# @configure_input@ # ----------------------------------------------------------------------------- # File name : doxyfile-config-python.txt # Description : Doxygen config for Python libSBML API manual # Original author(s): Michael Hucka # Organization : California Institute of Technology # ----------------------------------------------------------------------------- # Include libSBML's common Doxygen settings: @INCLUDE = doxygen-config-common.txt # ----------------------------------------------------------------------------- # Beginning of C++ specific configuration settings # ----------------------------------------------------------------------------- # The PROJECT_NAME tag is a single word (or a sequence of words surrounded # by quotes) that should identify the project. PROJECT_NAME = "@PACKAGE_NAME@ Python API" # The PROJECT_NUMBER tag can be used to enter a project or revision number. # This could be handy for archiving the generated documentation or # if some version control system is used. PROJECT_NUMBER = "@PACKAGE_VERSION@" # The HTML_OUTPUT tag is used to specify where the HTML docs will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `html' will be used as the default path. HTML_OUTPUT = ../formatted/python-api # If you use STL classes (i.e. std::string, std::vector, etc.) but do not # want to include (a tag file for) the STL sources as input, then you should # set this tag to YES in order to let doxygen match functions declarations # and definitions whose arguments contain STL classes # (e.g. func(std::string); v.s. func(std::string) {}). This also make the # inheritance and collaboration diagrams that involve STL classes more # complete and accurate. BUILTIN_STL_SUPPORT = YES # The PREDEFINED tag can be used to specify one or more macro names that # are defined before the preprocessor is started (similar to the -D option of # gcc). The argument of the tag is a list of macros of the form: name # or name=definition (no spaces). If the definition and the = are # omitted =1 is assumed. PREDEFINED = __cplusplus \ LIBSBML_EXTERN:="" \ BEGIN_C_DECLS:="" \ END_C_DECLS:="" \ LIBSBML_CPP_NAMESPACE_BEGIN:="" \ LIBSBML_CPP_NAMESPACE_END:="" \ SWIG=1 \ doxygen_ignore # The ENABLED_SECTIONS tag can be used to enable conditional # documentation sections, marked by \if sectionname ... \endif. # In libSBML, we use the following section names for the languages: # # java: only Java # python: only Python # perl: only Perl # cpp: only C++ # csharp: only C# # conly: only C # clike: C, C++ # notcpp: not C++ # notclike: not C or C++ ENABLED_SECTIONS = python notclike notcpp doxygenPythonOnly # Because of how we construct the Python documentation, we don't want # the first sentence to be assumed to be the brief description. BRIEF_MEMBER_DESC = NO # Override the settings in doxygen-config-common.txt to refer to just # the files relevant for the Python bindings. INPUT = \ libsbml-accessing.txt \ libsbml-changes.txt \ libsbml-coding.txt \ libsbml-communications.txt \ libsbml-converters.txt \ libsbml-core-versus-packages.txt \ libsbml-extending.txt \ libsbml-extension-support-classes.txt \ libsbml-features.txt \ libsbml-groups.txt \ libsbml-howto-implement-extension.txt \ libsbml-installation.txt \ libsbml-issues.txt \ libsbml-license.txt \ libsbml-mainpage.txt \ libsbml-math.txt \ libsbml-news.txt \ libsbml-old-news.txt \ libsbml-other.txt \ libsbml-programming.txt \ libsbml-python-creating-model.txt \ libsbml-python-example-files.txt \ libsbml-python-reading-files.txt \ libsbml-release-info.txt \ libsbml.py \ ../../src/sbml/common/common-documentation.h \ ../../src/sbml/common/common-sbmlerror-codes.h LAYOUT_FILE = doxygen-layout-python.xml # The INPUT_FILTER tag can be used to specify a program that doxygen should # invoke to filter for each input file. Doxygen will invoke the filter program # by executing (via popen()) the command , where # is the value of the INPUT_FILTER tag, and is the name of an # input file. Doxygen will then use the output that the filter program writes # to standard output. INPUT_FILTER = "${PYTHON_EXECUTABLE} filters/doc-filter-python.py" # Because of the way the proxies are done, @param never works properly. # So don't bother telling us. WARN_IF_DOC_ERROR = YES # According to the Doxygen 1.5.4 docs, you're supposed to set this for Python. OPTIMIZE_OUTPUT_JAVA = YES # Ignore some symbols from the output. We use this to hide some classes that we # don't expose outside of the core. # # 2011-12-15 Note: because of the way Python code # works, the only symbols handed to the matcher are the class names and the # function names, SEPARATELY. You can't use a path pattern like # SBasePlugin::connectToParent; it will simply never match. I traced # Doxygen's code in a debugger, and found that what the code handling # EXCLUDE_SYMBOLS sees is "SBasePlugin" at one point and "connectToParent" # at another point -- not connected at all. Therefore, this drastically # limits what we can do with EXCLUDE_SYMBOLS to hide things. You don't # want to put methods in this list unless you're absolutely sure that # the methods should be removed no matter what class they may appear on. # So, right now, we use this mainly to hide classes that don't get # hidden by other means, and methods that should be universally hidden # (or have completely unique names, so there's no chance of accidentally # hiding more than intended). EXCLUDE_SYMBOLS = \ ISBMLExtensionNamespaces \ SBMLExtension \ SBMLFunctionDefinitionConverter_init \ SBMLInitialAssignmentConverter_init \ SBMLLevelVersionConverter_init \ SBMLRuleConverter_init \ SBMLStripPackageConverter_init \ SBMLTransforms \ SBMLUnitsConverter_init \ SBaseExtensionPoint \ SwigPyIterator \ XMLInputStream \ XMLOutputStream \ swig_import_helper \ weakref_proxy \ _newclass \ accept \ string EXAMPLE_PATH = common-text . ../.. ../../examples/c++ \ ../../examples/c++/comp ../../examples/c++/layout \ ../../examples/c++/fbc ../../examples/c++/groups \ ../../examples/c++/qual ../../examples/c++/multi