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
|
###############################################################################
#
# Description : CMake script for constructing a libSBML python source package
# Original author(s): Frank Bergmann <fbergman@caltech.edu>
# 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) 2013-2018 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
#
###############################################################################
# checking arguments
if ("${OUT_DIR}" STREQUAL "" OR
"${SRC_DIR}" STREQUAL "" OR
"${BIN_DIR}" STREQUAL "" )
message ( FATAL_ERROR
"
Need three arguments:
OUT_DIR: directory where to create the package
SRC_DIR: libsbml/src directory
BIN_DIR: build directory, that has been configured with python & swigged
"
)
endif()
SET(CURRENT_DIR ${SRC_DIR}/../dev/utilities/python_package)
# delete prior builds
if (EXISTS ${OUT_DIR}/build)
file (REMOVE_RECURSE ${OUT_DIR}/build )
endif()
# delete prior distributions
if (EXISTS ${OUT_DIR}/dist)
file (REMOVE_RECURSE ${OUT_DIR}/dist )
endif()
# delete prior base files
if (EXISTS ${OUT_DIR}/base)
file (REMOVE_RECURSE ${OUT_DIR}/base )
endif()
# create base dir
file (MAKE_DIRECTORY ${OUT_DIR}/base)
# # list directories to copy files from (old way)
# set(DIRECTORIES
# sbml
# sbml/annotation
# sbml/common
# sbml/compress
# sbml/conversion
# sbml/extension
# sbml/math
# sbml/packages
# sbml/packages/comp/common
# sbml/packages/comp/extension
# sbml/packages/comp/sbml
# sbml/packages/comp/util
# sbml/packages/comp/validator
# sbml/packages/comp/validator/constraints
# sbml/packages/fbc/common
# sbml/packages/fbc/extension
# sbml/packages/fbc/sbml
# sbml/packages/fbc/util
# sbml/packages/fbc/validator
# sbml/packages/fbc/validator/constraints
# sbml/packages/layout/common
# sbml/packages/layout/extension
# sbml/packages/layout/sbml
# sbml/packages/layout/util
# sbml/packages/layout/validator
# sbml/packages/layout/validator/constraints
# sbml/packages/render/common
# sbml/packages/render/extension
# sbml/packages/render/sbml
# sbml/packages/render/util
# sbml/packages/render/validator
# sbml/packages/render/validator/constraints
# sbml/packages/qual/common
# sbml/packages/qual/extension
# sbml/packages/qual/sbml
# sbml/packages/qual/util
# sbml/packages/qual/validator
# sbml/packages/qual/validator/constraints
# sbml/packages/multi/common
# sbml/packages/multi/extension
# sbml/packages/multi/sbml
# sbml/packages/multi/validator
# sbml/packages/multi/validator/constraints
# sbml/packages/groups/common
# sbml/packages/groups/extension
# sbml/packages/groups/sbml
# sbml/packages/groups/util
# sbml/packages/groups/validator
# sbml/packages/groups/validator/constraints
# sbml/packages/l3v2extendedmath/common
# sbml/packages/l3v2extendedmath/extension
# sbml/packages/l3v2extendedmath/validator
# sbml/packages/l3v2extendedmath/validator/constraints
# sbml/units
# sbml/util
# sbml/validator
# sbml/validator/constraints
# sbml/xml
# )
# new way to list directories
IF (${CMAKE_VERSION} VERSION_GREATER 3.2.3)
message("\nCMake ${CMAKE_VERSION} detected using sane directory tree strategy.")
MACRO(GET_SBML_SRC_TREE result curdir)
FILE(GLOB_RECURSE children LIST_DIRECTORIES true RELATIVE ${curdir} ${curdir}/*)
SET(dirlist "sbml")
FOREACH(subdir ${children})
IF(IS_DIRECTORY ${curdir}/${subdir})
IF(subdir MATCHES "test$" OR subdir MATCHES "test-data$"
OR subdir MATCHES "/test/" OR subdir MATCHES "/test-data/")
#message("${subdir}")
ELSE()
#message("sbml/${subdir}")
LIST(APPEND dirlist "sbml/${subdir}")
ENDIF()
ENDIF()
ENDFOREACH()
SET(${result} ${dirlist})
ENDMACRO()
GET_SBML_SRC_TREE(DIRECTORIES "${SRC_DIR}/sbml")
ELSE ()
message("\nCMake ${CMAKE_VERSION} detected using directory tree hack.")
MACRO(SUBDIRLIST result curdir)
FILE(GLOB children ABSOLUTE ${curdir} ${curdir}/*)
SET(dirlist "")
FOREACH(subdir ${children})
IF(IS_DIRECTORY ${subdir})
IF(subdir MATCHES "test$" OR subdir MATCHES "test-data$"
OR subdir MATCHES "/test/" OR subdir MATCHES "/test-data/")
#message("${subdir}")
ELSE()
LIST(APPEND dirlist ${subdir})
ENDIF()
ENDIF()
ENDFOREACH()
LIST(APPEND "${result}" ${dirlist})
ENDMACRO()
MACRO(ADD_SUBDIR outlist inlist)
FOREACH(subdir ${inlist})
SUBDIRLIST(temp_dirs "${subdir}")
LIST(APPEND "${outlist}" ${temp_dirs})
ENDFOREACH()
list(REMOVE_DUPLICATES ${outlist})
ENDMACRO()
# get the actual list
SUBDIRLIST(DIRECTORIES "${SRC_DIR}/sbml")
# get 3 subdirectory levels
ADD_SUBDIR(DIRECTORIES "${DIRECTORIES}")
ADD_SUBDIR(DIRECTORIES "${DIRECTORIES}")
ADD_SUBDIR(DIRECTORIES "${DIRECTORIES}")
# postprocess
SET(ALL_DIRS)
STRING(LENGTH "${SRC_DIR}/sbml" SRC_DIR_LEN)
MATH(EXPR SRC_DIR_LEN_FIXED "${SRC_DIR_LEN} - 4")
FOREACH(dir ${DIRECTORIES})
STRING(SUBSTRING ${dir} ${SRC_DIR_LEN_FIXED} -1 dirfix)
LIST(APPEND ALL_DIRS ${dirfix})
ENDFOREACH()
SET(DIRECTORIES ${ALL_DIRS})
ENDIF(${CMAKE_VERSION} VERSION_GREATER 3.2.3)
list(SORT DIRECTORIES)
# # DEBUG
# message("${SRC_DIR}/sbml")
# FOREACH(sdir ${DIRECTORIES})
# message("${sdir}")
# ENDFOREACH()
# copy files
foreach( directory ${DIRECTORIES} )
file (MAKE_DIRECTORY ${OUT_DIR}/base/${directory})
file (GLOB SOURCE_FILES RELATIVE ${CMAKE_CURRENT_SOURCE_DIR}
${SRC_DIR}/${directory}/*.cpp
${SRC_DIR}/${directory}/*.c
${SRC_DIR}/${directory}/*.h
${SRC_DIR}/${directory}/*.in
${SRC_DIR}/${directory}/*.cxx)
file(
COPY ${SOURCE_FILES}
DESTINATION ${OUT_DIR}/base/${directory}
)
endforeach()
# remove expat / xerces files
file (GLOB SOURCE_FILES
${OUT_DIR}/base/sbml/xml/Expat*.*
${OUT_DIR}/base/sbml/xml/Xerces*.*
)
file(REMOVE ${SOURCE_FILES})
# copy swigable files
file (GLOB SOURCE_FILES RELATIVE ${CMAKE_CURRENT_SOURCE_DIR}
${SRC_DIR}/bindings/python/*.cpp
${SRC_DIR}/bindings/python/*.h
${SRC_DIR}/bindings/python/*.i
${SRC_DIR}/bindings/python/*.cxx
${SRC_DIR}/bindings/swig/*.cpp
${SRC_DIR}/bindings/swig/*.h
${SRC_DIR}/bindings/swig/*.i
${SRC_DIR}/bindings/swig/*.cxx
)
file(
COPY ${SOURCE_FILES}
DESTINATION ${OUT_DIR}/base/
)
file (GLOB HEADER_FILES
${BIN_DIR}/src/sbml/common/*.h
)
file(
COPY ${HEADER_FILES}
DESTINATION ${OUT_DIR}/base/sbml/common
)
file (GLOB BIN_BASE_FILES
${BIN_DIR}/src/bindings/python/*.cpp
${BIN_DIR}/src/bindings/python/*.h
)
# copy swigged files
file(
COPY ${BIN_BASE_FILES}
DESTINATION ${OUT_DIR}/base/
)
if (EXISTS ${OUT_DIR}/swig)
file (REMOVE_RECURSE ${OUT_DIR}/swig )
endif()
file (MAKE_DIRECTORY ${OUT_DIR}/swig)
# copy swig directory (needed as it is referenced directly)
file (GLOB SOURCE_FILES RELATIVE ${CMAKE_CURRENT_SOURCE_DIR}
${SRC_DIR}/bindings/swig/*.cpp
${SRC_DIR}/bindings/swig/*.h
${SRC_DIR}/bindings/swig/*.i
${SRC_DIR}/bindings/swig/*.cxx
)
file(
COPY ${SOURCE_FILES}
DESTINATION ${OUT_DIR}/swig/
)
# copy files generated in the swig dir
file (GLOB EXTENSION_FILES
${BIN_DIR}/src/sbml/extension/*.cxx
${BIN_DIR}/src/sbml/extension/*.cpp
${BIN_DIR}/src/sbml/extension/*.h
)
# copy swigged files
file(
COPY ${EXTENSION_FILES}
DESTINATION ${OUT_DIR}/base/sbml/extension/
)
# copy files generated in the swig dir
file (GLOB BIN_SWIG_FILES
${BIN_DIR}/src/bindings/swig/*.cpp
${BIN_DIR}/src/bindings/swig/*.h
)
# copy swigged files
file(
COPY ${BIN_SWIG_FILES}
DESTINATION ${OUT_DIR}/swig/
)
# remove previous python scripts
if (EXISTS ${OUT_DIR}/libsbml)
file (REMOVE_RECURSE ${OUT_DIR}/libsbml )
endif()
file (MAKE_DIRECTORY ${OUT_DIR}/libsbml)
file (MAKE_DIRECTORY ${OUT_DIR}/script)
# copy new python script
file(
COPY
${BIN_DIR}/src/bindings/python/libsbml.py
DESTINATION ${OUT_DIR}/script
)
# rename python script
file(
RENAME
${OUT_DIR}/script/libsbml.py
${OUT_DIR}/script/libsbml2.py
)
# generate a version compatible with python 3.x
file(READ ${OUT_DIR}/script/libsbml2.py init_script)
string(REPLACE
"class SBase(_object):"
"class SBase(_object, metaclass=AutoProperty):"
init3_script ${init_script}
)
string(REPLACE
"class SBase(object):"
"class SBase(object, metaclass=AutoProperty):"
init3_script ${init3_script}
)
string(REPLACE
"class SBasePlugin(_object):"
"class SBasePlugin(_object, metaclass=AutoProperty):"
init3_script ${init3_script}
)
string(REPLACE
"class SBasePlugin(object):"
"class SBasePlugin(object, metaclass=AutoProperty):"
init3_script ${init3_script}
)
file(WRITE ${OUT_DIR}/script/libsbml3.py ${init3_script})
# discover current version (default to 5.9.0)
set(LIBSBML_VERSION "5.9.0")
if(EXISTS "${SRC_DIR}/../VERSION.txt")
file(STRINGS "${SRC_DIR}/../VERSION.txt" VersionString NEWLINE_CONSUME)
string(STRIP "${VersionString}" 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(${versionLength} GREATER 3)
list(GET VersionString 3 LIBSBML_VERSION_RELEASE )
endif()
set(LIBSBML_VERSION "${LIBSBML_VERSION_MAJOR}.${LIBSBML_VERSION_MINOR}.${LIBSBML_VERSION_PATCH}")
endif()
# copy manifest template
file(
COPY
${CURRENT_DIR}/MANIFEST.in
DESTINATION ${OUT_DIR}/
)
#configure version in setup.py
configure_file(${CURRENT_DIR}/setup.py.in ${OUT_DIR}/setup.py)
|
