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Commit cf4c2287 authored by Peter Eastman's avatar Peter Eastman
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Use Doxygen to generate API docs for Python. This involved lots of changes... 

Use Doxygen to generate API docs for Python.  This involved lots of changes both to Python API generation and to Doxygen doc generation.
parent c8764170
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CMakeLists.txt
View file @ cf4c2287
...@@ -491,42 +491,75 @@ ENDIF (EXECUTABLE_OUTPUT_PATH) ...@@ -491,42 +491,75 @@ ENDIF (EXECUTABLE_OUTPUT_PATH)
find_package(Doxygen QUIET) find_package(Doxygen QUIET)
mark_as_advanced(CLEAR DOXYGEN_EXECUTABLE) mark_as_advanced(CLEAR DOXYGEN_EXECUTABLE)
IF(DOXYGEN_EXECUTABLE) IF(DOXYGEN_EXECUTABLE)
SET(DOXY_CONFIG "${CMAKE_CURRENT_BINARY_DIR}/Doxyfile") # Generate C++ API documentation
CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/docs/Doxyfile.in
${DOXY_CONFIG} SET(DOXY_CONFIG_C++ "${CMAKE_CURRENT_BINARY_DIR}/DoxyfileC++")
CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/docs/DoxyfileC++.in
${DOXY_CONFIG_C++}
@ONLY ) @ONLY )
FILE(GLOB_RECURSE OPENMM_INCLUDES "openmm/include/*.h") FILE(GLOB_RECURSE OPENMM_INCLUDES "openmm/include/*.h")
FILE(GLOB_RECURSE OLLA_INCLUDES "olla/include/*.h") FILE(GLOB_RECURSE OLLA_INCLUDES "olla/include/*.h")
ADD_CUSTOM_COMMAND( ADD_CUSTOM_COMMAND(
OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/html/index.html" OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/api-c++/index.html"
COMMAND ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG} COMMAND ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG_C++}
DEPENDS ${OPENMM_INCLUDES} ${OLLA_INCLUDES} DEPENDS ${OPENMM_INCLUDES} ${OLLA_INCLUDES}
WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}" WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
COMMENT "Generating API documentation using Doxygen") COMMENT "Generating C++ API documentation using Doxygen")
ADD_CUSTOM_TARGET(DoxygenApiDocs ADD_CUSTOM_TARGET(C++ApiDocs
DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/html/index.html" DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/api-c++/index.html"
COMMENT "Generating API documentation using Doxygen" COMMENT "Generating C++ API documentation using Doxygen"
SOURCES SOURCES
"${CMAKE_CURRENT_SOURCE_DIR}/docs/Doxyfile.in" "${CMAKE_CURRENT_SOURCE_DIR}/docs/DoxyfileC++.in"
${OPENMM_INCLUDES} ${OPENMM_INCLUDES}
${OLLA_INCLUDES} ${OLLA_INCLUDES}
) )
FILE(MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/html/") FILE(MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/api-c++/")
INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/html/" INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/api-c++/"
DESTINATION "docs/api/") DESTINATION "docs/api-c++/")
INSTALL(FILES "docs/API Reference.html" INSTALL(FILES "docs/API Reference.html"
DESTINATION "docs/") DESTINATION "docs/")
ADD_CUSTOM_TARGET(DoxygenApiDocs
DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/api-c++/index.html"
COMMENT "Generating C++ API documentation using Doxygen"
SOURCES
"${CMAKE_CURRENT_SOURCE_DIR}/docs/DoxyfileC++.in"
"${CMAKE_CURRENT_SOURCE_DIR}/docs/DoxyfilePython.in"
${OPENMM_INCLUDES}
${OLLA_INCLUDES}
)
set(OPENMM_GENERATE_API_DOCS OFF CACHE BOOL "Whether to create API documentation using Doxygen") set(OPENMM_GENERATE_API_DOCS OFF CACHE BOOL "Whether to create API documentation using Doxygen")
if(OPENMM_GENERATE_API_DOCS) IF (OPENMM_GENERATE_API_DOCS)
ADD_CUSTOM_TARGET(GenerateDoxygenApiDocs ALL SET_TARGET_PROPERTIES(DoxygenApiDocs PROPERTIES EXCLUDE_FROM_ALL FALSE)
DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/html/index.html" ENDIF (OPENMM_GENERATE_API_DOCS)
COMMENT "Generating API documentation using Doxygen"
# Generate Python API documentation
IF (OPENMM_BUILD_PYTHON_WRAPPERS)
SET(DOXY_CONFIG_PYTHON "${CMAKE_CURRENT_BINARY_DIR}/DoxyfilePython")
CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/docs/DoxyfilePython.in
${DOXY_CONFIG_PYTHON}
@ONLY )
ADD_CUSTOM_COMMAND(
OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/api-python/index.html"
COMMAND ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG_PYTHON}
DEPENDS RunSwig
WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
COMMENT "Generating Python API documentation using Doxygen")
ADD_CUSTOM_TARGET(PythonApiDocs
DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/api-python/index.html"
COMMENT "Generating Python API documentation using Doxygen"
SOURCES SOURCES
"${CMAKE_CURRENT_SOURCE_DIR}/docs/Doxyfile.in" "${CMAKE_CURRENT_SOURCE_DIR}/docs/DoxyfilePython.in"
${OPENMM_INCLUDES} ${OPENMM_INCLUDES}
${OLLA_INCLUDES} ${OLLA_INCLUDES}
) )
endif(OPENMM_GENERATE_API_DOCS) FILE(MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/api-python/")
INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/api-python/"
DESTINATION "docs/api-python/")
INSTALL(FILES "docs/API Reference.html"
DESTINATION "docs/")
ADD_DEPENDENCIES(DoxygenApiDocs PythonApiDocs)
ENDIF (OPENMM_BUILD_PYTHON_WRAPPERS)
ENDIF(DOXYGEN_EXECUTABLE) ENDIF(DOXYGEN_EXECUTABLE)
install(FILES docs/UsersGuide/OpenMMUsersGuide.pdf install(FILES docs/UsersGuide/OpenMMUsersGuide.pdf
......
docs/Doxyfile.in → docs/DoxyfileC++.in
View file @ cf4c2287
...@@ -85,7 +85,7 @@ RECURSIVE = YES ...@@ -85,7 +85,7 @@ RECURSIVE = YES
EXCLUDE = EXCLUDE =
EXCLUDE_SYMLINKS = NO EXCLUDE_SYMLINKS = NO
EXCLUDE_PATTERNS = */tests/* \ EXCLUDE_PATTERNS = */tests/* \
*/src/* \ */openmmapi/src/* \
*/.svn/* \ */.svn/* \
*/olla/include/openmm/kernels.h */olla/include/openmm/kernels.h
EXCLUDE_SYMBOLS = EXCLUDE_SYMBOLS =
...@@ -117,7 +117,7 @@ IGNORE_PREFIX = ...@@ -117,7 +117,7 @@ IGNORE_PREFIX =
# configuration options related to the HTML output # configuration options related to the HTML output
#--------------------------------------------------------------------------- #---------------------------------------------------------------------------
GENERATE_HTML = YES GENERATE_HTML = YES
HTML_OUTPUT = html HTML_OUTPUT = api-c++
HTML_FILE_EXTENSION = .html HTML_FILE_EXTENSION = .html
HTML_HEADER = HTML_HEADER =
HTML_FOOTER = HTML_FOOTER =
...@@ -200,7 +200,7 @@ SKIP_FUNCTION_MACROS = YES ...@@ -200,7 +200,7 @@ SKIP_FUNCTION_MACROS = YES
# Configuration::additions related to external references # Configuration::additions related to external references
#--------------------------------------------------------------------------- #---------------------------------------------------------------------------
TAGFILES = TAGFILES =
GENERATE_TAGFILE = "html/@PROJECT_NAME@DoxygenTagfile" GENERATE_TAGFILE = "api-c++/@PROJECT_NAME@DoxygenTagfile"
ALLEXTERNALS = NO ALLEXTERNALS = NO
EXTERNAL_GROUPS = YES EXTERNAL_GROUPS = YES
PERL_PATH = /usr/bin/perl PERL_PATH = /usr/bin/perl
......
docs/DoxyfilePython.in 0 → 100644
View file @ cf4c2287
# Doxyfile 1.5.3
#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------
DOXYFILE_ENCODING = UTF-8
PROJECT_NAME = @PROJECT_NAME@
PROJECT_NUMBER =
OUTPUT_DIRECTORY =
CREATE_SUBDIRS = NO
OUTPUT_LANGUAGE = English
BRIEF_MEMBER_DESC = YES
REPEAT_BRIEF = YES
ABBREVIATE_BRIEF =
ALWAYS_DETAILED_SEC = NO
INLINE_INHERITED_MEMB = NO
FULL_PATH_NAMES = NO
STRIP_FROM_PATH =
STRIP_FROM_INC_PATH =
SHORT_NAMES = NO
JAVADOC_AUTOBRIEF = YES
QT_AUTOBRIEF = NO
MULTILINE_CPP_IS_BRIEF = NO
DETAILS_AT_TOP = YES
INHERIT_DOCS = YES
SEPARATE_MEMBER_PAGES = NO
TAB_SIZE = 4
ALIASES =
OPTIMIZE_OUTPUT_FOR_C = NO
OPTIMIZE_OUTPUT_JAVA = YES
BUILTIN_STL_SUPPORT = NO
CPP_CLI_SUPPORT = NO
DISTRIBUTE_GROUP_DOC = YES
SUBGROUPING = YES
#---------------------------------------------------------------------------
# Build related configuration options
#---------------------------------------------------------------------------
EXTRACT_ALL = YES
EXTRACT_PRIVATE = NO
EXTRACT_STATIC = NO
EXTRACT_LOCAL_CLASSES = YES
EXTRACT_LOCAL_METHODS = NO
EXTRACT_ANON_NSPACES = NO
HIDE_UNDOC_MEMBERS = NO
HIDE_UNDOC_CLASSES = NO
HIDE_FRIEND_COMPOUNDS = NO
HIDE_IN_BODY_DOCS = YES
INTERNAL_DOCS = NO
CASE_SENSE_NAMES = YES
HIDE_SCOPE_NAMES = YES
SHOW_INCLUDE_FILES = YES
INLINE_INFO = YES
SORT_MEMBER_DOCS = YES
SORT_BRIEF_DOCS = NO
SORT_BY_SCOPE_NAME = NO
GENERATE_TODOLIST = YES
GENERATE_TESTLIST = YES
GENERATE_BUGLIST = YES
GENERATE_DEPRECATEDLIST= YES
ENABLED_SECTIONS =
MAX_INITIALIZER_LINES = 30
SHOW_USED_FILES = YES
SHOW_DIRECTORIES = YES
FILE_VERSION_FILTER =
SHOW_NAMESPACES = NO
SHOW_FILES = NO
SHOW_DIRECTORIES = NO
#---------------------------------------------------------------------------
# configuration options related to warning and progress messages
#---------------------------------------------------------------------------
QUIET = NO
WARNINGS = YES
WARN_IF_UNDOCUMENTED = YES
WARN_IF_DOC_ERROR = YES
WARN_NO_PARAMDOC = NO
WARN_FORMAT = "$file:$line: $text "
WARN_LOGFILE =
#---------------------------------------------------------------------------
# configuration options related to the input files
#---------------------------------------------------------------------------
INPUT = "@CMAKE_BINARY_DIR@/python/simtk/openmm" "@CMAKE_BINARY_DIR@/python/simtk/openmm/app"
INPUT_ENCODING = UTF-8
FILE_PATTERNS =
RECURSIVE = NO
EXCLUDE =
EXCLUDE_SYMLINKS = NO
EXCLUDE_PATTERNS =
EXCLUDE_SYMBOLS =
EXAMPLE_PATH =
EXAMPLE_PATTERNS =
EXAMPLE_RECURSIVE = NO
IMAGE_PATH =
INPUT_FILTER = "@PYTHON_EXECUTABLE@ @CMAKE_BINARY_DIR@/python/filterPythonFiles.py"
FILTER_PATTERNS =
FILTER_SOURCE_FILES = YES
#---------------------------------------------------------------------------
# configuration options related to source browsing
#---------------------------------------------------------------------------
SOURCE_BROWSER = NO
INLINE_SOURCES = NO
STRIP_CODE_COMMENTS = YES
REFERENCED_BY_RELATION = YES
REFERENCES_RELATION = YES
REFERENCES_LINK_SOURCE = YES
USE_HTAGS = NO
VERBATIM_HEADERS = YES
#---------------------------------------------------------------------------
# configuration options related to the alphabetical class index
#---------------------------------------------------------------------------
ALPHABETICAL_INDEX = NO
COLS_IN_ALPHA_INDEX = 5
IGNORE_PREFIX =
#---------------------------------------------------------------------------
# configuration options related to the HTML output
#---------------------------------------------------------------------------
GENERATE_HTML = YES
HTML_OUTPUT = api-python
HTML_FILE_EXTENSION = .html
HTML_HEADER =
HTML_FOOTER =
HTML_STYLESHEET =
HTML_ALIGN_MEMBERS = YES
GENERATE_HTMLHELP = NO
HTML_DYNAMIC_SECTIONS = YES
CHM_FILE =
HHC_LOCATION =
GENERATE_CHI = NO
BINARY_TOC = NO
TOC_EXPAND = NO
DISABLE_INDEX = NO
ENUM_VALUES_PER_LINE = 4
GENERATE_TREEVIEW = YES
TREEVIEW_WIDTH = 250
#---------------------------------------------------------------------------
# configuration options related to the LaTeX output
#---------------------------------------------------------------------------
GENERATE_LATEX = NO
LATEX_OUTPUT = latex
LATEX_CMD_NAME = latex
MAKEINDEX_CMD_NAME = makeindex
COMPACT_LATEX = NO
PAPER_TYPE = a4wide
EXTRA_PACKAGES =
LATEX_HEADER =
PDF_HYPERLINKS = NO
USE_PDFLATEX = NO
LATEX_BATCHMODE = NO
LATEX_HIDE_INDICES = NO
#---------------------------------------------------------------------------
# configuration options related to the RTF output
#---------------------------------------------------------------------------
GENERATE_RTF = NO
RTF_OUTPUT = rtf
COMPACT_RTF = NO
RTF_HYPERLINKS = NO
RTF_STYLESHEET_FILE =
RTF_EXTENSIONS_FILE =
#---------------------------------------------------------------------------
# configuration options related to the man page output
#---------------------------------------------------------------------------
GENERATE_MAN = NO
MAN_OUTPUT = man
MAN_EXTENSION = .3
MAN_LINKS = NO
#---------------------------------------------------------------------------
# configuration options related to the XML output
#---------------------------------------------------------------------------
GENERATE_XML = NO
XML_OUTPUT = xml
XML_SCHEMA =
XML_DTD =
XML_PROGRAMLISTING = YES
#---------------------------------------------------------------------------
# configuration options for the AutoGen Definitions output
#---------------------------------------------------------------------------
GENERATE_AUTOGEN_DEF = NO
#---------------------------------------------------------------------------
# configuration options related to the Perl module output
#---------------------------------------------------------------------------
GENERATE_PERLMOD = NO
PERLMOD_LATEX = NO
PERLMOD_PRETTY = YES
PERLMOD_MAKEVAR_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the preprocessor
#---------------------------------------------------------------------------
ENABLE_PREPROCESSING = YES
MACRO_EXPANSION = YES
EXPAND_ONLY_PREDEF = YES
SEARCH_INCLUDES = YES
INCLUDE_PATH =
INCLUDE_FILE_PATTERNS =
PREDEFINED =
EXPAND_AS_DEFINED =
SKIP_FUNCTION_MACROS = YES
#---------------------------------------------------------------------------
# Configuration::additions related to external references
#---------------------------------------------------------------------------
TAGFILES =
GENERATE_TAGFILE = "api-python/@PROJECT_NAME@DoxygenTagfile"
ALLEXTERNALS = NO
EXTERNAL_GROUPS = YES
PERL_PATH = /usr/bin/perl
#---------------------------------------------------------------------------
# Configuration options related to the dot tool
#---------------------------------------------------------------------------
CLASS_DIAGRAMS = YES
MSCGEN_PATH = /Applications/Doxygen.app/Contents/Resources/
HIDE_UNDOC_RELATIONS = YES
HAVE_DOT = NO
CLASS_GRAPH = YES
COLLABORATION_GRAPH = YES
GROUP_GRAPHS = YES
UML_LOOK = NO
TEMPLATE_RELATIONS = YES
INCLUDE_GRAPH = YES
INCLUDED_BY_GRAPH = YES
CALL_GRAPH = NO
CALLER_GRAPH = NO
GRAPHICAL_HIERARCHY = YES
DIRECTORY_GRAPH = YES
DOT_IMAGE_FORMAT = png
DOT_PATH =
DOTFILE_DIRS =
DOT_GRAPH_MAX_NODES = 50
MAX_DOT_GRAPH_DEPTH = 0
DOT_TRANSPARENT = NO
DOT_MULTI_TARGETS = NO
GENERATE_LEGEND = YES
DOT_CLEANUP = YES
#---------------------------------------------------------------------------
# Configuration::additions related to the search engine
#---------------------------------------------------------------------------
SEARCHENGINE = YES
wrappers/python/CMakeLists.txt
View file @ cf4c2287
...@@ -83,9 +83,6 @@ endif(SWIG_VERSION_ERROR) ...@@ -83,9 +83,6 @@ endif(SWIG_VERSION_ERROR)
find_package(Doxygen REQUIRED) find_package(Doxygen REQUIRED)
mark_as_advanced(CLEAR DOXYGEN_EXECUTABLE) mark_as_advanced(CLEAR DOXYGEN_EXECUTABLE)
find_package(Java REQUIRED)
mark_as_advanced(CLEAR JAVA_RUNTIME)
# SWIG_OPENMM_DIR is package area where swig files will be created/used # SWIG_OPENMM_DIR is package area where swig files will be created/used
set(SWIG_OPENMM_DIR "${OPENMM_PYTHON_STAGING_DIR}/src/swig_doxygen") set(SWIG_OPENMM_DIR "${OPENMM_PYTHON_STAGING_DIR}/src/swig_doxygen")
file(MAKE_DIRECTORY ${SWIG_OPENMM_DIR}/swig_lib/python) file(MAKE_DIRECTORY ${SWIG_OPENMM_DIR}/swig_lib/python)
...@@ -100,32 +97,13 @@ configure_file( ...@@ -100,32 +97,13 @@ configure_file(
# Step 2 - Run doxygen in non-package area # Step 2 - Run doxygen in non-package area
add_custom_command( add_custom_command(
OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/xml/index.xml" "${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/xml/combine.xslt" OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/xml/index.xml"
COMMAND "${DOXYGEN_EXECUTABLE}" COMMAND "${DOXYGEN_EXECUTABLE}"
DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/Doxyfile" DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/Doxyfile"
WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen" WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen"
COMMENT "Parsing OpenMM header files with doxygen..." COMMENT "Parsing OpenMM header files with doxygen..."
) )
# Step 3 - Run xslt to create combined xml file
add_custom_command(
OUTPUT "${SWIG_OPENMM_DIR}/OpenMM_headers.xml"
COMMAND ${JAVA_RUNTIME}
-jar "${CMAKE_SOURCE_DIR}/wrappers/saxonb9-1-0-7j/saxon9.jar"
-t
-s:"${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/xml/index.xml"
-xsl:"${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/xml/combine.xslt"
-o:OpenMM_headers.xml
DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/xml/index.xml" "${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/xml/combine.xslt"
WORKING_DIRECTORY "${SWIG_OPENMM_DIR}"
COMMENT "Creating combined OpenMM API xml file..."
)
add_custom_target(CreateCombinedXmlFile DEPENDS
"${SWIG_OPENMM_DIR}/OpenMM_headers.xml"
"${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/xml/index.xml"
"${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/xml/combine.xslt"
${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/Doxyfile)
# OpenMM REFERENCE platform first # OpenMM REFERENCE platform first
# Files which will be created by python script and used by swig (dynamically generated) # Files which will be created by python script and used by swig (dynamically generated)
...@@ -153,7 +131,7 @@ set(SWIG_INPUT_FILES2 ...@@ -153,7 +131,7 @@ set(SWIG_INPUT_FILES2
add_custom_command( add_custom_command(
OUTPUT ${SWIG_INPUT_FILES_REF} OUTPUT ${SWIG_INPUT_FILES_REF}
COMMAND ${PYTHON_EXECUTABLE} "${SWIG_OPENMM_DIR}/swigInputBuilder.py" COMMAND ${PYTHON_EXECUTABLE} "${SWIG_OPENMM_DIR}/swigInputBuilder.py"
-i OpenMM_headers.xml -i "${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/xml"
-c swigInputConfig.py -c swigInputConfig.py
-d OpenMM_docstring.i -d OpenMM_docstring.i
-o OpenMM_headers.i -o OpenMM_headers.i
...@@ -163,7 +141,7 @@ add_custom_command( ...@@ -163,7 +141,7 @@ add_custom_command(
DEPENDS DEPENDS
"${SWIG_OPENMM_DIR}/swigInputConfig.py" "${SWIG_OPENMM_DIR}/swigInputConfig.py"
"${SWIG_OPENMM_DIR}/swigInputBuilder.py" "${SWIG_OPENMM_DIR}/swigInputBuilder.py"
"${SWIG_OPENMM_DIR}/OpenMM_headers.xml" "${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/xml/index.xml"
COMMENT "Creating OpenMM Python swig input files..." COMMENT "Creating OpenMM Python swig input files..."
) )
......
wrappers/python/filterPythonFiles.py 0 → 100644
View file @ cf4c2287
import sys
# Doxygen does a bad job of generating documentation based on docstrings. This script is run as a filter
# on each file, and converts the docstrings into Doxygen style comments so we get better documentation.
input = open(sys.argv[1])
while True:
line = input.readline()
if len(line) == 0:
break
stripped = line.lstrip()
if stripped.startswith('def') or stripped.startswith('class'):
prefix = line[:len(line)-len(stripped)]
split = stripped.split()
if split[0] == 'class' and split[1][0].islower():
# Classes that start with a lowercase letter were defined by SWIG. We want to hide them.
print "%s## @private" % prefix
if split[1][0] == '_' and split[1][1] != '_':
# Names starting with a single _ are assumed to be private.
print "%s## @private" % prefix
# We're at the start of a class or function definition. Find all lines that contain the declaration.
declaration = line
while len(line) > 0 and line.find(':') == -1:
line = input.readline()
declaration += line
# Now look for a docstring.
docstrings = []
line = input.readline()
stripped = line.lstrip()
if stripped.startswith('"""'):
line = stripped[3:]
readingParameters = False
while line.find('"""') == -1:
docstrings.append(line)
line = input.readline()
if line.strip() == 'Parameters:':
readingParameters = True
line = input.readline()
stripped = line.lstrip()
if readingParameters and stripped.startswith('- '):
line = "@param %s" % stripped[2:]
elif stripped.startswith('Returns:'):
line = "@return %s" % stripped[8:]
line = line[:line.find('"""')]
docstrings.append(line)
# Print out the docstring in Doxygen syntax, followed by the declaration.
for s in docstrings:
print "%s##%s" % (prefix, s.rstrip())
print declaration
if len(docstrings) == 0:
print line
else:
print line
\ No newline at end of file
wrappers/python/simtk/openmm/app/forcefield.py
View file @ cf4c2287
...@@ -251,7 +251,7 @@ class ForceField(object): ...@@ -251,7 +251,7 @@ class ForceField(object):
Allowed values are None, HBonds, AllBonds, or HAngles. Allowed values are None, HBonds, AllBonds, or HAngles.
- rigidWater (boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument - rigidWater (boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument
- removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System - removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System
- Arbitrary additional keyword arguments may also be specified. This allows extra parameters to be specified that are specific to - - Arbitrary additional keyword arguments may also be specified. This allows extra parameters to be specified that are specific to
particular force fields. particular force fields.
Returns: the newly created System Returns: the newly created System
""" """
...@@ -525,7 +525,7 @@ def _findAtomMatches(atoms, template, bondedTo, externalBonds, matches, hasMatch ...@@ -525,7 +525,7 @@ def _findAtomMatches(atoms, template, bondedTo, externalBonds, matches, hasMatch
# and returns the corresponding generator object; 2) a createForce() method that constructs the Force object and adds it # and returns the corresponding generator object; 2) a createForce() method that constructs the Force object and adds it
# to the System. The static method should be added to the parsers map. # to the System. The static method should be added to the parsers map.
## @private
class HarmonicBondGenerator: class HarmonicBondGenerator:
"""A HarmonicBondGenerator constructs a HarmonicBondForce.""" """A HarmonicBondGenerator constructs a HarmonicBondForce."""
...@@ -572,6 +572,7 @@ class HarmonicBondGenerator: ...@@ -572,6 +572,7 @@ class HarmonicBondGenerator:
parsers["HarmonicBondForce"] = HarmonicBondGenerator.parseElement parsers["HarmonicBondForce"] = HarmonicBondGenerator.parseElement
## @private
class HarmonicAngleGenerator: class HarmonicAngleGenerator:
"""A HarmonicAngleGenerator constructs a HarmonicAngleForce.""" """A HarmonicAngleGenerator constructs a HarmonicAngleForce."""
...@@ -640,6 +641,7 @@ class HarmonicAngleGenerator: ...@@ -640,6 +641,7 @@ class HarmonicAngleGenerator:
parsers["HarmonicAngleForce"] = HarmonicAngleGenerator.parseElement parsers["HarmonicAngleForce"] = HarmonicAngleGenerator.parseElement
## @private
class PeriodicTorsion: class PeriodicTorsion:
"""A PeriodicTorsion records the information for a periodic torsion definition.""" """A PeriodicTorsion records the information for a periodic torsion definition."""
...@@ -652,6 +654,7 @@ class PeriodicTorsion: ...@@ -652,6 +654,7 @@ class PeriodicTorsion:
self.phase = [] self.phase = []
self.k = [] self.k = []
## @private
class PeriodicTorsionGenerator: class PeriodicTorsionGenerator:
"""A PeriodicTorsionGenerator constructs a PeriodicTorsionForce.""" """A PeriodicTorsionGenerator constructs a PeriodicTorsionForce."""
...@@ -739,6 +742,7 @@ class PeriodicTorsionGenerator: ...@@ -739,6 +742,7 @@ class PeriodicTorsionGenerator:
parsers["PeriodicTorsionForce"] = PeriodicTorsionGenerator.parseElement parsers["PeriodicTorsionForce"] = PeriodicTorsionGenerator.parseElement
## @private
class RBTorsion: class RBTorsion:
"""An RBTorsion records the information for a Ryckaert-Bellemans torsion definition.""" """An RBTorsion records the information for a Ryckaert-Bellemans torsion definition."""
...@@ -749,6 +753,7 @@ class RBTorsion: ...@@ -749,6 +753,7 @@ class RBTorsion:
self.types4 = types[3] self.types4 = types[3]
self.c = c self.c = c
## @private
class RBTorsionGenerator: class RBTorsionGenerator:
"""An RBTorsionGenerator constructs an RBTorsionForce.""" """An RBTorsionGenerator constructs an RBTorsionForce."""
...@@ -832,6 +837,7 @@ class RBTorsionGenerator: ...@@ -832,6 +837,7 @@ class RBTorsionGenerator:
parsers["RBTorsionForce"] = RBTorsionGenerator.parseElement parsers["RBTorsionForce"] = RBTorsionGenerator.parseElement
## @private
class CMAPTorsion: class CMAPTorsion:
"""A CMAPTorsion records the information for a CMAP torsion definition.""" """A CMAPTorsion records the information for a CMAP torsion definition."""
...@@ -843,6 +849,7 @@ class CMAPTorsion: ...@@ -843,6 +849,7 @@ class CMAPTorsion:
self.types5 = types[4] self.types5 = types[4]
self.map = map self.map = map
## @private
class CMAPTorsionGenerator: class CMAPTorsionGenerator:
"""A CMAPTorsionGenerator constructs a CMAPTorsionForce.""" """A CMAPTorsionGenerator constructs a CMAPTorsionForce."""
...@@ -922,6 +929,7 @@ class CMAPTorsionGenerator: ...@@ -922,6 +929,7 @@ class CMAPTorsionGenerator:
parsers["CMAPTorsionForce"] = CMAPTorsionGenerator.parseElement parsers["CMAPTorsionForce"] = CMAPTorsionGenerator.parseElement
## @private
class NonbondedGenerator: class NonbondedGenerator:
"""A NonbondedGenerator constructs a NonbondedForce.""" """A NonbondedGenerator constructs a NonbondedForce."""
...@@ -983,6 +991,7 @@ class NonbondedGenerator: ...@@ -983,6 +991,7 @@ class NonbondedGenerator:
parsers["NonbondedForce"] = NonbondedGenerator.parseElement parsers["NonbondedForce"] = NonbondedGenerator.parseElement
## @private
class GBSAOBCGenerator: class GBSAOBCGenerator:
"""A GBSAOBCGenerator constructs a GBSAOBCForce.""" """A GBSAOBCGenerator constructs a GBSAOBCForce."""
...@@ -1025,6 +1034,7 @@ class GBSAOBCGenerator: ...@@ -1025,6 +1034,7 @@ class GBSAOBCGenerator:
parsers["GBSAOBCForce"] = GBSAOBCGenerator.parseElement parsers["GBSAOBCForce"] = GBSAOBCGenerator.parseElement
## @private
class GBVIGenerator: class GBVIGenerator:
"""A GBVIGenerator constructs a GBVIForce.""" """A GBVIGenerator constructs a GBVIForce."""
...@@ -1112,6 +1122,7 @@ class GBVIGenerator: ...@@ -1112,6 +1122,7 @@ class GBVIGenerator:
parsers["GBVIForce"] = GBVIGenerator.parseElement parsers["GBVIForce"] = GBVIGenerator.parseElement
## @private
class CustomBondGenerator: class CustomBondGenerator:
"""A CustomBondGenerator constructs a CustomBondForce.""" """A CustomBondGenerator constructs a CustomBondForce."""
...@@ -1158,6 +1169,7 @@ class CustomBondGenerator: ...@@ -1158,6 +1169,7 @@ class CustomBondGenerator:
parsers["CustomBondForce"] = CustomBondGenerator.parseElement parsers["CustomBondForce"] = CustomBondGenerator.parseElement
## @private
class CustomAngleGenerator: class CustomAngleGenerator:
"""A CustomAngleGenerator constructs a CustomAngleForce.""" """A CustomAngleGenerator constructs a CustomAngleForce."""
...@@ -1208,6 +1220,7 @@ class CustomAngleGenerator: ...@@ -1208,6 +1220,7 @@ class CustomAngleGenerator:
parsers["CustomAngleForce"] = CustomAngleGenerator.parseElement parsers["CustomAngleForce"] = CustomAngleGenerator.parseElement
## @private
class CustomTorsion: class CustomTorsion:
"""A CustomTorsion records the information for a custom torsion definition.""" """A CustomTorsion records the information for a custom torsion definition."""
...@@ -1218,6 +1231,7 @@ class CustomTorsion: ...@@ -1218,6 +1231,7 @@ class CustomTorsion:
self.types4 = types[3] self.types4 = types[3]
self.paramValues = paramValues self.paramValues = paramValues
## @private
class CustomTorsionGenerator: class CustomTorsionGenerator:
"""A CustomTorsionGenerator constructs a CustomTorsionForce.""" """A CustomTorsionGenerator constructs a CustomTorsionForce."""
...@@ -1307,6 +1321,7 @@ class CustomTorsionGenerator: ...@@ -1307,6 +1321,7 @@ class CustomTorsionGenerator:
parsers["CustomTorsionForce"] = CustomTorsionGenerator.parseElement parsers["CustomTorsionForce"] = CustomTorsionGenerator.parseElement
## @private
class CustomGBGenerator: class CustomGBGenerator:
"""A CustomGBGenerator constructs a CustomGBForce.""" """A CustomGBGenerator constructs a CustomGBForce."""
...@@ -1401,6 +1416,7 @@ def countConstraint(data): ...@@ -1401,6 +1416,7 @@ def countConstraint(data):
print "Constraints bond=%d angle=%d total=%d" % (bondCount, angleCount, (bondCount+angleCount)) print "Constraints bond=%d angle=%d total=%d" % (bondCount, angleCount, (bondCount+angleCount))
## @private
class AmoebaHarmonicBondGenerator: class AmoebaHarmonicBondGenerator:
#============================================================================================= #=============================================================================================
...@@ -1515,6 +1531,7 @@ def addAngleConstraint(angle, idealAngle, data, sys): ...@@ -1515,6 +1531,7 @@ def addAngleConstraint(angle, idealAngle, data, sys):
return return
#============================================================================================= #=============================================================================================
## @private
class AmoebaHarmonicAngleGenerator: class AmoebaHarmonicAngleGenerator:
#============================================================================================= #=============================================================================================
...@@ -1730,6 +1747,7 @@ parsers["AmoebaHarmonicAngleForce"] = AmoebaHarmonicAngleGenerator.parseElement ...@@ -1730,6 +1747,7 @@ parsers["AmoebaHarmonicAngleForce"] = AmoebaHarmonicAngleGenerator.parseElement
# AmoebaHarmonicInPlaneAngleForce # AmoebaHarmonicInPlaneAngleForce
#============================================================================================= #=============================================================================================
## @private
class AmoebaOutOfPlaneBendGenerator: class AmoebaOutOfPlaneBendGenerator:
#============================================================================================= #=============================================================================================
...@@ -2010,6 +2028,7 @@ parsers["AmoebaOutOfPlaneBendForce"] = AmoebaOutOfPlaneBendGenerator.parseElemen ...@@ -2010,6 +2028,7 @@ parsers["AmoebaOutOfPlaneBendForce"] = AmoebaOutOfPlaneBendGenerator.parseElemen
#============================================================================================= #=============================================================================================
## @private
class AmoebaTorsionGenerator: class AmoebaTorsionGenerator:
#============================================================================================= #=============================================================================================
...@@ -2129,6 +2148,7 @@ parsers["AmoebaTorsionForce"] = AmoebaTorsionGenerator.parseElement ...@@ -2129,6 +2148,7 @@ parsers["AmoebaTorsionForce"] = AmoebaTorsionGenerator.parseElement
#============================================================================================= #=============================================================================================
## @private
class AmoebaPiTorsionGenerator: class AmoebaPiTorsionGenerator:
#============================================================================================= #=============================================================================================
...@@ -2247,6 +2267,7 @@ parsers["AmoebaPiTorsionForce"] = AmoebaPiTorsionGenerator.parseElement ...@@ -2247,6 +2267,7 @@ parsers["AmoebaPiTorsionForce"] = AmoebaPiTorsionGenerator.parseElement
#============================================================================================= #=============================================================================================
## @private
class AmoebaTorsionTorsionGenerator: class AmoebaTorsionTorsionGenerator:
#============================================================================================= #=============================================================================================
...@@ -2493,6 +2514,7 @@ parsers["AmoebaTorsionTorsionForce"] = AmoebaTorsionTorsionGenerator.parseElemen ...@@ -2493,6 +2514,7 @@ parsers["AmoebaTorsionTorsionForce"] = AmoebaTorsionTorsionGenerator.parseElemen
#============================================================================================= #=============================================================================================
## @private
class AmoebaStretchBendGenerator: class AmoebaStretchBendGenerator:
#============================================================================================= #=============================================================================================
...@@ -2641,6 +2663,7 @@ parsers["AmoebaStretchBendForce"] = AmoebaStretchBendGenerator.parseElement ...@@ -2641,6 +2663,7 @@ parsers["AmoebaStretchBendForce"] = AmoebaStretchBendGenerator.parseElement
#============================================================================================= #=============================================================================================
## @private
class AmoebaVdwGenerator: class AmoebaVdwGenerator:
"""A AmoebaVdwGenerator constructs a AmoebaVdwForce.""" """A AmoebaVdwGenerator constructs a AmoebaVdwForce."""
...@@ -2832,6 +2855,7 @@ parsers["AmoebaVdwForce"] = AmoebaVdwGenerator.parseElement ...@@ -2832,6 +2855,7 @@ parsers["AmoebaVdwForce"] = AmoebaVdwGenerator.parseElement
#============================================================================================= #=============================================================================================
## @private
class AmoebaMultipoleGenerator: class AmoebaMultipoleGenerator:
#============================================================================================= #=============================================================================================
...@@ -3501,6 +3525,7 @@ parsers["AmoebaMultipoleForce"] = AmoebaMultipoleGenerator.parseElement ...@@ -3501,6 +3525,7 @@ parsers["AmoebaMultipoleForce"] = AmoebaMultipoleGenerator.parseElement
#============================================================================================= #=============================================================================================
## @private
class AmoebaWcaDispersionGenerator: class AmoebaWcaDispersionGenerator:
"""A AmoebaWcaDispersionGenerator constructs a AmoebaWcaDispersionForce.""" """A AmoebaWcaDispersionGenerator constructs a AmoebaWcaDispersionForce."""
...@@ -3591,6 +3616,7 @@ parsers["AmoebaWcaDispersionForce"] = AmoebaWcaDispersionGenerator.parseElement ...@@ -3591,6 +3616,7 @@ parsers["AmoebaWcaDispersionForce"] = AmoebaWcaDispersionGenerator.parseElement
#============================================================================================= #=============================================================================================
## @private
class AmoebaGeneralizedKirkwoodGenerator: class AmoebaGeneralizedKirkwoodGenerator:
"""A AmoebaGeneralizedKirkwoodGenerator constructs a AmoebaGeneralizedKirkwoodForce.""" """A AmoebaGeneralizedKirkwoodGenerator constructs a AmoebaGeneralizedKirkwoodForce."""
...@@ -3864,6 +3890,7 @@ parsers["AmoebaGeneralizedKirkwoodForce"] = AmoebaGeneralizedKirkwoodGenerator.p ...@@ -3864,6 +3890,7 @@ parsers["AmoebaGeneralizedKirkwoodForce"] = AmoebaGeneralizedKirkwoodGenerator.p
#============================================================================================= #=============================================================================================
## @private
class AmoebaUreyBradleyGenerator: class AmoebaUreyBradleyGenerator:
#============================================================================================= #=============================================================================================
......
wrappers/python/simtk/openmm/app/modeller.py
View file @ cf4c2287
...@@ -426,16 +426,20 @@ class Modeller(object): ...@@ -426,16 +426,20 @@ class Modeller(object):
Aspartic acid: Aspartic acid:
ASH: Neutral form with a hydrogen on one of the delta oxygens ASH: Neutral form with a hydrogen on one of the delta oxygens
ASP: Negatively charged form without a hydrogen on either delta oxygen ASP: Negatively charged form without a hydrogen on either delta oxygen
Cysteine: Cysteine:
CYS: Neutral form with a hydrogen on the sulfur CYS: Neutral form with a hydrogen on the sulfur
CYX: No hydrogen on the sulfur (either negatively charged, or part of a disulfide bond) CYX: No hydrogen on the sulfur (either negatively charged, or part of a disulfide bond)
Glutamic acid: Glutamic acid:
GLH: Neutral form with a hydrogen on one of the epsilon oxygens GLH: Neutral form with a hydrogen on one of the epsilon oxygens
GLU: Negatively charged form without a hydrogen on either epsilon oxygen GLU: Negatively charged form without a hydrogen on either epsilon oxygen
Histidine: Histidine:
HID: Neutral form with a hydrogen on the ND1 atom HID: Neutral form with a hydrogen on the ND1 atom
HIE: Neutral form with a hydrogen on the NE2 atom HIE: Neutral form with a hydrogen on the NE2 atom
HIP: Positively charged form with hydrogens on both ND1 and NE2 HIP: Positively charged form with hydrogens on both ND1 and NE2
Lysine: Lysine:
LYN: Neutral form with two hydrogens on the zeta nitrogen LYN: Neutral form with two hydrogens on the zeta nitrogen
LYS: Positively charged form with three hydrogens on the zeta nitrogen LYS: Positively charged form with three hydrogens on the zeta nitrogen
......
wrappers/python/src/swig_doxygen/swigInputBuilder.py
View file @ cf4c2287
...@@ -17,6 +17,8 @@ import xml.etree.ElementTree as etree ...@@ -17,6 +17,8 @@ import xml.etree.ElementTree as etree
INDENT = " "; INDENT = " ";
docTags = {'emphasis':'i', 'bold':'b', 'itemizedlist':'ul', 'listitem':'li', 'preformatted':'pre', 'computeroutput':'tt'}
def trimToSingleSpace(text): def trimToSingleSpace(text):
if text is None or len(text) == 0: if text is None or len(text) == 0:
return "" return ""
...@@ -29,13 +31,30 @@ def trimToSingleSpace(text): ...@@ -29,13 +31,30 @@ def trimToSingleSpace(text):
t = "%s " % t t = "%s " % t
return t return t
def getNodeText(node):
if node.text is not None:
s = node.text
else:
s = ""
for n in node:
if n.tag == "para":
s = "%s%s\n\n" % (s, getNodeText(n))
elif n.tag == "ref":
s = "%s%s" % (s, getNodeText(n))
else:
if n.tag in docTags:
tag = docTags[n.tag]
s = "%s<%s>%s</%s>" % (s, tag, getNodeText(n), tag)
if n.tail is not None:
s = "%s%s" % (s, n.tail)
return s
def getText(subNodePath, node): def getText(subNodePath, node):
s="" s = ""
for n in node.findall(subNodePath): for n in node.findall(subNodePath):
s = "%s%s" % (s, trimToSingleSpace(n.text)) s = "%s%s" % (s, trimToSingleSpace(getNodeText(n)))
for r in n.findall("ref"): if n.tag == "para":
s = "%s%s%s" % (s, trimToSingleSpace(r.text), trimToSingleSpace(r.tail)) s = "%s\n\n" % s
s = "%s%s" % (s, trimToSingleSpace(n.tail))
return s.strip() return s.strip()
OPENMM_RE_PATTERN=re.compile("(.*)OpenMM:[a-zA-Z:]*:(.*)") OPENMM_RE_PATTERN=re.compile("(.*)OpenMM:[a-zA-Z:]*:(.*)")
...@@ -92,7 +111,7 @@ def getClassMethodList(classNode, skipMethods): ...@@ -92,7 +111,7 @@ def getClassMethodList(classNode, skipMethods):
class SwigInputBuilder: class SwigInputBuilder:
def __init__(self, def __init__(self,
inputFilename, inputDirname,
configFilename, configFilename,
outputFilename=None, outputFilename=None,
docstringFilename=None, docstringFilename=None,
...@@ -110,7 +129,12 @@ class SwigInputBuilder: ...@@ -110,7 +129,12 @@ class SwigInputBuilder:
items[2]=int(items[2]) items[2]=int(items[2])
self.skipMethods.append(tuple(items)) self.skipMethods.append(tuple(items))
self.doc = etree.parse(inputFilename) # Read all the XML files and merge them into a single document.
self.doc = etree.ElementTree(etree.Element('root'))
for file in os.listdir(inputDirname):
root = etree.parse(os.path.join(inputDirname, file)).getroot()
for node in root:
self.doc.getroot().append(node)
if outputFilename: if outputFilename:
self.fOut = open(outputFilename, 'w') self.fOut = open(outputFilename, 'w')
...@@ -220,6 +244,11 @@ class SwigInputBuilder: ...@@ -220,6 +244,11 @@ class SwigInputBuilder:
self.fOut.write("\n/* Class Declarations */\n\n") self.fOut.write("\n/* Class Declarations */\n\n")
for classNode in self._orderedClassNodes: for classNode in self._orderedClassNodes:
className = stripOpenmmPrefix(getText("compoundname", classNode)) className = stripOpenmmPrefix(getText("compoundname", classNode))
if self.fOutDocstring:
dNode = classNode.find('detaileddescription')
if dNode is not None:
docstring = getNodeText(dNode).strip().replace('"', '\\"')
self.fOutDocstring.write('%%feature("docstring") %s "%s";\n' % (className, docstring))
self.fOut.write("class %s" % className) self.fOut.write("class %s" % className)
if className in self.configModule.MISSING_BASE_CLASSES: if className in self.configModule.MISSING_BASE_CLASSES:
self.fOut.write(" : public %s" % self.fOut.write(" : public %s" %
...@@ -498,10 +527,13 @@ class SwigInputBuilder: ...@@ -498,10 +527,13 @@ class SwigInputBuilder:
dString=description dString=description
except IndexError: except IndexError:
pass pass
for pNode in findNodes(dNode, 'para/parameterlist/parameteritem'): params = findNodes(dNode, 'para/parameterlist/parameteritem')
if len(params) > 0:
dString="%s\n Parameters:" % dString
for pNode in params:
argName = getText('parameternamelist/parametername', pNode) argName = getText('parameternamelist/parametername', pNode)
argDoc = getText('parameterdescription/para', pNode) argDoc = getText('parameterdescription/para', pNode)
dString="%s\n %s -- %s" % (dString, argName, argDoc) dString="%s\n - %s %s" % (dString, argName, argDoc)
dString.strip() dString.strip()
if dString: if dString:
dString=re.sub(r'([^\\])"', r'\g<1>\"', dString) dString=re.sub(r'([^\\])"', r'\g<1>\"', dString)
...@@ -527,7 +559,7 @@ class SwigInputBuilder: ...@@ -527,7 +559,7 @@ class SwigInputBuilder:
def parseCommandLine(): def parseCommandLine():
opts, args_proper = getopt.getopt(sys.argv[1:], 'hi:c:o:d:a:z:s:') opts, args_proper = getopt.getopt(sys.argv[1:], 'hi:c:o:d:a:z:s:')
inputFilename = None inputDirname = None
configFilename = None configFilename = None
outputFilename = "" outputFilename = ""
docstringFilename = "" docstringFilename = ""
...@@ -536,24 +568,24 @@ def parseCommandLine(): ...@@ -536,24 +568,24 @@ def parseCommandLine():
skipAdditionalMethods = [] skipAdditionalMethods = []
for option, parameter in opts: for option, parameter in opts:
if option=='-h': usageError() if option=='-h': usageError()
if option=='-i': inputFilename = parameter if option=='-i': inputDirname = parameter
if option=='-c': configFilename=parameter if option=='-c': configFilename=parameter
if option=='-o': outputFilename = parameter if option=='-o': outputFilename = parameter
if option=='-d': docstringFilename = parameter if option=='-d': docstringFilename = parameter
if option=='-a': pythonprependFilename=parameter if option=='-a': pythonprependFilename=parameter
if option=='-z': pythonappendFilename=parameter if option=='-z': pythonappendFilename=parameter
if option=='-s': skipAdditionalMethods.append(parameter) if option=='-s': skipAdditionalMethods.append(parameter)
if not inputFilename: usageError() if not inputDirname: usageError()
if not configFilename: usageError() if not configFilename: usageError()
return (args_proper, inputFilename, configFilename, outputFilename, return (args_proper, inputDirname, configFilename, outputFilename,
docstringFilename, docstringFilename,
pythonprependFilename, pythonappendFilename, skipAdditionalMethods) pythonprependFilename, pythonappendFilename, skipAdditionalMethods)
def main(): def main():
(args_proper, inputFilename, configFilename, outputFilename, (args_proper, inputDirname, configFilename, outputFilename,
docstringFilename, pythonprependFilename, pythonappendFilename, docstringFilename, pythonprependFilename, pythonappendFilename,
skipAdditionalMethods) = parseCommandLine() skipAdditionalMethods) = parseCommandLine()
sBuilder = SwigInputBuilder(inputFilename, configFilename, outputFilename, sBuilder = SwigInputBuilder(inputDirname, configFilename, outputFilename,
docstringFilename, pythonprependFilename, docstringFilename, pythonprependFilename,
pythonappendFilename, skipAdditionalMethods) pythonappendFilename, skipAdditionalMethods)
#print "Calling writeSwigFile\n" #print "Calling writeSwigFile\n"
...@@ -568,7 +600,7 @@ def usageError(): ...@@ -568,7 +600,7 @@ def usageError():
% os.path.basename(sys.argv[0])) % os.path.basename(sys.argv[0]))
sys.stdout.write(' %s -c inputConfigFilename\n' \ sys.stdout.write(' %s -c inputConfigFilename\n' \
% (' '*len(os.path.basename(sys.argv[0])))) % (' '*len(os.path.basename(sys.argv[0]))))
sys.stdout.write(' %s[-o swigInputFilename]\n' \ sys.stdout.write(' %s[-o swigInputDirname]\n' \
% (' '*len(os.path.basename(sys.argv[0])))) % (' '*len(os.path.basename(sys.argv[0]))))
sys.stdout.write(' %s[-d docstringFilename]\n' \ sys.stdout.write(' %s[-d docstringFilename]\n' \
% (' '*len(os.path.basename(sys.argv[0])))) % (' '*len(os.path.basename(sys.argv[0]))))
......
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