From nobody Sat May 27 04:25:36 2023 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4QSpcd1XfCz4VCST; Sat, 27 May 2023 04:25:37 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4QSpcd0cwyz4DPm; Sat, 27 May 2023 04:25:37 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1685161537; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=fvQqXd3GCgS+wMbEJ9TMBZ/jp8QJ7ZA7CHxhAC3EeGY=; b=MIBaQM/fMk50WDm3y80N37ZXz7xtSvNCyeyPXVJFVc647RMWByFsIESwAAnfciWg66an4B QknVG4XXvYjOjtEuNx3BR8yUNnXFL8CYq9nwt/ndBDfknaL2fdjxbwVE7K2ZAzgiJbjhnz p3C3wgWMLrIFvhNBOH9evChhBnwSiet4reT/bp0KK0W+KqnEKvfkEjWlfyAsvPiS+IEVwd pz0L7zkr16znvz/e2LCzqVTs+ledP7DHvzbUjDR02veYC6HcAsM0Yi2f+56pQm6u59JdwF x/YgS6NJxMCzNy7kBvC6spHvqUG9EbP/2fG4+mZCLb2wFqRqCtA3W0SXqq3lvg== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1685161537; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=fvQqXd3GCgS+wMbEJ9TMBZ/jp8QJ7ZA7CHxhAC3EeGY=; b=Yb5ozftK0cjBIGfhhwGLel23GwCDXTIEAp3pIs8AltgqRFTU/N+Weyv0LZJdOs6e8BZ/lN 6XihYf4j9vpomH1zkS/b6hye4mUKazOWFNhcrWob/0KT32QmEINSQ9bgKzn3sNoL9KFcvv 5++rVQrXxUH2ehSfFhGauVWQ8LQJNsguyLFmcDjTldOq80msTi/BUH+BxvFaLW7xYwNYu8 GjuNb1kCoCnyfP4N0JqI5Ct5YLi9bBiQeTQmdvZTUeLdrN546pSSW80hv2BaZ45MsmgRBQ JUSMZmLg21mDkEI9IuWBjIeiluqIjRwhapUKfw3gcN6Zc5xGGkJDbCfbTR7Ixw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1685161537; a=rsa-sha256; cv=none; b=seIoRimmJwQKDgSv2duImJslScEfx1PzDr+fPXrpTiMZuMIZhJvrpG72VMiRourBJd0aZY PbzkEAxXkXWiCIfctMvOu42fugODDQ1nmMpRLKQWeNdLDuip+1R1G3anvMMaUwAZNW3Feg 28zFaZrN4jIdcwKNj46V+DYMJHb029x69r27GCwdidvaW43VnfpthE3GCXZSESBENB7brI 4btd5w4w4tSPXXWpEMzhvMUNfUwENG7cq0TY+ZyNeb1PYyZHOK4iQyClS3aA3PJCoaxExD 8+FVOcF5KJ31YOQ1u/9kbWZG5nYcmAzw/dW3H08kthOFR1IQjMOBAhaabiDa9Q== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4QSpcc6WVFzZTS; Sat, 27 May 2023 04:25:36 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 34R4PaHe023803; Sat, 27 May 2023 04:25:36 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 34R4Paap023802; Sat, 27 May 2023 04:25:36 GMT (envelope-from git) Date: Sat, 27 May 2023 04:25:36 GMT Message-Id: <202305270425.34R4Paap023802@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Po-Chuan Hsieh Subject: git: f98de8beb064 - main - biology/libsbml: Update to 5.20.0 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: sunpoet X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: f98de8beb06429de26f80be627eb78e0044bc826 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by sunpoet: URL: https://cgit.FreeBSD.org/ports/commit/?id=f98de8beb06429de26f80be627eb78e0044bc826 commit f98de8beb06429de26f80be627eb78e0044bc826 Author: Po-Chuan Hsieh AuthorDate: 2023-05-27 04:07:11 +0000 Commit: Po-Chuan Hsieh CommitDate: 2023-05-27 04:07:11 +0000 biology/libsbml: Update to 5.20.0 - Update MASTER_SITES - Update WWW - Sort PLIST Changes: https://github.com/sbmlteam/libsbml/releases --- biology/libsbml/Makefile | 44 ++- biology/libsbml/distinfo | 6 +- biology/libsbml/files/patch-CMakeLists.txt | 60 +++- ...-bindings-python-doc-converter-rewrite_pydoc.py | 279 --------------- biology/libsbml/pkg-plist | 376 ++++++--------------- 5 files changed, 199 insertions(+), 566 deletions(-) diff --git a/biology/libsbml/Makefile b/biology/libsbml/Makefile index 5d2aaca36803..791aaaac5e39 100644 --- a/biology/libsbml/Makefile +++ b/biology/libsbml/Makefile @@ -1,9 +1,7 @@ PORTNAME= libsbml -PORTVERSION= 5.19.0 -PORTREVISION= 2 +PORTVERSION= 5.20.0 +DISTVERSIONPREFIX= v CATEGORIES= biology devel -MASTER_SITES= SF/sbml/libsbml/${PORTVERSION}/stable -DISTNAME= libSBML-${PORTVERSION}-core-src MAINTAINER= sunpoet@FreeBSD.org COMMENT= API Library for Working with SBML File @@ -14,22 +12,46 @@ WWW= https://sbml.org/software/libsbml/ \ LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/COPYING.txt -USES= cmake iconv:build pathfix +USES= cmake:testing iconv:build pathfix -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 -CMAKE_ON= LIBSBML_SHARED_VERSION WITH_BZIP2 WITH_SWIG WITH_ZLIB +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 +CMAKE_ON= LIBSBML_SHARED_VERSION \ + WITH_BZIP2 \ + WITH_SWIG \ + WITH_THREADSAFE_PARSER \ + WITH_ZLIB +CMAKE_TESTING_ON= WITH_CHECK USE_CXXSTD= c++98 USE_LDCONFIG= yes -WRKSRC= ${WRKDIR}/libsbml-${PORTVERSION} PLIST_SUB= PORTVERSION=${PORTVERSION} +USE_GITHUB= yes +GH_ACCOUNT= sbmlteam + OPTIONS_DEFINE= EXAMPLES PYTHON RUBY OPTIONS_SINGLE= XML OPTIONS_SINGLE_XML= EXPAT LIBXML2 XERCES OPTIONS_DEFAULT=LIBXML2 PYTHON OPTIONS_SUB= yes +EXAMPLES_CMAKE_BOOL= WITH_EXAMPLES EXPAT_CMAKE_BOOL= WITH_EXPAT EXPAT_LIB_DEPENDS= libexpat.so:textproc/expat2 LIBXML2_CMAKE_BOOL= WITH_LIBXML @@ -37,7 +59,7 @@ LIBXML2_USE= GNOME=libxml2 LIBXML2_USES= gnome PYTHON_BUILD_DEPENDS= swig:devel/swig PYTHON_CMAKE_BOOL= WITH_PYTHON -PYTHON_USES= python:3.6+ +PYTHON_USES= python:3.7+ PYTHON_CMAKE_ON= WITH_SWIG RUBY_BUILD_DEPENDS= swig:devel/swig RUBY_CMAKE_BOOL= WITH_RUBY @@ -49,7 +71,7 @@ post-patch: @${REINPLACE_CMD} -e 's|/usr/local|${LOCALBASE}|g' ${WRKSRC}/CMakeLists.txt post-install-EXAMPLES-on: - ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} - cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} '! -name *Makefile*' + ${MV} ${STAGEDIR}${DATADIR}/examples ${STAGEDIR}${EXAMPLESDIR} + ${RMDIR} ${STAGEDIR}${DATADIR} .include diff --git a/biology/libsbml/distinfo b/biology/libsbml/distinfo index 2610d16e3336..30a1bfe42dfa 100644 --- a/biology/libsbml/distinfo +++ b/biology/libsbml/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1607539653 -SHA256 (libSBML-5.19.0-core-src.tar.gz) = 9d2837378e77a8732588d481327bb10c721ec06dd6cd72f8041d67d3b53d4e56 -SIZE (libSBML-5.19.0-core-src.tar.gz) = 14600103 +TIMESTAMP = 1684104306 +SHA256 (sbmlteam-libsbml-v5.20.0_GH0.tar.gz) = 400f1e1039ef0fc9addc99660a3a2559fefe9cb2c8315b1b488014b6101c438f +SIZE (sbmlteam-libsbml-v5.20.0_GH0.tar.gz) = 28776286 diff --git a/biology/libsbml/files/patch-CMakeLists.txt b/biology/libsbml/files/patch-CMakeLists.txt index 16351bdf126e..037277324c79 100644 --- a/biology/libsbml/files/patch-CMakeLists.txt +++ b/biology/libsbml/files/patch-CMakeLists.txt @@ -1,9 +1,56 @@ ---- CMakeLists.txt.orig 2020-11-19 11:17:49 UTC +--- CMakeLists.txt.orig 2023-04-03 10:48:28 UTC +++ CMakeLists.txt -@@ -1297,22 +1297,6 @@ endif() +@@ -430,8 +430,6 @@ if(WITH_EXPAT) + set(LIBSBML_XML_LIBRARY_INCLUDE ${EXPAT_INCLUDE_DIR}) + set(LIBSBML_XML_LIBRARY_LIBS ${EXPAT_LIBRARY}) + +- list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindEXPAT.cmake") +- + endif(WITH_EXPAT) + + +@@ -452,8 +450,6 @@ if(WITH_LIBXML) + set(LIBSBML_XML_LIBRARY_INCLUDE ${LIBXML_INCLUDE_DIR}) + set(LIBSBML_XML_LIBRARY_LIBS ${LIBXML_LIBRARY}) + +- list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindLIBXML.cmake") +- + endif(WITH_LIBXML) + + +@@ -473,8 +469,6 @@ if(WITH_XERCES) + set(LIBSBML_XML_LIBRARY_INCLUDE ${XERCES_INCLUDE_DIR}) + set(LIBSBML_XML_LIBRARY_LIBS ${XERCES_LIBRARY}) + +- list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindXERCES.cmake") +- + endif(WITH_XERCES) ############################################################################### - # +@@ -498,7 +492,6 @@ if(WITH_BZIP2) + set(USE_BZ2 ON) + add_definitions( -DUSE_BZ2 ) + list(APPEND SWIG_EXTRA_ARGS -DUSE_BZ2) +- list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindBZ2.cmake") + endif(WITH_BZIP2) + + +@@ -608,8 +601,6 @@ valid. It should contain the file zlib.h, but it does + INTERFACE_INCLUDE_DIRECTORIES "${LIBZ_INCLUDE_DIR}") + endif() + +- list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindZLIB.cmake") +- + endif(WITH_ZLIB) + + # install find scripts only for used dependencies +@@ -981,22 +972,6 @@ if(WITH_DOXYGEN) + add_subdirectory(docs) + endif() + +- +-############################################################################### +-# -# Install documentation -# - @@ -17,9 +64,6 @@ -) - -install(FILES ${DOCUMENTATION_FILES} DESTINATION ${MISC_PREFIX}) -- --############################################################################### --# - # Write libsbml.pc - # + ############################################################################### + # diff --git a/biology/libsbml/files/patch-src-bindings-python-doc-converter-rewrite_pydoc.py b/biology/libsbml/files/patch-src-bindings-python-doc-converter-rewrite_pydoc.py deleted file mode 100644 index fb1a6b0be7d9..000000000000 --- a/biology/libsbml/files/patch-src-bindings-python-doc-converter-rewrite_pydoc.py +++ /dev/null @@ -1,279 +0,0 @@ -Obtained from: https://github.com/sbmlteam/libsbml/commit/4f01a15fde1d8afa9eaffb4c13dfc83a3404f183 (based on) - ---- src/bindings/python/doc-converter/rewrite_pydoc.py.orig 2020-11-25 11:03:01 UTC -+++ src/bindings/python/doc-converter/rewrite_pydoc.py -@@ -118,7 +118,273 @@ import re - import sys - import os - import textwrap --from formatter import NullWriter, AbstractFormatter -+try: -+ from formatter import NullWriter, AbstractFormatter -+except Exception: -+ # issue 173 these classes have been removed in 3.10, so -+ # as per the 3.10 release notes: Existing users should copy whatever -+ # classes they use into their code. (Contributed by Dong-hee Na and -+ # Terry J. Reedy in bpo-42299.) -+ # -+ # So here they are: -+ -+ -+ class NullWriter: -+ """Minimal writer interface to use in testing & inheritance. -+ -+ A writer which only provides the interface definition; no actions are -+ taken on any methods. This should be the base class for all writers -+ which do not need to inherit any implementation methods. -+ -+ """ -+ def __init__(self): pass -+ def flush(self): pass -+ def new_alignment(self, align): pass -+ def new_font(self, font): pass -+ def new_margin(self, margin, level): pass -+ def new_spacing(self, spacing): pass -+ def new_styles(self, styles): pass -+ def send_paragraph(self, blankline): pass -+ def send_line_break(self): pass -+ def send_hor_rule(self, *args, **kw): pass -+ def send_label_data(self, data): pass -+ def send_flowing_data(self, data): pass -+ def send_literal_data(self, data): pass -+ -+ class AbstractFormatter: -+ """The standard formatter. -+ -+ This implementation has demonstrated wide applicability to many writers, -+ and may be used directly in most circumstances. It has been used to -+ implement a full-featured World Wide Web browser. -+ -+ """ -+ -+ # Space handling policy: blank spaces at the boundary between elements -+ # are handled by the outermost context. "Literal" data is not checked -+ # to determine context, so spaces in literal data are handled directly -+ # in all circumstances. -+ -+ def __init__(self, writer): -+ self.writer = writer # Output device -+ self.align = None # Current alignment -+ self.align_stack = [] # Alignment stack -+ self.font_stack = [] # Font state -+ self.margin_stack = [] # Margin state -+ self.spacing = None # Vertical spacing state -+ self.style_stack = [] # Other state, e.g. color -+ self.nospace = 1 # Should leading space be suppressed -+ self.softspace = 0 # Should a space be inserted -+ self.para_end = 1 # Just ended a paragraph -+ self.parskip = 0 # Skipped space between paragraphs? -+ self.hard_break = 1 # Have a hard break -+ self.have_label = 0 -+ -+ def end_paragraph(self, blankline): -+ if not self.hard_break: -+ self.writer.send_line_break() -+ self.have_label = 0 -+ if self.parskip < blankline and not self.have_label: -+ self.writer.send_paragraph(blankline - self.parskip) -+ self.parskip = blankline -+ self.have_label = 0 -+ self.hard_break = self.nospace = self.para_end = 1 -+ self.softspace = 0 -+ -+ def add_line_break(self): -+ if not (self.hard_break or self.para_end): -+ self.writer.send_line_break() -+ self.have_label = self.parskip = 0 -+ self.hard_break = self.nospace = 1 -+ self.softspace = 0 -+ -+ def add_hor_rule(self, *args, **kw): -+ if not self.hard_break: -+ self.writer.send_line_break() -+ self.writer.send_hor_rule(*args, **kw) -+ self.hard_break = self.nospace = 1 -+ self.have_label = self.para_end = self.softspace = self.parskip = 0 -+ -+ def add_label_data(self, format, counter, blankline = None): -+ if self.have_label or not self.hard_break: -+ self.writer.send_line_break() -+ if not self.para_end: -+ self.writer.send_paragraph((blankline and 1) or 0) -+ if isinstance(format, str): -+ self.writer.send_label_data(self.format_counter(format, counter)) -+ else: -+ self.writer.send_label_data(format) -+ self.nospace = self.have_label = self.hard_break = self.para_end = 1 -+ self.softspace = self.parskip = 0 -+ -+ def format_counter(self, format, counter): -+ label = '' -+ for c in format: -+ if c == '1': -+ label = label + ('%d' % counter) -+ elif c in 'aA': -+ if counter > 0: -+ label = label + self.format_letter(c, counter) -+ elif c in 'iI': -+ if counter > 0: -+ label = label + self.format_roman(c, counter) -+ else: -+ label = label + c -+ return label -+ -+ def format_letter(self, case, counter): -+ label = '' -+ while counter > 0: -+ counter, x = divmod(counter-1, 26) -+ # This makes a strong assumption that lowercase letters -+ # and uppercase letters form two contiguous blocks, with -+ # letters in order! -+ s = chr(ord(case) + x) -+ label = s + label -+ return label -+ -+ def format_roman(self, case, counter): -+ ones = ['i', 'x', 'c', 'm'] -+ fives = ['v', 'l', 'd'] -+ label, index = '', 0 -+ # This will die of IndexError when counter is too big -+ while counter > 0: -+ counter, x = divmod(counter, 10) -+ if x == 9: -+ label = ones[index] + ones[index+1] + label -+ elif x == 4: -+ label = ones[index] + fives[index] + label -+ else: -+ if x >= 5: -+ s = fives[index] -+ x = x-5 -+ else: -+ s = '' -+ s = s + ones[index]*x -+ label = s + label -+ index = index + 1 -+ if case == 'I': -+ return label.upper() -+ return label -+ -+ def add_flowing_data(self, data): -+ if not data: return -+ prespace = data[:1].isspace() -+ postspace = data[-1:].isspace() -+ data = " ".join(data.split()) -+ if self.nospace and not data: -+ return -+ elif prespace or self.softspace: -+ if not data: -+ if not self.nospace: -+ self.softspace = 1 -+ self.parskip = 0 -+ return -+ if not self.nospace: -+ data = ' ' + data -+ self.hard_break = self.nospace = self.para_end = \ -+ self.parskip = self.have_label = 0 -+ self.softspace = postspace -+ self.writer.send_flowing_data(data) -+ -+ def add_literal_data(self, data): -+ if not data: return -+ if self.softspace: -+ self.writer.send_flowing_data(" ") -+ self.hard_break = data[-1:] == '\n' -+ self.nospace = self.para_end = self.softspace = \ -+ self.parskip = self.have_label = 0 -+ self.writer.send_literal_data(data) -+ -+ def flush_softspace(self): -+ if self.softspace: -+ self.hard_break = self.para_end = self.parskip = \ -+ self.have_label = self.softspace = 0 -+ self.nospace = 1 -+ self.writer.send_flowing_data(' ') -+ -+ def push_alignment(self, align): -+ if align and align != self.align: -+ self.writer.new_alignment(align) -+ self.align = align -+ self.align_stack.append(align) -+ else: -+ 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] -+ self.writer.new_alignment(align) -+ else: -+ self.align = None -+ self.writer.new_alignment(None) -+ -+ def push_font(self, font): -+ size, i, b, tt = font -+ if self.softspace: -+ self.hard_break = self.para_end = self.softspace = 0 -+ 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: diff --git a/biology/libsbml/pkg-plist b/biology/libsbml/pkg-plist index b357279ef9f7..7a382979c5e4 100644 --- a/biology/libsbml/pkg-plist +++ b/biology/libsbml/pkg-plist @@ -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 @@ -196,53 +198,31 @@ include/sbml/xml/XercesHandler.h include/sbml/xml/XercesNamespaces.h include/sbml/xml/XercesParser.h include/sbml/xml/XercesTranscode.h -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 +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%% +%%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/FormulaGraphvizFormatter.h -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addCVTerms.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addModelHistory.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addingEvidenceCodes_1.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addingEvidenceCodes_2.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/appendAnnotation.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/convertSBML.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/createExampleSBML.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/drawMath.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/echoSBML.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/evaluateMath.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printAnnotation.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printMath.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printNotes.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printRegisteredPackages.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printSBML.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printSupported.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printUnits.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/promoteParameters.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/readSBML.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/stripPackage.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/translateL3Math.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/translateMath.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/unsetAnnotation.c -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/unsetNotes.c -%%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 @@ -258,15 +238,6 @@ lib/cmake/sbml-static-config.cmake %%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 @@ -278,6 +249,7 @@ lib/cmake/sbml-static-config.cmake %%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 @@ -288,219 +260,95 @@ lib/cmake/sbml-static-config.cmake %%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%%%%EXAMPLESDIR%%/c/FormulaGraphvizFormatter.h +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addCVTerms.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addModelHistory.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addingEvidenceCodes_1.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/addingEvidenceCodes_2.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/appendAnnotation.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/convertSBML.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/createExampleSBML.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/drawMath.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/echoSBML.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/evaluateMath.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printAnnotation.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printMath.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printNotes.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printRegisteredPackages.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printSBML.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printSupported.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printUnits.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/promoteParameters.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/readSBML.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/stripPackage.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/translateL3Math.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/translateMath.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/unsetAnnotation.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/unsetNotes.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/util.c +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/util.h +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/validateSBML.c +%%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