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libcifpp
Commit 98e3c47c by Maarten L. Hekkelman
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remove configure

parent 390b230c
Showing with 0 additions and 929 deletions
GNUmakefile.in deleted 100644 → 0
# SPDX-License-Identifier: BSD-2-Clause
#
# Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# makefile for libcifpp
.PHONY: firstTarget
firstTarget: all
CXX = @CXX@
CXXFLAGS = @BOOST_CPPFLAGS@ \
@CPPFLAGS@ \
@CXXFLAGS@ \
@PTHREAD_CFLAGS@
LDFLAGS = @BOOST_LDFLAGS@ \
@LDFLAGS@ \
@LIBS@
LIBS = @PTHREAD_LIBS@ \
@BOOST_IOSTREAMS_LIB@ \
@BOOST_DATE_TIME_LIB@ \
@BOOST_REGEX_LIB@ \
@LIBS@
prefix = $(DESTDIR)@prefix@
exec_prefix = @exec_prefix@
libdir = @libdir@
includedir = @includedir@
datarootdir = @datarootdir@
datadir = @datadir@
docdir = @docdir@
pkgconfigdir = $(libdir)/pkgconfig
CCP4DIR = @CCP4@
CLIBD = $(CCP4DIR:%=%/lib/data)
CACHE_DIR = $(DESTDIR)@DATA_CACHE_DIR@
DATA_DIR = @DATA_LIB_DIR@
CRON_DIR = $(DESTDIR)/etc/cron.weekly
DEFINES += CACHE_DIR='"$(CACHE_DIR)"' DATA_DIR='"$(DATA_DIR)"'
DEFINES += USE_RSRC=@USE_RSRC@
GNUmakefile: config.status GNUmakefile.in
$(SHELL) ./config.status
LIB_NAME = @PACKAGE_NAME@
LIB_VERSION = @LIBCIF_LT_VERSION@
LIB_CURRENT = @LIBCIF_LT_CURRENT@
LIB_TARGET = $(LIB_NAME).la
VERSION = @LIBCIF_SEMANTIC_VERSION@
DIST_NAME = @PACKAGE_NAME@-$(subst :,.,$(VERSION))
SKIP_DOWNLOAD_CCD = @SKIP_DOWNLOAD_CCD@
ifneq "$(SKIP_DOWNLOAD_CCD)" "1"
COMPONENTS_CIF = components.cif
endif
# libtool stuff
LIBTOOL_DEPS = @LIBTOOL_DEPS@
libtool: $(LIBTOOL_DEPS)
$(SHELL) ./config.status libtool
LIBTOOL = $(SHELL) @abs_top_builddir@/libtool
CXXCOMPILE = $(LIBTOOL) --silent --tag=CXX --mode=compile $(CXX) $(CXXFLAGS)
CXXLINK = $(LIBTOOL) --silent --tag=CXX --mode=link $(CXX) $(CXXFLAGS) $(LDFLAGS) -version-info $(LIB_VERSION) -o $@
# main build variables
CXXFLAGS += -Wall -Wno-multichar -I include
# Use the DEBUG flag to build debug versions of the code
DEBUG = @DEBUG@
ifeq "$(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)
OBJECTS = $(OBJDIR)/AtomType.lo \
$(OBJDIR)/BondMap.lo \
$(OBJDIR)/Cif2PDB.lo \
$(OBJDIR)/Cif++.lo \
$(OBJDIR)/CifParser.lo \
$(OBJDIR)/CifUtils.lo \
$(OBJDIR)/CifValidator.lo \
$(OBJDIR)/Compound.lo \
$(OBJDIR)/PDB2Cif.lo \
$(OBJDIR)/PDB2CifRemark3.lo \
$(OBJDIR)/Point.lo \
$(OBJDIR)/Secondary.lo \
$(OBJDIR)/Structure.lo \
$(OBJDIR)/Symmetry.lo \
$(OBJDIR)/TlsParser.lo
ifneq "$(CCP4DIR)" ""
# 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 $@
$(OBJDIR)/Symmetry.lo: src/SymOpTable_data.cpp
endif
ifneq "$(COMPONENTS_CIF)" ""
data/components.cif.gz:
mkdir -p data
wget -O $@ ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
data/components.cif: data/components.cif.gz
gunzip -c $^ > $@
endif
# We have development releases and official releases, for each we
# maintain different versioning schemes.
ifneq "x@UPDATE_REVISION@" "x"
REVISION = $(shell git log --pretty=format:%h --max-count=1)
REVISION_FILE = version-info-$(REVISION).txt
$(REVISION_FILE):
rm -f version-info-*.txt
@ echo libcifpp-version: $(VERSION) > $@
@ git describe --match=build --dirty >> $@
@ git log --pretty=medium --date=iso8601 -1 >> $@
src/revision.hpp: $(REVISION_FILE)
@ echo 'const char kRevision[] = R"(' > $@
@ cat $? >> $@
@ echo ')";' >> $@
else
src/revision.hpp:
@ echo 'const char kRevision[] = R"(' > $@
@ echo libcifpp-version: $(VERSION) >> $@
@ echo Date: $$(TZ=GMT date +"%Y-%m-%d") >> $@
@ echo ')";' >> $@
endif
$(OBJDIR)/CifUtils.o: src/revision.hpp
$(OBJDIR)/CifUtils.lo: src/revision.hpp
$(LIB_TARGET): $(OBJECTS)
$(CXXLINK) -rpath $(libdir) $(OBJECTS) $(LIBS)
.PHONY: lib
lib: $(LIB_TARGET)
.PHONY: all
all: $(LIB_TARGET)
-include $(OBJECTS:%.lo=%.d)
$(OBJECTS:.lo=.d):
$(OBJDIR)/%.lo: %.cpp | $(OBJDIR)
@ echo ">>" $<
@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(OBJDIR)/$*.d -c -o $@ $<
$(OBJDIR)/%.o: %.cpp | $(OBJDIR)
@ echo ">>" $<
@ $(CXX) $(CXXFLAGS) -MT $@ -MD -MP -MF $(OBJDIR)/$*.d -c -o $@ $<
.PHONY: clean
clean:
rm -rf .libs $(OBJDIR)/* $(LIB_TARGET)
rm -f $(TESTS:%=test/%-test)
.PHONY: distclean
distclean: clean
rm -f libtool config.lt
rm -f config.status config.cache config.log configure.lineno config.status.lineno
rm -f GNUmakefile
# Test rules
examples/pdb1cbs.ent: examples/pdb1cbs.ent.gz
gunzip -c $? > $@
pdb2cif_PARAMS = ../examples/pdb1cbs.ent
define TEST_template =
-include $$(OBJDIR)/$(1)-test.d
$(1)_OBJECTS = $$(OBJDIR)/$(1)-test.o
test/$(1)-test: $(LIB_TARGET) $$($(1)_OBJECTS) data/components.cif examples/pdb1cbs.ent
@ echo ">>> building $(1)-test"
$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $$@ $$($(1)_OBJECTS) -L.libs -lcifpp -lboost_program_options $(LIBS)
.PHONY: $(1)-test
$(1)-test: test/$(1)-test
cd test; LD_LIBRARY_PATH=../.libs ./$(1)-test $$($(1)_PARAMS)
endef
TESTS = unit pdb2cif rename-compound
$(foreach part,$(TESTS),$(eval $(call TEST_template,$(part))))
.PHONY: test
test: $(TESTS:%=%-test)
HEADERS = \
AtomType.hpp \
BondMap.hpp \
CifParser.hpp \
Compound.hpp \
PDB2CifRemark3.hpp \
Structure.hpp \
Cif2PDB.hpp \
CifUtils.hpp \
Point.hpp \
Symmetry.hpp \
Cif++.hpp \
CifValidator.hpp \
PDB2Cif.hpp \
Secondary.hpp \
TlsParser.hpp
.PHONY: install-data
ifneq "$(COMPONENTS_CIF)" ""
install-data: data/components.cif.gz
install -d $(datadir)/libcifpp
install -m644 data/components.cif.gz $(datadir)/libcifpp/
else
install-data:
endif
.PHONY: install-lib
install: install-lib
install -d $(libdir)
$(LIBTOOL) --mode=install install $(LIB_TARGET) $(libdir)
install -d $(datadir)/libcifpp
for d in mmcif_ddl.dic mmcif_pdbx_v50.dic; do \
install -m644 rsrc/$$d $(datadir)/libcifpp; \
gzip -f $(datadir)/libcifpp/$$d; \
done
install -d $(CACHE_DIR)
install -d $(CRON_DIR)
if [ ! -f /etc/libcifpp.conf ] ; then \
echo "# Uncomment the next line to enable automatic updates" > /etc/libcifpp.conf; \
echo "# update=true" >> /etc/libcifpp.conf; \
echo ""; \
echo "Update the /etc/libcifpp.conf file to enable automatic updates"; \
echo ""; \
fi
install -m755 tools/update-dictionary-script $(CRON_DIR)/libcifpp
install -d $(includedir)/cif++
for f in $(HEADERS); do install include/cif++/$$f $(includedir)/cif++/$$f; done
install -d $(pkgconfigdir)
install -m 644 $(LIB_NAME).pc $(pkgconfigdir)/$(LIB_NAME).pc
.PHONY: install
install: install-lib install-data
dist-clean: clean
.PHONY: dist
dist:
rm -rf $(DIST_NAME)
mkdir $(DIST_NAME)
git archive trunk | tar -x -C $(DIST_NAME)
tar czf $(DIST_NAME).tgz $(DIST_NAME)
rm -rf $(DIST_NAME)
FORCE:
config/ltmain.sh deleted 100644 → 0
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config/m4/ax_filesystem.m4 deleted 100644 → 0
# SPDX-License-Identifier: BSD-2-Clause
#
# Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Description: m4 macro to detect std::filesystem and optionally the linker flags to use it
AC_DEFUN([AX_FILESYSTEM],
[
AC_CHECK_HEADER([filesystem], [], [AC_MSG_ERROR([The file <filesystem> is missing, perhaps you should install a more recent libstdc++ implementation.])])
dnl check if we need stdc++fs as library
AC_TRY_LINK(
[#include <filesystem>],
[(void)std::filesystem::current_path();],
[],
[
LIBS="$LIBS -lstdc++fs"
AC_TRY_LINK(
[#include <filesystem>],
[(void)std::filesystem::current_path();],
[],
[
AC_MSG_ERROR([Could not link filesystem])
]
)
]
)
])
config/m4/ax_mrc.m4 deleted 100644 → 0
# SPDX-License-Identifier: BSD-2-Clause
#
# Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Description: m4 macro to detect mrc, the resource compiler
AC_DEFUN([AX_MRC],
[
AC_ARG_VAR([MRC], [Specify a location for the mrc executable])
dnl using resources?
USE_RSRC=0
if test "x$MRC" = "x"; then
AC_PATH_PROG([MRC], [mrc])
fi
if test "x$MRC" = "x"; then
AC_MSG_WARN([The mrc application was not found, not using resources.])
else
AC_ARG_ENABLE(
resources,
[AS_HELP_STRING([--disable-resources], [Do not use mrc to store data in resources])])
AS_IF([test "x$enable_resources" != "xno" ], [
USE_RSRC=1
])
fi
AC_SUBST([USE_RSRC], [$USE_RSRC])
AC_DEFINE_UNQUOTED([USE_RSRC], [$USE_RSRC], [Use mrc to store resources])
])
\ No newline at end of file
config/m4/ax_z_bz2.m4 deleted 100644 → 0
# SPDX-License-Identifier: BSD-2-Clause
#
# Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Description: m4 macro to detect whether the z and bz2 libraries needs to be linked
# when using boost::iostreams
AC_DEFUN([read_test], [
AC_LANG_SOURCE(esyscmd(config/tools/m4esc.sh config/test/$1))])
AC_DEFUN([AX_IOSTREAMS_Z],
[
AC_MSG_CHECKING([need to link zlib])
save_CPPFLAGS="$CPPFLAGS"
CPPFLAGS="$BOOST_CPPFLAGS $CPPFLAGS "
save_LDFLAGS="$LDFLAGS"
LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
save_LIBS="$LIBS"
LIBS="$LIBS $BOOST $BOOST_IOSTREAMS_LIB"
NEED_ZLIB=0
AC_LINK_IFELSE(
[read_test(iostreams-zlib-test.cpp)],
[AC_MSG_RESULT([no])],
[
LIBS="$LIBS -lz"
AC_LINK_IFELSE(
[read_test(iostreams-zlib-test.cpp)],
[
AC_MSG_RESULT([yes])
NEED_ZLIB=1
],
[AC_MSG_ERROR([Could not link iostreams, even with zlib])])
])
CPPFLAGS="$save_CPPFLAGS"
LDFLAGS="$save_LDFLAGS"
LIBS="$save_LIBS"
if [ test "x$NEED_ZLIB" != "x" ]; then
LIBS="$LIBS -lz"
fi
])
AC_DEFUN([AX_IOSTREAMS_BZ2],
[
AC_MSG_CHECKING([need to link bzip2])
save_CPPFLAGS="$CPPFLAGS"
CPPFLAGS="$BOOST_CPPFLAGS $CPPFLAGS "
save_LDFLAGS="$LDFLAGS"
LDFLAGS="$LDFLAGS $BOOST_LDFLAGS"
save_LIBS="$LIBS"
LIBS="$LIBS $BOOST $BOOST_IOSTREAMS_LIB"
NEED_BZLIB=0
AC_LINK_IFELSE(
[read_test(iostreams-bzip2-test.cpp)],
[AC_MSG_RESULT([no])],
[
LIBS="$LIBS -lbz2"
AC_LINK_IFELSE(
[read_test(iostreams-bzip2-test.cpp)],
[
AC_MSG_RESULT([yes])
NEED_BZLIB=1
],
[AC_MSG_ERROR([Could not link iostreams, even with bzip2])])
])
CPPFLAGS="$save_CPPFLAGS"
LDFLAGS="$save_LDFLAGS"
LIBS="$save_LIBS"
if [ test "x$NEED_BZLIB" != "x" ]; then
LIBS="$LIBS -lbz2"
fi
])
\ No newline at end of file
config/m4/libtool.m4 deleted 100644 → 0
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config/m4/ltsugar.m4 deleted 100644 → 0
# ltsugar.m4 -- libtool m4 base layer. -*-Autoconf-*-
#
# Copyright (C) 2004-2005, 2007-2008, 2011-2015 Free Software
# Foundation, Inc.
# Written by Gary V. Vaughan, 2004
#
# This file is free software; the Free Software Foundation gives
# unlimited permission to copy and/or distribute it, with or without
# modifications, as long as this notice is preserved.
# serial 6 ltsugar.m4
# This is to help aclocal find these macros, as it can't see m4_define.
AC_DEFUN([LTSUGAR_VERSION], [m4_if([0.1])])
# lt_join(SEP, ARG1, [ARG2...])
# -----------------------------
# Produce ARG1SEPARG2...SEPARGn, omitting [] arguments and their
# associated separator.
# Needed until we can rely on m4_join from Autoconf 2.62, since all earlier
# versions in m4sugar had bugs.
m4_define([lt_join],
[m4_if([$#], [1], [],
[$#], [2], [[$2]],
[m4_if([$2], [], [], [[$2]_])$0([$1], m4_shift(m4_shift($@)))])])
m4_define([_lt_join],
[m4_if([$#$2], [2], [],
[m4_if([$2], [], [], [[$1$2]])$0([$1], m4_shift(m4_shift($@)))])])
# lt_car(LIST)
# lt_cdr(LIST)
# ------------
# Manipulate m4 lists.
# These macros are necessary as long as will still need to support
# Autoconf-2.59, which quotes differently.
m4_define([lt_car], [[$1]])
m4_define([lt_cdr],
[m4_if([$#], 0, [m4_fatal([$0: cannot be called without arguments])],
[$#], 1, [],
[m4_dquote(m4_shift($@))])])
m4_define([lt_unquote], $1)
# lt_append(MACRO-NAME, STRING, [SEPARATOR])
# ------------------------------------------
# Redefine MACRO-NAME to hold its former content plus 'SEPARATOR''STRING'.
# Note that neither SEPARATOR nor STRING are expanded; they are appended
# to MACRO-NAME as is (leaving the expansion for when MACRO-NAME is invoked).
# No SEPARATOR is output if MACRO-NAME was previously undefined (different
# than defined and empty).
#
# This macro is needed until we can rely on Autoconf 2.62, since earlier
# versions of m4sugar mistakenly expanded SEPARATOR but not STRING.
m4_define([lt_append],
[m4_define([$1],
m4_ifdef([$1], [m4_defn([$1])[$3]])[$2])])
# lt_combine(SEP, PREFIX-LIST, INFIX, SUFFIX1, [SUFFIX2...])
# ----------------------------------------------------------
# Produce a SEP delimited list of all paired combinations of elements of
# PREFIX-LIST with SUFFIX1 through SUFFIXn. Each element of the list
# has the form PREFIXmINFIXSUFFIXn.
# Needed until we can rely on m4_combine added in Autoconf 2.62.
m4_define([lt_combine],
[m4_if(m4_eval([$# > 3]), [1],
[m4_pushdef([_Lt_sep], [m4_define([_Lt_sep], m4_defn([lt_car]))])]]dnl
[[m4_foreach([_Lt_prefix], [$2],
[m4_foreach([_Lt_suffix],
]m4_dquote(m4_dquote(m4_shift(m4_shift(m4_shift($@)))))[,
[_Lt_sep([$1])[]m4_defn([_Lt_prefix])[$3]m4_defn([_Lt_suffix])])])])])
# lt_if_append_uniq(MACRO-NAME, VARNAME, [SEPARATOR], [UNIQ], [NOT-UNIQ])
# -----------------------------------------------------------------------
# Iff MACRO-NAME does not yet contain VARNAME, then append it (delimited
# by SEPARATOR if supplied) and expand UNIQ, else NOT-UNIQ.
m4_define([lt_if_append_uniq],
[m4_ifdef([$1],
[m4_if(m4_index([$3]m4_defn([$1])[$3], [$3$2$3]), [-1],
[lt_append([$1], [$2], [$3])$4],
[$5])],
[lt_append([$1], [$2], [$3])$4])])
# lt_dict_add(DICT, KEY, VALUE)
# -----------------------------
m4_define([lt_dict_add],
[m4_define([$1($2)], [$3])])
# lt_dict_add_subkey(DICT, KEY, SUBKEY, VALUE)
# --------------------------------------------
m4_define([lt_dict_add_subkey],
[m4_define([$1($2:$3)], [$4])])
# lt_dict_fetch(DICT, KEY, [SUBKEY])
# ----------------------------------
m4_define([lt_dict_fetch],
[m4_ifval([$3],
m4_ifdef([$1($2:$3)], [m4_defn([$1($2:$3)])]),
m4_ifdef([$1($2)], [m4_defn([$1($2)])]))])
# lt_if_dict_fetch(DICT, KEY, [SUBKEY], VALUE, IF-TRUE, [IF-FALSE])
# -----------------------------------------------------------------
m4_define([lt_if_dict_fetch],
[m4_if(lt_dict_fetch([$1], [$2], [$3]), [$4],
[$5],
[$6])])
# lt_dict_filter(DICT, [SUBKEY], VALUE, [SEPARATOR], KEY, [...])
# --------------------------------------------------------------
m4_define([lt_dict_filter],
[m4_if([$5], [], [],
[lt_join(m4_quote(m4_default([$4], [[, ]])),
lt_unquote(m4_split(m4_normalize(m4_foreach(_Lt_key, lt_car([m4_shiftn(4, $@)]),
[lt_if_dict_fetch([$1], _Lt_key, [$2], [$3], [_Lt_key ])])))))])[]dnl
])
config/m4/ltversion.m4 deleted 100644 → 0
# ltversion.m4 -- version numbers -*- Autoconf -*-
#
# Copyright (C) 2004, 2011-2015 Free Software Foundation, Inc.
# Written by Scott James Remnant, 2004
#
# This file is free software; the Free Software Foundation gives
# unlimited permission to copy and/or distribute it, with or without
# modifications, as long as this notice is preserved.
# @configure_input@
# serial 4179 ltversion.m4
# This file is part of GNU Libtool
m4_define([LT_PACKAGE_VERSION], [2.4.6])
m4_define([LT_PACKAGE_REVISION], [2.4.6])
AC_DEFUN([LTVERSION_VERSION],
[macro_version='2.4.6'
macro_revision='2.4.6'
_LT_DECL(, macro_version, 0, [Which release of libtool.m4 was used?])
_LT_DECL(, macro_revision, 0)
])
config/m4/lt~obsolete.m4 deleted 100644 → 0
# lt~obsolete.m4 -- aclocal satisfying obsolete definitions. -*-Autoconf-*-
#
# Copyright (C) 2004-2005, 2007, 2009, 2011-2015 Free Software
# Foundation, Inc.
# Written by Scott James Remnant, 2004.
#
# This file is free software; the Free Software Foundation gives
# unlimited permission to copy and/or distribute it, with or without
# modifications, as long as this notice is preserved.
# serial 5 lt~obsolete.m4
# These exist entirely to fool aclocal when bootstrapping libtool.
#
# In the past libtool.m4 has provided macros via AC_DEFUN (or AU_DEFUN),
# which have later been changed to m4_define as they aren't part of the
# exported API, or moved to Autoconf or Automake where they belong.
#
# The trouble is, aclocal is a bit thick. It'll see the old AC_DEFUN
# in /usr/share/aclocal/libtool.m4 and remember it, then when it sees us
# using a macro with the same name in our local m4/libtool.m4 it'll
# pull the old libtool.m4 in (it doesn't see our shiny new m4_define
# and doesn't know about Autoconf macros at all.)
#
# So we provide this file, which has a silly filename so it's always
# included after everything else. This provides aclocal with the
# AC_DEFUNs it wants, but when m4 processes it, it doesn't do anything
# because those macros already exist, or will be overwritten later.
# We use AC_DEFUN over AU_DEFUN for compatibility with aclocal-1.6.
#
# Anytime we withdraw an AC_DEFUN or AU_DEFUN, remember to add it here.
# Yes, that means every name once taken will need to remain here until
# we give up compatibility with versions before 1.7, at which point
# we need to keep only those names which we still refer to.
# This is to help aclocal find these macros, as it can't see m4_define.
AC_DEFUN([LTOBSOLETE_VERSION], [m4_if([1])])
m4_ifndef([AC_LIBTOOL_LINKER_OPTION], [AC_DEFUN([AC_LIBTOOL_LINKER_OPTION])])
m4_ifndef([AC_PROG_EGREP], [AC_DEFUN([AC_PROG_EGREP])])
m4_ifndef([_LT_AC_PROG_ECHO_BACKSLASH], [AC_DEFUN([_LT_AC_PROG_ECHO_BACKSLASH])])
m4_ifndef([_LT_AC_SHELL_INIT], [AC_DEFUN([_LT_AC_SHELL_INIT])])
m4_ifndef([_LT_AC_SYS_LIBPATH_AIX], [AC_DEFUN([_LT_AC_SYS_LIBPATH_AIX])])
m4_ifndef([_LT_PROG_LTMAIN], [AC_DEFUN([_LT_PROG_LTMAIN])])
m4_ifndef([_LT_AC_TAGVAR], [AC_DEFUN([_LT_AC_TAGVAR])])
m4_ifndef([AC_LTDL_ENABLE_INSTALL], [AC_DEFUN([AC_LTDL_ENABLE_INSTALL])])
m4_ifndef([AC_LTDL_PREOPEN], [AC_DEFUN([AC_LTDL_PREOPEN])])
m4_ifndef([_LT_AC_SYS_COMPILER], [AC_DEFUN([_LT_AC_SYS_COMPILER])])
m4_ifndef([_LT_AC_LOCK], [AC_DEFUN([_LT_AC_LOCK])])
m4_ifndef([AC_LIBTOOL_SYS_OLD_ARCHIVE], [AC_DEFUN([AC_LIBTOOL_SYS_OLD_ARCHIVE])])
m4_ifndef([_LT_AC_TRY_DLOPEN_SELF], [AC_DEFUN([_LT_AC_TRY_DLOPEN_SELF])])
m4_ifndef([AC_LIBTOOL_PROG_CC_C_O], [AC_DEFUN([AC_LIBTOOL_PROG_CC_C_O])])
m4_ifndef([AC_LIBTOOL_SYS_HARD_LINK_LOCKS], [AC_DEFUN([AC_LIBTOOL_SYS_HARD_LINK_LOCKS])])
m4_ifndef([AC_LIBTOOL_OBJDIR], [AC_DEFUN([AC_LIBTOOL_OBJDIR])])
m4_ifndef([AC_LTDL_OBJDIR], [AC_DEFUN([AC_LTDL_OBJDIR])])
m4_ifndef([AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH], [AC_DEFUN([AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH])])
m4_ifndef([AC_LIBTOOL_SYS_LIB_STRIP], [AC_DEFUN([AC_LIBTOOL_SYS_LIB_STRIP])])
m4_ifndef([AC_PATH_MAGIC], [AC_DEFUN([AC_PATH_MAGIC])])
m4_ifndef([AC_PROG_LD_GNU], [AC_DEFUN([AC_PROG_LD_GNU])])
m4_ifndef([AC_PROG_LD_RELOAD_FLAG], [AC_DEFUN([AC_PROG_LD_RELOAD_FLAG])])
m4_ifndef([AC_DEPLIBS_CHECK_METHOD], [AC_DEFUN([AC_DEPLIBS_CHECK_METHOD])])
m4_ifndef([AC_LIBTOOL_PROG_COMPILER_NO_RTTI], [AC_DEFUN([AC_LIBTOOL_PROG_COMPILER_NO_RTTI])])
m4_ifndef([AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE], [AC_DEFUN([AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE])])
m4_ifndef([AC_LIBTOOL_PROG_COMPILER_PIC], [AC_DEFUN([AC_LIBTOOL_PROG_COMPILER_PIC])])
m4_ifndef([AC_LIBTOOL_PROG_LD_SHLIBS], [AC_DEFUN([AC_LIBTOOL_PROG_LD_SHLIBS])])
m4_ifndef([AC_LIBTOOL_POSTDEP_PREDEP], [AC_DEFUN([AC_LIBTOOL_POSTDEP_PREDEP])])
m4_ifndef([LT_AC_PROG_EGREP], [AC_DEFUN([LT_AC_PROG_EGREP])])
m4_ifndef([LT_AC_PROG_SED], [AC_DEFUN([LT_AC_PROG_SED])])
m4_ifndef([_LT_CC_BASENAME], [AC_DEFUN([_LT_CC_BASENAME])])
m4_ifndef([_LT_COMPILER_BOILERPLATE], [AC_DEFUN([_LT_COMPILER_BOILERPLATE])])
m4_ifndef([_LT_LINKER_BOILERPLATE], [AC_DEFUN([_LT_LINKER_BOILERPLATE])])
m4_ifndef([_AC_PROG_LIBTOOL], [AC_DEFUN([_AC_PROG_LIBTOOL])])
m4_ifndef([AC_LIBTOOL_SETUP], [AC_DEFUN([AC_LIBTOOL_SETUP])])
m4_ifndef([_LT_AC_CHECK_DLFCN], [AC_DEFUN([_LT_AC_CHECK_DLFCN])])
m4_ifndef([AC_LIBTOOL_SYS_DYNAMIC_LINKER], [AC_DEFUN([AC_LIBTOOL_SYS_DYNAMIC_LINKER])])
m4_ifndef([_LT_AC_TAGCONFIG], [AC_DEFUN([_LT_AC_TAGCONFIG])])
m4_ifndef([AC_DISABLE_FAST_INSTALL], [AC_DEFUN([AC_DISABLE_FAST_INSTALL])])
m4_ifndef([_LT_AC_LANG_CXX], [AC_DEFUN([_LT_AC_LANG_CXX])])
m4_ifndef([_LT_AC_LANG_F77], [AC_DEFUN([_LT_AC_LANG_F77])])
m4_ifndef([_LT_AC_LANG_GCJ], [AC_DEFUN([_LT_AC_LANG_GCJ])])
m4_ifndef([AC_LIBTOOL_LANG_C_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_C_CONFIG])])
m4_ifndef([_LT_AC_LANG_C_CONFIG], [AC_DEFUN([_LT_AC_LANG_C_CONFIG])])
m4_ifndef([AC_LIBTOOL_LANG_CXX_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_CXX_CONFIG])])
m4_ifndef([_LT_AC_LANG_CXX_CONFIG], [AC_DEFUN([_LT_AC_LANG_CXX_CONFIG])])
m4_ifndef([AC_LIBTOOL_LANG_F77_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_F77_CONFIG])])
m4_ifndef([_LT_AC_LANG_F77_CONFIG], [AC_DEFUN([_LT_AC_LANG_F77_CONFIG])])
m4_ifndef([AC_LIBTOOL_LANG_GCJ_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_GCJ_CONFIG])])
m4_ifndef([_LT_AC_LANG_GCJ_CONFIG], [AC_DEFUN([_LT_AC_LANG_GCJ_CONFIG])])
m4_ifndef([AC_LIBTOOL_LANG_RC_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_RC_CONFIG])])
m4_ifndef([_LT_AC_LANG_RC_CONFIG], [AC_DEFUN([_LT_AC_LANG_RC_CONFIG])])
m4_ifndef([AC_LIBTOOL_CONFIG], [AC_DEFUN([AC_LIBTOOL_CONFIG])])
m4_ifndef([_LT_AC_FILE_LTDLL_C], [AC_DEFUN([_LT_AC_FILE_LTDLL_C])])
m4_ifndef([_LT_REQUIRED_DARWIN_CHECKS], [AC_DEFUN([_LT_REQUIRED_DARWIN_CHECKS])])
m4_ifndef([_LT_AC_PROG_CXXCPP], [AC_DEFUN([_LT_AC_PROG_CXXCPP])])
m4_ifndef([_LT_PREPARE_SED_QUOTE_VARS], [AC_DEFUN([_LT_PREPARE_SED_QUOTE_VARS])])
m4_ifndef([_LT_PROG_ECHO_BACKSLASH], [AC_DEFUN([_LT_PROG_ECHO_BACKSLASH])])
m4_ifndef([_LT_PROG_F77], [AC_DEFUN([_LT_PROG_F77])])
m4_ifndef([_LT_PROG_FC], [AC_DEFUN([_LT_PROG_FC])])
m4_ifndef([_LT_PROG_CXX], [AC_DEFUN([_LT_PROG_CXX])])
config/test/iostreams-bzip2-test.cpp deleted 100644 → 0
#include <boost/iostreams/filtering_stream.hpp>
#include <boost/iostreams/filter/bzip2.hpp>
namespace io = boost::iostreams;
int main()
{
io::filtering_stream<io::input> in;
in.push(io::bzip2_decompressor());
return 0;
}
config/test/iostreams-zlib-test.cpp deleted 100644 → 0
#include <boost/iostreams/filtering_stream.hpp>
#include <boost/iostreams/filter/gzip.hpp>
namespace io = boost::iostreams;
int main()
{
io::filtering_stream<io::input> in;
in.push(io::gzip_decompressor());
return 0;
}
config/tools/m4esc.sh deleted 100755 → 0
#!/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 < "$file"
echo -n "]]"
configure deleted 100755 → 0
This source diff could not be displayed because it is too large. You can view the blob instead.
configure.ac deleted 100644 → 0
AC_PREREQ([2.69])
m4_define([libcifpp_version_major],[1])
m4_define([libcifpp_version_minor],[1])
m4_define([libcifpp_version_micro],[0])
m4_define([libcifpp_version_extra],[])
m4_define([libcifpp_version],[libcifpp_version_major().libcifpp_version_minor().libcifpp_version_micro()libcifpp_version_extra])
AC_INIT([libcifpp], [libcifpp_version], [m.hekkelman@nki.nl])
dnl Switch to a C++ compiler, and check if it works.
AC_LANG(C++)
AX_CXX_COMPILE_STDCXX_17([noext])
AX_CHECK_COMPILE_FLAG([-fstandalone-debug],
[
CXXFLAGS="$CXXFLAGS -fstandalone-debug"
] , , [-Werror])
AC_CONFIG_SRCDIR([src/Cif++.cpp])
AC_CONFIG_AUX_DIR(config)
AC_CONFIG_MACRO_DIR([config/m4])
AC_CONFIG_HEADERS([src/Config.hpp])
AC_PREFIX_DEFAULT(/usr/local)
AX_FILESYSTEM
AC_PROG_INSTALL
PKG_PROG_PKG_CONFIG
AX_PTHREAD
AC_ARG_VAR([DEBUG], [Build a debug version of the application])
dnl disable shared libraries, they break the build on MacOS... sigh
LT_INIT([disable-shared pic-only])
AC_SUBST(LIBTOOL_DEPS)
dnl versioning, for libtool
LIBCIF_CURRENT=1
LIBCIF_REVISION=1
LIBCIF_AGE=1
LIBCIF_LT_CURRENT="${LIBCIF_CURRENT}"
LIBCIF_LT_VERSION="${LIBCIF_CURRENT}:${LIBCIF_REVISION}:${LIBCIF_AGE}"
AC_SUBST(LIBCIF_LT_CURRENT)
AC_SUBST(LIBCIF_LT_VERSION)
dnl and now for the semantic version
LIBCIF_SEMANTIC_VERSION=libcifpp_version
AC_SUBST(LIBCIF_SEMANTIC_VERSION)
AC_ARG_VAR([CCP4], [The location where CCP4 is installed. CCP4 is only required if you want to rebuild the symmetry operations table.])
AX_MRC
dnl revision numbering is something used internally at the NKI
AC_ARG_ENABLE(
revision,
[AS_HELP_STRING([--disable-revision], [Create a build number as revision])])
AS_IF([test "x$enable_revision" != "xno" ], [
UPDATE_REVISION=1
])
AC_SUBST([UPDATE_REVISION], [$UPDATE_REVISION])
dnl Do not download CCD components file during make (for travis, won't work)
AC_ARG_ENABLE(
download-ccd,
[AS_HELP_STRING([--disable-download-ccd], [Do not try to download a CCD components.cif file during build])])
AS_IF([test "x$enable_download_ccd" != "xno" ], [
SKIP_DOWNLOAD_CCD=1
])
AC_SUBST([SKIP_DOWNLOAD_CCD], [$SKIP_DOWNLOAD_CCD])
AX_FILESYSTEM
AC_CHECK_FUNCS([floor pow rint sqrt strchr strerror])
AC_CHECK_HEADERS([sys/ioctl.h])
AC_CHECK_HEADERS([termios.h])
AC_CHECK_HEADER_STDBOOL
AC_CHECK_TYPES([ptrdiff_t])
AC_PROG_MAKE_SET
AX_BOOST_BASE([1.71], [], [AC_MSG_ERROR([Sorry, your boost is not found or not up-to-date.])])
AX_BOOST_IOSTREAMS
AX_BOOST_DATE_TIME
AX_BOOST_REGEX
AX_IOSTREAMS_Z
AX_IOSTREAMS_BZ2
dnl AC_CHECK_LIB([atomic], [atomic_flag_clear])
dnl Set output variables for the various directories
AC_ARG_VAR([DATA_LIB_DIR], [The location where to store packaged dictionary and CCD files])
AC_SUBST([DATA_LIB_DIR])
DATA_LIB_DIR=$datadir/libcifpp
AC_ARG_VAR([DATA_CACHE_DIR], [The location where to store cached dictionary and CCD files])
AC_SUBST([DATA_CACHE_DIR])
DATA_CACHE_DIR=/var/cache/libcifpp
AC_OUTPUT([GNUmakefile
libcifpp.pc
tools/update-dictionary-script])
src/CifUtils.cpp
...@@ -72,11 +72,7 @@ std::string get_version_nr() ...@@ -72,11 +72,7 @@ std::string get_version_nr()
rxVersionNr1(R"(build-(\d+)-g[0-9a-f]{7}(-dirty)?)"), rxVersionNr1(R"(build-(\d+)-g[0-9a-f]{7}(-dirty)?)"),
rxVersionNr2(R"(libcifpp-version: (\d+\.\d+\.\d+))"); rxVersionNr2(R"(libcifpp-version: (\d+\.\d+\.\d+))");
#if __has_include("revision.hpp")
#include "revision.hpp" #include "revision.hpp"
#else
const char *kRevision = "";
#endif
struct membuf : public std::streambuf struct membuf : public std::streambuf
{ {
......
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