mirror of
https://git.FreeBSD.org/ports.git
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biology/libsbml: Update to 5.20.0
- Update MASTER_SITES - Update WWW - Sort PLIST Changes: https://github.com/sbmlteam/libsbml/releases
This commit is contained in:
Po-Chuan Hsieh
parent
65881ff36b
commit
f98de8beb0
@ -1,9 +1,7 @@
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PORTNAME= libsbml
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PORTVERSION= 5.19.0
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PORTREVISION= 2
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PORTVERSION= 5.20.0
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DISTVERSIONPREFIX= v
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CATEGORIES= biology devel
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MASTER_SITES= SF/sbml/libsbml/${PORTVERSION}/stable
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DISTNAME= libSBML-${PORTVERSION}-core-src
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MAINTAINER= sunpoet@FreeBSD.org
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COMMENT= API Library for Working with SBML File
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@ -14,22 +12,46 @@ WWW= https://sbml.org/software/libsbml/ \
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LICENSE= LGPL21
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LICENSE_FILE= ${WRKSRC}/COPYING.txt
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USES= cmake iconv:build pathfix
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USES= cmake:testing iconv:build pathfix
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CMAKE_OFF= EXIT_ON_ERROR LIBSBML_USE_STRICT_INCLUDES PYTHON_USE_API2_WARNINGS WITH_ALL_PACKAGES WITH_CHECK WITH_CPP_NAMESPACE WITH_CSHARP WITH_DOXYGEN WITH_JAVA WITH_JAVASCRIPT WITH_MATLAB WITH_OCTAVE WITH_PERL WITH_PHP WITH_R WITH_STABLE_PACKAGES WITH_WALL
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CMAKE_ON= LIBSBML_SHARED_VERSION WITH_BZIP2 WITH_SWIG WITH_ZLIB
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CMAKE_OFF= EXIT_ON_ERROR \
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LIBSBML_USE_STRICT_INCLUDES \
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PYTHON_USE_API2_WARNINGS \
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WITH_ALL_PACKAGES \
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WITH_CHECK \
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WITH_CPP_NAMESPACE \
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WITH_CSHARP \
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WITH_DOXYGEN \
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WITH_JAVA \
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WITH_JAVASCRIPT \
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WITH_MATLAB \
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WITH_OCTAVE \
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WITH_PERL \
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WITH_PHP \
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WITH_R \
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WITH_STABLE_PACKAGES \
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WITH_WALL
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CMAKE_ON= LIBSBML_SHARED_VERSION \
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WITH_BZIP2 \
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WITH_SWIG \
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WITH_THREADSAFE_PARSER \
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WITH_ZLIB
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CMAKE_TESTING_ON= WITH_CHECK
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USE_CXXSTD= c++98
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USE_LDCONFIG= yes
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WRKSRC= ${WRKDIR}/libsbml-${PORTVERSION}
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PLIST_SUB= PORTVERSION=${PORTVERSION}
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USE_GITHUB= yes
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GH_ACCOUNT= sbmlteam
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OPTIONS_DEFINE= EXAMPLES PYTHON RUBY
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OPTIONS_SINGLE= XML
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OPTIONS_SINGLE_XML= EXPAT LIBXML2 XERCES
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OPTIONS_DEFAULT=LIBXML2 PYTHON
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OPTIONS_SUB= yes
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EXAMPLES_CMAKE_BOOL= WITH_EXAMPLES
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EXPAT_CMAKE_BOOL= WITH_EXPAT
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EXPAT_LIB_DEPENDS= libexpat.so:textproc/expat2
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LIBXML2_CMAKE_BOOL= WITH_LIBXML
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@ -37,7 +59,7 @@ LIBXML2_USE= GNOME=libxml2
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LIBXML2_USES= gnome
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PYTHON_BUILD_DEPENDS= swig:devel/swig
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PYTHON_CMAKE_BOOL= WITH_PYTHON
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PYTHON_USES= python:3.6+
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PYTHON_USES= python:3.7+
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PYTHON_CMAKE_ON= WITH_SWIG
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RUBY_BUILD_DEPENDS= swig:devel/swig
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RUBY_CMAKE_BOOL= WITH_RUBY
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@ -49,7 +71,7 @@ post-patch:
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@${REINPLACE_CMD} -e 's|/usr/local|${LOCALBASE}|g' ${WRKSRC}/CMakeLists.txt
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post-install-EXAMPLES-on:
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${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
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cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} '! -name *Makefile*'
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${MV} ${STAGEDIR}${DATADIR}/examples ${STAGEDIR}${EXAMPLESDIR}
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${RMDIR} ${STAGEDIR}${DATADIR}
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.include <bsd.port.mk>
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@ -1,3 +1,3 @@
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TIMESTAMP = 1607539653
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SHA256 (libSBML-5.19.0-core-src.tar.gz) = 9d2837378e77a8732588d481327bb10c721ec06dd6cd72f8041d67d3b53d4e56
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SIZE (libSBML-5.19.0-core-src.tar.gz) = 14600103
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TIMESTAMP = 1684104306
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SHA256 (sbmlteam-libsbml-v5.20.0_GH0.tar.gz) = 400f1e1039ef0fc9addc99660a3a2559fefe9cb2c8315b1b488014b6101c438f
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SIZE (sbmlteam-libsbml-v5.20.0_GH0.tar.gz) = 28776286
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@ -1,9 +1,56 @@
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--- CMakeLists.txt.orig 2020-11-19 11:17:49 UTC
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--- CMakeLists.txt.orig 2023-04-03 10:48:28 UTC
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+++ CMakeLists.txt
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@@ -1297,22 +1297,6 @@ endif()
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@@ -430,8 +430,6 @@ if(WITH_EXPAT)
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set(LIBSBML_XML_LIBRARY_INCLUDE ${EXPAT_INCLUDE_DIR})
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set(LIBSBML_XML_LIBRARY_LIBS ${EXPAT_LIBRARY})
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- list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindEXPAT.cmake")
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-
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endif(WITH_EXPAT)
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@@ -452,8 +450,6 @@ if(WITH_LIBXML)
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set(LIBSBML_XML_LIBRARY_INCLUDE ${LIBXML_INCLUDE_DIR})
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set(LIBSBML_XML_LIBRARY_LIBS ${LIBXML_LIBRARY})
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- list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindLIBXML.cmake")
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-
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endif(WITH_LIBXML)
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@@ -473,8 +469,6 @@ if(WITH_XERCES)
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set(LIBSBML_XML_LIBRARY_INCLUDE ${XERCES_INCLUDE_DIR})
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set(LIBSBML_XML_LIBRARY_LIBS ${XERCES_LIBRARY})
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- list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindXERCES.cmake")
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-
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endif(WITH_XERCES)
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###############################################################################
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#
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@@ -498,7 +492,6 @@ if(WITH_BZIP2)
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set(USE_BZ2 ON)
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add_definitions( -DUSE_BZ2 )
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list(APPEND SWIG_EXTRA_ARGS -DUSE_BZ2)
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- list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindBZ2.cmake")
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endif(WITH_BZIP2)
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@@ -608,8 +601,6 @@ valid. It should contain the file zlib.h, but it does
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INTERFACE_INCLUDE_DIRECTORIES "${LIBZ_INCLUDE_DIR}")
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endif()
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- list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindZLIB.cmake")
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-
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endif(WITH_ZLIB)
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# install find scripts only for used dependencies
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@@ -981,22 +972,6 @@ if(WITH_DOXYGEN)
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add_subdirectory(docs)
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endif()
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-
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-###############################################################################
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-#
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-# Install documentation
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-#
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-
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@ -17,9 +64,6 @@
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-)
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-
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-install(FILES ${DOCUMENTATION_FILES} DESTINATION ${MISC_PREFIX})
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-
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-###############################################################################
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-#
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# Write libsbml.pc
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#
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###############################################################################
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#
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@ -1,279 +0,0 @@
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Obtained from: https://github.com/sbmlteam/libsbml/commit/4f01a15fde1d8afa9eaffb4c13dfc83a3404f183 (based on)
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--- src/bindings/python/doc-converter/rewrite_pydoc.py.orig 2020-11-25 11:03:01 UTC
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+++ src/bindings/python/doc-converter/rewrite_pydoc.py
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@@ -118,7 +118,273 @@ import re
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import sys
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import os
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import textwrap
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-from formatter import NullWriter, AbstractFormatter
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+try:
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+ from formatter import NullWriter, AbstractFormatter
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+except Exception:
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+ # issue 173 these classes have been removed in 3.10, so
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+ # as per the 3.10 release notes: Existing users should copy whatever
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+ # classes they use into their code. (Contributed by Dong-hee Na and
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+ # Terry J. Reedy in bpo-42299.)
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+ #
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+ # So here they are:
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+
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+
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+ class NullWriter:
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+ """Minimal writer interface to use in testing & inheritance.
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+
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+ A writer which only provides the interface definition; no actions are
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+ taken on any methods. This should be the base class for all writers
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+ which do not need to inherit any implementation methods.
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+
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+ """
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+ def __init__(self): pass
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+ def flush(self): pass
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+ def new_alignment(self, align): pass
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+ def new_font(self, font): pass
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+ def new_margin(self, margin, level): pass
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+ def new_spacing(self, spacing): pass
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+ def new_styles(self, styles): pass
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+ def send_paragraph(self, blankline): pass
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+ def send_line_break(self): pass
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+ def send_hor_rule(self, *args, **kw): pass
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+ def send_label_data(self, data): pass
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+ def send_flowing_data(self, data): pass
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+ def send_literal_data(self, data): pass
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+
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+ class AbstractFormatter:
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+ """The standard formatter.
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+
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+ This implementation has demonstrated wide applicability to many writers,
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+ and may be used directly in most circumstances. It has been used to
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+ implement a full-featured World Wide Web browser.
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+
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+ """
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+
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+ # Space handling policy: blank spaces at the boundary between elements
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+ # are handled by the outermost context. "Literal" data is not checked
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+ # to determine context, so spaces in literal data are handled directly
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+ # in all circumstances.
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+
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+ def __init__(self, writer):
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+ self.writer = writer # Output device
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+ self.align = None # Current alignment
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+ self.align_stack = [] # Alignment stack
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+ self.font_stack = [] # Font state
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+ self.margin_stack = [] # Margin state
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+ self.spacing = None # Vertical spacing state
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+ self.style_stack = [] # Other state, e.g. color
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+ self.nospace = 1 # Should leading space be suppressed
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+ self.softspace = 0 # Should a space be inserted
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+ self.para_end = 1 # Just ended a paragraph
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+ self.parskip = 0 # Skipped space between paragraphs?
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+ self.hard_break = 1 # Have a hard break
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+ self.have_label = 0
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+
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+ def end_paragraph(self, blankline):
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+ if not self.hard_break:
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+ self.writer.send_line_break()
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+ self.have_label = 0
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+ if self.parskip < blankline and not self.have_label:
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+ self.writer.send_paragraph(blankline - self.parskip)
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+ self.parskip = blankline
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+ self.have_label = 0
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+ self.hard_break = self.nospace = self.para_end = 1
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+ self.softspace = 0
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+
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+ def add_line_break(self):
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+ if not (self.hard_break or self.para_end):
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+ self.writer.send_line_break()
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+ self.have_label = self.parskip = 0
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+ self.hard_break = self.nospace = 1
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+ self.softspace = 0
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+
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+ def add_hor_rule(self, *args, **kw):
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+ if not self.hard_break:
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+ self.writer.send_line_break()
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+ self.writer.send_hor_rule(*args, **kw)
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+ self.hard_break = self.nospace = 1
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+ self.have_label = self.para_end = self.softspace = self.parskip = 0
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+
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+ def add_label_data(self, format, counter, blankline = None):
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+ if self.have_label or not self.hard_break:
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+ self.writer.send_line_break()
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+ if not self.para_end:
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+ self.writer.send_paragraph((blankline and 1) or 0)
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+ if isinstance(format, str):
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+ self.writer.send_label_data(self.format_counter(format, counter))
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+ else:
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+ self.writer.send_label_data(format)
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+ self.nospace = self.have_label = self.hard_break = self.para_end = 1
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+ self.softspace = self.parskip = 0
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+
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+ def format_counter(self, format, counter):
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+ label = ''
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+ for c in format:
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+ if c == '1':
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+ label = label + ('%d' % counter)
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+ elif c in 'aA':
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+ if counter > 0:
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+ label = label + self.format_letter(c, counter)
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+ elif c in 'iI':
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+ if counter > 0:
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+ label = label + self.format_roman(c, counter)
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+ else:
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+ label = label + c
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+ return label
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+
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+ def format_letter(self, case, counter):
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+ label = ''
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+ while counter > 0:
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+ counter, x = divmod(counter-1, 26)
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+ # This makes a strong assumption that lowercase letters
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+ # and uppercase letters form two contiguous blocks, with
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+ # letters in order!
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+ s = chr(ord(case) + x)
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+ label = s + label
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+ return label
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+
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+ def format_roman(self, case, counter):
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+ ones = ['i', 'x', 'c', 'm']
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+ fives = ['v', 'l', 'd']
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+ label, index = '', 0
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+ # This will die of IndexError when counter is too big
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+ while counter > 0:
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+ counter, x = divmod(counter, 10)
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+ if x == 9:
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+ label = ones[index] + ones[index+1] + label
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+ elif x == 4:
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+ label = ones[index] + fives[index] + label
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+ else:
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+ if x >= 5:
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+ s = fives[index]
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+ x = x-5
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+ else:
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+ s = ''
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+ s = s + ones[index]*x
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+ label = s + label
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+ index = index + 1
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+ if case == 'I':
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+ return label.upper()
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+ return label
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+
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+ def add_flowing_data(self, data):
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+ if not data: return
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+ prespace = data[:1].isspace()
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+ postspace = data[-1:].isspace()
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+ data = " ".join(data.split())
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+ if self.nospace and not data:
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+ return
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+ elif prespace or self.softspace:
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+ if not data:
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+ if not self.nospace:
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+ self.softspace = 1
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+ self.parskip = 0
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+ return
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+ if not self.nospace:
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+ data = ' ' + data
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+ self.hard_break = self.nospace = self.para_end = \
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+ self.parskip = self.have_label = 0
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+ self.softspace = postspace
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+ self.writer.send_flowing_data(data)
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+
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+ def add_literal_data(self, data):
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+ if not data: return
|
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+ if self.softspace:
|
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+ self.writer.send_flowing_data(" ")
|
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+ self.hard_break = data[-1:] == '\n'
|
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+ self.nospace = self.para_end = self.softspace = \
|
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+ self.parskip = self.have_label = 0
|
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+ self.writer.send_literal_data(data)
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+
|
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+ def flush_softspace(self):
|
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+ if self.softspace:
|
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+ self.hard_break = self.para_end = self.parskip = \
|
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+ self.have_label = self.softspace = 0
|
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+ self.nospace = 1
|
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+ self.writer.send_flowing_data(' ')
|
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+
|
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+ def push_alignment(self, align):
|
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+ if align and align != self.align:
|
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+ self.writer.new_alignment(align)
|
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+ self.align = align
|
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+ self.align_stack.append(align)
|
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+ else:
|
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+ self.align_stack.append(self.align)
|
||||
+
|
||||
+ def pop_alignment(self):
|
||||
+ if self.align_stack:
|
||||
+ del self.align_stack[-1]
|
||||
+ if self.align_stack:
|
||||
+ self.align = align = self.align_stack[-1]
|
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+ self.writer.new_alignment(align)
|
||||
+ else:
|
||||
+ self.align = None
|
||||
+ self.writer.new_alignment(None)
|
||||
+
|
||||
+ def push_font(self, font):
|
||||
+ size, i, b, tt = font
|
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+ if self.softspace:
|
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+ self.hard_break = self.para_end = self.softspace = 0
|
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+ self.nospace = 1
|
||||
+ self.writer.send_flowing_data(' ')
|
||||
+ if self.font_stack:
|
||||
+ csize, ci, cb, ctt = self.font_stack[-1]
|
||||
+ if size is AS_IS: size = csize
|
||||
+ if i is AS_IS: i = ci
|
||||
+ if b is AS_IS: b = cb
|
||||
+ if tt is AS_IS: tt = ctt
|
||||
+ font = (size, i, b, tt)
|
||||
+ self.font_stack.append(font)
|
||||
+ self.writer.new_font(font)
|
||||
+
|
||||
+ def pop_font(self):
|
||||
+ if self.font_stack:
|
||||
+ del self.font_stack[-1]
|
||||
+ if self.font_stack:
|
||||
+ font = self.font_stack[-1]
|
||||
+ else:
|
||||
+ font = None
|
||||
+ self.writer.new_font(font)
|
||||
+
|
||||
+ def push_margin(self, margin):
|
||||
+ self.margin_stack.append(margin)
|
||||
+ fstack = filter(None, self.margin_stack)
|
||||
+ if not margin and fstack:
|
||||
+ margin = fstack[-1]
|
||||
+ self.writer.new_margin(margin, len(fstack))
|
||||
+
|
||||
+ def pop_margin(self):
|
||||
+ if self.margin_stack:
|
||||
+ del self.margin_stack[-1]
|
||||
+ fstack = filter(None, self.margin_stack)
|
||||
+ if fstack:
|
||||
+ margin = fstack[-1]
|
||||
+ else:
|
||||
+ margin = None
|
||||
+ self.writer.new_margin(margin, len(fstack))
|
||||
+
|
||||
+ def set_spacing(self, spacing):
|
||||
+ self.spacing = spacing
|
||||
+ self.writer.new_spacing(spacing)
|
||||
+
|
||||
+ def push_style(self, *styles):
|
||||
+ if self.softspace:
|
||||
+ self.hard_break = self.para_end = self.softspace = 0
|
||||
+ self.nospace = 1
|
||||
+ self.writer.send_flowing_data(' ')
|
||||
+ for style in styles:
|
||||
+ self.style_stack.append(style)
|
||||
+ self.writer.new_styles(tuple(self.style_stack))
|
||||
+
|
||||
+ def pop_style(self, n=1):
|
||||
+ del self.style_stack[-n:]
|
||||
+ self.writer.new_styles(tuple(self.style_stack))
|
||||
+
|
||||
+ def assert_line_data(self, flag=1):
|
||||
+ self.nospace = self.hard_break = not flag
|
||||
+ self.para_end = self.parskip = self.have_label = 0
|
||||
+
|
||||
+
|
||||
try:
|
||||
from htmllib import HTMLParser
|
||||
except Exception:
|
||||
@ -75,6 +75,7 @@ include/sbml/compress/zip.h
|
||||
include/sbml/compress/zipfstream.h
|
||||
include/sbml/conversion/ConversionOption.h
|
||||
include/sbml/conversion/ConversionProperties.h
|
||||
include/sbml/conversion/ExpressionAnalyser.h
|
||||
include/sbml/conversion/SBMLConverter.h
|
||||
include/sbml/conversion/SBMLConverterRegister.h
|
||||
include/sbml/conversion/SBMLConverterRegistry.h
|
||||
@ -87,6 +88,7 @@ include/sbml/conversion/SBMLLevel1Version1Converter.h
|
||||
include/sbml/conversion/SBMLLevelVersionConverter.h
|
||||
include/sbml/conversion/SBMLLocalParameterConverter.h
|
||||
include/sbml/conversion/SBMLRateOfConverter.h
|
||||
include/sbml/conversion/SBMLRateRuleConverter.h
|
||||
include/sbml/conversion/SBMLReactionConverter.h
|
||||
include/sbml/conversion/SBMLRuleConverter.h
|
||||
include/sbml/conversion/SBMLStripPackageConverter.h
|
||||
@ -196,24 +198,68 @@ include/sbml/xml/XercesHandler.h
|
||||
include/sbml/xml/XercesNamespaces.h
|
||||
include/sbml/xml/XercesParser.h
|
||||
include/sbml/xml/XercesTranscode.h
|
||||
lib/cmake/sbml-config-version.cmake
|
||||
lib/cmake/sbml-config.cmake
|
||||
lib/cmake/sbml-static-config-version.cmake
|
||||
lib/cmake/sbml-static-config.cmake
|
||||
lib/cmake/sbml-static-targets-%%CMAKE_BUILD_TYPE%%.cmake
|
||||
lib/cmake/sbml-static-targets.cmake
|
||||
lib/cmake/sbml-targets-%%CMAKE_BUILD_TYPE%%.cmake
|
||||
lib/cmake/sbml-targets.cmake
|
||||
lib/libsbml-static.a
|
||||
lib/libsbml.so
|
||||
lib/libsbml.so.5
|
||||
lib/libsbml.so.%%PORTVERSION%%
|
||||
libdata/pkgconfig/libsbml.pc
|
||||
lib/cmake/sbml-config-release.cmake
|
||||
lib/cmake/sbml-config-version.cmake
|
||||
lib/cmake/sbml-config.cmake
|
||||
lib/cmake/sbml-static-config-release.cmake
|
||||
lib/cmake/sbml-static-config-version.cmake
|
||||
lib/cmake/sbml-static-config.cmake
|
||||
%%PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml.pth
|
||||
%%PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/_libsbml.so
|
||||
%%PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/libsbml.py
|
||||
%%PYTHON_SITELIBDIR%%/libsbml.pth
|
||||
%%PYTHON_SITELIBDIR%%/libsbml/_libsbml.so
|
||||
%%PYTHON_SITELIBDIR%%/libsbml/libsbml.py
|
||||
%%RUBY%%%%RUBY_SITEARCHLIBDIR%%/libSBML.so
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CMakeLists.txt
|
||||
libdata/pkgconfig/libsbml.pc
|
||||
@comment share/cmake/Modules/FindBZ2.cmake
|
||||
@comment share/cmake/Modules/FindCHECK.cmake
|
||||
@comment share/cmake/Modules/FindEXPAT.cmake
|
||||
share/cmake/Modules/FindLIBSBML.cmake
|
||||
@comment share/cmake/Modules/FindLIBXML.cmake
|
||||
@comment share/cmake/Modules/FindXERCES.cmake
|
||||
@comment share/cmake/Modules/FindZLIB.cmake
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README.txt
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/CMakeLists.txt
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addCVTerms.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addCustomValidator.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addModelHistory.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addingEvidenceCodes_1.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addingEvidenceCodes_2.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/appendAnnotation.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/callExternalValidator.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/convertReactions.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/convertSBML.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/convertToL1V1.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/createExampleSBML.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/echoSBML.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/getAllElementsWithNotes.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/inferUnits.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/inlineFunctionDefintions.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printAnnotation.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printMath.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printNotes.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printRegisteredPackages.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printSBML.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printSupported.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printUnits.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/promoteParameters.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/readSBML.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/renameSId.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/rngvalidator.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/setAnnotation.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/setIdFromNames.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/setNamesFromIds.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/stripPackage.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/translateL3Math.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/translateMath.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/unsetAnnotation.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/unsetNotes.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/util.c
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/util.h
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/validateSBML.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/FormulaGraphvizFormatter.h
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addCVTerms.c
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addModelHistory.c
|
||||
@ -242,265 +288,67 @@ lib/cmake/sbml-static-config.cmake
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/util.c
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/util.h
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/validateSBML.c
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/CMakeLists.txt
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addCVTerms.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addCustomValidator.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addModelHistory.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addingEvidenceCodes_1.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addingEvidenceCodes_2.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/appendAnnotation.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/callExternalValidator.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/convertReactions.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/convertSBML.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/convertToL1V1.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/createExampleSBML.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/echoSBML.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/getAllElementsWithNotes.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/inferUnits.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/inlineFunctionDefintions.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/CMakeLists.txt
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/addLayout.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/convertLayout.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example1-L3.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example1.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example2-L3.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example2.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example3-L3.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/layout/example3.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printAnnotation.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printMath.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printNotes.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printRegisteredPackages.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printSBML.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printSupported.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printUnits.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/promoteParameters.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/readSBML.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/renameSId.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/rngvalidator.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/setIdFromNames.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/setNamesFromIds.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/stripPackage.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/translateL3Math.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/translateMath.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/unsetAnnotation.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/unsetNotes.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/util.c
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/util.h
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/validateSBML.cpp
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/CMakeLists.txt
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/GetAllElementsWithNotes.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/SetIdFromNames.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/addCVTerms.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/addCustomValidator.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/addModelHistory.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/addingEvidenceCodes_1.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/addingEvidenceCodes_2.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/appendAnnotation.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/callExternalValidator.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/convertSBML.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/createExampleSBML.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/echoSBML.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/evaluateCustomMath.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/inlineInitialAssignments.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/layout/CMakeLists.txt
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/layout/example1-L3.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printAnnotation.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printMath.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printNotes.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printRegisteredPackages.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printSBML.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printUnits.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/printsupported.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/promoteParameters.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/readSBML.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/replaceOneFD.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/stripPackage.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/translateMath.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/unsetAnnotation.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/unsetNotes.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/validateSBML.cs
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/CMakeLists.txt
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/README.txt
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addCVTerms.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addCustomValidator.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addModelHistory.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addingEvidenceCodes_1.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addingEvidenceCodes_2.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/appendAnnotation.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/callExternalValidator.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/convertSBML.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/createExampleSBML.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/echoSBML.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/evaluateCustomMath.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/evaluateMath.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/getAllElementsWithNotes.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/inlineInitialAssignments.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/layout/CMakeLists.txt
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/layout/SimpleLayoutConverter.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/layout/layout_example1.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/layout/layout_example1_L3.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printAnnotation.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printMath.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printNotes.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printRegisteredPackages.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printSBML.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printUnits.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printsupported.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/promoteParameters.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/readSBML.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/replaceOneFD.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/setIdFromNames.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/stripPackage.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/translateMath.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/unsetAnnotation.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/unsetNotes.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/validateSBML.java
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/addCVTerms.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/addModelHistory.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/addingEvidenceCodes_1.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/addingEvidenceCodes_2.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/appendAnnotation.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/callExternalValidator.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/convertSBML.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/createExampleSBML.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/echoSBML.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/printAnnotation.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/printMath.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/printNotes.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/printRegisteredPackages.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/printSBML.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/printUnits.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/printsupported.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/promoteParameters.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/readSBML.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/stripPackage.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/translateMath.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/unsetAnnotation.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/unsetNotes.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/javascript/validateSBML.js
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout-package.cmake
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/README.txt
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/addCVTerms.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/addCustomValidator.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/addModelHistory.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/addingEvidenceCodes_1.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/addingEvidenceCodes_2.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/appendAnnotation.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/callExternalValidator.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/convertSBML.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/createExampleSBML.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/echoSBML.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/evaluateMath.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/extractReactionInfo.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/extractReactions.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/layout/example1-L3.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printAnnotation.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printMath.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printNotes.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printRegisteredPackages.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printSBML.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printUnits.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printsupported.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/promoteParameters.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/readSBML.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/renameSId.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/stripPackage.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/translateMath.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/unsetAnnotation.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/unsetNotes.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/validateSBML.pl
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/php/createExampleSBML.php
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/php/echoSBML.php
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/php/validateSBML.php
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addCVTerms.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addCustomValidator.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addModelHistory.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addingEvidenceCodes_1.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/addingEvidenceCodes_2.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/append_to_note.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/appendAnnotation.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/callExternalValidator.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/convertSBML.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/createExampleSBML.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/createSimpleModel.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/echoSBML.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/evaluateCustomMath.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/getAllElementsWithNotes.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/inlineFunctionDefinitions.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/inlineInitialAssignments.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/layout/convertLayout.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/layout/example1-L3.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/layout/example1.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printAnnotation.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printMath.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printNotes.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printRegisteredPackages.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printSBML.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printUnits.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/printsupported.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/promoteParameters.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/readSBML.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/renameSId.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/replaceOneFD.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/setIdFromNames.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/stringInput.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/stripPackage.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/translateMath.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/unsetAnnotation.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/unsetNotes.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/validateSBML.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/validateSBMLWithCallback.py
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/addCVTerms.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/addModelHistory.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/addingEvidenceCodes_1.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/addingEvidenceCodes_2.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/appendAnnotation.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/convertSBML.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/createExampleSBML.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/echoSBML.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/evaluateMath.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printAnnotation.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printMath.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printNotes.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printRegisteredPackages.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printSBML.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printSupported.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/printUnits.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/promoteParameters.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/readSBML.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/stripPackage.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/translateMath.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/unsetAnnotation.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/unsetNotes.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/r/validateSBML.R
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/addCVTerms.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/addCustomValidator.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/addModelHistory.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/addingEvidenceCodes_1.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/addingEvidenceCodes_2.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/appendAnnotation.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/callExternalValidator.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/convertSBML.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/createExampleSBML.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/echoSBML.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/layout/example1-L3.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printAnnotation.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printMath.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printNotes.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printRegisteredPackages.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printSBML.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printUnits.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printsupported.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/promoteParameters.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/readSBML.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/stripPackage.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/translateMath.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/unsetAnnotation.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/unsetNotes.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/validateSBML.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/README.txt
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/README.txt
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/addCVTerms.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/addCustomValidator.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/addModelHistory.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/add_function_definition.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/addingEvidenceCodes_1.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/addingEvidenceCodes_2.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/appendAnnotation.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/append_to_note.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/callExternalValidator.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/convertSBML.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/createExampleSBML.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/createSimpleModel.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/echoSBML.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/evaluateCustomMath.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/getAllElementsWithNotes.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/inlineFunctionDefinitions.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/inlineInitialAssignments.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/printAnnotation.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/printMath.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/printNotes.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/printRegisteredPackages.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/printSBML.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/printUnits.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/printsupported.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/promoteParameters.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/readSBML.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/renameSId.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/replaceOneFD.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/setIdFromNames.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/setNamesFromIds.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/stringInput.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/stripPackage.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/translateMath.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/unsetAnnotation.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/unsetNotes.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/validateSBML.py
|
||||
%%PORTEXAMPLES%%%%PYTHON%%%%EXAMPLESDIR%%/python/validateSBMLWithCallback.py
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/addCVTerms.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/addCustomValidator.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/addModelHistory.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/addingEvidenceCodes_1.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/addingEvidenceCodes_2.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/appendAnnotation.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/callExternalValidator.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/convertSBML.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/createExampleSBML.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/echoSBML.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/printAnnotation.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/printMath.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/printNotes.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/printRegisteredPackages.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/printSBML.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/printUnits.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/printsupported.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/promoteParameters.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/readSBML.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/stripPackage.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/translateMath.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/unsetAnnotation.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/unsetNotes.rb
|
||||
%%PORTEXAMPLES%%%%RUBY%%%%EXAMPLESDIR%%/ruby/validateSBML.rb
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/algebraicrules.xml
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/assignmentrules.xml
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/boundarycondition.xml
|
||||
@ -513,7 +361,6 @@ lib/cmake/sbml-static-config.cmake
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/overdetermined.xml
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/twodimensional.xml
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/units.xml
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/README.txt
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/algebraicrules.xml
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/assignmentrules.xml
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/boundarycondition.xml
|
||||
@ -531,4 +378,3 @@ lib/cmake/sbml-static-config.cmake
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/overdetermined.xml
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/twoalgebraicrules.xml
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/twodimensional.xml
|
||||
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xslt/layout/layout2svg.xsl
|
||||
|
||||
Loading…
Reference in New Issue
Block a user