAGS)
	DEFINES                 += $(RELEASE_DEFINES)
endif

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 -lpopt
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 ))
LIBRARY                     := ./lib


simplex_sources = $(shell find import/simplex/src/ -type f -name '*.cxx')
simplex_objects = $(subst import/simplex/src, obj/simplex, $(simplex_sources:.cxx=.o))

GP_sources      = $(shell find src/GP/ -type f -name 'Rbt*.cxx')
GP_objects      = $(subst src/GP/, obj/GP/, $(GP_sources:.cxx=.o))

RBT_sources     = $(shell find src/lib/ -type f -name '*.cxx')
RBT_objects     = $(subst src/lib/, obj/, $(RBT_sources:.cxx=.o))

tests_sources   = $(shell find tests/src/ -type f -name '*.cpp')
tests_objects   = tests/obj/catch_amalgamated.o $(subst tests/src/, tests/obj/, $(tests_sources:.cpp=.o))

objects         = $(RBT_objects) $(simplex_objects) $(GP_objects)

objdirs         = $(sort $(dir $(objects)))
$(shell mkdir -p $(objdirs) ./lib ./bin)

bin_names   = rbdock rbcavity rbmoegrid rblist rbcalcgrid
bins        = $(addprefix bin/, $(bin_names))


.PHONY:	\
	install \
	target_folders build_directories \
	lib bin scripts \
	build build_lib build_bin \
	test test_dock_run test_rbcavity \
	clean clean_bin clean_lib veryclean \
	lint lint-check \
	targets help \

## User directed targets

build: build_lib build_bin scripts ## build the library and binaries (default target)

install: build target_folders ## install the library, binaries, and headers in PREFIX folder
	@cp -r bin/* $(PREFIX)/bin
	@cp -r lib/* $(PREFIX)/lib
	$(MAKE) install-include
	@cp -r data $(RBT_ROOT)

install-include: target_folders
	@cp -r include/* $(PREFIX)/include/rdock

full: ## equivalent to veryclean build test install
	$(MAKE) veryclean
	$(MAKE) build
	$(MAKE) test
	$(MAKE) install

build_bin: build_directories
	$(MAKE) $(bins)

build_lib: build_directories
	$(MAKE) lib

build_tests: tests_directories build
	$(MAKE) tests_bin

retest: build
	$(MAKE) clean_tests
	$(MAKE) test

test: build ## run the tests suite
	$(MAKE) test_rbcavity test_dock_run test_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
	
	@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

clean: ## removes the object files and folder
	@rm -rf obj

clean_bin: ## removes the compiled binaries and bin folder
	@rm -f $(bins)

clean_lib: ## removes the compiled library file, libRbt.so
	@rm -f lib/libRbt.so

clean_tests: ## removes the files generated by test execution
	@mv tests/data/1YET_reference_out.as tests/data/1YET_reference_out.as.bak
	@rm -rf tests/results tests/data/*.as
	@mv tests/data/1YET_reference_out.as.bak tests/data/1YET_reference_out.as

clean_tests_objects: ## removes the object files generated by the tests
	@rm -rf tests/obj
	@rm -f tests/bin/test_suite

veryclean: clean clean_bin clean_lib clean_tests clean_tests_objects ## equivalent to clean clean_bin clean_lib clean_tests clean_tests_objects

lint: ## format the code using clang-format. Requires clang-format to be installed
	@clang-format --style=file -i $(shell find src/ include/ tests/ -iname '*.cxx' -o -iname '*.h' -o -iname '*.cpp')

## Internal targets

target_folders:
	@mkdir -p $(PREFIX)/bin $(PREFIX)/lib $(PREFIX)/include/rdock $(RBT_ROOT)

build_directories:
	@mkdir -p $(objdirs) ./lib ./bin ./log ./tests/tmp

obj/%.o: src/lib/%.cxx
	@echo $(CXX) $(CXX_FLAGS) $(INCLUDE) -c -o $@ $<
	@$(CXX) $(CXX_FLAGS) $(INCLUDE) -c -o $@ $<

obj/simplex/%.o: import/simplex/src/%.cxx
	@echo $(CXX) $(CXX_FLAGS) $(INCLUDE) -c -o $@ $<
	$(CXX) $(CXX_FLAGS) $(INCLUDE) -c -o $@ $<

obj/GP/%.o: src/GP/%.cxx
	@echo $(CXX) $(CXX_FLAGS) $(INCLUDE) -c -o $@ $<
	$(CXX) $(CXX_FLAGS) $(INCLUDE) -c -o $@ $<

scripts: build_directories
	@cp -r scripts/* bin/

lib: lib/libRbt.so

lib/libRbt.so: $(objects)
	$(CXX) $(CXX_FLAGS) -shared -L$(LIBRARY) $^ -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

tests_directories:
	@mkdir -p tests/obj tests/bin

tests_bin: $(tests_objects)
	$(CXX) $(CXX_FLAGS) $(TESTS_INCLUDE) -L$(LIBRARY) -o tests/bin/test_suite $^ $(LIBS)

tests/obj/catch_amalgamated.o: import/catch2/catch_amalgamated.cpp
	@echo $(CXX) $(CXX_FLAGS) $(TESTS_INCLUDE) -c -o $@ $<
	$(CXX) $(CXX_FLAGS) $(TESTS_INCLUDE) -c -o $@ $<

tests/obj/%.o: tests/src/%.cpp
	@echo $(CXX) $(CXX_FLAGS) $(TESTS_INCLUDE) -c -o $@ $<
	$(CXX) $(CXX_FLAGS) $(TESTS_INCLUDE) -c -o $@ $<

lint-check:
	@echo "Checking code style..."
	# --ferror-limit=1 is used to stop the execution after the first error until we fix all the code
	@clang-format --style=file -Werror --dry-run --ferror-limit=1 $(shell find src/ include/ -iname '*.cxx' -o -iname '*.h')

targets:  ## Display this help
	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) |\
	awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-20s\033[0m %s\n", $$1, $$2}'

help:  ## detailed help
	@ awk '/^#/ {print; next} {if (NR>1) exit}' $(MAKEFILE_LIST) | sed -e 's/^#//'