1## @configure_input@ 2## 3## Filename : Makefile.in 4## Description : Makefile template for use by 'configure' 5## Author(s) : SBML Team <sbml-team@googlegroups.com> 6## Organization: California Institute of Technology 7## Created : 2004-05-31 8## 9## <!-------------------------------------------------------------------------- 10## This file is part of libSBML. Please visit http://sbml.org for more 11## information about SBML, and the latest version of libSBML. 12## 13## Copyright (C) 2013-2017 jointly by the following organizations: 14## 1. California Institute of Technology, Pasadena, CA, USA 15## 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK 16## 3. University of Heidelberg, Heidelberg, Germany 17## 18## Copyright (C) 2009-2013 jointly by the following organizations: 19## 1. California Institute of Technology, Pasadena, CA, USA 20## 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK 21## 22## Copyright (C) 2006-2008 by the California Institute of Technology, 23## Pasadena, CA, USA 24## 25## Copyright (C) 2002-2005 jointly by the following organizations: 26## 1. California Institute of Technology, Pasadena, CA, USA 27## 2. Japan Science and Technology Agency, Japan 28## 29## This library is free software; you can redistribute it and/or modify it 30## under the terms of the GNU Lesser General Public License as published by 31## the Free Software Foundation. A copy of the license agreement is provided 32## in the file named "LICENSE.txt" included with this software distribution 33## and also available online as http://sbml.org/software/libsbml/license.html 34## ------------------------------------------------------------------------ --> 35 36 37# ----------------------------------------------------------------------------- 38# Configuration variables 39# ----------------------------------------------------------------------------- 40# Some of the following are substituted automatically by `configure'. If 41# you are looking at "Makefile", do not edit these values; instead, run the 42# configure script at the top level of the src tree. It will recreate 43# "Makefile". 44 45include @top_srcdir@/config/makefile-common-vars.mk 46 47# `srcdir' points to the current directory, but should be set by configure. 48# `subdir' must be set manually to the relative dir under `srcdir'. Don't 49# set `subdir' to an absolute path, or some make actions will fail. 50 51srcdir = @srcdir@ 52thisdir = . 53 54# Variables `examples' and `xml-schemas' are local variables reused below. 55# SK removed xml-schema files 56 57examples = \ 58 examples/README.txt \ 59 examples/CMakeLists.txt \ 60 examples/layout-package.cmake \ 61 examples/c/CMakeLists.txt \ 62 examples/c++/CMakeLists.txt \ 63 examples/csharp/CMakeLists.txt \ 64 examples/java/CMakeLists.txt \ 65 examples/c/FormulaGraphvizFormatter.h \ 66 examples/c/Makefile.in \ 67 examples/c/addCVTerms.c \ 68 examples/c/addingEvidenceCodes_1.c \ 69 examples/c/addingEvidenceCodes_2.c \ 70 examples/c/addModelHistory.c \ 71 examples/c/appendAnnotation.c \ 72 examples/c/convertSBML.c \ 73 examples/c/createExampleSBML.c \ 74 examples/c/drawMath.c \ 75 examples/c/echoSBML.c \ 76 examples/c/evaluateMath.c \ 77 examples/c/printAnnotation.c \ 78 examples/c/printMath.c \ 79 examples/c/printNotes.c \ 80 examples/c/printRegisteredPackages.c \ 81 examples/c/printSBML.c \ 82 examples/c/printSupported.c \ 83 examples/c/printUnits.c \ 84 examples/c/promoteParameters.c \ 85 examples/c/readSBML.c \ 86 examples/c/stripPackage.c \ 87 examples/c/translateMath.c \ 88 examples/c/translateL3Math.c \ 89 examples/c/util.c \ 90 examples/c/util.h \ 91 examples/c/validateSBML.c \ 92 examples/c/unsetNotes.c \ 93 examples/c/unsetAnnotation.c \ 94 examples/c++/Makefile.in \ 95 examples/c++/addCVTerms.cpp \ 96 examples/c++/addCustomValidator.cpp \ 97 examples/c++/renameSId.cpp \ 98 examples/c++/setIdFromNames.cpp \ 99 examples/c++/setNamesFromIds.cpp \ 100 examples/c++/addModelHistory.cpp \ 101 examples/c++/addingEvidenceCodes_1.cpp \ 102 examples/c++/addingEvidenceCodes_2.cpp \ 103 examples/c++/appendAnnotation.cpp \ 104 examples/c++/callExternalValidator.cpp \ 105 examples/c++/convertToL1V1.cpp \ 106 examples/c++/convertSBML.cpp \ 107 examples/c++/createExampleSBML.cpp \ 108 examples/c++/echoSBML.cpp \ 109 examples/c++/getAllElementsWithNotes.cpp \ 110 examples/c++/inferUnits.cpp \ 111 examples/c++/inlineFunctionDefintions.cpp \ 112 examples/c++/convertReactions.cpp \ 113 examples/c++/printAnnotation.cpp \ 114 examples/c++/printMath.cpp \ 115 examples/c++/printNotes.cpp \ 116 examples/c++/printRegisteredPackages.cpp \ 117 examples/c++/printSBML.cpp \ 118 examples/c++/printSupported.cpp \ 119 examples/c++/printUnits.cpp \ 120 examples/c++/promoteParameters.cpp \ 121 examples/c++/readSBML.cpp \ 122 examples/c++/rngvalidator.cpp \ 123 examples/c++/stripPackage.cpp \ 124 examples/c++/translateMath.cpp \ 125 examples/c++/translateL3Math.cpp \ 126 examples/c++/unsetAnnotation.cpp \ 127 examples/c++/unsetNotes.cpp \ 128 examples/c++/util.c \ 129 examples/c++/util.h \ 130 examples/c++/validateSBML.cpp \ 131 examples/c++/layout/CMakeLists.txt \ 132 examples/c++/layout/Makefile.in \ 133 examples/c++/layout/addLayout.cpp \ 134 examples/c++/layout/convertLayout.cpp \ 135 examples/c++/layout/example1.cpp \ 136 examples/c++/layout/example1-L3.cpp \ 137 examples/c++/layout/example2.cpp \ 138 examples/c++/layout/example2-L3.cpp \ 139 examples/c++/layout/example3.cpp \ 140 examples/c++/layout/example3-L3.cpp \ 141 examples/xslt/layout/layout2svg.xsl \ 142 examples/layout/README.txt \ 143 examples/csharp/Makefile.in \ 144 examples/csharp/addCustomValidator.cs \ 145 examples/csharp/addCVTerms.cs \ 146 examples/csharp/addingEvidenceCodes_1.cs \ 147 examples/csharp/addingEvidenceCodes_2.cs \ 148 examples/csharp/addModelHistory.cs \ 149 examples/csharp/appendAnnotation.cs \ 150 examples/csharp/callExternalValidator.cs \ 151 examples/csharp/convertSBML.cs \ 152 examples/csharp/createExampleSBML.cs \ 153 examples/csharp/echoSBML.cs \ 154 examples/csharp/printAnnotation.cs \ 155 examples/csharp/printMath.cs \ 156 examples/csharp/printNotes.cs \ 157 examples/csharp/printRegisteredPackages.cs \ 158 examples/csharp/printSBML.cs \ 159 examples/csharp/printsupported.cs \ 160 examples/csharp/printUnits.cs \ 161 examples/csharp/promoteParameters.cs \ 162 examples/csharp/readSBML.cs \ 163 examples/csharp/stripPackage.cs \ 164 examples/csharp/translateMath.cs \ 165 examples/csharp/unsetAnnotation.cs \ 166 examples/csharp/unsetNotes.cs \ 167 examples/csharp/validateSBML.cs \ 168 examples/csharp/SetIdFromNames.cs \ 169 examples/csharp/GetAllElementsWithNotes.cs \ 170 examples/csharp/inlineInitialAssignments.cs \ 171 examples/csharp/replaceOneFD.cs \ 172 examples/csharp/evaluateCustomMath.cs \ 173 examples/java/Makefile.in \ 174 examples/java/README.txt \ 175 examples/java/addCustomValidator.java \ 176 examples/java/addCVTerms.java \ 177 examples/java/addingEvidenceCodes_1.java \ 178 examples/java/addingEvidenceCodes_2.java \ 179 examples/java/addModelHistory.java \ 180 examples/java/appendAnnotation.java \ 181 examples/java/callExternalValidator.java \ 182 examples/java/convertSBML.java \ 183 examples/java/createExampleSBML.java \ 184 examples/java/echoSBML.java \ 185 examples/java/evaluateMath.java \ 186 examples/java/getAllElementsWithNotes.java \ 187 examples/java/printAnnotation.java \ 188 examples/java/printMath.java \ 189 examples/java/printNotes.java \ 190 examples/java/printRegisteredPackages.java \ 191 examples/java/printSBML.java \ 192 examples/java/printsupported.java \ 193 examples/java/printUnits.java \ 194 examples/java/promoteParameters.java \ 195 examples/java/readSBML.java \ 196 examples/java/stripPackage.java \ 197 examples/java/setIdFromNames.java \ 198 examples/java/translateMath.java \ 199 examples/java/unsetAnnotation.java \ 200 examples/java/unsetNotes.java \ 201 examples/java/validateSBML.java \ 202 examples/java/inlineInitialAssignments.java \ 203 examples/java/replaceOneFD.java \ 204 examples/java/evaluateCustomMath.java \ 205 examples/java/layout/CMakeLists.txt \ 206 examples/java/layout/layout_example1.java \ 207 examples/java/layout/SimpleLayoutConverter.java \ 208 examples/java/layout/layout_example1_L3.java \ 209 examples/javascript/addCVTerms.js \ 210 examples/javascript/addingEvidenceCodes_1.js \ 211 examples/javascript/addingEvidenceCodes_2.js \ 212 examples/javascript/addModelHistory.js \ 213 examples/javascript/appendAnnotation.js \ 214 examples/javascript/callExternalValidator.js \ 215 examples/javascript/convertSBML.js \ 216 examples/javascript/createExampleSBML.js \ 217 examples/javascript/echoSBML.js \ 218 examples/javascript/printAnnotation.js \ 219 examples/javascript/printMath.js \ 220 examples/javascript/printNotes.js \ 221 examples/javascript/printRegisteredPackages.js \ 222 examples/javascript/printSBML.js \ 223 examples/javascript/printsupported.js \ 224 examples/javascript/printUnits.js \ 225 examples/javascript/promoteParameters.js \ 226 examples/javascript/readSBML.js \ 227 examples/javascript/stripPackage.js \ 228 examples/javascript/translateMath.js \ 229 examples/javascript/unsetAnnotation.js \ 230 examples/javascript/unsetNotes.js \ 231 examples/javascript/validateSBML.js \ 232 examples/perl/layout/example1-L3.pl \ 233 examples/ruby/layout/example1-L3.rb \ 234 examples/csharp/layout/CMakeLists.txt \ 235 examples/csharp/layout/example1-L3.cs \ 236 examples/python/layout/example1-L3.py \ 237 examples/python/layout/convertLayout.py \ 238 examples/python/layout/example1.py \ 239 examples/perl/addCVTerms.pl \ 240 examples/perl/addCustomValidator.pl \ 241 examples/perl/addingEvidenceCodes_1.pl \ 242 examples/perl/addingEvidenceCodes_2.pl \ 243 examples/perl/addModelHistory.pl \ 244 examples/perl/appendAnnotation.pl \ 245 examples/perl/callExternalValidator.pl \ 246 examples/perl/convertSBML.pl \ 247 examples/perl/createExampleSBML.pl \ 248 examples/perl/echoSBML.pl \ 249 examples/perl/stripPackage.pl \ 250 examples/perl/evaluateMath.pl \ 251 examples/perl/extractReactionInfo.pl \ 252 examples/perl/extractReactions.pl \ 253 examples/perl/printAnnotation.pl \ 254 examples/perl/printMath.pl \ 255 examples/perl/printNotes.pl \ 256 examples/perl/printRegisteredPackages.pl \ 257 examples/perl/printSBML.pl \ 258 examples/perl/printsupported.pl \ 259 examples/perl/printUnits.pl \ 260 examples/perl/promoteParameters.pl \ 261 examples/perl/readSBML.pl \ 262 examples/perl/renameSId.pl \ 263 examples/perl/translateMath.pl \ 264 examples/perl/unsetAnnotation.pl \ 265 examples/perl/unsetNotes.pl \ 266 examples/perl/validateSBML.pl \ 267 examples/python/addCustomValidator.py \ 268 examples/python/addCVTerms.py \ 269 examples/python/addingEvidenceCodes_1.py \ 270 examples/python/addingEvidenceCodes_2.py \ 271 examples/python/addModelHistory.py \ 272 examples/python/append_to_note.py \ 273 examples/python/appendAnnotation.py \ 274 examples/python/callExternalValidator.py \ 275 examples/python/convertSBML.py \ 276 examples/python/createExampleSBML.py \ 277 examples/python/createSimpleModel.py \ 278 examples/python/getAllElementsWithNotes.py \ 279 examples/python/echoSBML.py \ 280 examples/python/stripPackage.py \ 281 examples/python/printAnnotation.py \ 282 examples/python/printMath.py \ 283 examples/python/printNotes.py \ 284 examples/python/printRegisteredPackages.py \ 285 examples/python/printSBML.py \ 286 examples/python/printsupported.py \ 287 examples/python/printUnits.py \ 288 examples/python/promoteParameters.py \ 289 examples/python/readSBML.py \ 290 examples/python/renameSId.py \ 291 examples/python/stringInput.py \ 292 examples/python/setIdFromNames.py \ 293 examples/python/translateMath.py \ 294 examples/python/unsetAnnotation.py \ 295 examples/python/unsetNotes.py \ 296 examples/python/validateSBML.py \ 297 examples/python/inlineInitialAssignments.py \ 298 examples/python/replaceOneFD.py \ 299 examples/python/evaluateCustomMath.py \ 300 examples/python/inlineFunctionDefinitions.py \ 301 examples/python/validateSBMLWithCallback.py \ 302 examples/php/createExampleSBML.php \ 303 examples/php/echoSBML.php \ 304 examples/php/validateSBML.php \ 305 examples/r/addCVTerms.R \ 306 examples/r/addModelHistory.R \ 307 examples/r/addingEvidenceCodes_1.R \ 308 examples/r/addingEvidenceCodes_2.R \ 309 examples/r/appendAnnotation.R \ 310 examples/r/convertSBML.R \ 311 examples/r/createExampleSBML.R \ 312 examples/r/echoSBML.R \ 313 examples/r/evaluateMath.R \ 314 examples/r/printAnnotation.R \ 315 examples/r/printMath.R \ 316 examples/r/printNotes.R \ 317 examples/r/printRegisteredPackages.R \ 318 examples/r/printSBML.R \ 319 examples/r/printSupported.R \ 320 examples/r/printUnits.R \ 321 examples/r/promoteParameters.R \ 322 examples/r/readSBML.R \ 323 examples/r/stripPackage.R \ 324 examples/r/translateMath.R \ 325 examples/r/unsetAnnotation.R \ 326 examples/r/unsetNotes.R \ 327 examples/r/validateSBML.R \ 328 examples/ruby/addCustomValidator.rb \ 329 examples/ruby/addCVTerms.rb \ 330 examples/ruby/addingEvidenceCodes_1.rb \ 331 examples/ruby/addingEvidenceCodes_2.rb \ 332 examples/ruby/addModelHistory.rb \ 333 examples/ruby/appendAnnotation.rb \ 334 examples/ruby/callExternalValidator.rb \ 335 examples/ruby/convertSBML.rb \ 336 examples/ruby/createExampleSBML.rb \ 337 examples/ruby/stripPackage.rb \ 338 examples/ruby/echoSBML.rb \ 339 examples/ruby/printAnnotation.rb \ 340 examples/ruby/printMath.rb \ 341 examples/ruby/printNotes.rb \ 342 examples/ruby/printRegisteredPackages.rb \ 343 examples/ruby/printSBML.rb \ 344 examples/ruby/printsupported.rb \ 345 examples/ruby/printUnits.rb \ 346 examples/ruby/promoteParameters.rb \ 347 examples/ruby/readSBML.rb \ 348 examples/ruby/translateMath.rb \ 349 examples/ruby/unsetAnnotation.rb \ 350 examples/ruby/unsetNotes.rb \ 351 examples/ruby/validateSBML.rb \ 352 examples/sample-models/README.txt \ 353 examples/sample-models/from-spec/level-2/README.txt \ 354 examples/sample-models/from-spec/level-2/algebraicrules.xml \ 355 examples/sample-models/from-spec/level-2/assignmentrules.xml \ 356 examples/sample-models/from-spec/level-2/boundarycondition.xml \ 357 examples/sample-models/from-spec/level-2/delay.xml \ 358 examples/sample-models/from-spec/level-2/dimerization.xml \ 359 examples/sample-models/from-spec/level-2/enzymekinetics.xml \ 360 examples/sample-models/from-spec/level-2/events.xml \ 361 examples/sample-models/from-spec/level-2/functiondef.xml \ 362 examples/sample-models/from-spec/level-2/multicomp.xml \ 363 examples/sample-models/from-spec/level-2/overdetermined.xml \ 364 examples/sample-models/from-spec/level-2/twodimensional.xml \ 365 examples/sample-models/from-spec/level-2/units.xml \ 366 examples/sample-models/from-spec/level-3/README.txt \ 367 examples/sample-models/from-spec/level-3/algebraicrules.xml \ 368 examples/sample-models/from-spec/level-3/assignmentrules.xml \ 369 examples/sample-models/from-spec/level-3/boundarycondition.xml \ 370 examples/sample-models/from-spec/level-3/conversionfactor1.xml \ 371 examples/sample-models/from-spec/level-3/delay.xml \ 372 examples/sample-models/from-spec/level-3/dimerization.xml \ 373 examples/sample-models/from-spec/level-3/enzymekineticext.xml \ 374 examples/sample-models/from-spec/level-3/enzymekinetics.xml \ 375 examples/sample-models/from-spec/level-3/events.xml \ 376 examples/sample-models/from-spec/level-3/fullydeterminedevent.xml \ 377 examples/sample-models/from-spec/level-3/functiondef.xml \ 378 examples/sample-models/from-spec/level-3/membrane.xml \ 379 examples/sample-models/from-spec/level-3/multicomp.xml \ 380 examples/sample-models/from-spec/level-3/overdetermined.xml \ 381 examples/sample-models/from-spec/level-3/twoalgebraicrules.xml \ 382 examples/sample-models/from-spec/level-3/twodimensional.xml \ 383 examples/sample-models/from-spec/level-3/conversionfactor2.xml 384 385# The files listed in 'r bindings' have to be included the dist files, even 386# though they can't be created by gnumake. 387 388rbindings = \ 389 src/bindings/r/CMakeLists.txt \ 390 src/bindings/r/create_package.cmake \ 391 src/bindings/r/configure \ 392 src/bindings/r/configure.in \ 393 src/bindings/r/configure.win \ 394 src/bindings/r/Makevars.in \ 395 src/bindings/r/Makevars.win \ 396 src/bindings/r/swig-binding.cmake \ 397 src/bindings/r/DESCRIPTION.in \ 398 src/bindings/r/NAMESPACE \ 399 src/bindings/r/libsbml.i \ 400 src/bindings/r/local-downcast-extension-layout.cpp \ 401 src/bindings/r/local-downcast-extension-l3v2extendedmath.cpp \ 402 src/bindings/r/local-downcast-astplugins-l3v2extendedmath.cpp \ 403 src/bindings/r/local-downcast-astplugins.cpp.in \ 404 src/bindings/r/local-downcast-extension.cpp.in \ 405 src/bindings/r/local-downcast-namespaces-layout.cpp \ 406 src/bindings/r/local-downcast-namespaces-l3v2extendedmath.cpp \ 407 src/bindings/r/local-downcast-namespaces.cpp.in \ 408 src/bindings/r/local-downcast-packages-layout.cpp \ 409 src/bindings/r/local-downcast-packages-l3v2extendedmath.cpp \ 410 src/bindings/r/local-downcast-converters.cpp.in \ 411 src/bindings/r/local-downcast-converters-layout.cpp \ 412 src/bindings/r/local-downcast-plugins-layout.cpp \ 413 src/bindings/r/local-downcast-plugins-l3v2extendedmath.cpp \ 414 src/bindings/r/local-downcast-plugins.cpp.in \ 415 src/bindings/r/local-downcast.cpp.in \ 416 src/bindings/r/create-r-package.cmake \ 417 src/bindings/r/cmake-r-install.cmake.in \ 418 src/bindings/r/libsbml_rtype.swg \ 419 src/bindings/r/local-layout.i \ 420 src/bindings/r/local-l3v2extendedmath.i \ 421 src/bindings/r/local-packages.i.in \ 422 src/bindings/r/local.cpp \ 423 src/bindings/r/local.i \ 424 src/bindings/r/patch-swig-file.cmake 425 426# The files listed in 'javscript bindings' have to be included the dist files, even 427# though they can't be created by gnumake. 428 429jsbindings = \ 430 src/bindings/javascript/binding.gyp.in \ 431 src/bindings/javascript/CMakeLists.txt \ 432 src/bindings/javascript/compile-native-files.cmake \ 433 src/bindings/javascript/libsbml.i \ 434 src/bindings/javascript/local.cpp \ 435 src/bindings/javascript/local-downcast-astplugins-l3v2extendedmath.cpp \ 436 src/bindings/javascript/local-downcast-astplugins.cpp.in \ 437 src/bindings/javascript/local-downcast-converters.cpp.in \ 438 src/bindings/javascript/local-downcast-converters-layout.cpp \ 439 src/bindings/javascript/local-downcast.cpp.in \ 440 src/bindings/javascript/local-downcast-extension.cpp.in \ 441 src/bindings/javascript/local-downcast-extension-layout.cpp \ 442 src/bindings/javascript/local-downcast-extension-l3v2extendedmath.cpp \ 443 src/bindings/javascript/local-downcast-namespaces.cpp.in \ 444 src/bindings/javascript/local-downcast-namespaces-layout.cpp \ 445 src/bindings/javascript/local-downcast-namespaces-l3v2extendedmath.cpp \ 446 src/bindings/javascript/local-downcast-packages-layout.cpp \ 447 src/bindings/javascript/local-downcast-packages-l3v2extendedmath.cpp \ 448 src/bindings/javascript/local-downcast-plugins.cpp.in \ 449 src/bindings/javascript/local-downcast-plugins-layout.cpp \ 450 src/bindings/javascript/local-downcast-plugins-l3v2extendedmath.cpp \ 451 src/bindings/javascript/local.i \ 452 src/bindings/javascript/local-layout.i \ 453 src/bindings/javascript/local-l3v2extendedmath.i \ 454 src/bindings/javascript/local-packages.i.in \ 455 456 457# The files listed in 'php bindings' have to be included the dist files, even 458# though they can't be created by gnumake. 459 460phpbindings = \ 461 src/bindings/php/CMakeLists.txt \ 462 src/bindings/php/libsbml.i \ 463 src/bindings/php/local-downcast-converters-layout.cpp \ 464 src/bindings/php/local-downcast-astplugins.cpp.in \ 465 src/bindings/php/local-downcast-astplugins-l3v2extendedmath.cpp \ 466 src/bindings/php/local-downcast-converters.cpp.in \ 467 src/bindings/php/local-downcast-extension-layout.cpp \ 468 src/bindings/php/local-downcast-extension-l3v2extendedmath.cpp \ 469 src/bindings/php/local-downcast-extension.cpp.in \ 470 src/bindings/php/local-downcast-namespaces-layout.cpp \ 471 src/bindings/php/local-downcast-namespaces-l3v2extendedmath.cpp \ 472 src/bindings/php/local-downcast-namespaces.cpp.in \ 473 src/bindings/php/local-downcast-packages-layout.cpp \ 474 src/bindings/php/local-downcast-packages-l3v2extendedmath.cpp \ 475 src/bindings/php/local-downcast-plugins-layout.cpp \ 476 src/bindings/php/local-downcast-plugins-l3v2extendedmath.cpp \ 477 src/bindings/php/local-downcast-plugins.cpp.in \ 478 src/bindings/php/local-downcast.cpp.in \ 479 src/bindings/php/local-layout.i \ 480 src/bindings/php/local-l3v2extendedmath.i \ 481 src/bindings/php/local-packages.i.in \ 482 src/bindings/php/local.cpp \ 483 src/bindings/php/local.i \ 484 485 486# The files listed in `docs' are copied to the documentation directory 487# during a `make install'. 488 489docs = \ 490 docs/historical/AUTHORS.txt \ 491 COPYING.html \ 492 COPYING.txt \ 493 FUNDING.txt \ 494 LICENSE.txt \ 495 LICENSE.html \ 496 NEWS.txt \ 497 docs/historical/OLD_NEWS.txt \ 498 README.md \ 499 VERSION.txt \ 500 $(examples) 501 502 503# Variables `subdirs', `headers', `sources', `libraries', `extra_CPPFLAGS', 504# `extra_CXXFLAGS', `extra_LDFLAGS', `extra_clean', and `distfiles' are 505# used by the default rules in `makefile-common-actions.mk' included at the 506# end. 507 508subdirs = src docs macosx 509 510# `distfile' is the list of files used for creating distributions, 511# something that only the libSBML developers should do. The list of files 512# here is in addition to the subdirectories listed in `subdirs'. The 513# latter are the object of `make dist' and the files that are collected 514# are under the control of the makefiles in the subdirectories. 515 516distfiles = \ 517 docs/historical/AUTHORS.txt \ 518 COPYING.html \ 519 COPYING.txt \ 520 FUNDING.txt \ 521 LICENSE.txt \ 522 LICENSE.html \ 523 Makefile.in \ 524 docs/historical/OLD_NEWS.txt \ 525 NEWS.txt \ 526 README.md \ 527 VERSION.txt \ 528 VERSION_PACKAGES.ac \ 529 aclocal.m4 \ 530 acinclude.m4 \ 531 config/chk_swig_version.sh.in \ 532 config/config.guess \ 533 config/config.sub \ 534 config/doxygen.m4 \ 535 config/expat.m4 \ 536 config/install-sh \ 537 config/java.m4 \ 538 config/libcheck.m4 \ 539 config/libxml.m4 \ 540 config/dolt.m4 \ 541 config/ltmain.sh \ 542 config/libtool.m4 \ 543 config/lt_link_helper.sh.in \ 544 config/machine.m4 \ 545 config/makefile-common-actions.mk \ 546 config/makefile-common-vars.mk.in \ 547 config/matlab.m4 \ 548 config/missing \ 549 config/mkinstalldirs \ 550 config/mkoctfile_wrapper.sh.in \ 551 config/octave.m4 \ 552 config/perl.m4 \ 553 config/platform.m4 \ 554 config/printJavaDataModel.java \ 555 config/python.m4 \ 556 config/ruby.m4 \ 557 config/csharp.m4 \ 558 config/runldpath.m4 \ 559 config/swig.m4 \ 560 config/xercesc.m4 \ 561 config/zlib.m4 \ 562 config/bzip2.m4 \ 563 configure \ 564 configure.ac \ 565 libsbml.spec.in \ 566 cmake_uninstall.cmake.in \ 567 CMakeLists.txt \ 568 common.cmake \ 569 layout-package.cmake \ 570 l3v2extendedmath-package.cmake \ 571 $(examples) \ 572 $(jsbindings) \ 573 $(rbindings) \ 574 $(phpbindings) 575 576# The files listed in `extra_distclean' are items created by configure or 577# make, and that are removed by the default rules for `make distclean' in 578# makefile-common-actions.mk. 579 580extra_distclean = config.status config.cache config.log autom4te.cache \ 581 src/sbml/common/config.h src/sbml/common/stamp-h1 config/lt_link_helper.sh \ 582 config/mkoctfile_wrapper.sh libtool doltlibtool doltcompile \ 583 config/makefile-common-vars.mk config/chk_swig_version.sh \ 584 examples/c/Makefile examples/c++/Makefile examples/csharp/Makefile \ 585 examples/java/Makefile 586 587# It's safer to remove and recreate the copy of the include files (in the 588# 'include' directory) after a make clean. Previously we did it in a make 589# distclean only, but I've run into situations where the copy didn't get 590# updated. This is a bit of a sledgehammer, but it's not too bad. 591 592extra_clean = include libsbml.pc libsbml.spec config/*.class 593 594ifeq "$(HOST_TYPE)" "cygwin" 595 extra_clean += libsbml.la 596endif 597 598# Misc things used later below. 599 600define nodoxygen 601 602 Cannot create manuals, either because libSBML was not 603 configured using --with-doxygen, or 'doxygen' cannot be found, or 604 the version of 'doxygen' found is too old. Please reconfigure with 605 a suitable value for the configuration flag --with-doxygen 606endef 607 608 609# ----------------------------------------------------------------------------- 610# Primary build actions. 611# ----------------------------------------------------------------------------- 612 613# The default rules in `makefile-common-actions.mk' know to interpret goals 614# of the form `foo-recursive' to run 'make foo' in directories defined in 615# variable `subdirs'. 616 617all: configure Makefile all-recursive libsbml.pc 618 619docs:; 620# Only in the case of Java can we make the docs without doxygen. 621ifndef USE_JAVA 622ifeq "$(USE_DOXYGEN)" "" 623# Doxygen hasn't been configured suitably. 624 $(error $(nodoxygen)) 625endif 626endif 627ifneq "$(MAKEFLAGS)" "" 628 $(MAKE) -$(MAKEFLAGS) -w -C docs $(MAKECMDGOALS) 629else 630 $(MAKE) -w -C docs $(MAKECMDGOALS) 631endif 632 633# 634# Create a package (.dmg file) for MacOSX 635# 636# Executing "make create-dmg" will create a 637# libsbml-${VERSION}-${XML_PARSER}_macosx-installer.dmg 638# in the top directory of source tree. 639# 640# Install prefix, underlying XML parser (expat, libxml2, or xerces), language 641# bindings and etc. are determined by options passed to the configure script. 642# 643# For example, a created package will install libSBML (depends on expat) as 644# universal binaries (i386 and ppc) in /usr/local/ directory (default path) 645# with Java and Python bindings if the configure script is run as follows: 646# 647# ./configure --with-expat --enable-universal-binary --with-java --with-python 648# 649 650create-dmg: 651ifneq "$(MAKEFLAGS)" "" 652 $(MAKE) -$(MAKEFLAGS) -w -C macosx $(MAKECMDGOALS) 653else 654 $(MAKE) -w -C macosx $(MAKECMDGOALS) 655endif 656 657# 658# Create an RPM distribution. 659# 660 661create-rpm: libsbml.spec 662 rpmbuild -ba libsbml.spec --with java --with csharp --with python \ 663 --with ruby --with perl --with octave 664 665libsbml.spec: libsbml.spec.in $(TOP_SRCDIR)/configure \ 666 $(TOP_SRCDIR)/config/makefile-common-vars.mk 667 cd $(TOP_BUILDDIR) && $(SHELL) ./config.status $@ 668 669 670# ----------------------------------------------------------------------------- 671# Checking. 672# ----------------------------------------------------------------------------- 673 674check: all check-recursive 675 676 677# ----------------------------------------------------------------------------- 678# Tags. 679# ----------------------------------------------------------------------------- 680 681tags: etags-recursive ctags-recursive 682 683 684# ----------------------------------------------------------------------------- 685# libsbml.pc. 686# ----------------------------------------------------------------------------- 687 688base-libs = -lstdc++ -lm 689 690COMPRESS_CPFLAGS = ${ZLIB_CPPFLAGS} ${BZ2_CPPFLAGS} 691COMPRESS_LDFLAGS = ${ZLIB_LDFLAGS} ${BZ2_LDFLAGS} 692COMPRESS_LIBS = ${ZLIB_LIBS} ${BZ2_LIBS} 693 694XML_CPFLAGS = ${XERCES_CPPFLAGS} ${EXPAT_CPPFLAGS} ${LIBXML_CPPFLAGS} 695XML_LDFLAGS = ${XERCES_LDFLAGS} ${EXPAT_LDFLAGS} ${LIBXML_LDFLAGS} 696XML_LIBS = ${XERCES_LIBS} ${EXPAT_LIBS} ${LIBXML_LIBS} 697 698DEPENDENCY_CPPFLAGS = ${XML_CPPFLAGS} ${COMPRESS_CPPFLAGS} 699DEPENDENCY_LIBFLAGS = ${XML_LDFLAGS} ${COMPRESS_LDFLAGS} ${XML_LIBS} ${COMPRESS_LIBS} 700 701libsbml.pc: Makefile 702 @rm -f libsbml.pc 703 @echo "Name: @PACKAGE_NAME@" > libsbml.pc 704 @echo "Description: A library for reading/writing/manipulating SBML" >> libsbml.pc 705 @echo "URL: http://sbml.org/Software/libSBML" >> libsbml.pc 706 @echo "Version: @PACKAGE_VERSION@" >> libsbml.pc 707 @echo "" >> libsbml.pc 708 @echo "prefix=@prefix@" >> libsbml.pc 709 @echo "libdir=@libdir@" >> libsbml.pc 710 @echo "includedir=@includedir@" >> libsbml.pc 711 @echo "" >> libsbml.pc 712 @echo "Libs: -L\$${libdir} -lsbml" >> libsbml.pc 713 @echo "Libs.private: ${DEPENDENCY_LIBFLAGS} ${base-libs}" >> libsbml.pc 714 @echo "Cflags: -I\$${includedir}" >> libsbml.pc 715ifdef USE_XERCES 716 @echo "Conflicts: xerces-c = 2.6.0" >> libsbml.pc 717endif 718ifdef USE_LIBXML 719 @echo "Requires.private: libxml-2.0 >= 2.6.22" >> libsbml.pc 720endif 721 722# ----------------------------------------------------------------------------- 723# Installation. 724# ----------------------------------------------------------------------------- 725 726define install-linux-warning-msg 727 728 The installation of libSBML is finished. On certain platforms 729 (such as Linux), you will also need to do one of the following: 730 1) run 'ldconfig' (see the man page if this is unfamiliar) 731 2) set the LD_LIBRARY_PATH (or equivalent) environment variable 732 to contain the path "$(DESTDIR)$(LIBDIR)" so that programs can 733 find the libSBML library at run-time. 734 735endef 736define install-darwin-warning-msg 737 738 The installation of libSBML is finished. To use the library, you 739 may also need to set your DYLD_LIBRARY_PATH environment to contain 740 the path "$(DESTDIR)$(LIBDIR)" so that programs can find the 741 libSBML library at run-time. 742 743endef 744define uninstall-warning-msg 745 746 Uninstallation complete. WARNING: if you have run libSBML's 'configure' 747 utility since the time of the last installation of libSBML on this computer, 748 the uninstallation just performed may not have removed all of the libSBML 749 files. The 'make uninstall' command only knows about the files installed 750 by libSBML according to its MOST RECENT CONFIGURATION. 751 752endef 753 754install: all install-recursive install-warnings install-pc 755 756# Only in the case of Java can we make the docs without doxygen. 757ifdef USE_JAVA 758install-docs: install-docs-recursive 759else 760ifeq "$(USE_DOXYGEN)" "" 761# Doxygen hasn't been configured suitably. 762install-docs: 763 $(error $(nodoxygen)) 764else 765install-docs: install-docs-recursive 766endif 767endif 768 769installcheck: installcheck-recursive 770 771install-warnings: 772ifeq "$(HOST_TYPE)" "darwin" 773 $(warning $(install-darwin-warning-msg)) 774else 775 $(warning $(install-linux-warning-msg)) 776endif 777 778install-pc: libsbml.pc 779 $(INSTALL_SH) libsbml.pc -m 0644 "$(DESTDIR)$(LIBDIR)/pkgconfig/libsbml.pc" 780 781uninstall: uninstall-recursive uninstall-libsbml-pc 782 @if test -d "$(DESTDIR)$(LIBDIR)"; then \ 783 if test -n "`find $(DESTDIR)$(LIBDIR) -maxdepth 0 -empty`"; then \ 784 echo rmdir "$(DESTDIR)$(LIBDIR)"; \ 785 rmdir "$(DESTDIR)$(LIBDIR)"; \ 786 else \ 787 echo "Directory $(DESTDIR)$(LIBDIR) not empty; leaving it alone"; \ 788 fi; \ 789 fi; \ 790 if test -d "$(DESTDIR)$(INCLUDEDIR)"; then \ 791 if test -n "`find $(DESTDIR)$(INCLUDEDIR) -maxdepth 0 -empty`"; then \ 792 echo rmdir "$(DESTDIR)$(INCLUDEDIR)"; \ 793 rmdir "$(DESTDIR)$(INCLUDEDIR)"; \ 794 else \ 795 echo "Directory $(DESTDIR)$(INCLUDEDIR) not empty; leaving it alone"; \ 796 fi; \ 797 fi; \ 798 if test -d "$(DESTDIR)"; then \ 799 if test -n "`find $(DESTDIR) -maxdepth 0 -empty`"; then \ 800 echo rmdir "$(DESTDIR)"; \ 801 rmdir "$(DESTDIR)"; \ 802 else \ 803 echo "Directory $(DESTDIR) not empty; leaving it alone"; \ 804 fi; \ 805 fi; 806 $(warning $(uninstall-warning-msg)) 807 808uninstall-libsbml-pc: 809 @target="$(DESTDIR)$(LIBDIR)/pkgconfig/libsbml.pc"; \ 810 if test -f $$target ; then \ 811 echo rm $$target; \ 812 rm $$target; \ 813 fi; \ 814 if test -d "$(DESTDIR)$(LIBDIR)/pkgconfig"; then \ 815 if test -n "`find $(DESTDIR)$(LIBDIR) -maxdepth 0 -empty`"; then \ 816 echo rmdir "$(DESTDIR)$(LIBDIR)/pkgconfig"; \ 817 rmdir "$(DESTDIR)$(LIBDIR)/pkgconfig"; \ 818 else \ 819 echo "Directory $(DESTDIR)$(LIBDIR)/pkgconfig not empty; leaving it alone"; \ 820 fi; \ 821 fi; 822 823# ----------------------------------------------------------------------------- 824# Cleaning. 825# ----------------------------------------------------------------------------- 826 827clean: clean-normal clean-recursive 828 829distclean: distclean-normal distclean-recursive 830 831mostlyclean: mostlyclean-normal mostlyclean-recursive 832 833maintainer-clean: maintainer-clean-normal maintainer-clean-recursive 834 835 836# ----------------------------------------------------------------------------- 837# Creating distribution (for libSBML maintainers only) 838# ----------------------------------------------------------------------------- 839 840# The `make dist' command is only available from this top-level makefile. 841 842touch_distdir = \ 843 { find "$(archive_basename)" -print0 | xargs -0 gtouch -d '1 day ago'; } 844 845remove_distdir = \ 846 { test ! -d $(DISTDIR) \ 847 || { find $(DISTDIR) -type d ! -perm -200 -exec chmod u+w {} ';' \ 848 && rm -fr $(DISTDIR); }; } 849 850# Don't use GNU make's $(basename ...) command in the following; it behaves 851# differently in a critical way (specifically, in its handling of dots). 852 853archive_basename = $(shell basename $(DISTDIR)) 854tar_archive = $(archive_basename)-src.tar.gz 855zip_archive = $(archive_basename)-src.zip 856 857dist: dist-all dist-gzip dist-zip 858 if test -d $(DISTDIR); then \ 859 $(remove_distdir); \ 860 fi 861 862TAR := $(shell gnutar --version 2>/dev/null) 863ifdef TAR 864 TAR:=gnutar 865else 866 TAR:=tar 867endif 868 869dist-gzip: config-check dist-all 870 if test -d $(DISTDIR); then \ 871 $(TAR) -C $(DISTDIR)/.. -czf $(tar_archive) $(notdir $(DISTDIR)); \ 872 fi 873 874# The dependency on dist-gzip is to make sure that one is done first, because 875# this one resets the file time stamps before creating the archive: 876 877dist-zip: dist-gzip 878 if test -d $(DISTDIR); then \ 879 cd $(DISTDIR)/..; \ 880 $(touch_distdir); \ 881 zip -Xyvr9 $(zip_archive) "$(archive_basename)"; \ 882 fi 883 884# For `make dist' to work properly, we need the developer to configure 885# libsbml with certain flags, so that certain auto-generated files are 886# present when `make dist' runs and looks for them. 887 888# 2009-01-02 Lisp is now disabled, and thus not in the list below. 889 890check_vars_list = USE_JAVA USE_PYTHON USE_PERL USE_RUBY USE_CSHARP 891num_vars = $(words $(check_vars_list)) 892num_vars_set = $(words $(foreach var,$(check_vars_list),$($(var)))) 893 894config-check: 895 @if test $(num_vars_set) != $(num_vars); then \ 896 echo "Please reconfigure with options $(check_vars_list)"; \ 897 echo "before running 'make dist'"; \ 898 exit 2; \ 899 fi 900 901dist-all: $(distfiles) 902ifneq "$(MAKEFLAGS)" "" 903 $(MAKE) -$(MAKEFLAGS) all 904else 905 $(MAKE) all 906endif 907 -rm -f $(tar_archive) $(zip_archive) 908 @$(remove_distdir) 909 mkdir -p $(DISTDIR) 910 @list='$(distfiles)'; for file in $$list; do \ 911 if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \ 912 dir=`echo "$$file" | sed -e 's,/[^/]*$$,,'`; \ 913 if test "$$dir" != "$$file" && test "$$dir" != "."; then \ 914 dir="$$dir"; \ 915 $(MKINSTALLDIRS) "$(DISTDIR)/$$dir"; \ 916 else \ 917 dir=''; \ 918 fi; \ 919 if test -d $$d/$$file; then \ 920 if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \ 921 cp -pR $(srcdir)/$$file $(DISTDIR)/$$dir || exit 1; \ 922 fi; \ 923 cp -pR $$d/$$file $(DISTDIR)/$$dir || exit 1; \ 924 else \ 925 test -f $(DISTDIR)/$$file \ 926 || cp -p $$d/$$file $(DISTDIR)/$$file \ 927 || exit 1; \ 928 fi; \ 929 done 930 @list='$(subdirs)'; for subdir in $$list; do \ 931 if test "$$subdir" = .; then :; else \ 932 test -d $(DISTDIR)/$$subdir \ 933 || mkdir $(DISTDIR)/$$subdir \ 934 || exit 1; \ 935 $(MAKE) -$(MAKEFLAGS) -C $$subdir \ 936 TOP_DISTDIR="$(TOP_DISTDIR)" \ 937 DISTDIR=$(DISTDIR) \ 938 dist \ 939 || exit 1; \ 940 fi; \ 941 done 942 -@find $(DISTDIR) -type d ! -perm -777 -exec chmod a+rwx {} \; -o \ 943 ! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \ 944 ! -type d ! -perm -400 -exec chmod a+r {} \; -o \ 945 ! -type d ! -perm -444 -exec $(SHELL) $(INSTALL_SH) -c -m a+r {} {} \; \ 946 || chmod -R a+r $(DISTDIR) 947 948docs_tar_archive = $(archive_basename)-docs.tar.gz 949docs_zip_archive = $(archive_basename)-docs.zip 950 951docs_archive_contents = \ 952 docs/*.txt \ 953 docs/*.html \ 954 docs/*.docx \ 955 docs/*.pdf \ 956 docs/.graphics \ 957 docs/formatted/cpp-api \ 958 docs/formatted/csharp-api \ 959 docs/formatted/java-api \ 960 docs/formatted/matlab-api \ 961 docs/formatted/octave-api \ 962 docs/formatted/python-api 963 964dist-docs: 965 make docs 966 $(TAR) -czf $(docs_tar_archive) $(docs_archive_contents) 967 zip -Xyvr9 $(docs_zip_archive) $(docs_archive_contents) 968 969## This target untars the dist file and tries a VPATH configuration. Then 970## it guarantees that the distribution is self-contained by making another 971## tarfile. 972#distcheck: dist 973# $(remove_distdir) 974# GZIP=$(gzip_env) gunzip -c $(distdir).tar.gz | $(AMTAR) xf - 975# chmod -R a-w $(distdir); chmod a+w $(distdir) 976# mkdir $(distdir)/=build 977# mkdir $(distdir)/=inst 978# chmod a-w $(distdir) 979# dc_install_base=`$(am__cd) $(distdir)/=inst && pwd` \ 980# && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \ 981# && cd $(distdir)/=build \ 982# && ../configure --srcdir=.. --prefix="$$dc_install_base" \ 983# $(DISTCHECK_CONFIGURE_FLAGS) \ 984# && $(MAKE) $(AM_MAKEFLAGS) \ 985# && $(MAKE) $(AM_MAKEFLAGS) dvi \ 986# && $(MAKE) $(AM_MAKEFLAGS) check \ 987# && $(MAKE) $(AM_MAKEFLAGS) install \ 988# && $(MAKE) $(AM_MAKEFLAGS) installcheck \ 989# && $(MAKE) $(AM_MAKEFLAGS) uninstall \ 990# && $(MAKE) $(AM_MAKEFLAGS) distuninstallcheck_dir="$$dc_install_base" \ 991# distuninstallcheck \ 992# && chmod -R a-w "$$dc_install_base" \ 993# && ({ \ 994# (cd ../.. && $(MKINSTALLDIRS) "$$dc_destdir") \ 995# && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" install \ 996# && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" uninstall \ 997# && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" \ 998# distuninstallcheck_dir="$$dc_destdir" distuninstallcheck; \ 999# } || { rm -rf "$$dc_destdir"; exit 1; }) \ 1000# && rm -rf "$$dc_destdir" \ 1001# && $(MAKE) $(AM_MAKEFLAGS) dist-gzip \ 1002# && rm -f $(distdir).tar.gz \ 1003# && $(MAKE) $(AM_MAKEFLAGS) distcleancheck 1004# $(remove_distdir) 1005# @echo "$(distdir).tar.gz is ready for distribution" | \ 1006# sed 'h;s/./=/g;p;x;p;x' 1007 1008#distuninstallcheck: 1009# cd $(distuninstallcheck_dir) \ 1010# && test `find . -type f -print | wc -l` -le 1 \ 1011# || { echo "ERROR: files left after uninstall:" ; \ 1012# if test -n "$(DESTDIR)"; then \ 1013# echo " (check DESTDIR support)"; \ 1014# fi ; \ 1015# find . -type f -print ; \ 1016# exit 1; } >&2 1017 1018#distcleancheck: distclean 1019# if test '$(srcdir)' = . ; then \ 1020# echo "ERROR: distcleancheck can only run from a VPATH build" ; \ 1021# exit 1 ; \ 1022# fi 1023# test `find . -type f -print | wc -l` -eq 0 \ 1024# || { echo "ERROR: files left in build directory after distclean:" ; \ 1025# find -type f -print ; \ 1026# exit 1; } >&2 1027 1028 1029# ----------------------------------------------------------------------------- 1030# Miscellaneous. 1031# ----------------------------------------------------------------------------- 1032 1033printJavaDataModel: config/printJavaDataModel.java 1034 $(JAVAC) config/printJavaDataModel.java 1035 1036 1037# ----------------------------------------------------------------------------- 1038# Common default rules. 1039# ----------------------------------------------------------------------------- 1040 1041include @top_srcdir@/config/makefile-common-actions.mk 1042 1043 1044# ----------------------------------------------------------------------------- 1045# End. 1046# ----------------------------------------------------------------------------- 1047 1048