configure script

a3cf3343 · Maarten L. Hekkelman · 188fa4e5 · a3cf3343 · a3cf3343 · a3cf3343
Commit a3cf3343 authored Jun 15, 2020 by Maarten L. Hekkelman
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Showing with 505 additions and 15 deletions

GNUmakefile.in
+400 -0

README.md
+3 -15

config-tests/clipper-test.cpp
+9 -0

configure.ac
+80 -0

tools/m4esc.sh
+13 -0

No files found.
--- a/GNUmakefile.in
+++ b/GNUmakefile.in
+# makefile for libcif++
+
+.PHONY: firstTarget
+firstTarget: all
+
+CXX					= @CXX@
+CXXFLAGS			= @CXXFLAGS@
+
+CXXFLAGS			+= @BOOST_CPPFLAGS@
+LDFLAGS				+= @BOOST_LDFLAGS@
+
+prefix				= @prefix@
+exec_prefix			= @exec_prefix@
+libdir				= @libdir@
+includedir			= @includedir@
+
+
+LIB_NAME			= libcif++
+
+# DIST_NAME           = $(LIB_NAME)$(VERSION)
+# SO_NAME             = $(LIB_NAME).so.$(VERSION_MAJOR)
+# SHARED_LIB_NAME     = $(SO_NAME).$(VERSION_MINOR)
+STATIC_LIB_NAME		= $(LIB_NAME).a
+
+OUTPUT				= ./
+
+# SHARED_LIB			= $(OUTPUT)/$(SHARED_LIB_NAME)
+STATIC_LIB			= $(OUTPUT)/$(STATIC_LIB_NAME)
+
+LIBDIR              ?= $(PREFIX)/lib
+INCDIR              ?= $(PREFIX)/include
+MANDIR              ?= $(PREFIX)/man/man3
+DOCDIR              ?= $(PREFIX)/share/doc/libzeep-doc
+
+# main build variables
+CXXFLAGS            += -I. -pthread -I include/
+CXXFLAGS            += -Wall -Wno-multichar
+
+PACKAGES			+= 
+
+ifneq ($(PACKAGES),)
+CXXFLAGS			+= $(shell PKG_CONFIG_PATH=$(PKG_CONFIG_PATH) pkg-config --cflags $(PACKAGES))
+LDFLAGS				+= $(shell PKG_CONFIG_PATH=$(PKG_CONFIG_PATH) pkg-config --libs $(PACKAGES) )
+endif
+
+# Use the DEBUG flag to build debug versions of the code
+DEBUG               = @DEBUG@
+
+ifeq "$(DEBUG)" "1"
+DEFINES				+= DEBUG
+CXXFLAGS            += -g -O0
+LDFLAGS				+= -g
+else
+CXXFLAGS			+= -O2
+DEFINES				+= NDEBUG
+endif
+
+# targets
+
+VPATH += src:test
+
+CXXFLAGS			+= $(DEFINES:%=-D%)
+
+OBJDIR = obj
+ifeq "$(DEBUG)" "1"
+	OBJDIR	:= $(OBJDIR).dbg
+endif
+
+$(OBJDIR):
+	mkdir -p $(OBJDIR)
+
+LIBCIF_SRC		= AtomShape.cpp \
+				  AtomType.cpp \
+				  BondMap.cpp \
+				  Cif2PDB.cpp \
+				  Cif++.cpp \
+				  CifParser.cpp \
+				  CifUtils.cpp \
+				  CifValidator.cpp \
+				  Compound.cpp \
+				  DistanceMap.cpp \
+				  MapMaker.cpp \
+				  PDB2Cif.cpp \
+				  PDB2CifRemark3.cpp \
+				  Point.cpp \
+				  ResolutionCalculator.cpp \
+				  Secondary.cpp \
+				  Statistics.cpp \
+				  Structure.cpp \
+				  Symmetry.cpp \
+				  TlsParser.cpp
+
+SOURCES			= $(addprefix src/,$(LIBCIF_SRC))
+OBJECTS			= $(addprefix $(OBJDIR)/, $(notdir $(SOURCES:%.cpp=%.o)))
+
+# Special rules to generate symmetry operation number table
+tools/symop-map-generator: tools/symop-map-generator.cpp
+
+src/SymOpTable_data.cpp: tools/symop-map-generator $(CLIBD)/symop.lib
+	tools/symop-map-generator > $@
+
+$(OBJDIR)/Symmetry.o: src/SymOpTable_data.cpp
+
+$(STATIC_LIB): $(OBJECTS)
+	ar rc $@ $(OBJECTS)
+	ranlib $@
+
+$(SHARED_LIB): $(OBJECTS)
+	$(CXX) -shared -o $(SHARED_LIB) -Wl,-soname=$(SO_NAME) $(OBJECTS) $(LDFLAGS)
+	ln -fs $(SHARED_LIB_NAME) $(OUTPUT)/$(SO_NAME)
+	ln -fs $(SHARED_LIB_NAME) $(OUTPUT)/$(LIB_NAME).so
+
+ifeq "$(BUILD_STATIC_LIB)" "1"
+BUILD_LIBS = $(STATIC_LIB)
+endif
+
+ifeq "$(BUILD_SHARED_LIB)" "1"
+BUILD_LIBS += $(SHARED_LIB)
+endif
+
+libs: $(BUILD_LIBS)
+.PHONY: libs
+
+static-lib: $(STATIC_LIB)
+.PHONY: static-lib
+
+shared-lib: $(SHARED_LIB)
+.PHONY: shared-lib
+
+install-libs: $(SHARED_LIB)
+	install -d $(LIBDIR)
+	install $(SHARED_LIB) $(LIBDIR)/$(SHARED_LIB_NAME)
+	strip --strip-unneeded $(LIBDIR)/$(SHARED_LIB_NAME)
+	ln -Tfs $(SHARED_LIB_NAME) $(LIBDIR)/$(SO_NAME)
+	ln -Tfs $(SHARED_LIB_NAME) $(LIBDIR)/$(LIB_NAME).so
+	$(LD_CONFIG) -n $(LIBDIR)
+
+install-dev: $(STATIC_LIB)
+	install -d $(LIBDIR) $(INCDIR)/zeep/xml $(INCDIR)/zeep/http $(INCDIR)/zeep/http/webapp
+	for f in $(HEADERS); do install ../include/$$f $(INCDIR)/$$f; done
+	install $(STATIC_LIB) $(LIBDIR)/$(STATIC_LIB_NAME)
+	strip -SX $(LIBDIR)/$(STATIC_LIB_NAME)
+
+install: install-libs install-dev
+
+-include $(OBJECTS:%.o=%.d)
+
+$(OBJECTS:.o=.d):
+
+$(OBJDIR)/%.o: %.cpp | $(OBJDIR)
+	@ echo ">>" $<
+	@ $(CXX) -MD -c -o $@ $< $(CFLAGS) $(CXXFLAGS)
+
+.PHONY: clean
+clean:
+	rm -rf $(OBJDIR)/* $(OUTPUT)/$(LIB_NAME)*
+
+# Test rules
+
+BOOST_LIBS = 
+
+define TEST_template =
+
+-include $$(OBJDIR)/$(1)-test.d
+
+$(1)_OBJECTS = $$(OBJECTS) $$(OBJDIR)/$(1)-test.o
+
+test/$(1)-test: $$($(1)_OBJECTS)
+	@ echo ">>> building $(1)-test"
+	@ $(CXX) -o $$@ $$($(1)_OBJECTS) $$(CFLAGS) $$(CXXFLAGS) $(LDFLAGS) $(BOOST_LIBS:%=-lboost_%) -lstdc++fs
+
+.PHONY: $(1)-test
+$(1)-test: test/$(1)-test
+	cd test; ./$(1)-test $$($(1)_PARAMS)
+
+endef
+
+TESTS = unit
+
+$(foreach part,$(TESTS),$(eval $(call TEST_template,$(part))))
+
+.PHONY: test
+test: $(TESTS:%=%-test)
+
+dist-clean: clean
+
+FORCE:
+
+
+# ifeq ($(CLIB),)
+# $(warning "")
+# $(warning "The CCP4 environment seems to be unavailable, please source it")
+# $(warning "")
+
+# CLIBD ?= $(CLIB)/lib/data
+
+# make.config:
+# 	@ echo "No make.config file, writing a default one"
+# 	@ echo "#NO_RSRC = 1 # uncomment this line to disable resources" > make.config
+# 	@ echo "" >> make.config
+# 	@ echo "NEWUOA_DIR = # Please specify" >> make.config
+# 	@ echo "" >> make.config
+# 	@ echo "INCLUDE_DIR += \$$(NEWUOA_DIR:%=%/include) $(CINCL)" >> make.config
+# 	@ echo "LIBRARY_DIR += \$$(NEWUOA_DIR:%=%/lib) $(CLIB)" >> make.config
+# 	@ echo
+# 	@ echo "The default make.config now contains:"
+# 	@ cat make.config
+# 	@ echo
+# 	@ echo "Please update this make.config file to include the correct paths"
+
+# MRC					?= mrc
+
+# ifeq ($(NO_RSRC),)
+# ifeq ($(shell which $(MRC)),)
+# $(warning "")
+# $(warning "The executable mrc is not found in your path.")
+# $(warning "Please consider installing it to enable built-in data files.")
+# $(warning "See https://github.com/mhekkel/mrc")
+# $(warning "")
+# else
+# 	DEFINES			+= USE_RSRC
+# endif
+# endif
+
+# SO_NAME				= libcif++.so.1
+
+# CPU					= $(shell uname -m)
+# OS					= $(shell uname -o)
+# SYSLIBDIR			= /usr/lib
+
+# ifeq "$(OS)" "GNU/Linux"
+# 	SYSLIBDIR		:= $(SYSLIBDIR)/$(CPU)-linux-gnu
+# endif
+
+# WARNINGS			= all no-multichar no-unknown-pragmas no-deprecated-declarations
+
+# RANLIB				?= ranlib
+
+# INCLUDE_DIR			+= ./include
+# LIBRARY_DIR			+= 
+
+# CFLAGS				+= -std=c++17 -pthread -fPIC
+# CFLAGS				+= -ffunction-sections -fdata-sections
+# CFLAGS				+= $(addprefix -I, $(INCLUDE_DIR))
+
+# # generic defines
+
+# CFLAGS				+= $(addprefix -W, $(WARNINGS))
+# CFLAGS				+= $(addprefix -D, $(DEFINES))
+
+# LIBS				+= newuoa
+# # LDFLAGS				+= $(LIBRARY_DIR:%=-L %) $(LIBS:%=-l%) -g
+
+# OBJDIR				= obj
+
+# ifneq ($(DEBUG),1)
+# CFLAGS				+= -O3 -ffunction-sections -fdata-sections -DNDEBUG -g
+# else
+# CFLAGS				+= -g -DDEBUG 
+# OBJDIR				:= $(OBJDIR).dbg
+# endif
+
+# ifeq ($(PROFILE),1)
+# CFLAGS				+= -pg
+# LDFLAGS				+= -pg
+# OBJDIR				:= $(OBJDIR).profile
+# endif
+
+# CXXFLAGS			= $(CFLAGS)
+
+# LIBCIF_SRC		= AtomShape.cpp \
+# 				  AtomType.cpp \
+# 				  BondMap.cpp \
+# 				  Cif2PDB.cpp \
+# 				  Cif++.cpp \
+# 				  CifParser.cpp \
+# 				  CifUtils.cpp \
+# 				  CifValidator.cpp \
+# 				  Compound.cpp \
+# 				  DistanceMap.cpp \
+# 				  MapMaker.cpp \
+# 				  PDB2Cif.cpp \
+# 				  PDB2CifRemark3.cpp \
+# 				  Point.cpp \
+# 				  ResolutionCalculator.cpp \
+# 				  Secondary.cpp \
+# 				  Statistics.cpp \
+# 				  Structure.cpp \
+# 				  Symmetry.cpp \
+# 				  TlsParser.cpp
+
+# SOURCES			= $(addprefix src/,$(LIBCIF_SRC))
+# OBJECTS			= $(addprefix $(OBJDIR)/, $(notdir $(SOURCES:%.cpp=%.o)))
+
+# SOURCE_DIRS		= $(sort $(dir $(SOURCES)))
+
+# empty = 
+# space = $(empty) $(empty)
+# SRC_VPATH = $(subst $(space),:,$(SOURCE_DIRS))
+
+# VPATH += $(SRC_VPATH)
+
+# $(OBJDIR)/%.o: %.cpp | $(OBJDIR)
+# 	@ echo ">>" $<
+# 	@ $(CXX) -MD -c -o $@ $< $(CFLAGS) $(CXXFLAGS)
+
+# -include $(OBJECTS:%.o=%.d)
+
+# $(OBJECTS:.o=.d):
+
+# $(OBJDIR):
+# 	@ test -d $@ || mkdir -p $@
+
+# # Special rules to generate symmetry operation number table
+# tools/symop-map-generator: tools/symop-map-generator.cpp
+
+# src/SymOpTable_data.cpp: tools/symop-map-generator $(CLIBD)/symop.lib
+# 	tools/symop-map-generator > $@
+
+# $(OBJDIR)/Symmetry.o: src/SymOpTable_data.cpp
+
+# .PHONY: clean all
+# clean:
+# 	rm -rf $(OBJDIR)/* libcif++.a
+
+# .PHONY: static-lib
+# static-lib: libcif++.a
+
+# libcif++.a: $(OBJECTS)
+# 	ar rc $@ $^
+# 	$(RANLIB) $@
+
+# .PHONY: shared-lib
+# shared-lib: libcif++.a
+
+# libcif++.so: $(OBJECTS)
+# 	$(CXX) -shared -o $(SO_NAME) $^ $(LDFLAGS) -Wl,-soname=$(SO_NAME)
+# 	ln -fs $(SO_NAME) $@
+
+# BOOST_LIB_DIR		?= $(SYSLIBDIR)
+
+# BOOST_LIBS			= date_time iostreams program_options filesystem thread math_c99 math_c99f timer chrono system regex random
+# BOOST_LIBS			:= $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX))
+# BOOST_LIBS			:= $(BOOST_LIBS:%=$(BOOST_LIB_DIR)/lib%.a)
+
+# CLIPPER_LIBS		= clipper-ccp4 clipper-minimol clipper-mmdb clipper-cns clipper-phs clipper-contrib clipper-core
+# CLIPPER_LIB_DIR		?= $(CLIB)
+# ifeq ($(STATIC_CPP4_LIBS),1)
+# CLIPPER_LIBS		:= $(CLIPPER_LIBS:%=$(CLIPPER_LIB_DIR)/lib%.a)
+# else
+# CLIPPER_LIBS		:= $(CLIPPER_LIBS:%=-l%)
+# endif
+
+# ZEEP_LIBS			?= xml el generic
+# ZEEP_LIBS			:= $(ZEEP_LIBS:%=-lzeep-%)
+
+# CCP4_LIBS			+= ccp4c mmdb2 rfftw fftw
+# CCP4_LIB_DIR		?= $(CLIB)
+# ifeq ($(STATIC_CPP4_LIBS),1)
+# CCP4_LIBS			:= $(CCP4_LIBS:%=$(CCP4_LIB_DIR)/lib%.a)
+# else
+# CCP4_LIBS			:= $(CCP4_LIB_DIR:%=-L%) $(CCP4_LIBS:%=-l%)
+# endif
+
+# TEST_LIBS			= $(LIBS)
+# TEST_LIBS			+= m rt
+# TEST_LIBS			:= $(TEST_LIBS:%=-l%)
+# TEST_LIBS			+= $(ZEEP_LIBS) $(BOOST_LIBS) $(CLIPPER_LIBS) $(CCP4_LIBS) -lz -lbz2 -lpthread 
+
+# TEST_LDFLAGS		= $(LDFLAGS)
+# TEST_LDFLAGS		+= $(LIBRARY_DIR:%=-L %) $(TEST_LIBS) -g
+# TEST_LDFLAGS		+= -Wl,-rpath=$(CLIB)
+
+# VPATH += test
+
+# define TEST_template =
+
+# $$(OBJDIR)/$(1)_rsrc.o: rsrc/dictionaries
+# 	$(MRC) -o $$@ $$^
+
+# test/$(1)-test: $$(OBJECTS) $$(OBJDIR)/$(1)-test.o libcif++.a $$(OBJDIR)/$(1)_rsrc.o
+# 	@ echo ">>> building $(1)-test"
+# 	@ $(CXX) -o $$@ $$(OBJDIR)/$(1)-test.o $$(OBJDIR)/$(1)_rsrc.o $$(OBJECTS) $$(CFLAGS) $$(CXXFLAGS) $(TEST_LDFLAGS)
+
+# .PHONY: $(1)-test
+# $(1)-test: test/$(1)-test
+# 	test/$(1)-test $$($(1)_PARAMS)
+
+# -include $$(OBJDIR)/$(1)-test.d
+
+# endef
+
+# TESTS = unit
+# $(foreach part,$(TESTS),$(eval $(call TEST_template,$(part))))
+
+# .PHONY: test
+# test: $(TESTS:%=%-test)
+
+# all: static-lib
+
--- a/README.md
+++ b/README.md
-libcif++ and pdb-redo tools
-===========================
+libcif++
+========

-This is the README file for libcif++ and the suite of PDB-REDO tools
-using this library.
+This is the README file for libcif++.

 Requirements
 ------------
@@ -23,17 +22,6 @@ Other requirements are:
  functionality.
 - [newuoa-cpp](https://github.com/elsid/newuoa-cpp), required to
  calculate atom radii.
- [libzeep](https://github.com/mhekkel/libzeep), a library that
-  contains a full validating XML parser as well as a complete HTTP,
-  SOAP and REST server implementation.
- [nlohmann/json](https://github.com/nlohmann/json), a header only
-  library to parse and write JSON. This is only a requirement if you
-  have a libzeep version older than version 4.
-
-As stated, the nlohmann library is only needed if you use libzeep 3.0.x
-which is bundled with Debian and derivatives (`apt-get install libzeep-dev`).
-If you clone the version of libzeep on github the nlohmann json library will
-not be used.

 Building
 --------

--- a/config-tests/clipper-test.cpp
+++ b/config-tests/clipper-test.cpp
+// test to see if the clipper version is up-to-date enough
+
+#include <clipper/core/atomsf.h>
+
+int main()
+{
+  auto sf = clipper::ScatteringFactors::instance()["C"];
+  return 0;
+}
--- a/configure.ac
+++ b/configure.ac
+AC_INIT([libcif++], 1.0, [m.hekkelman@nki.nl])
+
+dnl Switch to a C++ compiler, and check if it works.
+AC_LANG(C++)
+AX_CXX_COMPILE_STDCXX_14([noext])
+
+AC_CONFIG_SRCDIR([src/AtomShape.cpp])
+AC_CONFIG_AUX_DIR(config)
+AC_CONFIG_MACRO_DIR([config/m4])
+
+AC_PREFIX_DEFAULT(/usr/local)
+
+AC_DEFUN([read_test], [AC_LANG_SOURCE(
+	esyscmd(tools/m4esc.sh config-tests/$1))])
+
+AX_BOOST_BASE([1.73])
+
+AC_PROG_INSTALL
+
+AC_ARG_VAR([DEBUG], [Build a debug version of the library])
+
+AC_PATH_PROG([PKG_CONFIG], [pkg-config])
+
+AC_ARG_VAR([CCP4], [The location where CCP4 is installed])
+
+AS_IF([test x"$CCP4" != x""],
+	  [
+		CPPFLAGS="$CPPFLAGS -I ${CCP4}/include"
+		CXXFLAGS="$CXXFLAGS -I ${CCP4}/include"
+	  ])
+
+AC_ARG_WITH([clipper],
+	AS_HELP_STRING([--with-clipper=@<:@location@:>@],
+		[Use the clipper library as specified.
+		@<:@location=$CCP4@:>@]),
+		[
+			CPPFLAGS="$CPPFLAGS -I ${withval}/include"
+			CXXFLAGS="$CXXFLAGS -I ${withval}/include"
+		])
+
+AC_ARG_WITH([newuoa],
+	AS_HELP_STRING([--with-newuoa=@<:@location@:>@],
+		[Use the newuoa library as specified.]),
+		[
+			CPPFLAGS="$CPPFLAGS -I ${withval}/include"
+			CXXFLAGS="$CXXFLAGS -I ${withval}/include"
+		])
+
+AC_CHECK_HEADER(
+	[clipper/clipper.h],
+	[],
+	[AC_MSG_ERROR([
+Can't find the main clipper include file clipper/clipper.h. Please
+specify either the CCP4 location of the location of the installed
+clipper using --with-clipper=<path>
+])])
+
+AC_MSG_CHECKING([clipper version])
+AC_COMPILE_IFELSE(
+	[read_test(clipper-test.cpp)],
+	[],
+	[AC_MSG_ERROR([The version of clipper is not up to date])])
+
+AC_CHECK_HEADER(
+	[newuoa.h],
+	[],
+	[AC_MSG_ERROR([
+Can't find the newuoa include file newuoa.h. Please install this
+library and specify its location with --with-newuoa=<path>.
+You can find newuoa at https://github.com/elsid/newuoa-cpp.git
+])])
+
+# AC_ARG_ENABLE(
+# 	debug,
+# 	[AS_HELP_STRING([--enable-debug], [Generate a debug version of the library])],
+# 	[],
+# 	[enable_debug=auto])
+
+dnl Process Makefile.in to create Makefile
+AC_OUTPUT([GNUmakefile])
--- a/tools/m4esc.sh
+++ b/tools/m4esc.sh
+#!/bin/bash
+
+set -e
+
+file="$1"
+
+echo -n "[["
+while IFS= read -r line; do
+	echo $line | sed -e 's/\[/@<:@/g' -e 's/\]/@:>@/g' -e 's/#/@%:@/g' -e 's/\$/@S|@/g'
+	echo
+done < "$file"
+
+echo -n "]]"