-
Notifications
You must be signed in to change notification settings - Fork 28
/
CMakeLists.txt
1195 lines (982 loc) · 40.2 KB
/
CMakeLists.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
###############################################################################
#
# Description : CMake build script for libSBML
# Original author(s): Frank Bergmann <[email protected]>
# Organization : California Institute of Technology
#
# This file is part of libSBML. Please visit http://sbml.org for more
# information about SBML, and the latest version of libSBML.
#
# Copyright (C) 2013-2017 jointly by the following organizations:
# 1. California Institute of Technology, Pasadena, CA, USA
# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
# 3. University of Heidelberg, Heidelberg, Germany
#
# Copyright (C) 2009-2013 jointly by the following organizations:
# 1. California Institute of Technology, Pasadena, CA, USA
# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
#
# Copyright (C) 2006-2008 by the California Institute of Technology,
# Pasadena, CA, USA
#
# Copyright (C) 2002-2005 jointly by the following organizations:
# 1. California Institute of Technology, Pasadena, CA, USA
# 2. Japan Science and Technology Agency, Japan
#
# This library is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation. A copy of the license agreement is provided
# in the file named "LICENSE.txt" included with this software distribution
# and also available online as http://sbml.org/software/libsbml/license.html
#
###############################################################################
cmake_minimum_required(VERSION 2.8.12...3.19)
project(libsbml)
set(LIBSBML_ROOT_SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}" CACHE PATH
"Path to the libSBML root source directory")
set(LIBSBML_ROOT_BINARY_DIR "${CMAKE_CURRENT_BINARY_DIR}" CACHE PATH
"Path to the libSBML root build directory")
include (CMakeTestCCompiler)
include (CheckCSourceCompiles)
include (CheckCXXSourceCompiles)
include (CheckStructHasMember)
include (CheckLibraryExists)
include (CheckFunctionExists)
include (CheckCCompilerFlag)
include (CheckCSourceRuns)
include (CheckSymbolExists)
include (CheckTypeSize)
if (${CMAKE_VERSION} VERSION_GREATER 2.8.4)
include(GNUInstallDirs)
else ()
set (CMAKE_INSTALL_DATADIR "share/libsbml/")
set (CMAKE_INSTALL_LIBDIR "lib")
set (CMAKE_INSTALL_INCLUDEDIR "include")
set (CMAKE_INSTALL_BINDIR "bin")
set (CMAKE_INSTALL_DATADIR "share")
set (CMAKE_INSTALL_FULL_LIBDIR "${CMAKE_INSTALL_PREFIX}/lib")
set (CMAKE_INSTALL_FULL_INCLUDEDIR "${CMAKE_INSTALL_PREFIX}/include")
endif ()
###############################################################################
#
# Parse VERSION.txt to determine the package version
#
set(LIBSBML_VERSION_MAJOR)
set(LIBSBML_VERSION_MINOR)
set(LIBSBML_VERSION_PATCH)
set(LIBSBML_VERSION_RELEASE)
set(LIBSBML_DOTTED_VERSION)
if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/VERSION.txt")
file(STRINGS "${CMAKE_CURRENT_SOURCE_DIR}/VERSION.txt" VersionString NEWLINE_CONSUME)
string(STRIP "${VersionString}" VersionString)
set(LIBSBML_DOTTED_VERSION ${VersionString})
string(REPLACE "." ";" VersionString "${VersionString}" )
string(REPLACE "-" ";" VersionString "${VersionString}" )
list(LENGTH VersionString versionLength)
list(GET VersionString 0 LIBSBML_VERSION_MAJOR )
list(GET VersionString 1 LIBSBML_VERSION_MINOR )
list(GET VersionString 2 LIBSBML_VERSION_PATCH )
if(${versionLength} GREATER 3)
list(GET VersionString 3 LIBSBML_VERSION_RELEASE )
endif()
endif()
# version number needs to be calculated correctly
MATH(EXPR LIBSBML_VERSION_NUMERIC "${LIBSBML_VERSION_MAJOR} * 10000 + ${LIBSBML_VERSION_MINOR} * 100 + ${LIBSBML_VERSION_PATCH}" )
set(PACKAGE_VERSION "${LIBSBML_VERSION_MAJOR}.${LIBSBML_VERSION_MINOR}.${LIBSBML_VERSION_PATCH}${LIBSBML_VERSION_RELEASE}")
set(PACKAGE_NAME "libSBML")
set(PACKAGE_CONFIG_DIR "${CMAKE_INSTALL_LIBDIR}/cmake" CACHE PATH
"Path into which the cmake config files should be installed")
# PACKAGE_VERSION gets overridden by using other packages, so setting
# the PROJECT_VERSION, which will be used when exporting targets in
# src/CMakeLists.txt
set(PROJECT_VERSION ${PACKAGE_VERSION})
if (WITH_DOXYGEN OR WITH_PYTHON)
# configure the version for documentation / bindings
configure_file(
${CMAKE_CURRENT_SOURCE_DIR}/docs/src/common-text/libsbml-version.html.in
${CMAKE_CURRENT_SOURCE_DIR}/docs/src/common-text/libsbml-version.html
)
endif()
# add make dist and make check target as they are already familiar for
# everyone using the gnumake build
add_custom_target(dist COMMAND ${CMAKE_MAKE_PROGRAM} package_source)
add_custom_target(check COMMAND ${CMAKE_MAKE_PROGRAM} test)
###############################################################################
#
# The next lines configure the parameters for packaging the binaries.
# They can be invoked with "make package" or "nmake package" or by using
# cpack -G zip|deb|rpm|dmg|nsis
#
set(CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS ON)
include(InstallRequiredSystemLibraries)
set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "An API library for reading/writing/manipulating SBML.")
set(CPACK_PACKAGE_NAME "${PACKAGE_NAME}")
set(CPACK_PACKAGE_VENDOR "The libSBML Team")
set(CPACK_PACKAGE_CONTACT "LibSBML Team <[email protected]>")
set(CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_CURRENT_SOURCE_DIR}/README.md")
set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/COPYING.txt")
set(CPACK_PACKAGE_VERSION_MAJOR "${LIBSBML_VERSION_MAJOR}")
set(CPACK_PACKAGE_VERSION_MINOR "${LIBSBML_VERSION_MINOR}")
set(CPACK_PACKAGE_VERSION_PATCH "${LIBSBML_VERSION_PATCH}")
set(CPACK_RPM_PACKAGE_LICENSE "LGPL")
set(CPACK_RPM_PACKAGE_GROUP "Libraries/Development")
set(CPACK_DEBIAN_PACKAGE_SECTION "Libraries")
set(CPACK_SOURCE_IGNORE_FILES "${CMAKE_CURRENT_BINARY_DIR};/.vs/;/.vscode/;/.svn/;/.libs/;/.deps/;/.bzr/;.*.o$;.*.lo$;.*.la$;${CPACK_SOURCE_IGNORE_FILES};/.DS_Store;/.svnignore;blib;libsbml-dist")
if(UNIX)
set(CPACK_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
set(CPACK_SET_DESTDIR "ON")
endif()
if(CMAKE_SIZEOF_VOID_P EQUAL 4)
set(CPACK_DEBIAN_PACKAGE_ARCHITECTURE "i386")
set(CPACK_RPM_PACKAGE_ARCHITECTURE "i386")
else()
set(CPACK_DEBIAN_PACKAGE_ARCHITECTURE "amd64")
set(CPACK_RPM_PACKAGE_ARCHITECTURE "x86_64")
endif()
include(CPack)
# add local modules to module path
set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules;${CMAKE_MODULE_PATH}")
# install find modules, so they can readily be used by others: start with libSBML
set (LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindLIBSBML.cmake")
###############################################################################
#
# Here we have the main configuration options for libsbml.
#
# Build static / shared library
#
# Here we check whether the user has defined BUILD_SHARED_LIBS. If it is
# defined we will honor the value, otherwise we continue to use the
# LIBSBML_SKIP variables to determine whether to build shared or static
# libraries.
if(DEFINED BUILD_SHARED_LIBS)
if (BUILD_SHARED_LIBS)
set(LIBSBML_SKIP_SHARED_LIBRARY OFF)
set(LIBSBML_SKIP_STATIC_LIBRARY ON)
else()
set(LIBSBML_SKIP_SHARED_LIBRARY ON)
set(LIBSBML_SKIP_STATIC_LIBRARY OFF)
endif()
endif()
# Whether to compile examples
option(WITH_EXAMPLES "Compile the libSBML example programs." OFF)
option(WITH_CHECK "Enable testing of libSBML." OFF)
# Which language bindings should be built
option(WITH_CSHARP "Generate the C# language interface for libSBML." OFF)
option(WITH_JAVA "Generate the Java language interface for libSBML." OFF)
option(WITH_PYTHON "Generate the Python language interface for libSBML." OFF)
option(WITH_PERL "Generate the Perl language interface for libSBML." OFF)
option(WITH_PHP "Generate the PHP language interface for libSBML." OFF)
option(WITH_RUBY "Generate the Ruby language interface for libSBML" OFF)
option(WITH_R "Generate the R language interface for libSBML" OFF)
option(WITH_OCTAVE "Generate the Octave language interface for libSBML." OFF)
option(WITH_MATLAB "Generate the MATLAB language interface for libSBML." OFF)
option(WITH_JAVASCRIPT "Generate the experimental Node.js language interface for libSBML." OFF)
option(WITH_STABLE_PACKAGES "Compile libSBML with all stable packages." OFF)
option(WITH_ALL_PACKAGES "Compile libSBML with all packages." OFF)
if (WITH_ALL_PACKAGES)
set(_EXPERIMENTAL_PACKGES "arrays;dyn;REQUIREDELEMENTS")
foreach(package ${_EXPERIMENTAL_PACKGES})
string(TOUPPER ${package} package_upper)
string(CONCAT package_option "ENABLE_" ${package_upper})
set(${package_option} ON CACHE BOOL "Enable package" FORCE)
endforeach()
set(WITH_STABLE_PACKAGES ON CACHE BOOL "Enable stable packages" FORCE)
endif(WITH_ALL_PACKAGES)
if (WITH_STABLE_PACKAGES)
set(_STABLE_PACKGES "comp;distrib;fbc;groups;layout;multi;qual;render;spatial")
foreach(package ${_STABLE_PACKGES})
string(TOUPPER ${package} package_upper)
string(CONCAT package_option "ENABLE_" ${package_upper})
set(${package_option} ON CACHE BOOL "Enable package" FORCE)
endforeach()
endif(WITH_STABLE_PACKAGES)
if (WITH_JAVASCRIPT)
set(_PF86 "ProgramFiles(x86)")
find_program(NODE_GYP_EXECUTABLE
NAMES node-gyp node-gyp.cmd
PATHS
/usr/local/bin
/opt/local/bin
/usr/bin
"$ENV{ProgramFilesProgramFiles}/nodejs/"
"$ENV{ProgramW6432}/nodejs/"
DOC "The file name of the node-gyp executable."
)
find_program(NODEJS_EXECUTABLE
NAMES node nodeexe
PATHS
/usr/local/bin
/opt/local/bin
/usr/bin
"$ENV{ProgramFiles}/nodejs/"
"$ENV{ProgramW6432}/nodejs/"
DOC "The file name of the nodejs executable."
)
# check that we found node-gyp
if (NOT NODE_GYP_EXECUTABLE)
message(FATAL_ERROR
"In oder to build the JavaScript language interface, libSBML needs the
node-gyp executable. Please set the variable named NODE_GYP_EXECUTABLE.")
endif()
# ensure that the swig version is high enough for javascript
if (SWIG_VERSION AND NOT SWIG_VERSION VERSION_GREATER 3.0.1)
message(FATAL_ERROR
"SWIG version 3.0.2 or greater is needed in order to build the JavaScript
language interface for libSBML, but only version ${SWIG_VERSION} was found.")
endif()
endif()
# Add an option to compile with all warnings shown
option(WITH_WALL "Compile with -Wall, so that the compiler will display all warnings." OFF)
mark_as_advanced(WITH_WALL)
if(WITH_WALL)
if(MSVC OR USING_INTEL)
add_definitions(/W4)
string(REPLACE "/W3" "/W4" CMAKE_C_FLAGS "${CMAKE_C_FLAGS}")
string(REPLACE "/W3" "/W4" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
else()
add_definitions(-Wall)
endif()
endif()
# Add an option to instruct libSBML to not include SBMLTypes.h and other files internally.
option(LIBSBML_USE_STRICT_INCLUDES
"Compile using 'strict includes' rules: libSBML header files won't
use SBMLTypes.h, among others." OFF)
if(LIBSBML_USE_STRICT_INCLUDES)
add_definitions(-DLIBSBML_USE_STRICT_INCLUDES)
endif(LIBSBML_USE_STRICT_INCLUDES)
mark_as_advanced(LIBSBML_USE_STRICT_INCLUDES)
set(LIBSBML_BUILD_TYPE "native")
if (CMAKE_SIZEOF_VOID_P EQUAL 4)
set(LIBSBML_BUILD_TYPE "32bit")
else()
set(LIBSBML_BUILD_TYPE "64bit")
endif()
if (APPLE AND ENABLE_UNIVERSAL)
set(LIBSBML_BUILD_TYPE "universal")
endif()
# When allocation of memory fails or the libSBML C API is unable to open
# a file, libSBML can exit the current process. By default this behavior
# is disabled.
#
option (EXIT_ON_ERROR "Call exit(-1) in case of allocation or file error." OFF)
mark_as_advanced(EXIT_ON_ERROR)
# Use the version number in the shared library.
#
option (LIBSBML_SHARED_VERSION
"Include version information into the compiled libSBML shared library." ON)
mark_as_advanced(LIBSBML_SHARED_VERSION)
# initial value for xml2 parser will default to ON,
# unless expat or xerces are chosen
set(WITH_LIBXML_INITIAL ON)
if (WITH_EXPAT OR WITH_XERCES)
set(WITH_LIBXML_INITIAL OFF)
endif()
# Choose the xml parsing library to be used.
option(WITH_EXPAT "Use the Expat XML parser library." OFF)
option(WITH_LIBXML "Use the libxml2 XML parser library." ${WITH_LIBXML_INITIAL})
option(WITH_XERCES "Use the Xerces XML parser library." OFF)
# Use C++ namespace.
option(WITH_CPP_NAMESPACE "Use a C++ namespace for libSBML." OFF)
option(WITH_THREADSAFE_PARSER "Use a threadsafe parser." OFF)
if(WITH_THREADSAFE_PARSER)
add_definitions(-DLIBSBML_WITH_THREADSAFE_PARSER=1)
endif()
# Generate documentation.
option(WITH_DOXYGEN "Generate documentation for libSBML using Doxygen." OFF )
# marks as advanced, so as to hide documentation generation
mark_as_advanced(WITH_DOXYGEN)
# Re-generate the swig bindings? This really should be on by default
# otherwise one might have the wrong wrapper code without support for
# the libsbml packages one wants.
option(WITH_SWIG "Regenerate the programming language interface code
(for Java, Python, etc.) using SWIG." ON )
# Set build type default.
set(CMAKE_BUILD_TYPE "Release" CACHE STRING
"Choose the type of build to perform. The options are: None (CMAKE_CXX_FLAGS
or CMAKE_C_FLAGS are used), Debug, Release, RelWithDebInfo, MinSizeRel.")
if("${CMAKE_BUILD_TYPE}" STREQUAL "")
set(CMAKE_BUILD_TYPE "Release" CACHE STRING
"Choose the type of build to perform. The options are: None (CMAKE_CXX_FLAGS
or CMAKE_C_FLAGS are used), Debug, Release, RelWithDebInfo, MinSizeRel." FORCE)
endif()
# Set the default dependency directory.
set(LIBSBML_DEPENDENCY_DIR ${LIBSBML_ROOT_SOURCE_DIR}/dependencies/ CACHE PATH
"Directory containing libraries that libSBML depends upon.
(Particularly important on Windows.)")
if("${LIBSBML_DEPENDENCY_DIR}" STREQUAL "")
set(LIBSBML_DEPENDENCY_DIR ${LIBSBML_ROOT_SOURCE_DIR}/dependencies/ CACHE PATH
"Directory containing libraries that libSBML depends upon.
(Particularly important on Windows.)" FORCE)
endif()
if (WITH_PYTHON)
# add option to enable Python API2 (with warnings)
option(PYTHON_USE_API2_WARNINGS "Enable the new Python API2 with warnings." OFF)
endif (WITH_PYTHON)
###############################################################################
#
# If WITH_SWIG is selected, we need to find swig
#
set(LIBSBML_USE_CPP_NAMESPACE OFF)
if(WITH_CPP_NAMESPACE)
add_definitions(-DLIBSBML_USE_CPP_NAMESPACE=1)
set(LIBSBML_USE_CPP_NAMESPACE ON)
endif()
if(WITH_SWIG)
find_program(SWIG_EXECUTABLE
NAMES swig
PATHS
c:/swigwin-3.0.10
c:/swigwin-3.0.9
c:/swigwin-3.0.8
c:/swigwin-3.0.7
c:/swigwin-3.0.6
c:/swigwin-3.0.5
c:/swigwin-3.0.4
c:/swigwin-3.0.3
c:/swigwin-3.0.2
c:/swigwin-3.0.1
c:/swigwin-2.0.12
c:/swigwin-2.0.11
c:/swigwin-2.0.10
c:/swigwin-2.0.9
c:/swigwin-2.0.8
c:/swigwin-2.0.7
c:/swigwin-2.0.6
c:/swigwin-2.0.5
c:/swigwin-2.0.4
c:/swigwin-2.0.3
c:/swigwin-2.0.2
c:/swigwin-2.0.1
c:/swigwin-2.0.0
/usr/local/bin
/opt/local/bin
/usr/bin
"C:/Program Files (x86)/Swig"
"C:/Program Files/Swig"
DOC "The file name of the SWIG executable."
)
find_package(SWIG)
if (SWIG_FOUND AND SWIG_VERSION VERSION_LESS "2.0.4")
message(WARNING
"You are using SWIG version ${SWIG_VERSION}. We strongly recommend
using version 2.0.4 or greater. For libSBML JavaScript support, you
will need version 3.0.1 at minimum.")
endif()
set(SWIG_EXTRA_ARGS -DLIBSBML_COMPILED_IN_SRC)
add_definitions(-DLIBSBML_COMPILED_IN_SRC)
set(SWIG_SWIGDOCDEFINES)
endif(WITH_SWIG)
###############################################################################
#
# Locate expat if needed
#
set(LIBSBML_XML_LIBRARY)
set(LIBSBML_XML_LIBRARY_INCLUDE)
set(LIBSBML_XML_LIBRARY_LIBS)
if(WITH_EXPAT)
if(NOT TARGET EXPAT::EXPAT)
find_package(EXPAT REQUIRED)
endif()
add_definitions( -DUSE_EXPAT )
list(APPEND SWIG_EXTRA_ARGS -DUSE_EXPAT)
set(LIBSBML_XML_LIBRARY "expat")
set(LIBSBML_XML_LIBRARY_INCLUDE ${EXPAT_INCLUDE_DIR})
set(LIBSBML_XML_LIBRARY_LIBS ${EXPAT_LIBRARY})
list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindEXPAT.cmake")
endif(WITH_EXPAT)
###############################################################################
#
# Locate Libxml2 if needed
#
set(USE_LIBXML OFF)
if(WITH_LIBXML)
find_package(LIBXML REQUIRED)
add_definitions( -DUSE_LIBXML )
list(APPEND SWIG_EXTRA_ARGS -DUSE_LIBXML)
set(USE_LIBXML ON)
set(LIBSBML_XML_LIBRARY "libxml2")
set(LIBSBML_XML_LIBRARY_INCLUDE ${LIBXML_INCLUDE_DIR})
set(LIBSBML_XML_LIBRARY_LIBS ${LIBXML_LIBRARY})
list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindLIBXML.cmake")
endif(WITH_LIBXML)
###############################################################################
#
# Locate xerces
#
if(WITH_XERCES)
find_package(XERCES REQUIRED)
add_definitions( -DUSE_XERCES )
list(APPEND SWIG_EXTRA_ARGS -DUSE_XERCES)
set(LIBSBML_XML_LIBRARY "xerces-c")
set(LIBSBML_XML_LIBRARY_INCLUDE ${XERCES_INCLUDE_DIR})
set(LIBSBML_XML_LIBRARY_LIBS ${XERCES_LIBRARY})
list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindXERCES.cmake")
endif(WITH_XERCES)
###############################################################################
#
# Locate bz2
#
set(BZIP_INITIAL_VALUE)
find_package(BZ2 QUIET)
if(EXISTS ${LIBBZ_LIBRARY})
set(BZIP_INITIAL_VALUE ON)
else()
set(BZIP_INITIAL_VALUE OFF)
endif()
option(WITH_BZIP2 "Enable the use of bzip2 compression." ${BZIP_INITIAL_VALUE})
set(USE_BZ2 OFF)
if(WITH_BZIP2)
find_package(BZ2 REQUIRED)
set(USE_BZ2 ON)
add_definitions( -DUSE_BZ2 )
list(APPEND SWIG_EXTRA_ARGS -DUSE_BZ2)
list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindBZ2.cmake")
endif(WITH_BZIP2)
###############################################################################
#
# list of additional files to link against.
#
set(EXTRA_LIBS "" CACHE STRING
"List of additional libraries to link against. Separate multiple
names using semicolons." )
set(EXTRA_INCLUDE_DIRS "" CACHE STRING
"List of additional include directories to use during compilation.
Separate multiple directories using semicolons." )
###############################################################################
#
# Locate zlib
#
find_package(ZLIB QUIET)
set(ZLIB_INITIAL_VALUE ON)
if(NOT TARGET ZLIB::ZLIB)
set(ZLIB_INITIAL_VALUE OFF)
endif()
option(WITH_ZLIB "Enable the use of zip compression." ${ZLIB_INITIAL_VALUE} )
set(USE_ZLIB OFF)
if(WITH_ZLIB)
find_package(ZLIB REQUIRED)
set(USE_ZLIB ON)
add_definitions( -DUSE_ZLIB )
list(APPEND SWIG_EXTRA_ARGS -DUSE_ZLIB)
list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindZLIB.cmake")
endif(WITH_ZLIB)
# install find scripts only for used dependencies
install(FILES ${LIBSBML_FIND_MODULES} DESTINATION share/cmake/Modules)
###############################################################################
#
# Find the C# compiler to use and set name for resulting library
#
if(WITH_CSHARP)
FILE(TO_CMAKE_PATH "$ENV{WINDIR}" windir)
find_program(CSHARP_COMPILER
NAMES gmcs csc mcs
PATHS
${windir}/Microsoft.NET/Framework/v2.0.50727/
${windir}/Microsoft.NET/Framework/v3.0/
/usr/bin
/usr/local/bin
DOC "The file name of the C# compiler for the libsbmlcs assembly."
)
find_program(CSHARP_EXAMPLE_COMPILER
NAMES gmcs csc mcs
PATHS
${windir}/Microsoft.NET/Framework/v4.0.30319/
${windir}/Microsoft.NET/Framework/v3.5/
${windir}/Microsoft.NET/Framework/v3.0/
${windir}/Microsoft.NET/Framework/v2.0.50727/
/usr/bin
/usr/local/bin
DOC "The file name of the C# compiler to be used for the examples."
)
if(UNIX)
else()
if(CMAKE_SIZEOF_VOID_P EQUAL 4)
# mark libsbml library as x86
set(CSHARP_EXTRA_ARGS -platform:x86 )
elseif(CMAKE_SIZEOF_VOID_P EQUAL 8)
# mark libsbml library as x64
set(CSHARP_EXTRA_ARGS -platform:x64 )
endif()
endif()
endif(WITH_CSHARP)
###############################################################################
#
# Enable support for testing ... can be invoked by running ctest
# or make test
#
if(WITH_CHECK)
# set test timeout to 3000 as the normal time limit is not sufficient
# for the comp tests
SET(DART_TESTING_TIMEOUT "3000" CACHE STRING "" FORCE)
enable_testing()
find_package(CHECK REQUIRED)
if (UNIX)
# setup valgrind
set(CMAKE_MEMORYCHECK_COMMAND valgrind)
set(CMAKE_MEMORYCHECK_COMMAND_OPTIONS
"--error-exitcode=1 --trace-children=yes --leak-check=full --show-reachable=yes --leak-resolution=high --track-origins=yes --error-limit=no ")
set(MEMCHECK_COMMAND
"${CMAKE_MEMORYCHECK_COMMAND} ${CMAKE_MEMORYCHECK_COMMAND_OPTIONS}")
separate_arguments(MEMCHECK_COMMAND)
endif(UNIX)
include(CTest)
endif(WITH_CHECK)
###############################################################################
#
# Need some variables set up, such as the name for the libSBML
# library and the Path and file separator characters. The
# MISC_PREFIX variable will cause libsbml bindings, examples and
# documentation to be installed in PREFIX/${MISC_PREFIX}.
#
set( MISC_PREFIX )
if(UNIX OR CYGWIN)
set(PATH_SEP "/")
set(FILE_SEP ":")
set( MISC_PREFIX "${CMAKE_INSTALL_DATADIR}/libsbml/" )
set(LIBSBML_LIBRARY sbml)
else()
set( MISC_PREFIX ".\\" )
set(PATH_SEP "\\")
set(FILE_SEP ";")
if(MINGW)
set(LIBSBML_LIBRARY sbml)
else()
set(LIBSBML_LIBRARY libsbml)
endif()
endif()
# On some Linux (64bit) systems (64bit) the libraries should be installed into lib64 rather
# than lib. It will default to 'lib' but can be overwritten.
set(CMAKE_INSTALL_LIBDIR lib CACHE PATH "Full path to the library output directory")
mark_as_advanced(CMAKE_INSTALL_LIBDIR)
###############################################################################
#
# Set up remaining variables, add option for universal binaries
#
set(USING_INTEL)
if (WIN32 AND CMAKE_C_COMPILER AND ${CMAKE_C_COMPILER} MATCHES ".*icl.*$")
message(STATUS "Detected Intel Compiler")
set(USING_INTEL TRUE)
endif ()
set(BUILD_DEFINITIONS)
if(UNIX)
if(APPLE)
# on osx starting with xcode 4.3 the system root is in
# the app bundle, however cmake (up to 2.8.8) does not seem
# to update the path, so lets try it here
if (CMAKE_OSX_SYSROOT AND NOT EXISTS ${CMAKE_OSX_SYSROOT})
if (EXISTS "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/${CMAKE_OSX_SYSROOT}")
set(CMAKE_OSX_SYSROOT "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/${CMAKE_OSX_SYSROOT}" CACHE STRING "The SDK root to be used" FORCE)
endif()
endif()
add_definitions(-DMACOSX)
set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DMACOSX")
# Since we are encountering errors with the use of libc++ on OSX
# this option allows to override which stdlib to use
if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
option(CLANG_USE_STDLIB "Use libstdc++ rather than libc++" OFF)
if (CLANG_USE_STDLIB)
SET( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libstdc++" )
endif()
endif()
# On OSX it is common to build universal binaries to support multiple
# processor architectures. The default behavior is not to build
# multiple architectures, as most users might not need that.
option(ENABLE_UNIVERSAL
"Create 'universal' binaries on Mac OS X. (Not available on
other operating systems.)" OFF)
set(CMAKE_OSX_ARCHITECTURES "${CMAKE_OSX_ARCHITECTURES}" CACHE STRING
"A semicolon-separated list of architectures for which libSBML should be built.")
if(ENABLE_UNIVERSAL)
# if universal binaries are requested and none defined so far
# overwrite them with all three common architectures. If the user
# specified their own list of architectures do not touch!
if(CMAKE_OSX_ARCHITECTURES STREQUAL "")
STRING(REGEX REPLACE "^.*MacOSX([0-9]*\\.[0-9]*)\\.sdk$" "\\1"
OSX_SDK_VERSION "${CMAKE_OSX_SYSROOT}")
if(OSX_SDK_VERSION VERSION_EQUAL "10.7" OR
OSX_SDK_VERSION VERSION_GREATER "10.7" OR
OSX_SDK_VERSION VERSION_EQUAL "10.8" OR
OSX_SDK_VERSION VERSION_GREATER "10.8")
# OSX Lion no longer supports ppc architecture
set(CMAKE_OSX_ARCHITECTURES "i386;x86_64" CACHE STRING
"A semicolon-separated list of architectures for which libSBML should be built." FORCE)
elseif(OSX_SDK_VERSION AND OSX_SDK_VERSION VERSION_LESS "10.7" )
set(CMAKE_OSX_ARCHITECTURES "i386;ppc;x86_64" CACHE STRING
"A semicolon-separated list of architectures for which libSBML should be built." FORCE)
else()
set(CMAKE_OSX_ARCHITECTURES "i386;x86_64" CACHE STRING
"A semicolon-separated list of architectures for which libSBML should be built." FORCE)
endif()
endif()
endif(ENABLE_UNIVERSAL)
else(APPLE)
add_definitions(-DLINUX)
if(NOT CYGWIN)
# on cygwin all code is position independent so -fPIC is not needed
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-strict-aliasing -fPIC")
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fno-strict-aliasing -fPIC")
endif()
set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DLINUX")
endif(APPLE)
else(UNIX)
# not needing these defines, and they do cause warnings
# add_definitions(-DPACKAGE_VERSION=\"${PACKAGE_VERSION}\" -DPACKAGE_NAME=\"${PROJECT_NAME}\")
add_definitions(-DWIN32 -DLIBSBML_EXPORTS -DLIBLAX_EXPORTS)
set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DWIN32 -DLIBSBML_EXPORTS -DLIBLAX_EXPORTS")
if(MSVC OR USING_INTEL)
add_definitions(-D_CRT_SECURE_NO_WARNINGS -D_CRT_NONSTDC_NO_DEPRECATE)
set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -D_CRT_SECURE_NO_WARNINGS")
option(WITH_STATIC_RUNTIME "Compile using the static MSVC Runtime." OFF)
if(WITH_STATIC_RUNTIME)
foreach(flag_var
CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE
CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO
CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE
CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO)
if(${flag_var} MATCHES "/MD")
string(REGEX REPLACE "/MD" "/MT" ${flag_var} "${${flag_var}}")
endif(${flag_var} MATCHES "/MD")
endforeach(flag_var)
add_definitions( -D_MT)
set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>")
endif(WITH_STATIC_RUNTIME)
# on VS enable multiprocessor build
SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /MP")
# Provide an easy way to use Visual Leak Detector (https://vld.codeplex.com)
option(LIBSBML_USE_VLD "When running debug builds with MSVC use Visual Leak Detector." OFF)
mark_as_advanced(LIBSBML_USE_VLD)
if (LIBSBML_USE_VLD)
find_path(VLD_INCLUDE_DIR
NAMES vld.h
PATHS ${LIBSBML_DEPENDENCY_DIR}/include
"$ENV{PROGRAMFILES}/Visual Leak Detector/include"
"$ENV{ProgramW6432}/Visual Leak Detector/include"
DOC "Directory containing VLD files."
)
if (NOT VLD_INCLUDE_DIR)
message(WARNING "VLD is not found on your system, please ensure you installed it correctly.")
else()
include_directories(${VLD_INCLUDE_DIR})
endif()
add_definitions( -DLIBSBML_USE_VLD)
endif (LIBSBML_USE_VLD)
# CMake no longer creates PDB files for static libraries after 2.8.11
# so we store debug information in the object files instead
if (${CMAKE_VERSION} VERSION_GREATER "2.8.11")
foreach(flag_var
CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE
CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO
CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE
CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO)
if(${flag_var} MATCHES "/Zi")
STRING(REPLACE "/Zi" "/Z7" "${flag_var}" "${${flag_var}}")
endif(${flag_var} MATCHES "/Zi")
endforeach(flag_var)
# add /bigobj to allow debug builds to work with swig and packages
ADD_DEFINITIONS(/bigobj)
SET(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} /bigobj")
SET(CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} /bigobj")
endif()
file(GLOB WIN32_BINARIES ${LIBSBML_DEPENDENCY_DIR}/bin/*.dll)
INSTALL(FILES ${WIN32_BINARIES} DESTINATION bin)
file(GLOB WIN32_DEPENDENCIES ${LIBSBML_DEPENDENCY_DIR}/lib/*.lib)
install(FILES ${WIN32_DEPENDENCIES} DESTINATION lib)
elseif(CYGWIN)
add_definitions(-DCYGWIN)
set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DCYGWIN")
elseif(MINGW)
if(WITH_LIBXML)
# this is necessary to build with libxml2 on mingw
add_definitions(-DLIBXML_STATIC)
endif(WITH_LIBXML)
endif(MSVC OR USING_INTEL)
endif(UNIX)
###############################################################################
#
# Disable in-source build
#
if("${LIBSBML_ROOT_SOURCE_DIR}" STREQUAL "${LIBSBML_ROOT_BINARY_DIR}" )
message(FATAL_ERROR "In-source builds of libSBML are disabled.
Please create a separate build directory.")
endif()
###############################################################################
#
# Add check that only one XML library was selection
#
set(LIBRARY_COUNT 0)
if(WITH_EXPAT)
math(EXPR LIBRARY_COUNT "${LIBRARY_COUNT} + 1")
endif()
if(WITH_LIBXML)
math(EXPR LIBRARY_COUNT "${LIBRARY_COUNT} + 1")
endif()
if(WITH_XERCES)
math(EXPR LIBRARY_COUNT "${LIBRARY_COUNT} + 1")
endif()
if(LIBRARY_COUNT GREATER 1)
message(FATAL_ERROR
"Only one XML library should be chosen. Please select only one of the
following options: WITH_LIBXML, WITH_EXPAT or WITH_XERCES.")
endif()
###############################################################################
#
# Add check that at least one XML library was selection
#
if(LIBRARY_COUNT EQUAL 0)
message(FATAL_ERROR
"A XML library must be selected. Please select one of the following
options: WITH_LIBXML, WITH_EXPAT or WITH_XERCES.")
endif()
###############################################################################
#
# Include options for all libSBML packages
#
set(LIBSBML_PACKAGE_INCLUDES)
set(LIBSBML_PACKAGE_SUMMARY)
file(GLOB PACKAGE_OPTIONS "*package.cmake")
foreach(package ${PACKAGE_OPTIONS})
include(${package})
endforeach()
if (LIBSBML_PACKAGE_INCLUDES)
list(REMOVE_DUPLICATES LIBSBML_PACKAGE_INCLUDES)
endif()
###############################################################################
#
# Build the actual libSBML library
#
add_subdirectory(src)
###############################################################################
#
# Build examples if specified
#
if(WITH_EXAMPLES)
# code that builds the examples
add_subdirectory(examples)
endif(WITH_EXAMPLES)
if(WITH_DOXYGEN)
add_subdirectory(docs)
endif()
###############################################################################
#
# Install documentation
#
set(DOCUMENTATION_FILES
COPYING.txt
FUNDING.txt
LICENSE.txt
NEWS.txt
README.md
VERSION.txt
)
install(FILES ${DOCUMENTATION_FILES} DESTINATION ${MISC_PREFIX})
###############################################################################
#
# Write libsbml.pc
#
set (PRIVATE_LIBS "-lstdc++ -lm")
if (WITH_ZLIB)
set (PRIVATE_LIBS "${LIBZ_LIBRARY} ${PRIVATE_LIBS}")
endif()
if (WITH_BZIP2)
set (PRIVATE_LIBS "${LIBBZ_LIBRARY} ${PRIVATE_LIBS}")
endif()
if (WITH_LIBXML)
set (PRIVATE_LIBS "${LIBXML_LIBRARY} ${PRIVATE_LIBS}")
endif()
if (WITH_EXPAT)
set (PRIVATE_LIBS "${LIBEXPAT_LIBRARY} ${PRIVATE_LIBS}")
endif()
if (WITH_XERCES)
set (PRIVATE_LIBS "${XERCES_LIBRARY} ${PRIVATE_LIBS}")
endif()
file(WRITE "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Name: ${PACKAGE_NAME}\n")
file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Description: A library for reading/writing/manipulating SBML\n")
file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "URL: http://sbml.org/Software/libSBML\n")
file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Version: ${PACKAGE_VERSION}\n")
file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "\n")
file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "prefix=${CMAKE_INSTALL_PREFIX}\n")
file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "libdir=${CMAKE_INSTALL_FULL_LIBDIR}\n")
file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "includedir=${CMAKE_INSTALL_FULL_INCLUDEDIR}\n")
file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "\n")
file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Libs: -L\${libdir} -lsbml\n")
file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Libs.private: ${PRIVATE_LIBS}\n")
file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Cflags: -I\${includedir}\n")
if (WITH_XERCES)
file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Conflicts: xerces-c = 2.6.0\n")
endif()
if (WITH_LIBXML)
file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Requires.private: libxml-2.0 >= 2.6.22\n")
endif()
if (UNIX OR MINGW)
install(FILES "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc"
DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
endif()
###############################################################################
#
# Print Summary
#
if (NOT HOSTNAME)
site_name(HOSTNAME)
endif()
message(STATUS "
----------------------------------------------------------------------