Fixed stdout output

versions of python

LICENSE

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+
+  CeCILL FREE SOFTWARE LICENSE AGREEMENT
+
+Version 2.1 dated 2013-06-21
+
+
+    Notice
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+
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+
+
+    Article 13 - GOVERNING LAW AND JURISDICTION
+
+13.1 The Agreement is governed by French law. The Parties agree to
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+jurisdiction, by the more diligent Party.

MANIFEST.in

@@ -1,11 +1,12 @@
 include setup.py
-recursive-include distutils.ext *.py *.c *.pem
-recursive-include python *.pyx *.pxd *.c *.h *.cfiles
+recursive-include python *.pyx *.pxd *.c *.h
 recursive-include src *.c *.h
+include src/CMakeLists.txt
 recursive-include doc/sphinx/source *.txt *.rst *.py
 recursive-include doc/sphinx/sphinxext *.py
 include doc/sphinx/Makefile
 include doc/sphinx/Doxyfile
-include README.txt
+include README.md
 include requirements.txt
+include scripts/obi
 

README.md

@@ -0,0 +1,41 @@
+The `OBITools3`: A package for the management of analyses and data in DNA metabarcoding   
+---------------------------------------------
+
+**Website: <https://metabarcoding.org/obitools3>**
+
+DNA metabarcoding offers new perspectives for biodiversity research [1]. This approach of ecosystem studies relies heavily on the use of Next-Generation Sequencing (NGS), and consequently requires the ability to to treat large volumes of data. The `OBITools` package  satisfies this requirement thanks to a set of programs specifically designed for analyzing NGS data in a DNA metabarcoding context [2] - <https://metabarcoding.org/obitools>. Their capacity to filter and edit sequences while taking into account taxonomic annotation helps to setup tailored-made analysis pipelines for a broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses.   
+
+
+
+**The `OBITools3`.** This new version of the `OBITools` looks to significantly improve the storage efficiency and the data processing speed. To this end, the `OBITools3` rely on an ad hoc database system, inside which all the data that a DNA metabarcoding experiment must consider is stored: the sequences, the metadata (describing for instance the samples), the database containing the reference sequences used for the taxonomic annotation, as well as the taxonomic databases. Besides the gain in efficiency, this new structure allows an easier access to all the data associated with an experiment.   
+
+
+
+**Column-oriented storage.** An analysis pipeline corresponds to a succession of commands, each computing one step of the analysis, and where the result of the command *n* is used by the command *n+1*. DNA metabarcoding data can easily be represented in the form of tables, and each command can be regarded as an operation transforming one or several 'input' tables into one or several 'output' tables, which can be used by the next command. Many of the basic operations in a pipeline copy without modification an important part of the input tables to the result tables, and use for their calculations only a small part of the input data. In the original `OBITools`, those tables are kept in the form of annotated sequence files in the FASTA or FASTQ format. This has two consequences: i) keeping the transitional results of the analysis pipeline means using disk space for an important volume of redundant data, ii) The coding and decoding of informations that are not actually used represent an important part of the treatment process. The new database system used by the `OBITools3` (called DMS for Data Management System) relies on column-oriented storage. The columns are immutable and can be assembled in views representing the data tables. This way, the data not modified by a command in an input table can easily be associated to the result table without duplicating any information ; and the data not used at all by a command can be associated with the result table without being read. This strategy results in a gain in disk space efficiency by limiting data redundancy, as well as a gain in execution time by limiting data reading, writing and conversion operations. Finally, as a mean to optimize data access, each column is stored in a binary file directly mapped in memory for reading and writing operations.   
+
+
+
+**Storage optimization.** DNA metabarcoding data is intrinsically very redundant. For example, the same sequence corresponding to a species will be present several thousand times across all samples. In order to limit the disk space used and make comparison operations more efficient, data in the form of character strings is stored in columns using a complex indexing structure, efficient on millions of values, coupling hash functions, Bloom filters and AVL trees. Finally, DNA sequences are compressed by encoding each nucleotide on two or four bits depending on whether the sequences contain only the four nucleotides (A, C, G, T) or use the IUPAC codes.   
+
+
+
+**Saving the data processing history.** The totality of the informations used by the `OBITools3` is stored in immutable data structures in the DMS. If a command has to modify a column used as input to produce its result, a new version of that column is created, leaving the initial version intact. This storage system enables to keep, at minimal cost, the totality of the transitional results produced by the pipeline. The storage of metadata describing all the operations that have produced a view (a result table) in the DMS makes possible the creation of an oriented hypergraph, where each node corresponds to a view and each arrow to an operation. By retracing the dependency relationships in this hypergraph, it is possible to rebuild *a posteriori* the entirety of the process that has produced a result table.   
+
+
+
+**Tools.** The `OBITools3` offer the same tools as the original `OBITools`, plus `ecoPCR` (*in silico* PCR) [4] and `Sumatra` (sequence alignment, not multithreaded yet) [5]. 
+Eventually, new versions of `ecoPrimers` (PCR primer design) [3], as well as `Sumaclust` (sequence alignment and clustering) [5] will be added, taking advantage of the database structure developed for the `OBITools3`.    
+
+
+
+**Implementation and disponibility.** The lower layers managing the DMS as well as all the compute-intensive functions are coded in `C99` for efficiency reasons. A `Cython` (<http://www.cython.org>) object layer allows for a simple but efficient implementation of the `OBITools3` commands in `Python 3`. The `OBITools3` are now being released, check the wiki for more information.
+
+
+
+**References.**
+
+1. Taberlet P, Coissac E, Hajibabaei M, Rieseberg LH: Environmental DNA. Mol Ecol 2012:1789–1793.
+2. Boyer F, Mercier C, Bonin A, Le Bras Y, Taberlet P, Coissac E: OBITools: a Unix-inspired software package for DNA metabarcoding. Mol Ecol Resour, 2016: 176-182.
+3. Riaz T, Shehzad W, Viari A, Pompanon F, Taberlet P, Coissac E: ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Res 2011, 39:e145.
+4. Ficetola GF, Coissac E, Zundel S, Riaz T, Shehzad W, Bessière J, Taberlet P, Pompanon F: An in silico approach for the evaluation of DNA barcodes. BMC Genomics 2010, 11:434.
+5. Mercier C, Boyer F, Bonin A, Coissac E (2013) SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences. Available: <http://metabarcoding.org/sumatra> and <http://metabarcoding.org/sumaclust>

c-sandbox/obicount/Makefile

@@ -1,18 +0,0 @@
-CC = gcc
-CFLAGS = -c -Wall
-LDFLAGS = 
-SOURCES = obicount.c ../obidmscolumn.c
-OBJECTS = $(SOURCES:.c=.o)
-EXECUTABLE = obicount
-
-all: $(SOURCES) $(EXECUTABLE)
-    
-$(EXECUTABLE): $(OBJECTS) 
-	$(CC) $(LDFLAGS) $(OBJECTS) -o $@
-
-.c.o:
-	$(CC) $(CFLAGS) $< -o $@
-
-clean:
-	rm *o
-	rm $(EXECUTABLE)

c-sandbox/obicount/obicount.c

@@ -1,87 +0,0 @@
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <sys/mman.h>	/* mmap() is defined in this header */
-#include <stdint.h>
-#include <fcntl.h>
-#include <sys/stat.h>
-
-#include "../obitypes.h"
-#include "../obidmscolumn.h"
-
-
-/**
- * @brief Computes the size to map.
- *
- * * @param OBIDMSColumn_file The file to map.
- * @return The size to map.
- */
-int get_size_to_map(int OBIDMSColumn_file)
-// compute size to map : file size minus size of the header
-{
-	int size;
-	struct stat s;
-
-	fstat(OBIDMSColumn_file, &s);
-	size = (s.st_size) - HEADER_SIZE;
-	return(size);
-}
-
-/**
- * @brief Computes and prints the total number of sequences by summing their counts.
- *
- * * @param The count file.
- */
-int main(int argc, char const *argv[])
-{
-	char* map;
-	int size;
-	int OBIDMSColumn_file;
-	int count;
-	char c;
-	char num_str[10] = "";
-	int num_int;
-	int i,j;
-
-	// initialize variables
-	OBIDMSColumn_file = open(argv[1], O_RDONLY);	//read only
-	count = 0;
-	j = 0;
-
-	// compute size to map
-	size = get_size_to_map(OBIDMSColumn_file);
-
-	// map the data
-	map = obi_map_read_only(OBIDMSColumn_file, HEADER_SIZE, size);
-
-	// sum the counts
-	for (i=0; i<size; i++)
-	{
-		c = map[i];
-
-		if (c != SEPARATOR)		// reading lines
-		{
-			num_str[j] = c;
-			j++;
-		}
-
-		else if (c == SEPARATOR)	// end of a line
-		{
-			num_int = atoi(num_str);	// turn number from character string to int
-			count = count + num_int;	// add the number to the sum
-			j = 0;
-			num_str[j] = '\0';
-		}
-	}
-
-	// print the final count of sequences
-	fprintf(stderr, "Sequence count = %d\n", count);
-
-	// unmap
-	obi_unmap(size);
-
-	// close file
-	close(OBIDMSColumn_file);
-
-	return(0);
-}

distutils.ext/obidistutils/command/build.py

@@ -1,42 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-
-from distutils.command.build import build as ori_build
-from obidistutils.serenity.checksystem import is_mac_system
-
-
-class build(ori_build):
-    
-    def has_ctools(self):
-        return self.distribution.has_ctools()
-
-    def has_files(self):
-        return self.distribution.has_files()
-
-    def has_executables(self):
-        return self.distribution.has_executables()
-    
-    def has_ext_modules(self):
-        return self.distribution.has_ext_modules()
-    
-    def has_littlebigman(self):
-        return True
-    
-    def has_pidname(self):
-        return is_mac_system()
-
-    def has_doc(self):
-        return True
-    
-    
-    sub_commands = [('littlebigman', has_littlebigman),
-                    ('pidname',has_pidname),
-                    ('build_ctools', has_ctools),
-                    ('build_files', has_files),
-                    ('build_cexe', has_executables)] \
-                   + ori_build.sub_commands + \
-                   [('build_sphinx',has_doc)]
-    

distutils.ext/obidistutils/command/build_cexe.py

@@ -1,73 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-
-from obidistutils.command.build_ctools import build_ctools
-from distutils.errors import DistutilsSetupError
-from distutils import log
-
-
-class build_cexe(build_ctools):
-
-    description = "build C/C++ executable distributed with Python extensions"
-
-
-    def initialize_options(self):
-        build_ctools.initialize_options(self)
-        self.built_files = None
-
-
-    def finalize_options(self):
-        # This might be confusing: both build-cexe and build-temp default
-        # to build-temp as defined by the "build" command.  This is because
-        # I think that C libraries are really just temporary build
-        # by-products, at least from the point of view of building Python
-        # extensions -- but I want to keep my options open.
-
-        build_cexe_dir = self.build_cexe
-        build_ctools.finalize_options(self)
-
-        if build_cexe_dir is None:
-            self.build_cexe=None
-            
-        self.set_undefined_options('build',
-                                   ('build_scripts',  'build_cexe'))
-
-        self.set_undefined_options('build_files',
-                                   ('files',  'built_files'))
-                   
-        self.executables = self.distribution.executables
-
-        if self.executables:
-            self.check_executable_list(self.executables)
-                            
-
-        # XXX same as for build_ext -- what about 'self.define' and
-        # 'self.undef' ?
-
-    def substitute_sources(self,exe_name,sources):
-        """
-        Substitutes source file name starting by an @ by the actual
-        name of the built file (see --> build_files)
-        """
-        sources = list(sources)
-        for i in range(len(sources)):
-            message = "%s :-> %s" % (exe_name,sources[i])
-            if sources[i][0]=='@':
-                try:
-                    filename = self.built_files[sources[i][1:]]
-                except KeyError:
-                    raise DistutilsSetupError(
-                         'The %s filename declared in the source '
-                         'files of the program %s have not been '
-                         'built by the installation process' % (sources[i],
-                                                                exe_name))
-                sources[i]=filename
-                log.info("%s changed to %s",message,filename)
-            else:
-                log.info("%s ok",message)
-
-        return sources
-    

distutils.ext/obidistutils/command/build_ctools.py

@@ -1,55 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-
-
-from obidistutils.command.build_exe import build_exe
-
-class build_ctools(build_exe):
-    description = "build C/C++ executable not distributed with Python extensions"
-
-    def initialize_options(self):
-        build_exe.initialize_options(self)
-        
-        # List of built tools
-        self.ctools = None
-        self.littlebigman = None
-
-
-    def finalize_options(self):
-        # This might be confusing: both build-cexe and build-temp default
-        # to build-temp as defined by the "build" command.  This is because
-        # I think that C libraries are really just temporary build
-        # by-products, at least from the point of view of building Python
-        # extensions -- but I want to keep my options open.
-            
-        build_exe.finalize_options(self)
-        
-        
-        self.set_undefined_options('build',
-                                    ('build_temp', 'build_cexe'))
-
-        self.set_undefined_options('littlebigman',
-                                   ('littlebigman',  'littlebigman'))
-                   
-        self.executables = self.distribution.ctools
-        self.check_executable_list(self.executables)
-        
-        if self.littlebigman =='-DLITTLE_END':
-            if self.define is None:
-                self.define=[('LITTLE_END',None)]
-            else:
-                self.define.append('LITTLE_END',None)
-
-        self.ctools = set()
-
-    def run(self):
-        
-        build_exe.run(self)
-        for e,p in self.executables:                                  # @UnusedVariable
-            self.ctools.add(e)
-            
-
-

distutils.ext/obidistutils/command/build_exe.py

@@ -1,210 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-
-import os
-
-from distutils.core import Command
-from distutils.sysconfig import customize_compiler
-from distutils.errors import DistutilsSetupError
-from distutils import log
-from distutils.ccompiler import show_compilers
-
-class build_exe(Command):
-    
-    description = "build an executable -- Abstract command "
-
-    user_options = [
-        ('build-cexe', 'x',
-         "directory to build C/C++ libraries to"),
-        ('build-temp', 't',
-         "directory to put temporary build by-products"),
-        ('debug', 'g',
-         "compile with debugging information"),
-        ('force', 'f',
-         "forcibly build everything (ignore file timestamps)"),
-        ('compiler=', 'c',
-         "specify the compiler type"),
-        ]
-
-    boolean_options = ['debug', 'force']
-
-    help_options = [
-        ('help-compiler', None,
-         "list available compilers", show_compilers),
-        ]
-
-    def initialize_options(self):
-        self.build_cexe = None
-        self.build_temp = None
-
-        # List of executables to build
-        self.executables = None
-
-        # Compilation options for all libraries
-        self.include_dirs = None
-        self.define = None
-        self.undef = None
-        self.extra_compile_args = None
-        self.debug = None
-        self.force = 0
-        self.compiler = None
-        self.sse = None
-        self.built_files=None
-
-    def finalize_options(self):
-        # This might be confusing: both build-cexe and build-temp default
-        # to build-temp as defined by the "build" command.  This is because
-        # I think that C libraries are really just temporary build
-        # by-products, at least from the point of view of building Python
-        # extensions -- but I want to keep my options open.
-        self.set_undefined_options('build',
-                                   ('build_temp', 'build_temp'),
-                                   ('compiler', 'compiler'),
-                                   ('debug', 'debug'),
-                                   ('force', 'force'))
-
-        if self.include_dirs is None:
-            self.include_dirs = self.distribution.include_dirs or []
-            
-        if isinstance(self.include_dirs, str):
-            self.include_dirs = self.include_dirs.split(os.pathsep)
-
-        self.sse = self.distribution.sse
-        
-        if self.sse is not None:
-            if self.extra_compile_args is None:
-                self.extra_compile_args=['-m%s' % self.sse]
-            else:
-                self.extra_compile_args.append('-m%s' % self.sse)
-
-        # XXX same as for build_ext -- what about 'self.define' and
-        # 'self.undef' ?
-
-    def run(self):
-
-        if not self.executables:
-            return
-
-        self.mkpath(self.build_cexe)
-
-        # Yech -- this is cut 'n pasted from build_ext.py!
-        from distutils.ccompiler import new_compiler
-        self.compiler = new_compiler(compiler=self.compiler,
-                                     dry_run=self.dry_run,
-                                     force=self.force)
-        customize_compiler(self.compiler)
-
-        if self.include_dirs is not None:
-            self.compiler.set_include_dirs(self.include_dirs)
-        if self.define is not None:
-            # 'define' option is a list of (name,value) tuples
-            for (name,value) in self.define:
-                self.compiler.define_macro(name, value)
-
-        if self.undef is not None:
-            for macro in self.undef:
-                self.compiler.undefine_macro(macro)
-                
-        self.build_executables(self.executables)
-
-
-    def check_executable_list(self, executables):
-        """Ensure that the list of executables is valid.
-
-        `executable` is presumably provided as a command option 'executables'.
-        This method checks that it is a list of 2-tuples, where the tuples
-        are (executable_name, build_info_dict).
-
-        Raise DistutilsSetupError if the structure is invalid anywhere;
-        just returns otherwise.
-        """
-        if not isinstance(executables, list):
-            raise DistutilsSetupError("'executables' option must be a list of tuples")
-
-        for exe in executables:
-            if not isinstance(exe, tuple) and len(exe) != 2:
-                raise DistutilsSetupError("each element of 'executables' must a 2-tuple")
-
-            name, build_info = exe
-
-            if not isinstance(name, str):
-                raise DistutilsSetupError(
-                      "first element of each tuple in 'executables' " 
-                      "must be a string (the executables name)")
-                
-            if '/' in name or (os.sep != '/' and os.sep in name):
-                raise DistutilsSetupError(
-                       "bad executable name '%s': " 
-                       "may not contain directory separators" % exe[0])
-
-            if not isinstance(build_info, dict):
-                raise DistutilsSetupError(
-                      "second element of each tuple in 'executables' " 
-                      "must be a dictionary (build info)")
-
-    def get_executable_names(self):
-        # Assume the executables list is valid -- 'check_executable_list()' is
-        # called from 'finalize_options()', so it should be!
-        if not self.executables:
-            return None
-
-        exe_names = []
-        for (exe_name, build_info) in self.executables:                     # @UnusedVariable
-            exe_names.append(exe_name)
-        return exe_names
-
-
-    def get_source_files(self):
-        self.check_executable_list(self.executables)
-        filenames = []
-        for (exe_name, build_info) in self.executables:                     # @UnusedVariable
-            sources = build_info.get('sources')
-            if sources is None or not isinstance(sources, (list, tuple)):
-                raise DistutilsSetupError(
-                       "in 'executables' option (library '%s'), "
-                       "'sources' must be present and must be "
-                       "a list of source filenames" % exe_name)
-
-            filenames.extend(sources)
-        return filenames
-    
-    def substitute_sources(self,exe_name,sources):
-        return list(sources)
-
-    def build_executables(self, executables):
-        for (exe_name, build_info) in executables:
-            sources = build_info.get('sources')
-            if sources is None or not isinstance(sources, (list, tuple)):
-                raise DistutilsSetupError(
-                       "in 'executables' option (library '%s'), " 
-                       "'sources' must be present and must be " 
-                       "a list of source filenames" % exe_name)
-                
-            sources = self.substitute_sources(exe_name,sources)
-
-            log.info("building '%s' program", exe_name)
-
-            # First, compile the source code to object files in the library
-            # directory.  (This should probably change to putting object
-            # files in a temporary build directory.)
-            macros = build_info.get('macros')
-            include_dirs = build_info.get('include_dirs')
-            extra_args = self.extra_compile_args or []
-            
-            objects = self.compiler.compile(sources,
-                                            output_dir=self.build_temp,
-                                            macros=macros,
-                                            include_dirs=include_dirs,
-                                            extra_postargs=extra_args,
-                                            debug=self.debug)
-
-            # Now "link" the object files together into a static library.
-            # (On Unix at least, this isn't really linking -- it just
-            # builds an archive.  Whatever.)
-            self.compiler.link_executable(objects, exe_name,
-                                            output_dir=self.build_cexe,
-                                            debug=self.debug)
-

distutils.ext/obidistutils/command/build_ext.py

@@ -1,93 +0,0 @@
-'''
-Created on 13 fevr. 2014
-
-@author: coissac
-'''
-
-from distutils import log
-import os
-
-from Cython.Distutils import build_ext  as ori_build_ext  # @UnresolvedImport
-    
-from distutils.errors import DistutilsSetupError
-
-class build_ext(ori_build_ext):
-    def modifyDocScripts(self):
-        build_dir_file=open("doc/build_dir.txt","w")
-        print(self.build_lib,file=build_dir_file)
-        build_dir_file.close()
-        
-    def initialize_options(self):
-        ori_build_ext.initialize_options(self)  # @UndefinedVariable
-        self.littlebigman = None
-        self.built_files = None
-
-    
-    def finalize_options(self):
-        ori_build_ext.finalize_options(self)  # @UndefinedVariable
-
-        self.set_undefined_options('littlebigman',
-                                   ('littlebigman',  'littlebigman'))
-        
-        self.set_undefined_options('build_files',
-                                   ('files',  'built_files'))
-
-        self.cython_c_in_temp = 1
-                   
-        if self.littlebigman =='-DLITTLE_END':
-            if self.define is None:
-                self.define=[('LITTLE_END',None)]
-            else:
-                self.define.append('LITTLE_END',None)
-        
-    def substitute_sources(self,exe_name,sources):
-        """
-        Substitutes source file name starting by an @ by the actual
-        name of the built file (see --> build_files)
-        """
-        sources = list(sources)
-        for i in range(len(sources)):
-            message = "%s :-> %s" % (exe_name,sources[i])
-            if sources[i][0]=='@':
-                try:
-                    filename = self.built_files[sources[i][1:]]
-                except KeyError:
-                    tmpfilename = os.path.join(self.build_temp,sources[i][1:])
-                    if os.path.isfile       (tmpfilename):
-                        filename = tmpfilename
-                    else:
-                        raise DistutilsSetupError(
-                             'The %s filename declared in the source '
-                             'files of the program %s have not been '
-                             'built by the installation process' % (sources[i],
-                                                                     exe_name))
-                sources[i]=filename
-                log.info("%s changed to %s",message,filename)
-            else:
-                log.info("%s ok",message)
-
-        return sources
-
-    def build_extensions(self):
-        # First, sanity-check the 'extensions' list
-        
-        for ext in self.extensions:
-            ext.sources = self.substitute_sources(ext.name,ext.sources)
-            
-        self.check_extensions_list(self.extensions)
-
-        for ext in self.extensions:
-            log.info("%s :-> %s",ext.name,ext.sources)
-            ext.sources = self.cython_sources(ext.sources, ext)
-            self.build_extension(ext)
-
-        
-    def run(self):
-        self.modifyDocScripts()
-        ori_build_ext.run(self)  # @UndefinedVariable
-        
-
-        
-
-
-        

distutils.ext/obidistutils/command/build_files.py

@@ -1,53 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-
-import os.path
-
-from distutils.core import Command
-from distutils import log
-
-class build_files(Command):
-            
-    def initialize_options(self):
-        self.files=None
-        self.ctools=None
-        self.build_temp=None
-        self.build_cexe=None
-
-    def finalize_options(self):
-        
-        self.set_undefined_options('build_ctools',
-                                   ('ctools',  'ctools'),
-                                   ('build_temp','build_temp'),
-                                   ('build_cexe','build_cexe'),
-                                   )
-        
-        self.files = {}
-        
-    def run(self):
-        
-        for dest,prog,command in self.distribution.files:
-            destfile = os.path.join(self.build_temp,dest)
-            if prog in self.ctools:
-                progfile = os.path.join(self.build_cexe,prog)
-            else:
-                progfile = prog 
-                
-            log.info("Building file : %s" % dest)
-            
-            commandline = command % {'prog' : progfile,
-                                     'dest' : destfile}
-
-            log.info("    --> %s" % commandline)
-            
-            os.system(commandline)
-            self.files[dest]=destfile
-            
-            log.info("Done.\n")
-            
-            
-            
-        

distutils.ext/obidistutils/command/build_scripts.py

@@ -1,104 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-
-import os.path
-
-from distutils.command.build_scripts import build_scripts as ori_build_scripts,\
-    first_line_re
-from distutils.util import convert_path
-from distutils import log, sysconfig
-from distutils.dep_util import newer
-from stat import ST_MODE
-
-
-
-class build_scripts(ori_build_scripts):
-            
-    def copy_scripts (self):
-        """Copy each script listed in 'self.scripts'; if it's marked as a
-        Python script in the Unix way (first line matches 'first_line_re',
-        ie. starts with "\#!" and contains "python"), then adjust the first
-        line to refer to the current Python interpreter as we copy.
-        """        
-        self.mkpath(self.build_dir)
-        rawbuild_dir = os.path.join(os.path.dirname(self.build_dir),'raw_scripts')
-        self.mkpath(rawbuild_dir)
-        
-        outfiles = []
-        for script in self.scripts:
-            adjust = 0
-            script = convert_path(script)
-            outfile = os.path.join(self.build_dir, os.path.splitext(os.path.basename(script))[0])
-            rawoutfile = os.path.join(rawbuild_dir, os.path.basename(script))
-            outfiles.append(outfile)
-
-            if not self.force and not newer(script, outfile):
-                log.debug("not copying %s (up-to-date)", script)
-                continue
-
-            # Always open the file but ignore failures in dry-run mode --
-            # that way, we'll get accurate feedback if we can read the
-            # script.
-            try:
-                f = open(script, "r")
-            except IOError:
-                if not self.dry_run:
-                    raise
-                f = None
-            else:
-                first_line = f.readline()
-                if not first_line:
-                    self.warn("%s is an empty file (skipping)" % script)
-                    continue
-
-                match = first_line_re.match(first_line)
-                if match:
-                    adjust = 1
-                    post_interp = match.group(1) or ''
-            
-            log.info("Store the raw script %s -> %s", script,rawoutfile)        
-            self.copy_file(script, rawoutfile)
-
-
-            if adjust:
-                log.info("copying and adjusting %s -> %s", script,
-                         self.build_dir)
-                if not self.dry_run:
-                    outf = open(outfile, "w")
-                    if not sysconfig.python_build:
-                        outf.write("#!%s%s\n" %
-                                   (self.executable,
-                                    post_interp))
-                    else:
-                        outf.write("#!%s%s\n" %
-                                   (os.path.join(
-                            sysconfig.get_config_var("BINDIR"),
-                           "python%s%s" % (sysconfig.get_config_var("VERSION"),
-                                           sysconfig.get_config_var("EXE"))),
-                                    post_interp))
-                    outf.writelines(f.readlines())
-                    outf.close()
-                if f:
-                    f.close()
-            else:
-                if f:
-                    f.close()
-                self.copy_file(script, outfile)
-
-        if os.name == 'posix':
-            for F in outfiles:
-                if self.dry_run:
-                    log.info("changing mode of %s", F)
-                else:
-                    oldmode = os.stat(F)[ST_MODE]
-                    oldmode = oldmode & 0o7777
-                    
-                    newmode = (oldmode | 0o555) & 0o7777
-                    if newmode != oldmode:
-                        log.info("changing mode of %s from %o to %o",
-                                 F, oldmode, newmode)
-                        os.chmod(F, newmode)
-

distutils.ext/obidistutils/command/build_sphinx.py

@@ -1,26 +0,0 @@
-'''
-Created on 10 mars 2015
-
-@author: coissac
-'''
-
-from sphinx.setup_command import BuildDoc as ori_build_sphinx  # @UnresolvedImport
-    
-class build_sphinx(ori_build_sphinx):
-    '''
-    Build Sphinx documentation in html, epub and man formats 
-    '''
-
-    description = __doc__
-
-    def run(self):
-        self.builder='html'
-        self.finalize_options()
-        ori_build_sphinx.run(self)
-        self.builder='epub'
-        self.finalize_options()
-        ori_build_sphinx.run(self)
-        self.builder='man'
-        self.finalize_options()
-        ori_build_sphinx.run(self)
-    

distutils.ext/obidistutils/command/install.py

@@ -1,14 +0,0 @@
-'''
-Created on 6 oct. 2014
-
-@author: coissac
-'''
-
-from distutils.command.install import install as install_ori
-
-class install(install_ori):
-    
-    def __init__(self,dist):
-        install_ori.__init__(self, dist)
-        self.sub_commands.insert(0, ('build',lambda self: True))
-        self.sub_commands.append(('install_sphinx',lambda self: self.distribution.serenity))

distutils.ext/obidistutils/command/install_scripts.py

@@ -1,43 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-from distutils.command.install_scripts import install_scripts as ori_install_scripts
-
-import os.path
-from distutils import log
-
-class install_scripts(ori_install_scripts):
-
-    def initialize_options(self):
-        ori_install_scripts.initialize_options(self)
-        self.public_dir = None
-                        
-                    
-    def install_public_link(self):
-        self.mkpath(self.public_dir)
-        for file in self.get_outputs():
-            if self.dry_run:
-                log.info("changing mode of %s", file)
-            else:
-                log.info("exporting file %s -> %s", file,os.path.join(self.public_dir,
-                                        os.path.split(file)[1]
-                                        ))
-                dest = os.path.join(self.public_dir,
-                                    os.path.split(file)[1]
-                                   )
-                if os.path.exists(dest):
-                    os.unlink(dest)
-                os.symlink(file,dest)
-                    
-
-
-    def run(self):
-        ori_install_scripts.run(self)
-        if self.distribution.serenity:
-            self.public_dir=os.path.join(self.install_dir,"../export/bin")
-            self.public_dir=os.path.abspath(self.public_dir)
-            self.install_public_link()
-
-

distutils.ext/obidistutils/command/install_sphinx.py

@@ -1,46 +0,0 @@
-'''
-Created on 10 mars 2015
-
-@author: coissac
-'''
-from distutils.core import Command
-import os.path
-import glob
-
-class install_sphinx(Command):
-    '''
-    Install the sphinx documentation
-    '''
-    
-    description = "Install the sphinx documentation in serenity mode"
-
-    boolean_options = ['force', 'skip-build']
-
-
-    def initialize_options (self):
-        self.install_doc = None
-        self.build_dir = None
-
-    def finalize_options (self):
-        self.set_undefined_options('build_sphinx', ('build_dir', 'build_dir'))
-        self.set_undefined_options('install',
-                                   ('install_scripts', 'install_doc'))
-
-    def run (self):
-        if self.distribution.serenity:
-            self.install_doc = os.path.join(self.install_doc,"../export/share")
-            self.install_doc=os.path.abspath(self.install_doc)
-            self.mkpath(self.install_doc)
-            self.mkpath(os.path.join(self.install_doc,'html'))
-            outfiles = self.copy_tree(os.path.join(self.build_dir,'html'),  # @UnusedVariable
-                                      os.path.join(self.install_doc,'html'))
-                
-            self.mkpath(os.path.join(self.install_doc,'man','man1'))
-            outfiles = self.copy_tree(os.path.join(self.build_dir,'man'),  # @UnusedVariable
-                                      os.path.join(self.install_doc,'man','man1'))
-
-            for epub in glob.glob(os.path.join(self.build_dir,'epub/*.epub')):
-                self.copy_file(os.path.join(epub), 
-                               os.path.join(self.install_doc,os.path.split(epub)[1]))
-            
-        

distutils.ext/obidistutils/command/littlebigman.py

@@ -1,59 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-
-import os
-
-from obidistutils.command.build_exe import build_exe
-from distutils import log
-
-import subprocess
-
-class littlebigman(build_exe):
-    
-    description = "build the littlebigman executable testing endianness of the CPU"
-
-
-    def initialize_options(self):
-        build_exe.initialize_options(self)
-
-        self.littlebigman = None
-
-
-    def finalize_options(self):
-        # This might be confusing: both build-cexe and build-temp default
-        # to build-temp as defined by the "build" command.  This is because
-        # I think that C libraries are really just temporary build
-        # by-products, at least from the point of view of building Python
-        # extensions -- but I want to keep my options open.
-        
-        build_exe.finalize_options(self)
-        
-        self.set_undefined_options('build',
-                                   ('build_temp', 'build_cexe'))
-
-        # self.ctools = self.distribution.ctools
-        
-        if os.path.isfile("distutils.ext/src/littlebigman.c"):
-            self.executables = [('littlebigman',{"sources":["distutils.ext/src/littlebigman.c"]})]
-            self.check_executable_list(self.executables)
-        else:
-            self.executables = []
-
-
-    def run_littlebigman(self):
-        p = subprocess.Popen("'%s'" % os.path.join(self.build_temp,
-                                                   'littlebigman'), 
-                             shell=True, 
-                             stdout=subprocess.PIPE)
-        little = p.communicate()[0]
-        return little
-
-    def run(self):
-        build_exe.run(self)
-        self.littlebigman=self.run_littlebigman()
-        log.info("Your CPU is in mode : %s" % self.littlebigman)
-        
-        

distutils.ext/obidistutils/command/pidname.py

@@ -1,51 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-
-import os
-
-from obidistutils.command.build_exe import build_exe
-from obidistutils.serenity.checksystem import is_mac_system
-
-
-class pidname(build_exe):
-    
-    description = "build the pidname executable returning the executable path from a PID on a mac"
-
-
-    def initialize_options(self):
-        build_exe.initialize_options(self)
-
-        self.pidname = False
-
-
-    def finalize_options(self):
-        # This might be confusing: both build-cexe and build-temp default
-        # to build-temp as defined by the "build" command.  This is because
-        # I think that C libraries are really just temporary build
-        # by-products, at least from the point of view of building Python
-        # extensions -- but I want to keep my options open.
-        
-        build_exe.finalize_options(self)
-        
-        self.set_undefined_options('build',
-                                   ('build_scripts', 'build_cexe'))
-
-        # self.ctools = self.distribution.ctools
-        
-        if os.path.isfile("distutils.ext/src/pidname.c"):
-            self.executables = [('pidname',{"sources":["distutils.ext/src/pidname.c"]})]
-            self.check_executable_list(self.executables)
-        else:
-            self.executables = []
-
-
-    def run(self):
-        if is_mac_system():
-            build_exe.run(self)
-            self.pidname=True
-        else:
-            self.pidname=False
-        

distutils.ext/obidistutils/command/sdist.py

@@ -1,42 +0,0 @@
-'''
-Created on 10 mars 2015
-
-@author: coissac
-'''
-
-import os.path
-
-from distutils.command.sdist import sdist as orig_sdist
-from distutils import dir_util
-
-class sdist(orig_sdist):
-
-    def make_distribution(self):
-        """Create the source distribution(s).  First, we create the release
-        tree with 'make_release_tree()'; then, we create all required
-        archive files (according to 'self.formats') from the release tree.
-        Finally, we clean up by blowing away the release tree (unless
-        'self.keep_temp' is true).  The list of archive files created is
-        stored so it can be retrieved later by 'get_archive_files()'.
-        """
-        # Don't warn about missing meta-data here -- should be (and is!)
-        # done elsewhere.
-        base_dir = self.distribution.get_fullname()
-        base_name = os.path.join(self.dist_dir,base_dir)
-
-        self.make_release_tree(os.path.join('tmp',base_dir), self.filelist.files)
-        archive_files = []              # remember names of files we create
-        # tar archive must be created last to avoid overwrite and remove
-        if 'tar' in self.formats:
-            self.formats.append(self.formats.pop(self.formats.index('tar')))
-
-        for fmt in self.formats:
-            file = self.make_archive(base_name, fmt, root_dir='tmp',base_dir=base_dir,
-                                     owner=self.owner, group=self.group)
-            archive_files.append(file)
-            self.distribution.dist_files.append(('sdist', '', file))
-
-        self.archive_files = archive_files
-
-        if not self.keep_temp:
-            dir_util.remove_tree(os.path.join('tmp',base_dir), dry_run=self.dry_run)

distutils.ext/obidistutils/core.py

@@ -1,197 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-
-from os import path
-import os.path
-import glob
-import sys
-
-
-from distutils.core import setup as ori_setup
-from distutils.extension import Extension
-
-from obidistutils.serenity.checkpackage import  install_requirements,\
-                                                check_requirements, \
-                                                RequirementError
-                                                
-from obidistutils.serenity.rerun import enforce_good_python
-from obidistutils.serenity.rerun import rerun_with_anothe_python
-from distutils import log
-
-from obidistutils.dist import Distribution
- 
- 
-def findPackage(root,base=None):
-    modules=[]
-    if base is None:
-        base=[]
-    for module in (path.basename(path.dirname(x)) 
-                   for x in glob.glob(path.join(root,'*','__init__.py'))):
-        modules.append('.'.join(base+[module]))
-        modules.extend(findPackage(path.join(root,module),base+[module]))
-    return modules
-    
-def findCython(root,base=None,pyrexs=None):
-    setupdir = os.path.dirname(sys.argv[0])
-    pyrexs=[]
-
-    if base is None:
-        base=[]
-    for module in (path.basename(path.dirname(x)) 
-                   for x in glob.glob(path.join(root,'*','__init__.py'))):
-                       
-                
-        for pyrex in glob.glob(path.join(root,module,'*.pyx')):
-            pyrexs.append(Extension('.'.join(base+[module,path.splitext(path.basename(pyrex))[0]]),
-                                    [pyrex]
-                                    )
-                          )
-            try:
-                cfiles = os.path.splitext(pyrex)[0]+".cfiles"
-                cfilesdir = os.path.dirname(cfiles)
-                cfiles = open(cfiles)
-                cfiles = [os.path.relpath(os.path.join(cfilesdir,y),setupdir).strip() 
-                          if y[0] !='@' else y.strip()
-                          for y in cfiles]
-                
-                log.info("Cython module : %s",cfiles)   
-                incdir = set(os.path.dirname(x) for x in cfiles if x[-2:]==".h")
-                cfiles = [x for x in cfiles if x[-2:]==".c"]                
-                pyrexs[-1].sources.extend(cfiles)
-                pyrexs[-1].include_dirs.extend(incdir)
-                pyrexs[-1].extra_compile_args.extend(['-msse2','-Wno-unused-function'])
-                
-            except IOError:
-                pass
-            
-        pyrexs.extend(findCython(path.join(root,module),base+[module]))
-    return pyrexs
-    
-
-def rootname(x):
-    return os.path.splitext(x.sources[0])[0]
-
-
-def prepare_commands():
-    from obidistutils.command.build import build
-    from obidistutils.command.littlebigman import littlebigman
-    from obidistutils.command.build_cexe import build_cexe
-    from obidistutils.command.build_sphinx import build_sphinx
-    from obidistutils.command.build_ext import build_ext
-    from obidistutils.command.build_ctools import build_ctools
-    from obidistutils.command.build_files import build_files
-    from obidistutils.command.build_scripts import build_scripts
-    from obidistutils.command.install_scripts import install_scripts
-    from obidistutils.command.install_sphinx import install_sphinx
-    from obidistutils.command.install import install
-    from obidistutils.command.pidname import pidname
-    from obidistutils.command.sdist import sdist
-
-    COMMANDS = {'build':build,
-                'littlebigman':littlebigman,
-                'pidname':pidname,
-                'build_ctools':build_ctools, 
-                'build_files':build_files,
-                'build_cexe':build_cexe, 
-                'build_ext': build_ext,
-                'build_scripts':build_scripts, 
-                'build_sphinx':build_sphinx, 
-                'install_scripts':install_scripts,
-                'install_sphinx':install_sphinx,
-                'install':install,
-                'sdist':sdist}
-    
-    return COMMANDS
-
-
-CTOOLS =[]
-CEXES  =[]
-FILES  =[]
-
-def setup(**attrs):
-    
-    log.set_threshold(log.INFO)
-    
-    minversion      = attrs.get("pythonmin",'3.4')
-    maxversion      = attrs.get('pythonmax',None)    
-    fork            = attrs.get('fork',False)
-    requirementfile = attrs.get('requirements','requirements.txt')
-
-    try:
-        del attrs['pythonmin']
-    except KeyError:
-        pass
-
-    try:
-        del attrs['pythonmax']
-    except KeyError:
-        pass
-
-    try:
-        del attrs['fork']
-    except KeyError:
-        pass
-
-    try:
-        del attrs['requirements']
-    except KeyError:
-        pass
-
-    
-    enforce_good_python(minversion, maxversion, fork)
-    
-    if (install_requirements(requirementfile)):
-        rerun_with_anothe_python(sys.executable,minversion,maxversion,fork)
-        
-    
-    try:
-        check_requirements(requirementfile)
-    except RequirementError as e :
-        log.error(e)                                   
-        sys.exit(1)
-        
-    if 'distclass' not in attrs:
-        attrs['distclass']=Distribution
-
-    if 'python_src' not in attrs:
-        SRC = 'python'
-    else:
-        SRC = attrs['python_src']
-        del(attrs['python_src'])
-    
-    if 'scripts' not in attrs:
-        attrs['scripts'] = glob.glob('%s/*.py' % SRC)
-
-    if 'package_dir' not in attrs:
-        attrs['package_dir'] = {'': SRC}
-
-    if 'packages' not in attrs:
-        attrs['packages'] = findPackage(SRC)
-    
-    if 'cmdclass' not in attrs:
-        attrs['cmdclass'] = prepare_commands()
-
-    if 'ctools' not in attrs:
-        attrs['ctools'] = CTOOLS
-    
-    if 'executables' not in attrs:
-        attrs['executables'] = CEXES
-        
-    if 'files' not in attrs:
-        attrs['files'] = FILES
-        
-    if 'sse' not in attrs:
-        attrs['sse']=None
-        
-    if 'serenity' not in attrs:
-        attrs['serenity']=False
-    
-    EXTENTION=findCython(SRC)
-    
-    if 'ext_modules' not in attrs:
-        attrs['ext_modules'] = EXTENTION
-    
-    ori_setup(**attrs)

distutils.ext/obidistutils/dist.py

@@ -1,45 +0,0 @@
-'''
-Created on 20 oct. 2012
-
-@author: coissac
-'''
-
-from distutils.dist import Distribution as ori_Distribution
-
-class Distribution(ori_Distribution):
-    
-    def __init__(self,attrs=None):
-        self.executables = None
-        self.ctools = None
-        self.files = None
-        self.build_cexe  = None
-        self.deprecated_scripts = None
-        self.zip_safe=False
-        self.sse = None
-        self.serenity=attrs['serenity']
-        
-        ori_Distribution.__init__(self, attrs)
-        
-        self.global_options.insert(0,('serenity', None, "install or build the package in a python virtualenv "
-                                                       "without polluting the installed python and with many "
-                                                       "checks during the installation process"
-                                     ))
-        self.global_options.insert(0,('virtualenv', None, "if the installation is done using the serenity mode "
-                                                        "this option allows for specifying the virtualenv name. "
-                                                        "By default the name is PACKAGE-VERSION"
-                                     ))
-        
-        
-    def has_executables(self):
-        return self.executables is not None and self.executables
-        
-    def has_ctools(self):
-        return self.ctools is not None and self.ctools
-        
-    def has_files(self):
-        return self.files is not None and self.files
-        
-    def has_deprecated_scripts(self):
-        return self.deprecated_scripts is not None and self.deprecated_scripts
-
-    

distutils.ext/obidistutils/serenity/__init__.py

@@ -1,108 +0,0 @@
-import sys
-
-from distutils import util
-from distutils import sysconfig
-from distutils import log
-from distutils.version import LooseVersion, StrictVersion
-import glob
-import os
-import subprocess
-import re 
-from distutils.errors import DistutilsError
-import tempfile
-
-import importlib
-import imp
-import zipimport
-
-import argparse
-
-import base64
-
-from .checkpython import is_python_version
-                        
-                        
-from obidistutils.serenity.rerun import  enforce_good_python
-from obidistutils.serenity.rerun import rerun_with_anothe_python
-
-from obidistutils.serenity.virtual import serenity_virtualenv
-                        
-from obidistutils.serenity.checksystem import is_mac_system, \
-                                              is_windows_system
-                        
-from obidistutils.serenity.checkpackage import install_requirements
-from obidistutils.serenity.checkpackage import check_requirements
-
-from obidistutils.serenity.util import save_argv
-                        
-from obidistutils.serenity.snake import snake
-                            
-    
-def serenity_snake(envname,package,version):
-    old = log.set_threshold(log.INFO)
-
-    log.info("Installing %s (%s) in serenity mode" % (package,version))
-
-    enforce_good_python()
-
-    virtualpython=serenity_virtualenv(envname,package,version)
-    
-    if virtualpython!=os.path.realpath(sys.executable):
-        log.info("Restarting installation within the %s virtualenv" % (envname))
-        rerun_with_anothe_python(virtualpython)
-        
-    log.info("%s will be installed with python : %s" % (package,virtualpython))
-        
-    if install_requirements():    
-        log.info("Restarting installation with all dependencies ok")
-        rerun_with_anothe_python(virtualpython)
-    
-    log.set_threshold(old)
-    
-def serenity_assert(version):
-    check_requirements()
-
-
-def is_serenity():
-    from obidistutils.serenity.globals import local_serenity
-    return local_serenity and local_serenity[0]
-
-def serenity_mode(package,version):
-    
-    save_argv()
-
-    
-    from obidistutils.serenity.globals import saved_args
-    from obidistutils.serenity.globals import local_serenity
-    
-
-    old = log.set_threshold(log.INFO)
-    
-    argparser = argparse.ArgumentParser(add_help=False)
-    argparser.add_argument('--serenity',
-                           dest='serenity', 
-                           action='store_true',
-                           default=False, 
-                           help='Switch the installer in serenity mode. Everythings are installed in a virtualenv')
-
-    argparser.add_argument('--virtualenv',
-                           dest='virtual', 
-                           type=str,
-                           action='store',
-                           default="%s-%s" % (package,version), 
-                           help='Specify the name of the virtualenv used by the serenity mode [default: %s-%s]' % (package,version))    
-    
-    args, unknown = argparser.parse_known_args()
-    sys.argv = [sys.argv[0]] + unknown
-    
-    if args.serenity:
-        local_serenity.append(True)
-        serenity_snake(args.virtual,package,version)
-    else:
-        local_serenity.append(False)       
-    
-    log.set_threshold(old)
-    
-    return args.serenity
-    
-    

distutils.ext/obidistutils/serenity/checkpackage.py

@@ -1,156 +0,0 @@
-'''
-Created on 2 oct. 2014
-
-@author: coissac
-'''
-
-import re
-import os
-
-import pip                                              # @UnresolvedImport
-from pip.utils import get_installed_distributions       # @UnresolvedImport
-from distutils.version import StrictVersion             # @UnusedImport
-from distutils.errors import DistutilsError
-from distutils import log
-
-class RequirementError(Exception):
-    pass
-
-def is_installed(requirement):
-    
-    
-    requirement_project,requirement_relation,requirement_version = parse_package_requirement(requirement)
-    
-    package = [x for x in get_installed_distributions() if x.project_name==requirement_project]
-    
-    if len(package)==1:
-        if requirement_version is not None and requirement_relation is not None:    
-            rep = (len(package)==1) and eval("StrictVersion('%s') %s StrictVersion('%s')" % (package[0].version,
-                                                                                           requirement_relation,
-                                                                                           requirement_version)
-                                             )
-        else:
-            rep=True
-    else:
-        rep=False
-    
-    if rep:
-        if requirement_version is not None and requirement_relation is not None:        
-            log.info("Look for package %s (%s%s) : ok version %s installed" % (requirement_project,
-                                                                               requirement_relation,
-                                                                               requirement_version,
-                                                                               package[0].version))
-        else:
-            log.info("Look for package %s : ok version %s installed" % (requirement_project,
-                                                                        package[0].version))
-    else:
-        if len(package)!=1:
-            log.info("Look for package %s (%s%s) : not installed" % (requirement_project,
-                                                                     requirement_relation,
-                                                                     requirement_version))
-        else:
-            log.info("Look for package %s (%s%s) : failed only version %s installed" % (requirement_project,
-                                                                                        requirement_relation,
-                                                                                        requirement_version,
-                                                                                        package[0].version))
-        
-    return rep
-
-
-def get_requirements(requirementfile='requirements.txt'):
-    
-    try:
-        requirements = open(requirementfile).readlines()
-        requirements = [x.strip() for x in requirements]
-        requirements = [x for x in requirements if x[0]!='-']
-    
-    except IOError:
-        requirements = []
-        
-    return requirements
-    
-    
-def install_requirements(requirementfile='requirements.txt'):
-    
-    install_something=False
-
-    requirements = get_requirements(requirementfile)
-
-    log.info("Required packages for the installation :")
-    for x in requirements:
-        ok = is_installed(x)
-        if not ok:
-            log.info("  Installing requirement : %s" % x)
-            pip_install_package(x)
-            install_something=True
-                
-    return install_something
- 
-
-def check_requirements(requirementfile='requirements.txt'):
-    
-    requirements = get_requirements(requirementfile)
-    
-    log.info("Required packages for the installation :")
-    for x in requirements:
-        ok = is_installed(x)
-        if not ok:
-            raise RequirementError("  Missing requirement : %s -- Package installation stopped" % x)
-                
- 
-
-
-def parse_package_requirement(requirement):
-    
-    version_pattern = re.compile('[=><]+(.*)$')
-    project_pattern  = re.compile('[^=><]+')
-    relationship_pattern = re.compile('[=><]+')
-    
-    try:
-        requirement_project = project_pattern.search(requirement).group(0)
-        requirement_version = version_pattern.search(requirement)
-        if requirement_version is not None:
-            requirement_version=requirement_version.group(1)
-        requirement_relation= relationship_pattern.search(requirement)
-        if requirement_relation is not None:
-            requirement_relation=requirement_relation.group(0)
-    except:
-        raise DistutilsError("Requirement : %s not correctly formated" % requirement)
-    
-    return requirement_project,requirement_relation,requirement_version
-    
-
-def get_package_requirement(package,requirementfile='requirements.txt'):            
-    requirements = get_requirements(requirementfile)
-    req = [x for x in requirements
-             if x[0:len(package)]==package
-          ]
-    
-    if len(req)==1:
-        return req[0]
-    else:
-        return None
-        
-        
-def pip_install_package(package,directory=None,upgrade=True):
-
-    log.info('installing %s in directory %s' % (package,str(directory)))
-
-    if 'http_proxy' in os.environ and 'https_proxy' not in os.environ:
-        os.environ['https_proxy']=os.environ['http_proxy']
-
-    args = ['install']
-    
-    if upgrade:
-        args.append('--upgrade')
-    
-    if 'http_proxy' in os.environ:
-        args.append('--proxy=%s' % os.environ['http_proxy'])
-        
-    if directory is not None:
-        args.append('--target=%s' % directory)
-    
-    args.append(package)
-        
-    return pip.main(args)
-

distutils.ext/obidistutils/serenity/checkpython.py

@@ -1,138 +0,0 @@
-'''
-Created on 24 mai 2015
-
-@author: coissac
-'''
-from distutils.version import StrictVersion
-from distutils import sysconfig
-import subprocess
-import os
-import glob
-import re
-
-from obidistutils.serenity.checksystem import is_windows_system
-import sys
-
-
-def is_python_version(path=None,minversion='3.4',maxversion=None):
-    '''
-    Checks that the python version is in the range {minversion,maxversion[
-    
-        @param path: if None consider the running python
-                     otherwise the python pointed by the path
-        @param minversion: the minimum version to consider
-        @param maxversion: the maximum version to consider (strictly inferior to)
-                     
-        @return: True if the python version match
-        @rtype: bool
-    '''
-    if path is None:
-        pythonversion = StrictVersion(sysconfig.get_python_version())
-    else:
-        command = """'%s' -c 'from distutils import sysconfig; """ \
-                  """print(sysconfig.get_python_version())'""" % path
-                  
-        p = subprocess.Popen(command, 
-                             shell=True, 
-                             stdout=subprocess.PIPE)
-        pythonversion=str(p.communicate()[0],'utf8').strip()
-        pythonversion = StrictVersion(pythonversion)
-                
-    return  (        pythonversion >=StrictVersion(minversion) 
-             and (   maxversion is None    
-                  or pythonversion < StrictVersion(maxversion))
-            )
-           
-
-def lookfor_good_python(minversion='3.4',maxversion=None,followLink=False):
-    '''
-    Look for all python interpreters present in the system path that
-    match the version constraints.
-    
-    @param minversion: the minimum version to consider
-    @param maxversion: the maximum version to consider (strictly inferior to)
-    @param followLink: a boolean value indicating if link must be substituted 
-                       by their real path.
-                       
-    @return: a list of path to interpreters
-    '''
-    exe = []
-    if not is_windows_system():
-        paths = os.environ['PATH'].split(os.pathsep)
-        for p in paths:
-            candidates = glob.glob(os.path.join(p,'python*')) 
-            pexe = []
-            pythonpat=re.compile('python([0-9]|[0-9]\.[0-9])?$')
-            for e in candidates:
-                print(e)
-                if pythonpat.search(e) is not None:
-                    if followLink and os.path.islink(e):
-                        e = os.path.realpath(e)
-                    if (os.path.isfile(e) and 
-                       os.access(e, os.X_OK) and 
-                       is_python_version(e,minversion,maxversion)):
-                        pexe.append(e)
-            exe.extend(set(pexe))
-        
-    return exe
-
-def is_a_virtualenv_python(path=None):
-    '''
-    Check if the python is belonging a virtualenv
-    
-        @param path: the path pointing to the python executable.
-                     if path is None then the running python is
-                     considered.
-        @param path: str or None 
-                     
-        @return: True if the python belongs a virtualenv
-                 False otherwise
-        @rtype: bool
-                 
-    '''
-    if path is None:
-        rep = sys.base_exec_prefix == sys.exec_prefix
-    else:
-        command = """'%s' -c 'import sys; print(sys.base_exec_prefix == sys.exec_prefix)'""" % path
-        p = subprocess.Popen(command, 
-                             shell=True, 
-                             stdout=subprocess.PIPE)
-        rep = eval(str(p.communicate()[0],'utf8'))
-        
-    return rep
-
-
-def which_virtualenv(path=None,full=False):
-    '''
-    Returns the name of the virtualenv.
-        @param path: the path to a python binary or None
-                     if you want to consider the running python
-        @type path: str or None
-                     
-        @param full: if set to True, returns the absolute path,
-                     otherwise only return a simple directory name
-        @type full: bool
-                 
-        @return: the virtual environment name or None if the
-                 path does not belong a virtualenv
-        @rtype: str or None
-    '''
-    if path is None:
-        path = sys.executable
-    
-    if is_a_virtualenv_python(path):
-        parts = path.split(os.sep)
-        try:
-            if full:
-                rep = os.sep.join(parts[0:parts.index('bin')])
-                rep = os.path.realpath(rep)
-            else:
-                rep = parts[parts.index('bin')-1]
-        except ValueError:
-            rep = None
-    else:
-        rep=None
-        
-    return rep
-        
-

distutils.ext/obidistutils/serenity/checksystem.py

@@ -1,18 +0,0 @@
-'''
-Created on 24 mai 2015
-
-@author: coissac
-'''
-
-from distutils import util
-
-def is_mac_system():
-    platform = util.get_platform().split('-')[0]
-    
-    return platform=='macosx'
-
-def is_windows_system():
-    platform = util.get_platform().split('-')[0]
-    
-    return platform=='Windows'
-        

distutils.ext/obidistutils/serenity/globals.py

@@ -1,14 +0,0 @@
-'''
-Created on 24 mai 2015
-
-@author: coissac
-'''
-
-
-saved_args=[]
-tmpdir=[]
-local_pip=[]
-local_virtualenv=[]
-local_cython=[]
-local_serenity=[]
-        

distutils.ext/obidistutils/serenity/rerun.py

@@ -1,61 +0,0 @@
-'''
-Created on 24 mai 2015
-
-@author: coissac
-'''
-
-import sys
-import os
-from distutils import log
-from distutils.errors import DistutilsError
-
-
-from obidistutils.serenity.globals import saved_args
-from obidistutils.serenity.checkpython import is_python_version,\
-    lookfor_good_python
-
-
-def rerun_with_anothe_python(path, minversion='3.4',maxversion=None, fork=False):
-        
-    if saved_args:
-        args = saved_args
-    else:
-        args = list(sys.argv)
-        
-          
-    assert is_python_version(path,minversion,maxversion), \
-           'the selected python is not adapted to the installation of this package'
-                   
-    args.insert(0, path)
-        
-    sys.stderr.flush()
-    sys.stdout.flush()
-    
-    if fork:
-        log.info('Forking a new install process')
-        os.system(' '.join(list(args)))
-        log.info('External process ended')
-        sys.exit(0)
-    else:
-        log.info('Install script restarting...')
-        os.execv(path,list(args))
-
-def enforce_good_python(minversion='3.4',maxversion=None, fork=False):
-    if is_python_version(minversion=minversion,maxversion=maxversion):
-        log.info('You are running the good python')
-        return True
-    
-    goodpython = lookfor_good_python(minversion,maxversion)
-    
-    if not goodpython:
-        raise DistutilsError('No good python identified on your system')
-
-    goodpython=goodpython[0]
-    
-    log.warn("========================================")    
-    log.warn("")
-    log.warn("    Switching to python : %s" % goodpython)
-    log.warn("")
-    log.warn("========================================")    
-
-    rerun_with_anothe_python(goodpython)

distutils.ext/obidistutils/serenity/snake.py

@@ -1,35 +0,0 @@
-'''
-Created on 2 oct. 2014
-
-@author: coissac
-'''
-
-snake ="""
-
-        ___
-      ,'._,`.
-     (-.___.-)
-     (-.___.-)
-     `-.___.-'
-      ((  @ @|              .            __
-       \   ` |         ,\   |`.    @|   |  |      _.-._
-      __`.`=-=mm===mm:: |   | |`.   |   |  |    ,'=` '=`.
-     (    `-'|:/  /:/  `/  @| | |   |, @| @|   /---)W(---\ 
-      \ \   / /  / /         @| |   '         (----| |----) ,~
-      |\ \ / /| / /            @|              \---| |---/  |
-      | \ V /||/ /                              `.-| |-,'   |
-      |  `-' |V /                                 \| |/    @'
-      |    , |-'                                 __| |__
-      |    .;: _,-.                         ,--""..| |..""--.
-      ;;:::' "    )                        (`--::__|_|__::--')
-    ,-"      _,  /                          \`--...___...--'/
-   (    -:--'/  /                           /`--...___...--'\  
-    "-._  `"'._/                           /`---...___...---'\  
-        "-._   "---.                      (`---....___....---')
-         .' ",._ ,' )                     |`---....___....---'|
-         /`._|  `|  |                     (`---....___....---')
-        (   \    |  /                      \`---...___...---'/
-         `.  `,  ^""                        `:--...___...--;'
-           `.,'               hh              `-._______.-'
-
-"""

distutils.ext/obidistutils/serenity/util.py

@@ -1,27 +0,0 @@
-'''
-Created on 2 oct. 2014
-
-@author: coissac
-'''
-
-import sys 
-import tempfile
-
-
-from obidistutils.serenity.globals import tmpdir         # @UnusedImport
-from obidistutils.serenity.globals import saved_args     # @UnusedImport
-
-def get_serenity_dir():
-    global tmpdir
-
-    if not tmpdir:
-        tmpdir.append(tempfile.mkdtemp())
-    return tmpdir[0]
-        
-def save_argv():
-    global saved_args
-
-    del saved_args[:]
-    saved_args.extend(list(sys.argv))
-
-           

distutils.ext/obidistutils/serenity/virtual.py

@@ -1,68 +0,0 @@
-'''
-Created on 2 oct. 2014
-
-@author: coissac
-'''
-
-import os
-import sys
-import venv
-
-from distutils.errors import DistutilsError
-from obidistutils.serenity.globals import local_virtualenv  # @UnusedImport
-from obidistutils.serenity.checkpython import   which_virtualenv,\
-                                                is_python_version, \
-                                                is_a_virtualenv_python
-                                                
-
-    
-    
-def serenity_virtualenv(envname,package,version,minversion='3.4',maxversion=None):
-        
-    #
-    # Checks if we are already running under the good virtualenv
-    #
-    ve = which_virtualenv(full=True)
-    if ve == os.path.realpath(envname) and is_python_version(minversion=minversion,maxversion=maxversion):
-        return sys.executable
-        
-    #
-    # Check if the virtualenv exist
-    # 
-        
-    python = None
-    
-    if os.path.isdir(envname):
-        python = os.path.join(envname,'bin','python')
-        ok = (is_python_version(python,
-                                minversion=minversion,
-                                maxversion=maxversion) and 
-              is_a_virtualenv_python(python))
-        
-        #
-        # The virtualenv already exist but it is not ok
-        #
-        if not ok:
-            raise DistutilsError("A virtualenv %s already exists but not with the required python")
-                 
-    else:
-        ok = False
-                
-        
-    #
-    # Creates a new virtualenv
-    #
-    if not ok:
-        venv.create(envname, 
-                    system_site_packages=False, 
-                    clear=True, 
-                    symlinks=False, 
-                    with_pip=True)
-        
-        # check the newly created virtualenv
-        return serenity_virtualenv(envname,package,version)
-    
-    return os.path.realpath(python)
-    
-    
-    

distutils.ext/src/littlebigman.c

@@ -1,24 +0,0 @@
-/*
- * littlebigman.c
- *
- *  Created on: 11 juil. 2012
- *      Author: coissac
- */
-
-#include<stdio.h>
-
-int main(int argc, char *argv[])
-{
-    union { int entier;
-            char caractere[4] ;
-    } test;
-
-    test.entier=0x01020304;
-
-    if (test.caractere[3] == 1)
-       printf("-DLITTLE_END");
-    else
-        printf("-DBIG_END");
-
-	return 0;
-}

distutils.ext/src/pidname.c

@@ -1,24 +0,0 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <errno.h>
-#include <libproc.h>
-
-int main (int argc, char* argv[])
-{
-	pid_t pid; int ret;
-	char pathbuf[PROC_PIDPATHINFO_MAXSIZE];
-
-	if ( argc > 1 ) {
-		pid = (pid_t) atoi(argv[1]);
-		ret = proc_pidpath (pid, pathbuf, sizeof(pathbuf));
-		if ( ret <= 0 ) {
-			fprintf(stderr, "PID %d: proc_pidpath ();\n", pid);
-			fprintf(stderr,	"    %s\n", strerror(errno));
-		} else {
-			printf("proc %d: %s\n", pid, pathbuf);
-		}
-	}
-
-	return 0;
-}

doc/.gitignore

@@ -1,3 +0,0 @@
-/build/
-/doxygen/
-/build_dir.txt

doc/Makefile

@@ -1,203 +0,0 @@
-# Makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-PAPER         =
-BUILDDIR      = build
-DOXYGENDIR    = doxygen
-
-# User-friendly check for sphinx-build
-ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
-$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
-endif
-
-# Internal variables.
-PAPEROPT_a4     = -D latex_paper_size=a4
-PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
-# the i18n builder cannot share the environment and doctrees with the others
-I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
-
-.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest coverage gettext
-
-help:
-	@echo "Please use \`make <target>' where <target> is one of"
-	@echo "  html       to make standalone HTML files"
-	@echo "  dirhtml    to make HTML files named index.html in directories"
-	@echo "  singlehtml to make a single large HTML file"
-	@echo "  pickle     to make pickle files"
-	@echo "  json       to make JSON files"
-	@echo "  htmlhelp   to make HTML files and a HTML help project"
-	@echo "  qthelp     to make HTML files and a qthelp project"
-	@echo "  applehelp  to make an Apple Help Book"
-	@echo "  devhelp    to make HTML files and a Devhelp project"
-	@echo "  epub       to make an epub"
-	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
-	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
-	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
-	@echo "  text       to make text files"
-	@echo "  man        to make manual pages"
-	@echo "  texinfo    to make Texinfo files"
-	@echo "  info       to make Texinfo files and run them through makeinfo"
-	@echo "  gettext    to make PO message catalogs"
-	@echo "  changes    to make an overview of all changed/added/deprecated items"
-	@echo "  xml        to make Docutils-native XML files"
-	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
-	@echo "  linkcheck  to check all external links for integrity"
-	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
-	@echo "  coverage   to run coverage check of the documentation (if enabled)"
-
-clean:
-	rm -rf $(BUILDDIR)/*
-	rm -rf $(DOXYGENDIR)/*
-
-html:
-	@echo "Generating Doxygen documentation..."
-	doxygen Doxyfile
-	@echo "Doxygen documentation generated. \n"
-	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
-	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
-
-dirhtml:
-	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
-	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
-
-singlehtml:
-	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
-	@echo
-	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
-
-pickle:
-	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
-	@echo
-	@echo "Build finished; now you can process the pickle files."
-
-json:
-	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
-	@echo
-	@echo "Build finished; now you can process the JSON files."
-
-htmlhelp:
-	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
-	@echo
-	@echo "Build finished; now you can run HTML Help Workshop with the" \
-	      ".hhp project file in $(BUILDDIR)/htmlhelp."
-
-qthelp:
-	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
-	@echo
-	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
-	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
-	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/OBITools-3.qhcp"
-	@echo "To view the help file:"
-	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/OBITools-3.qhc"
-
-applehelp:
-	$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
-	@echo
-	@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
-	@echo "N.B. You won't be able to view it unless you put it in" \
-	      "~/Library/Documentation/Help or install it in your application" \
-	      "bundle."
-
-devhelp:
-	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
-	@echo
-	@echo "Build finished."
-	@echo "To view the help file:"
-	@echo "# mkdir -p $$HOME/.local/share/devhelp/OBITools-3"
-	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/OBITools-3"
-	@echo "# devhelp"
-
-epub:
-	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
-	@echo
-	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
-
-latex:
-	@echo "Generating Doxygen documentation..."
-	doxygen Doxyfile
-	@echo "Doxygen documentation generated. \n"
-	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
-	@echo
-	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
-	@echo "Run \`make' in that directory to run these through (pdf)latex" \
-	      "(use \`make latexpdf' here to do that automatically)."
-
-latexpdf:
-	@echo "Generating Doxygen documentation..."
-	doxygen Doxyfile
-	@echo "Doxygen documentation generated. \n"
-	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
-	@echo "Running LaTeX files through pdflatex..."
-	$(MAKE) -C $(BUILDDIR)/latex all-pdf
-	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
-
-latexpdfja:
-	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
-	@echo "Running LaTeX files through platex and dvipdfmx..."
-	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
-	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
-
-text:
-	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
-	@echo
-	@echo "Build finished. The text files are in $(BUILDDIR)/text."
-
-man:
-	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
-	@echo
-	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
-
-texinfo:
-	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
-	@echo
-	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
-	@echo "Run \`make' in that directory to run these through makeinfo" \
-	      "(use \`make info' here to do that automatically)."
-
-info:
-	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
-	@echo "Running Texinfo files through makeinfo..."
-	make -C $(BUILDDIR)/texinfo info
-	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
-
-gettext:
-	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
-	@echo
-	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
-
-changes:
-	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
-	@echo
-	@echo "The overview file is in $(BUILDDIR)/changes."
-
-linkcheck:
-	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
-	@echo
-	@echo "Link check complete; look for any errors in the above output " \
-	      "or in $(BUILDDIR)/linkcheck/output.txt."
-
-doctest:
-	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
-	@echo "Testing of doctests in the sources finished, look at the " \
-	      "results in $(BUILDDIR)/doctest/output.txt."
-
-coverage:
-	$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
-	@echo "Testing of coverage in the sources finished, look at the " \
-	      "results in $(BUILDDIR)/coverage/python.txt."
-
-xml:
-	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
-	@echo
-	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
-
-pseudoxml:
-	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
-	@echo
-	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

doc/breathe/__init__.py

@@ -1,16 +0,0 @@
-
-__version__ = '4.0.0'
-
-
-def setup(app):
-
-    # We can't do the import at the module scope as setup.py has to be able to
-    # import this file to read __version__ without hitting any syntax errors
-    # from both Python 2 & Python 3.
-
-    # By the time this function is called, the directives code will have been
-    # converted with 2to3 if appropriate
-
-    from . import directives
-
-    directives.setup(app)

doc/breathe/directive/base.py

@@ -1,88 +0,0 @@
-
-from ..renderer.rst.doxygen.base import RenderContext
-from ..renderer.rst.doxygen import format_parser_error
-from ..parser import ParserError, FileIOError
-
-from docutils import nodes
-from docutils.parsers import rst
-
-
-class WarningHandler(object):
-
-    def __init__(self, state, context):
-        self.state = state
-        self.context = context
-
-    def warn(self, raw_text, rendered_nodes=None):
-        raw_text = self.format(raw_text)
-        if rendered_nodes is None:
-            rendered_nodes = [nodes.paragraph("", "", nodes.Text(raw_text))]
-        return [
-            nodes.warning("", *rendered_nodes),
-            self.state.document.reporter.warning(raw_text, line=self.context['lineno'])
-            ]
-
-    def format(self, text):
-        return text.format(**self.context)
-
-
-def create_warning(project_info, state, lineno, **kwargs):
-
-    tail = ''
-    if project_info:
-        tail = 'in doxygen xml output for project "{project}" from directory: {path}'.format(
-            project=project_info.name(),
-            path=project_info.project_path()
-            )
-
-    context = dict(
-        lineno=lineno,
-        tail=tail,
-        **kwargs
-        )
-
-    return WarningHandler(state, context)
-
-
-class BaseDirective(rst.Directive):
-
-    def __init__(self, root_data_object, renderer_factory_creator_constructor, finder_factory,
-                 project_info_factory, filter_factory, target_handler_factory, parser_factory, *args):
-        rst.Directive.__init__(self, *args)
-        self.directive_args = list(args)  # Convert tuple to list to allow modification.
-
-        self.root_data_object = root_data_object
-        self.renderer_factory_creator_constructor = renderer_factory_creator_constructor
-        self.finder_factory = finder_factory
-        self.project_info_factory = project_info_factory
-        self.filter_factory = filter_factory
-        self.target_handler_factory = target_handler_factory
-        self.parser_factory = parser_factory
-
-    def render(self, node_stack, project_info, options, filter_, target_handler, mask_factory):
-        "Standard render process used by subclasses"
-
-        renderer_factory_creator = self.renderer_factory_creator_constructor.create_factory_creator(
-            project_info,
-            self.state.document,
-            options,
-            target_handler
-            )
-
-        try:
-            renderer_factory = renderer_factory_creator.create_factory(
-                node_stack,
-                self.state,
-                self.state.document,
-                filter_,
-                target_handler,
-                )
-        except ParserError as e:
-            return format_parser_error("doxygenclass", e.error, e.filename, self.state,
-                                       self.lineno, True)
-        except FileIOError as e:
-            return format_parser_error("doxygenclass", e.error, e.filename, self.state, self.lineno)
-
-        context = RenderContext(node_stack, mask_factory, self.directive_args)
-        object_renderer = renderer_factory.create_renderer(context)
-        return object_renderer.render()

doc/breathe/directive/file.py

@@ -1,123 +0,0 @@
-
-from ..renderer.rst.doxygen.base import RenderContext
-from ..renderer.rst.doxygen.mask import NullMaskFactory
-from ..directive.base import BaseDirective
-from ..project import ProjectError
-from .base import create_warning
-
-from docutils.parsers.rst.directives import unchanged_required, flag
-from docutils.parsers import rst
-
-
-class BaseFileDirective(BaseDirective):
-    """Base class handle the main work when given the appropriate file and project info to work
-    from.
-    """
-
-    # We use inheritance here rather than a separate object and composition, because so much
-    # information is present in the Directive class from the docutils framework that we'd have to
-    # pass way too much stuff to a helper object to be reasonable.
-
-    def handle_contents(self, file_, project_info):
-
-        finder = self.finder_factory.create_finder(project_info)
-
-        finder_filter = self.filter_factory.create_file_finder_filter(file_)
-
-        matches = []
-        finder.filter_(finder_filter, matches)
-
-        if len(matches) > 1:
-            warning = create_warning(None, self.state, self.lineno, file=file_,
-                                     directivename=self.directive_name)
-            return warning.warn('{directivename}: Found multiple matches for file "{file} {tail}')
-
-        elif not matches:
-            warning = create_warning(None, self.state, self.lineno, file=file_,
-                                     directivename=self.directive_name)
-            return warning.warn('{directivename}: Cannot find file "{file} {tail}')
-
-        target_handler = self.target_handler_factory.create_target_handler(
-            self.options, project_info, self.state.document)
-        filter_ = self.filter_factory.create_file_filter(file_, self.options)
-
-        renderer_factory_creator = self.renderer_factory_creator_constructor.create_factory_creator(
-            project_info,
-            self.state.document,
-            self.options,
-            target_handler
-            )
-        node_list = []
-        for node_stack in matches:
-
-            renderer_factory = renderer_factory_creator.create_factory(
-                node_stack,
-                self.state,
-                self.state.document,
-                filter_,
-                target_handler,
-                )
-
-            mask_factory = NullMaskFactory()
-            context = RenderContext(node_stack, mask_factory, self.directive_args)
-            object_renderer = renderer_factory.create_renderer(context)
-            node_list.extend(object_renderer.render())
-
-        return node_list
-
-
-class DoxygenFileDirective(BaseFileDirective):
-
-    directive_name = 'doxygenfile'
-
-    required_arguments = 0
-    optional_arguments = 2
-    option_spec = {
-        "path": unchanged_required,
-        "project": unchanged_required,
-        "outline": flag,
-        "no-link": flag,
-        }
-    has_content = False
-
-    def run(self):
-        """Get the file from the argument and the project info from the factory."""
-
-        file_ = self.arguments[0]
-
-        try:
-            project_info = self.project_info_factory.create_project_info(self.options)
-        except ProjectError as e:
-            warning = create_warning(None, self.state, self.lineno)
-            return warning.warn('doxygenfile: %s' % e)
-
-        return self.handle_contents(file_, project_info)
-
-
-class AutoDoxygenFileDirective(BaseFileDirective):
-
-    directive_name = 'autodoxygenfile'
-
-    required_arguments = 1
-    option_spec = {
-        "project": unchanged_required,
-        "outline": flag,
-        "no-link": flag,
-        }
-    has_content = False
-
-    def run(self):
-        """Get the file from the argument and extract the associated project info for the named
-        project given that it is an auto-project.
-        """
-
-        file_ = self.arguments[0]
-
-        try:
-            project_info = self.project_info_factory.retrieve_project_info_for_auto(self.options)
-        except ProjectError as e:
-            warning = create_warning(None, self.state, self.lineno)
-            return warning.warn('autodoxygenfile: %s' % e)
-
-        return self.handle_contents(file_, project_info)
-

doc/breathe/directive/index.py

@@ -1,115 +0,0 @@
-
-from ..renderer.rst.doxygen.base import RenderContext
-from ..renderer.rst.doxygen.mask import NullMaskFactory
-from ..renderer.rst.doxygen import format_parser_error
-from ..directive.base import BaseDirective
-from ..project import ProjectError
-from ..parser import ParserError, FileIOError
-from .base import create_warning
-
-from docutils.parsers import rst
-from docutils.parsers.rst.directives import unchanged_required, flag
-
-
-class BaseIndexDirective(BaseDirective):
-    """Base class handle the main work when given the appropriate project info to work from.
-    """
-
-    # We use inheritance here rather than a separate object and composition, because so much
-    # information is present in the Directive class from the docutils framework that we'd have to
-    # pass way too much stuff to a helper object to be reasonable.
-
-    def handle_contents(self, project_info):
-
-        try:
-            finder = self.finder_factory.create_finder(project_info)
-        except ParserError as e:
-            return format_parser_error(self.name, e.error, e.filename, self.state,
-                                       self.lineno, True)
-        except FileIOError as e:
-            return format_parser_error(self.name, e.error, e.filename, self.state, self.lineno)
-
-        data_object = finder.root()
-
-        target_handler = self.target_handler_factory.create_target_handler(
-            self.options, project_info, self.state.document)
-        filter_ = self.filter_factory.create_index_filter(self.options)
-
-        renderer_factory_creator = self.renderer_factory_creator_constructor.create_factory_creator(
-            project_info,
-            self.state.document,
-            self.options,
-            target_handler
-            )
-        renderer_factory = renderer_factory_creator.create_factory(
-            [data_object],
-            self.state,
-            self.state.document,
-            filter_,
-            target_handler,
-            )
-
-        mask_factory = NullMaskFactory()
-        context = RenderContext([data_object, self.root_data_object], mask_factory, self.directive_args)
-        object_renderer = renderer_factory.create_renderer(context)
-
-        try:
-            node_list = object_renderer.render()
-        except ParserError as e:
-            return format_parser_error(self.name, e.error, e.filename, self.state,
-                                       self.lineno, True)
-        except FileIOError as e:
-            return format_parser_error(self.name, e.error, e.filename, self.state, self.lineno)
-
-        return node_list
-
-
-class DoxygenIndexDirective(BaseIndexDirective):
-
-    required_arguments = 0
-    optional_arguments = 2
-    option_spec = {
-        "path": unchanged_required,
-        "project": unchanged_required,
-        "outline": flag,
-        "no-link": flag,
-        }
-    has_content = False
-
-    def run(self):
-        """Extract the project info and pass it to the helper method"""
-
-        try:
-            project_info = self.project_info_factory.create_project_info(self.options)
-        except ProjectError as e:
-            warning = create_warning(None, self.state, self.lineno)
-            return warning.warn('doxygenindex: %s' % e)
-
-        return self.handle_contents(project_info)
-
-
-class AutoDoxygenIndexDirective(BaseIndexDirective):
-
-    required_arguments = 0
-    final_argument_whitespace = True
-    option_spec = {
-        "project": unchanged_required,
-        "outline": flag,
-        "no-link": flag,
-        }
-    has_content = False
-
-    def run(self):
-        """Extract the project info from the auto project info store and pass it to the helper
-        method
-        """
-
-        try:
-            project_info = self.project_info_factory.retrieve_project_info_for_auto(self.options)
-        except ProjectError as e:
-            warning = create_warning(None, self.state, self.lineno)
-            return warning.warn('autodoxygenindex: %s' % e)
-
-        return self.handle_contents(project_info)
-
-

doc/breathe/exception.py

@@ -1,3 +0,0 @@
-
-class BreatheError(Exception):
-    pass

doc/breathe/finder/core.py

@@ -1,45 +0,0 @@
-
-class FakeParentNode(object):
-
-    node_type = "fakeparent"
-
-
-class Finder(object):
-
-    def __init__(self, root, item_finder_factory):
-
-        self._root = root
-        self.item_finder_factory = item_finder_factory
-
-    def filter_(self, filter_, matches):
-        """Adds all nodes which match the filter into the matches list"""
-
-        item_finder = self.item_finder_factory.create_finder(self._root)
-        item_finder.filter_([FakeParentNode()], filter_, matches)
-
-    def root(self):
-
-        return self._root
-
-
-class FinderFactory(object):
-
-    def __init__(self, parser, item_finder_factory_creator):
-
-        self.parser = parser
-        self.item_finder_factory_creator = item_finder_factory_creator
-
-    def create_finder(self, project_info):
-
-        root = self.parser.parse(project_info)
-        item_finder_factory = self.item_finder_factory_creator.create_factory(project_info)
-
-        return Finder(root, item_finder_factory)
-
-    def create_finder_from_root(self, root, project_info):
-
-        item_finder_factory = self.item_finder_factory_creator.create_factory(project_info)
-
-        return Finder(root, item_finder_factory)
-
-

doc/breathe/finder/doxygen/__init__.py

@@ -1 +0,0 @@
-

doc/breathe/finder/doxygen/base.py

@@ -1,18 +0,0 @@
-
-class ItemFinder(object):
-
-    def __init__(self, project_info, data_object, item_finder_factory):
-
-        self.data_object = data_object
-        self.item_finder_factory = item_finder_factory
-        self.project_info = project_info
-
-
-def stack(element, list_):
-    """Stack an element on to the start of a list and return as a new list"""
-
-    # Copy list first so we have a new list to insert into
-    output = list_[:]
-    output.insert(0, element)
-    return output
-

doc/breathe/finder/doxygen/compound.py

@@ -1,75 +0,0 @@
-
-from .base import ItemFinder, stack
-
-
-class DoxygenTypeSubItemFinder(ItemFinder):
-
-    def filter_(self, ancestors, filter_, matches):
-        """Find nodes which match the filter. Doesn't test this node, only its children"""
-
-        node_stack = stack(self.data_object, ancestors)
-
-        compound_finder = self.item_finder_factory.create_finder(self.data_object.compounddef)
-        compound_finder.filter_(node_stack, filter_, matches)
-
-
-class CompoundDefTypeSubItemFinder(ItemFinder):
-
-    def filter_(self, ancestors, filter_, matches):
-        """Finds nodes which match the filter and continues checks to children"""
-
-        node_stack = stack(self.data_object, ancestors)
-
-        if filter_.allow(node_stack):
-            matches.append(node_stack)
-
-        for sectiondef in self.data_object.sectiondef:
-            finder = self.item_finder_factory.create_finder(sectiondef)
-            finder.filter_(node_stack, filter_, matches)
-
-        for innerclass in self.data_object.innerclass:
-            finder = self.item_finder_factory.create_finder(innerclass)
-            finder.filter_(node_stack, filter_, matches)
-
-
-class SectionDefTypeSubItemFinder(ItemFinder):
-
-    def filter_(self, ancestors, filter_, matches):
-        """Find nodes which match the filter. Doesn't test this node, only its children"""
-
-        node_stack = stack(self.data_object, ancestors)
-
-        if filter_.allow(node_stack):
-            matches.append(node_stack)
-
-        for memberdef in self.data_object.memberdef:
-            finder = self.item_finder_factory.create_finder(memberdef)
-            finder.filter_(node_stack, filter_, matches)
-
-
-class MemberDefTypeSubItemFinder(ItemFinder):
-
-    def filter_(self, ancestors, filter_, matches):
-
-        data_object = self.data_object
-        node_stack = stack(data_object, ancestors)
-
-        if filter_.allow(node_stack):
-            matches.append(node_stack)
-
-        if data_object.kind == 'enum':
-            for value in data_object.enumvalue:
-                value_stack = stack(value, node_stack)
-                if filter_.allow(value_stack):
-                    matches.append(value_stack)
-
-
-class RefTypeSubItemFinder(ItemFinder):
-
-    def filter_(self, ancestors, filter_, matches):
-
-        node_stack = stack(self.data_object, ancestors)
-
-        if filter_.allow(node_stack):
-            matches.append(node_stack)
-

doc/breathe/finder/doxygen/core.py

@@ -1,55 +0,0 @@
-
-from . import index as indexfinder
-from . import compound as compoundfinder
-
-
-class CreateCompoundTypeSubFinder(object):
-
-    def __init__(self, parser_factory, matcher_factory):
-
-        self.parser_factory = parser_factory
-        self.matcher_factory = matcher_factory
-
-    def __call__(self, project_info, *args):
-
-        compound_parser = self.parser_factory.create_compound_parser(project_info)
-        return indexfinder.CompoundTypeSubItemFinder(self.matcher_factory, compound_parser,
-                                                     project_info, *args)
-
-
-class DoxygenItemFinderFactory(object):
-
-    def __init__(self, finders, project_info):
-
-        self.finders = finders
-        self.project_info = project_info
-
-    def create_finder(self, data_object):
-
-        return self.finders[data_object.node_type](self.project_info, data_object, self)
-
-
-class DoxygenItemFinderFactoryCreator(object):
-
-    def __init__(self, parser_factory, filter_factory):
-
-        self.parser_factory = parser_factory
-        self.filter_factory = filter_factory
-
-    def create_factory(self, project_info):
-
-        finders = {
-            "doxygen": indexfinder.DoxygenTypeSubItemFinder,
-            "compound": CreateCompoundTypeSubFinder(self.parser_factory, self.filter_factory),
-            "member": indexfinder.MemberTypeSubItemFinder,
-            "doxygendef": compoundfinder.DoxygenTypeSubItemFinder,
-            "compounddef": compoundfinder.CompoundDefTypeSubItemFinder,
-            "sectiondef": compoundfinder.SectionDefTypeSubItemFinder,
-            "memberdef": compoundfinder.MemberDefTypeSubItemFinder,
-            "ref": compoundfinder.RefTypeSubItemFinder,
-            }
-
-        return DoxygenItemFinderFactory(finders, project_info)
-
-
-

doc/breathe/finder/doxygen/index.py

@@ -1,79 +0,0 @@
-
-from .base import ItemFinder, stack
-
-
-class DoxygenTypeSubItemFinder(ItemFinder):
-
-    def filter_(self, ancestors, filter_, matches):
-        """Find nodes which match the filter. Doesn't test this node, only its children"""
-
-        compounds = self.data_object.get_compound()
-
-        node_stack = stack(self.data_object, ancestors)
-
-        for compound in compounds:
-
-            compound_finder = self.item_finder_factory.create_finder(compound)
-            compound_finder.filter_(node_stack, filter_, matches)
-
-
-class CompoundTypeSubItemFinder(ItemFinder):
-
-    def __init__(self, filter_factory, compound_parser, *args):
-        ItemFinder.__init__(self, *args)
-
-        self.filter_factory = filter_factory
-        self.compound_parser = compound_parser
-
-    def filter_(self, ancestors, filter_, matches):
-        """Finds nodes which match the filter and continues checks to children
-
-        Requires parsing the xml files referenced by the children for which we use the compound
-        parser and continue at the top level of that pretending that this node is the parent of the
-        top level node of the compound file.
-        """
-
-        node_stack = stack(self.data_object, ancestors)
-
-        # Match against compound object
-        if filter_.allow(node_stack):
-            matches.append(node_stack)
-
-        # Descend to member children
-        members = self.data_object.get_member()
-        member_matches = []
-        for member in members:
-            member_finder = self.item_finder_factory.create_finder(member)
-            member_finder.filter_(node_stack, filter_, member_matches)
-
-        results = []
-
-        # If there are members in this compound that match the criteria
-        # then load up the file for this compound and get the member data objects
-        if member_matches:
-
-            file_data = self.compound_parser.parse(self.data_object.refid)
-            finder = self.item_finder_factory.create_finder(file_data)
-
-            for member_stack in member_matches:
-                ref_filter = self.filter_factory.create_id_filter('memberdef', member_stack[0].refid)
-                finder.filter_(node_stack, ref_filter, matches)
-
-        else:
-
-            # Read in the xml file referenced by the compound and descend into that as well
-            file_data = self.compound_parser.parse(self.data_object.refid)
-            finder = self.item_finder_factory.create_finder(file_data)
-
-            finder.filter_(node_stack, filter_, matches)
-
-
-class MemberTypeSubItemFinder(ItemFinder):
-
-    def filter_(self, ancestors, filter_, matches):
-
-        node_stack = stack(self.data_object, ancestors)
-
-        # Match against member object
-        if filter_.allow(node_stack):
-            matches.append(node_stack)

doc/breathe/parser/__init__.py

@@ -1,118 +0,0 @@
-
-import breathe.parser.doxygen.index
-import breathe.parser.doxygen.compound
-
-class ParserError(Exception):
-
-    def __init__(self, error, filename):
-        Exception.__init__(self, error)
-
-        self.error = error
-        self.filename = filename
-
-class FileIOError(Exception):
-
-    def __init__(self, error, filename):
-        Exception.__init__(self, error)
-
-        self.error = error
-        self.filename = filename
-
-class Parser(object):
-
-    def __init__(self, cache, path_handler, file_state_cache):
-
-        self.cache = cache
-        self.path_handler = path_handler
-        self.file_state_cache = file_state_cache
-
-class DoxygenIndexParser(Parser):
-
-    def __init__(self, cache, path_handler, file_state_cache):
-        Parser.__init__(self, cache, path_handler, file_state_cache)
-
-    def parse(self, project_info):
-
-        filename = self.path_handler.resolve_path(
-                project_info.project_path(),
-                "index.xml"
-                )
-
-        self.file_state_cache.update(filename)
-
-        try: 
-            # Try to get from our cache
-            return self.cache[filename]
-        except KeyError:
-
-            # If that fails, parse it afresh
-            try:
-                result = breathe.parser.doxygen.index.parse(filename)
-                self.cache[filename] = result
-                return result
-            except breathe.parser.doxygen.index.ParseError as e:
-                raise ParserError(e, filename)
-            except breathe.parser.doxygen.index.FileIOError as e:
-                raise FileIOError(e, filename)
-
-class DoxygenCompoundParser(Parser):
-
-    def __init__(self, cache, path_handler, file_state_cache, project_info):
-        Parser.__init__(self, cache, path_handler, file_state_cache)
-
-        self.project_info = project_info
-
-    def parse(self, refid):
-
-        filename = self.path_handler.resolve_path(
-                self.project_info.project_path(),
-                "%s.xml" % refid
-                )
-
-        self.file_state_cache.update(filename)
-
-        try: 
-            # Try to get from our cache
-            return self.cache[filename]
-        except KeyError:
-
-            # If that fails, parse it afresh
-            try:
-                result = breathe.parser.doxygen.compound.parse(filename)
-                self.cache[filename] = result
-                return result
-            except breathe.parser.doxygen.compound.ParseError as e:
-                raise ParserError(e, filename)
-            except breathe.parser.doxygen.compound.FileIOError as e:
-                raise FileIOError(e, filename)
-
-class CacheFactory(object):
-
-    def create_cache(self):
-
-        # Return basic dictionary as cache
-        return {}
-
-class DoxygenParserFactory(object):
-
-    def __init__(self, cache, path_handler, file_state_cache):
-
-        self.cache = cache
-        self.path_handler = path_handler
-        self.file_state_cache = file_state_cache
-
-    def create_index_parser(self):
-
-        return DoxygenIndexParser(self.cache, self.path_handler, self.file_state_cache)
-
-    def create_compound_parser(self, project_info):
-
-        return DoxygenCompoundParser(
-                self.cache,
-                self.path_handler,
-                self.file_state_cache,
-                project_info
-                )
-
-
-

doc/breathe/parser/doxygen/compound.py

@@ -1,964 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Generated Mon Feb  9 19:08:05 2009 by generateDS.py.
-"""
-
-from xml.dom import minidom
-from xml.dom import Node
-from xml.parsers.expat import ExpatError
-
-from . import compoundsuper as supermod
-from .compoundsuper import MixedContainer
-
-
-class DoxygenTypeSub(supermod.DoxygenType):
-
-    node_type = "doxygendef"
-
-    def __init__(self, version=None, compounddef=None):
-        supermod.DoxygenType.__init__(self, version, compounddef)
-supermod.DoxygenType.subclass = DoxygenTypeSub
-# end class DoxygenTypeSub
-
-
-class compounddefTypeSub(supermod.compounddefType):
-
-    node_type = "compounddef"
-
-    def __init__(self, kind=None, prot=None, id=None, compoundname='', title='',
-                 basecompoundref=None, derivedcompoundref=None, includes=None, includedby=None,
-                 incdepgraph=None, invincdepgraph=None, innerdir=None, innerfile=None,
-                 innerclass=None, innernamespace=None, innerpage=None, innergroup=None,
-                 templateparamlist=None, sectiondef=None, briefdescription=None,
-                 detaileddescription=None, inheritancegraph=None, collaborationgraph=None,
-                 programlisting=None, location=None, listofallmembers=None):
-
-        supermod.compounddefType.__init__(self, kind, prot, id, compoundname, title,
-                                          basecompoundref, derivedcompoundref, includes, includedby,
-                                          incdepgraph, invincdepgraph, innerdir, innerfile,
-                                          innerclass, innernamespace, innerpage, innergroup,
-                                          templateparamlist, sectiondef, briefdescription,
-                                          detaileddescription, inheritancegraph, collaborationgraph,
-                                          programlisting, location, listofallmembers)
-
-supermod.compounddefType.subclass = compounddefTypeSub
-# end class compounddefTypeSub
-
-
-class listofallmembersTypeSub(supermod.listofallmembersType):
-
-    node_type = "listofallmembers"
-
-    def __init__(self, member=None):
-        supermod.listofallmembersType.__init__(self, member)
-supermod.listofallmembersType.subclass = listofallmembersTypeSub
-# end class listofallmembersTypeSub
-
-
-class memberRefTypeSub(supermod.memberRefType):
-
-    node_type = "memberref"
-
-    def __init__(self, virt=None, prot=None, refid=None, ambiguityscope=None, scope='', name=''):
-        supermod.memberRefType.__init__(self, virt, prot, refid, ambiguityscope, scope, name)
-supermod.memberRefType.subclass = memberRefTypeSub
-# end class memberRefTypeSub
-
-
-class compoundRefTypeSub(supermod.compoundRefType):
-
-    node_type = "compoundref"
-
-    def __init__(self, virt=None, prot=None, refid=None, valueOf_='', mixedclass_=None,
-                 content_=None):
-        supermod.compoundRefType.__init__(self, mixedclass_, content_)
-supermod.compoundRefType.subclass = compoundRefTypeSub
-# end class compoundRefTypeSub
-
-
-class reimplementTypeSub(supermod.reimplementType):
-
-    node_type = "reimplement"
-
-    def __init__(self, refid=None, valueOf_='', mixedclass_=None, content_=None):
-        supermod.reimplementType.__init__(self, mixedclass_, content_)
-supermod.reimplementType.subclass = reimplementTypeSub
-# end class reimplementTypeSub
-
-
-class incTypeSub(supermod.incType):
-
-    node_type = "inc"
-
-    def __init__(self, local=None, refid=None, valueOf_='', mixedclass_=None, content_=None):
-        supermod.incType.__init__(self, mixedclass_, content_)
-supermod.incType.subclass = incTypeSub
-# end class incTypeSub
-
-
-class refTypeSub(supermod.refType):
-
-    node_type = "ref"
-
-    def __init__(self, node_name, prot=None, refid=None, valueOf_='', mixedclass_=None,
-                 content_=None):
-        supermod.refType.__init__(self, mixedclass_, content_)
-
-        self.node_name = node_name
-
-supermod.refType.subclass = refTypeSub
-
-
-class refTextTypeSub(supermod.refTextType):
-
-    node_type = "reftex"
-
-    def __init__(self, refid=None, kindref=None, external=None, valueOf_='', mixedclass_=None,
-                 content_=None):
-        supermod.refTextType.__init__(self, mixedclass_, content_)
-
-supermod.refTextType.subclass = refTextTypeSub
-# end class refTextTypeSub
-
-
-class sectiondefTypeSub(supermod.sectiondefType):
-
-    node_type = "sectiondef"
-
-    def __init__(self, kind=None, header='', description=None, memberdef=None):
-        supermod.sectiondefType.__init__(self, kind, header, description, memberdef)
-
-supermod.sectiondefType.subclass = sectiondefTypeSub
-# end class sectiondefTypeSub
-
-
-class memberdefTypeSub(supermod.memberdefType):
-
-    node_type = "memberdef"
-
-    def __init__(self, initonly=None, kind=None, volatile=None, const=None, raise_=None, virt=None,
-                 readable=None, prot=None, explicit=None, new=None, final=None, writable=None,
-                 add=None, static=None, remove=None, sealed=None, mutable=None, gettable=None,
-                 inline=None, settable=None, id=None, templateparamlist=None, type_=None,
-                 definition='', argsstring='', name='', read='', write='', bitfield='',
-                 reimplements=None, reimplementedby=None, param=None, enumvalue=None,
-                 initializer=None, exceptions=None, briefdescription=None, detaileddescription=None,
-                 inbodydescription=None, location=None, references=None, referencedby=None):
-
-        supermod.memberdefType.__init__(self, initonly, kind, volatile, const, raise_, virt,
-                                        readable, prot, explicit, new, final, writable, add, static,
-                                        remove, sealed, mutable, gettable, inline, settable, id,
-                                        templateparamlist, type_, definition, argsstring, name,
-                                        read, write, bitfield, reimplements, reimplementedby, param,
-                                        enumvalue, initializer, exceptions, briefdescription,
-                                        detaileddescription, inbodydescription, location,
-                                        references, referencedby)
-
-        self.parameterlist = supermod.docParamListType.factory()
-        self.parameterlist.kind = "param"
-
-    def buildChildren(self, child_, nodeName_):
-        supermod.memberdefType.buildChildren(self, child_, nodeName_)
-
-        if child_.nodeType == Node.ELEMENT_NODE and nodeName_ == 'param':
-
-            # Get latest param
-            param = self.param[-1]
-
-            # If it doesn't have a description we're done
-            if not param.briefdescription:
-                return
-
-            # Construct our own param list from the descriptions stored inline
-            # with the parameters
-            paramdescription = param.briefdescription
-            paramname = supermod.docParamName.factory()
-
-            # Add parameter name
-            obj_ = paramname.mixedclass_(MixedContainer.CategoryText, MixedContainer.TypeNone, '',
-                                         param.declname)
-            paramname.content_.append(obj_)
-
-            paramnamelist = supermod.docParamNameList.factory()
-            paramnamelist.parametername.append(paramname)
-
-            paramlistitem = supermod.docParamListItem.factory()
-            paramlistitem.parameternamelist.append(paramnamelist)
-
-            # Add parameter description
-            paramlistitem.parameterdescription = paramdescription
-
-            self.parameterlist.parameteritem.append(paramlistitem)
-
-        elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == 'detaileddescription':
-
-            if not self.parameterlist.parameteritem:
-                # No items in our list
-                return
-
-            # Assume supermod.memberdefType.buildChildren has already built the
-            # description object, we just want to slot our parameterlist in at
-            # a reasonable point
-
-            if not self.detaileddescription:
-                # Create one if it doesn't exist
-                self.detaileddescription = supermod.descriptionType.factory()
-
-            detaileddescription = self.detaileddescription
-
-            para = supermod.docParaType.factory()
-            para.parameterlist.append(self.parameterlist)
-
-            obj_ = detaileddescription.mixedclass_(MixedContainer.CategoryComplex,
-                                                   MixedContainer.TypeNone, 'para', para)
-
-            index = 0
-            detaileddescription.content_.insert(index, obj_)
-
-
-supermod.memberdefType.subclass = memberdefTypeSub
-# end class memberdefTypeSub
-
-
-class descriptionTypeSub(supermod.descriptionType):
-
-    node_type = "description"
-
-    def __init__(self, title='', para=None, sect1=None, internal=None, mixedclass_=None,
-                 content_=None):
-        supermod.descriptionType.__init__(self, mixedclass_, content_)
-
-supermod.descriptionType.subclass = descriptionTypeSub
-# end class descriptionTypeSub
-
-
-class enumvalueTypeSub(supermod.enumvalueType):
-
-    node_type = "enumvalue"
-
-    def __init__(self, prot=None, id=None, name='', initializer=None, briefdescription=None,
-                 detaileddescription=None, mixedclass_=None, content_=None):
-        supermod.enumvalueType.__init__(self, mixedclass_, content_)
-
-        self.initializer = None
-
-    def buildChildren(self, child_, nodeName_):
-        # Get text from <name> child and put it in self.name
-        if child_.nodeType == Node.ELEMENT_NODE and nodeName_ == 'name':
-            value_ = []
-            for text_ in child_.childNodes:
-                value_.append(text_.nodeValue)
-            valuestr_ = ''.join(value_)
-            self.name = valuestr_
-        elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == 'briefdescription':
-            obj_ = supermod.descriptionType.factory()
-            obj_.build(child_)
-            self.set_briefdescription(obj_)
-        elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == 'detaileddescription':
-            obj_ = supermod.descriptionType.factory()
-            obj_.build(child_)
-            self.set_detaileddescription(obj_)
-        elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == 'initializer':
-            childobj_ = supermod.linkedTextType.factory()
-            childobj_.build(child_)
-            obj_ = self.mixedclass_(MixedContainer.CategoryComplex, MixedContainer.TypeNone,
-                                    'initializer', childobj_)
-            self.set_initializer(obj_)
-            self.content_.append(obj_)
-
-supermod.enumvalueType.subclass = enumvalueTypeSub
-# end class enumvalueTypeSub
-
-
-class templateparamlistTypeSub(supermod.templateparamlistType):
-
-    node_type = "templateparamlist"
-
-    def __init__(self, param=None):
-        supermod.templateparamlistType.__init__(self, param)
-supermod.templateparamlistType.subclass = templateparamlistTypeSub
-# end class templateparamlistTypeSub
-
-
-class paramTypeSub(supermod.paramType):
-
-    node_type = "param"
-
-    def __init__(self, type_=None, declname='', defname='', array='', defval=None,
-                 briefdescription=None):
-        supermod.paramType.__init__(self, type_, declname, defname, array, defval, briefdescription)
-supermod.paramType.subclass = paramTypeSub
-# end class paramTypeSub
-
-
-class linkedTextTypeSub(supermod.linkedTextType):
-
-    node_type = "linkedtext"
-
-    def __init__(self, ref=None, mixedclass_=None, content_=None):
-        supermod.linkedTextType.__init__(self, mixedclass_, content_)
-supermod.linkedTextType.subclass = linkedTextTypeSub
-# end class linkedTextTypeSub
-
-
-class graphTypeSub(supermod.graphType):
-
-    node_type = "graph"
-
-    def __init__(self, node=None):
-        supermod.graphType.__init__(self, node)
-supermod.graphType.subclass = graphTypeSub
-# end class graphTypeSub
-
-
-class nodeTypeSub(supermod.nodeType):
-
-    node_type = "node"
-
-    def __init__(self, id=None, label='', link=None, childnode=None):
-        supermod.nodeType.__init__(self, id, label, link, childnode)
-supermod.nodeType.subclass = nodeTypeSub
-# end class nodeTypeSub
-
-
-class childnodeTypeSub(supermod.childnodeType):
-
-    node_type = "childnode"
-
-    def __init__(self, relation=None, refid=None, edgelabel=None):
-        supermod.childnodeType.__init__(self, relation, refid, edgelabel)
-supermod.childnodeType.subclass = childnodeTypeSub
-# end class childnodeTypeSub
-
-
-class linkTypeSub(supermod.linkType):
-
-    node_type = "link"
-
-    def __init__(self, refid=None, external=None, valueOf_=''):
-        supermod.linkType.__init__(self, refid, external)
-supermod.linkType.subclass = linkTypeSub
-# end class linkTypeSub
-
-
-class listingTypeSub(supermod.listingType):
-
-    node_type = "listing"
-
-    def __init__(self, codeline=None):
-        supermod.listingType.__init__(self, codeline)
-supermod.listingType.subclass = listingTypeSub
-# end class listingTypeSub
-
-
-class codelineTypeSub(supermod.codelineType):
-
-    node_type = "codeline"
-
-    def __init__(self, external=None, lineno=None, refkind=None, refid=None, highlight=None):
-        supermod.codelineType.__init__(self, external, lineno, refkind, refid, highlight)
-supermod.codelineType.subclass = codelineTypeSub
-# end class codelineTypeSub
-
-
-class highlightTypeSub(supermod.highlightType):
-
-    node_type = "highlight"
-
-    def __init__(self, class_=None, sp=None, ref=None, mixedclass_=None, content_=None):
-        supermod.highlightType.__init__(self, mixedclass_, content_)
-supermod.highlightType.subclass = highlightTypeSub
-# end class highlightTypeSub
-
-
-class referenceTypeSub(supermod.referenceType):
-
-    node_type = "reference"
-
-    def __init__(self, endline=None, startline=None, refid=None, compoundref=None, valueOf_='',
-                 mixedclass_=None, content_=None):
-        supermod.referenceType.__init__(self, mixedclass_, content_)
-supermod.referenceType.subclass = referenceTypeSub
-# end class referenceTypeSub
-
-
-class locationTypeSub(supermod.locationType):
-
-    node_type = "location"
-
-    def __init__(self, bodystart=None, line=None, bodyend=None, bodyfile=None, file=None,
-                 valueOf_=''):
-        supermod.locationType.__init__(self, bodystart, line, bodyend, bodyfile, file)
-supermod.locationType.subclass = locationTypeSub
-# end class locationTypeSub
-
-
-class docSect1TypeSub(supermod.docSect1Type):
-
-    node_type = "docsect1"
-
-    def __init__(self, id=None, title='', para=None, sect2=None, internal=None, mixedclass_=None,
-                 content_=None):
-        supermod.docSect1Type.__init__(self, mixedclass_, content_)
-supermod.docSect1Type.subclass = docSect1TypeSub
-# end class docSect1TypeSub
-
-
-class docSect2TypeSub(supermod.docSect2Type):
-
-    node_type = "docsect2"
-
-    def __init__(self, id=None, title='', para=None, sect3=None, internal=None, mixedclass_=None,
-                 content_=None):
-        supermod.docSect2Type.__init__(self, mixedclass_, content_)
-supermod.docSect2Type.subclass = docSect2TypeSub
-# end class docSect2TypeSub
-
-
-class docSect3TypeSub(supermod.docSect3Type):
-
-    node_type = "docsect3"
-
-    def __init__(self, id=None, title='', para=None, sect4=None, internal=None, mixedclass_=None,
-                 content_=None):
-        supermod.docSect3Type.__init__(self, mixedclass_, content_)
-supermod.docSect3Type.subclass = docSect3TypeSub
-# end class docSect3TypeSub
-
-
-class docSect4TypeSub(supermod.docSect4Type):
-
-    node_type = "docsect4"
-
-    def __init__(self, id=None, title='', para=None, internal=None, mixedclass_=None,
-                 content_=None):
-        supermod.docSect4Type.__init__(self, mixedclass_, content_)
-supermod.docSect4Type.subclass = docSect4TypeSub
-# end class docSect4TypeSub
-
-
-class docInternalTypeSub(supermod.docInternalType):
-
-    node_type = "docinternal"
-
-    def __init__(self, para=None, sect1=None, mixedclass_=None, content_=None):
-        supermod.docInternalType.__init__(self, mixedclass_, content_)
-supermod.docInternalType.subclass = docInternalTypeSub
-# end class docInternalTypeSub
-
-
-class docInternalS1TypeSub(supermod.docInternalS1Type):
-
-    node_type = "docinternals1"
-
-    def __init__(self, para=None, sect2=None, mixedclass_=None, content_=None):
-        supermod.docInternalS1Type.__init__(self, mixedclass_, content_)
-supermod.docInternalS1Type.subclass = docInternalS1TypeSub
-# end class docInternalS1TypeSub
-
-
-class docInternalS2TypeSub(supermod.docInternalS2Type):
-
-    node_type = "docinternals2"
-
-    def __init__(self, para=None, sect3=None, mixedclass_=None, content_=None):
-        supermod.docInternalS2Type.__init__(self, mixedclass_, content_)
-supermod.docInternalS2Type.subclass = docInternalS2TypeSub
-# end class docInternalS2TypeSub
-
-
-class docInternalS3TypeSub(supermod.docInternalS3Type):
-
-    node_type = "docinternals3"
-
-    def __init__(self, para=None, sect3=None, mixedclass_=None, content_=None):
-        supermod.docInternalS3Type.__init__(self, mixedclass_, content_)
-supermod.docInternalS3Type.subclass = docInternalS3TypeSub
-# end class docInternalS3TypeSub
-
-
-class docInternalS4TypeSub(supermod.docInternalS4Type):
-
-    node_type = "docinternals4"
-
-    def __init__(self, para=None, mixedclass_=None, content_=None):
-        supermod.docInternalS4Type.__init__(self, mixedclass_, content_)
-supermod.docInternalS4Type.subclass = docInternalS4TypeSub
-# end class docInternalS4TypeSub
-
-
-class docURLLinkSub(supermod.docURLLink):
-
-    node_type = "docurllink"
-
-    def __init__(self, url=None, valueOf_='', mixedclass_=None, content_=None):
-        supermod.docURLLink.__init__(self, mixedclass_, content_)
-supermod.docURLLink.subclass = docURLLinkSub
-# end class docURLLinkSub
-
-
-class docAnchorTypeSub(supermod.docAnchorType):
-
-    node_type = "docanchor"
-
-    def __init__(self, id=None, valueOf_='', mixedclass_=None, content_=None):
-        supermod.docAnchorType.__init__(self, mixedclass_, content_)
-supermod.docAnchorType.subclass = docAnchorTypeSub
-# end class docAnchorTypeSub
-
-
-class docFormulaTypeSub(supermod.docFormulaType):
-
-    node_type = "docformula"
-
-    def __init__(self, id=None, valueOf_='', mixedclass_=None, content_=None):
-        supermod.docFormulaType.__init__(self, mixedclass_, content_)
-supermod.docFormulaType.subclass = docFormulaTypeSub
-# end class docFormulaTypeSub
-
-
-class docIndexEntryTypeSub(supermod.docIndexEntryType):
-
-    node_type = "docindexentry"
-
-    def __init__(self, primaryie='', secondaryie=''):
-        supermod.docIndexEntryType.__init__(self, primaryie, secondaryie)
-supermod.docIndexEntryType.subclass = docIndexEntryTypeSub
-# end class docIndexEntryTypeSub
-
-
-class docListTypeSub(supermod.docListType):
-
-    node_type = "doclist"
-
-    def __init__(self, listitem=None, subtype=""):
-        self.node_subtype = "itemized"
-        if subtype is not "":
-            self.node_subtype = subtype
-        supermod.docListType.__init__(self, listitem)
-supermod.docListType.subclass = docListTypeSub
-# end class docListTypeSub
-
-
-class docListItemTypeSub(supermod.docListItemType):
-
-    node_type = "doclistitem"
-
-    def __init__(self, para=None):
-        supermod.docListItemType.__init__(self, para)
-supermod.docListItemType.subclass = docListItemTypeSub
-# end class docListItemTypeSub
-
-
-class docSimpleSectTypeSub(supermod.docSimpleSectType):
-
-    node_type = "docsimplesect"
-
-    def __init__(self, kind=None, title=None, para=None):
-        supermod.docSimpleSectType.__init__(self, kind, title, para)
-supermod.docSimpleSectType.subclass = docSimpleSectTypeSub
-# end class docSimpleSectTypeSub
-
-
-class docVarListEntryTypeSub(supermod.docVarListEntryType):
-
-    node_type = "docvarlistentry"
-
-    def __init__(self, term=None):
-        supermod.docVarListEntryType.__init__(self, term)
-supermod.docVarListEntryType.subclass = docVarListEntryTypeSub
-# end class docVarListEntryTypeSub
-
-
-class docRefTextTypeSub(supermod.docRefTextType):
-
-    node_type = "docreftext"
-
-    def __init__(self, refid=None, kindref=None, external=None, valueOf_='', mixedclass_=None,
-                 content_=None):
-        supermod.docRefTextType.__init__(self, mixedclass_, content_)
-
-        self.para = []
-
-    def buildChildren(self, child_, nodeName_):
-        supermod.docRefTextType.buildChildren(self, child_, nodeName_)
-
-        if child_.nodeType == Node.ELEMENT_NODE and nodeName_ == 'para':
-            obj_ = supermod.docParaType.factory()
-            obj_.build(child_)
-            self.para.append(obj_)
-
-supermod.docRefTextType.subclass = docRefTextTypeSub
-# end class docRefTextTypeSub
-
-
-class docTableTypeSub(supermod.docTableType):
-
-    node_type = "doctable"
-
-    def __init__(self, rows=None, cols=None, row=None, caption=None):
-        supermod.docTableType.__init__(self, rows, cols, row, caption)
-supermod.docTableType.subclass = docTableTypeSub
-# end class docTableTypeSub
-
-
-class docRowTypeSub(supermod.docRowType):
-
-    node_type = "docrow"
-
-    def __init__(self, entry=None):
-        supermod.docRowType.__init__(self, entry)
-supermod.docRowType.subclass = docRowTypeSub
-# end class docRowTypeSub
-
-
-class docEntryTypeSub(supermod.docEntryType):
-
-    node_type = "docentry"
-
-    def __init__(self, thead=None, para=None):
-        supermod.docEntryType.__init__(self, thead, para)
-supermod.docEntryType.subclass = docEntryTypeSub
-# end class docEntryTypeSub
-
-
-class docHeadingTypeSub(supermod.docHeadingType):
-
-    node_type = "docheading"
-
-    def __init__(self, level=None, valueOf_='', mixedclass_=None, content_=None):
-        supermod.docHeadingType.__init__(self, mixedclass_, content_)
-
-    def buildChildren(self, child_, nodeName_):
-        supermod.docHeadingType.buildChildren(self, child_, nodeName_)
-
-        # Account for styled content in the heading. This might need to be expanded to include other
-        # nodes as it seems from the xsd that headings can have a lot of different children but we
-        # really don't expect most of them to come up.
-        if child_.nodeType == Node.ELEMENT_NODE and (
-                nodeName_ == 'bold' or
-                nodeName_ == 'emphasis' or
-                nodeName_ == 'computeroutput' or
-                nodeName_ == 'subscript' or
-                nodeName_ == 'superscript' or
-                nodeName_ == 'center' or
-                nodeName_ == 'small'):
-            obj_ = supermod.docMarkupType.factory()
-            obj_.build(child_)
-            obj_.type_ = nodeName_
-            self.content_.append(obj_)
-
-supermod.docHeadingType.subclass = docHeadingTypeSub
-# end class docHeadingTypeSub
-
-
-class docImageTypeSub(supermod.docImageType):
-
-    node_type = "docimage"
-
-    def __init__(self, width=None, type_=None, name=None, height=None, valueOf_='',
-                 mixedclass_=None, content_=None):
-        supermod.docImageType.__init__(self, mixedclass_, content_)
-supermod.docImageType.subclass = docImageTypeSub
-# end class docImageTypeSub
-
-
-class docDotFileTypeSub(supermod.docDotFileType):
-
-    node_type = "docdocfile"
-
-    def __init__(self, name=None, valueOf_='', mixedclass_=None, content_=None):
-        supermod.docDotFileType.__init__(self, mixedclass_, content_)
-supermod.docDotFileType.subclass = docDotFileTypeSub
-# end class docDotFileTypeSub
-
-
-class docTocItemTypeSub(supermod.docTocItemType):
-
-    node_type = "doctocitem"
-
-    def __init__(self, id=None, valueOf_='', mixedclass_=None, content_=None):
-        supermod.docTocItemType.__init__(self, mixedclass_, content_)
-supermod.docTocItemType.subclass = docTocItemTypeSub
-# end class docTocItemTypeSub
-
-
-class docTocListTypeSub(supermod.docTocListType):
-
-    node_type = "doctoclist"
-
-    def __init__(self, tocitem=None):
-        supermod.docTocListType.__init__(self, tocitem)
-supermod.docTocListType.subclass = docTocListTypeSub
-# end class docTocListTypeSub
-
-
-class docLanguageTypeSub(supermod.docLanguageType):
-
-    node_type = "doclanguage"
-
-    def __init__(self, langid=None, para=None):
-        supermod.docLanguageType.__init__(self, langid, para)
-supermod.docLanguageType.subclass = docLanguageTypeSub
-# end class docLanguageTypeSub
-
-
-class docParamListTypeSub(supermod.docParamListType):
-
-    node_type = "docparamlist"
-
-    def __init__(self, kind=None, parameteritem=None):
-        supermod.docParamListType.__init__(self, kind, parameteritem)
-supermod.docParamListType.subclass = docParamListTypeSub
-# end class docParamListTypeSub
-
-
-class docParamListItemSub(supermod.docParamListItem):
-
-    node_type = "docparamlistitem"
-
-    def __init__(self, parameternamelist=None, parameterdescription=None):
-        supermod.docParamListItem.__init__(self, parameternamelist, parameterdescription)
-supermod.docParamListItem.subclass = docParamListItemSub
-# end class docParamListItemSub
-
-
-class docParamNameListSub(supermod.docParamNameList):
-
-    node_type = "docparamnamelist"
-
-    def __init__(self, parametername=None):
-        supermod.docParamNameList.__init__(self, parametername)
-supermod.docParamNameList.subclass = docParamNameListSub
-# end class docParamNameListSub
-
-
-class docParamNameSub(supermod.docParamName):
-
-    node_type = "docparamname"
-
-    def __init__(self, direction=None, ref=None, mixedclass_=None, content_=None):
-        supermod.docParamName.__init__(self, mixedclass_, content_)
-supermod.docParamName.subclass = docParamNameSub
-# end class docParamNameSub
-
-
-class docXRefSectTypeSub(supermod.docXRefSectType):
-
-    node_type = "docxrefsect"
-
-    def __init__(self, id=None, xreftitle=None, xrefdescription=None):
-        supermod.docXRefSectType.__init__(self, id, xreftitle, xrefdescription)
-supermod.docXRefSectType.subclass = docXRefSectTypeSub
-# end class docXRefSectTypeSub
-
-
-class docCopyTypeSub(supermod.docCopyType):
-
-    node_type = "doccopy"
-
-    def __init__(self, link=None, para=None, sect1=None, internal=None):
-        supermod.docCopyType.__init__(self, link, para, sect1, internal)
-supermod.docCopyType.subclass = docCopyTypeSub
-# end class docCopyTypeSub
-
-
-class docCharTypeSub(supermod.docCharType):
-
-    node_type = "docchar"
-
-    def __init__(self, char=None, valueOf_=''):
-        supermod.docCharType.__init__(self, char)
-supermod.docCharType.subclass = docCharTypeSub
-# end class docCharTypeSub
-
-
-class verbatimTypeSub(object):
-    """
-    New node type. Structure is largely pillaged from other nodes in order to
-    match the set.
-    """
-
-    node_type = "verbatim"
-
-    def __init__(self, valueOf_='', mixedclass_=None, content_=None):
-        if mixedclass_ is None:
-            self.mixedclass_ = MixedContainer
-        else:
-            self.mixedclass_ = mixedclass_
-        if content_ is None:
-            self.content_ = []
-        else:
-            self.content_ = content_
-        self.text = ""
-
-    def factory(*args, **kwargs):
-        return verbatimTypeSub(*args, **kwargs)
-
-    factory = staticmethod(factory)
-
-    def buildAttributes(self, attrs):
-        pass
-
-    def build(self, node_):
-        attrs = node_.attributes
-        self.buildAttributes(attrs)
-        self.valueOf_ = ''
-        for child_ in node_.childNodes:
-            nodeName_ = child_.nodeName.split(':')[-1]
-            self.buildChildren(child_, nodeName_)
-
-    def buildChildren(self, child_, nodeName_):
-        if child_.nodeType == Node.TEXT_NODE:
-            self.text += child_.nodeValue
-
-
-class docParaTypeSub(supermod.docParaType):
-
-    node_type = "docpara"
-
-    def __init__(self, char=None, valueOf_=''):
-        supermod.docParaType.__init__(self, char)
-
-        self.parameterlist = []
-        self.simplesects = []
-        self.content = []
-        self.programlisting = []
-        self.images = []
-
-    def buildChildren(self, child_, nodeName_):
-        supermod.docParaType.buildChildren(self, child_, nodeName_)
-
-        if child_.nodeType == Node.TEXT_NODE:
-            obj_ = self.mixedclass_(MixedContainer.CategoryText,
-                                    MixedContainer.TypeNone, '', child_.nodeValue)
-            self.content.append(obj_)
-        elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == "ref":
-            obj_ = supermod.docRefTextType.factory()
-            obj_.build(child_)
-            self.content.append(obj_)
-        elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == 'parameterlist':
-            obj_ = supermod.docParamListType.factory()
-            obj_.build(child_)
-            self.parameterlist.append(obj_)
-        elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == 'simplesect':
-            obj_ = supermod.docSimpleSectType.factory()
-            obj_.build(child_)
-            self.simplesects.append(obj_)
-        elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == 'programlisting':
-            obj_ = supermod.listingType.factory()
-            obj_.build(child_)
-            self.programlisting.append(obj_)
-        elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == 'image':
-            obj_ = supermod.docImageType.factory()
-            obj_.build(child_)
-            self.images.append(obj_)
-        elif child_.nodeType == Node.ELEMENT_NODE and (
-                nodeName_ == 'bold' or
-                nodeName_ == 'emphasis' or
-                nodeName_ == 'computeroutput' or
-                nodeName_ == 'subscript' or
-                nodeName_ == 'superscript' or
-                nodeName_ == 'center' or
-                nodeName_ == 'small'):
-            obj_ = supermod.docMarkupType.factory()
-            obj_.build(child_)
-            obj_.type_ = nodeName_
-            self.content.append(obj_)
-        elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == 'verbatim':
-            childobj_ = verbatimTypeSub.factory()
-            childobj_.build(child_)
-            obj_ = self.mixedclass_(MixedContainer.CategoryComplex, MixedContainer.TypeNone,
-                                    'verbatim', childobj_)
-            self.content.append(obj_)
-        elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == 'formula':
-            childobj_ = docFormulaTypeSub.factory()
-            childobj_.build(child_)
-            obj_ = self.mixedclass_(MixedContainer.CategoryComplex, MixedContainer.TypeNone,
-                                    'formula', childobj_)
-            self.content.append(obj_)
-        elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == "itemizedlist":
-            obj_ = supermod.docListType.factory(subtype="itemized")
-            obj_.build(child_)
-            self.content.append(obj_)
-        elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == "orderedlist":
-            obj_ = supermod.docListType.factory(subtype="ordered")
-            obj_.build(child_)
-            self.content.append(obj_)
-        elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == 'heading':
-            obj_ = supermod.docHeadingType.factory()
-            obj_.build(child_)
-            self.content.append(obj_)
-        elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == 'ulink':
-            obj_ = supermod.docURLLink.factory()
-            obj_.build(child_)
-            self.content.append(obj_)
-
-supermod.docParaType.subclass = docParaTypeSub
-# end class docParaTypeSub
-
-
-class docMarkupTypeSub(supermod.docMarkupType):
-
-    node_type = "docmarkup"
-
-    def __init__(self, valueOf_='', mixedclass_=None, content_=None):
-        supermod.docMarkupType.__init__(self, valueOf_, mixedclass_, content_)
-        self.type_ = None
-
-    def buildChildren(self, child_, nodeName_):
-        if child_.nodeType == Node.TEXT_NODE:
-            obj_ = self.mixedclass_(MixedContainer.CategoryText, MixedContainer.TypeNone, '',
-                                    child_.nodeValue)
-            self.content_.append(obj_)
-        elif child_.nodeType == Node.ELEMENT_NODE and nodeName_ == 'ref':
-            childobj_ = supermod.docRefTextType.factory()
-            childobj_.build(child_)
-            obj_ = self.mixedclass_(MixedContainer.CategoryComplex, MixedContainer.TypeNone, 'ref',
-                                    childobj_)
-            self.content_.append(obj_)
-        if child_.nodeType == Node.TEXT_NODE:
-            self.valueOf_ += child_.nodeValue
-        elif child_.nodeType == Node.CDATA_SECTION_NODE:
-            self.valueOf_ += '![CDATA[' + child_.nodeValue + ']]'
-
-supermod.docMarkupType.subclass = docMarkupTypeSub
-# end class docMarkupTypeSub
-
-
-class docTitleTypeSub(supermod.docTitleType):
-
-    node_type = "doctitle"
-
-    def __init__(self, valueOf_='', mixedclass_=None, content_=None):
-        supermod.docTitleType.__init__(self, valueOf_, mixedclass_, content_)
-        self.type_ = None
-
-supermod.docTitleType.subclass = docTitleTypeSub
-# end class docTitleTypeSub
-
-
-class ParseError(Exception):
-    pass
-
-
-class FileIOError(Exception):
-    pass
-
-
-def parse(inFilename):
-
-    try:
-        doc = minidom.parse(inFilename)
-    except IOError as e:
-        raise FileIOError(e)
-    except ExpatError as e:
-        raise ParseError(e)
-
-    rootNode = doc.documentElement
-    rootObj = supermod.DoxygenType.factory()
-    rootObj.build(rootNode)
-    return rootObj
-
-

doc/breathe/parser/doxygen/index.py

@@ -1,63 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Generated Mon Feb  9 19:08:05 2009 by generateDS.py.
-"""
-
-from xml.dom import minidom
-from xml.parsers.expat import ExpatError
-
-
-from . import indexsuper as supermod
-
-class DoxygenTypeSub(supermod.DoxygenType):
-
-    node_type = "doxygen"
-
-    def __init__(self, version=None, compound=None):
-        supermod.DoxygenType.__init__(self, version, compound)
-supermod.DoxygenType.subclass = DoxygenTypeSub
-# end class DoxygenTypeSub
-
-
-class CompoundTypeSub(supermod.CompoundType):
-    
-    node_type = "compound"
-
-    def __init__(self, kind=None, refid=None, name='', member=None):
-        supermod.CompoundType.__init__(self, kind, refid, name, member)
-supermod.CompoundType.subclass = CompoundTypeSub
-# end class CompoundTypeSub
-
-
-class MemberTypeSub(supermod.MemberType):
-
-    node_type = "member"
-
-    def __init__(self, kind=None, refid=None, name=''):
-        supermod.MemberType.__init__(self, kind, refid, name)
-supermod.MemberType.subclass = MemberTypeSub
-# end class MemberTypeSub
-
-
-class ParseError(Exception):
-    pass
-
-class FileIOError(Exception):
-    pass
-
-def parse(inFilename):
-
-    try:
-        doc = minidom.parse(inFilename)
-    except IOError as e:
-        raise FileIOError(e)
-    except ExpatError as e:
-        raise ParseError(e)
-
-    rootNode = doc.documentElement
-    rootObj = supermod.DoxygenType.factory()
-    rootObj.build(rootNode)
-
-    return rootObj
-

doc/breathe/parser/doxygen/indexsuper.py

@@ -1,362 +0,0 @@
-#!/usr/bin/env python
-
-#
-# Generated Thu Jun 11 18:43:54 2009 by generateDS.py.
-#
-
-import sys
-import getopt
-from xml.dom import minidom
-from xml.dom import Node
-
-#
-# User methods
-#
-# Calls to the methods in these classes are generated by generateDS.py.
-# You can replace these methods by re-implementing the following class
-#   in a module named generatedssuper.py.
-
-try:
-    from generatedssuper import GeneratedsSuper
-except ImportError as exp:
-
-    class GeneratedsSuper:
-        def format_string(self, input_data, input_name=''):
-            return input_data
-        def format_integer(self, input_data, input_name=''):
-            return '%d' % input_data
-        def format_float(self, input_data, input_name=''):
-            return '%f' % input_data
-        def format_double(self, input_data, input_name=''):
-            return '%e' % input_data
-        def format_boolean(self, input_data, input_name=''):
-            return '%s' % input_data
-
-
-#
-# If you have installed IPython you can uncomment and use the following.
-# IPython is available from http://ipython.scipy.org/.
-#
-
-## from IPython.Shell import IPShellEmbed
-## args = ''
-## ipshell = IPShellEmbed(args,
-##     banner = 'Dropping into IPython',
-##     exit_msg = 'Leaving Interpreter, back to program.')
-
-# Then use the following line where and when you want to drop into the
-# IPython shell:
-#    ipshell('<some message> -- Entering ipshell.\nHit Ctrl-D to exit')
-
-#
-# Globals
-#
-
-ExternalEncoding = 'ascii'
-
-#
-# Support/utility functions.
-#
-
-def showIndent(outfile, level):
-    for idx in range(level):
-        outfile.write('    ')
-
-def quote_xml(inStr):
-    s1 = (isinstance(inStr, basestring) and inStr or
-          '%s' % inStr)
-    s1 = s1.replace('&', '&amp;')
-    s1 = s1.replace('<', '&lt;')
-    s1 = s1.replace('>', '&gt;')
-    return s1
-
-def quote_attrib(inStr):
-    s1 = (isinstance(inStr, basestring) and inStr or
-          '%s' % inStr)
-    s1 = s1.replace('&', '&amp;')
-    s1 = s1.replace('<', '&lt;')
-    s1 = s1.replace('>', '&gt;')
-    if '"' in s1:
-        if "'" in s1:
-            s1 = '"%s"' % s1.replace('"', "&quot;")
-        else:
-            s1 = "'%s'" % s1
-    else:
-        s1 = '"%s"' % s1
-    return s1
-
-def quote_python(inStr):
-    s1 = inStr
-    if s1.find("'") == -1:
-        if s1.find('\n') == -1:
-            return "'%s'" % s1
-        else:
-            return "'''%s'''" % s1
-    else:
-        if s1.find('"') != -1:
-            s1 = s1.replace('"', '\\"')
-        if s1.find('\n') == -1:
-            return '"%s"' % s1
-        else:
-            return '"""%s"""' % s1
-
-
-class MixedContainer:
-    # Constants for category:
-    CategoryNone = 0
-    CategoryText = 1
-    CategorySimple = 2
-    CategoryComplex = 3
-    # Constants for content_type:
-    TypeNone = 0
-    TypeText = 1
-    TypeString = 2
-    TypeInteger = 3
-    TypeFloat = 4
-    TypeDecimal = 5
-    TypeDouble = 6
-    TypeBoolean = 7
-    def __init__(self, category, content_type, name, value):
-        self.category = category
-        self.content_type = content_type
-        self.name = name
-        self.value = value
-    def getCategory(self):
-        return self.category
-    def getContenttype(self, content_type):
-        return self.content_type
-    def getValue(self):
-        return self.value
-    def getName(self):
-        return self.name
-
-
-class _MemberSpec(object):
-    def __init__(self, name='', data_type='', container=0):
-        self.name = name
-        self.data_type = data_type
-        self.container = container
-    def set_name(self, name): self.name = name
-    def get_name(self): return self.name
-    def set_data_type(self, data_type): self.data_type = data_type
-    def get_data_type(self): return self.data_type
-    def set_container(self, container): self.container = container
-    def get_container(self): return self.container
-
-
-#
-# Data representation classes.
-#
-
-class DoxygenType(GeneratedsSuper):
-    subclass = None
-    superclass = None
-    def __init__(self, version=None, compound=None):
-        self.version = version
-        if compound is None:
-            self.compound = []
-        else:
-            self.compound = compound
-    def factory(*args_, **kwargs_):
-        if DoxygenType.subclass:
-            return DoxygenType.subclass(*args_, **kwargs_)
-        else:
-            return DoxygenType(*args_, **kwargs_)
-    factory = staticmethod(factory)
-    def get_compound(self): return self.compound
-    def set_compound(self, compound): self.compound = compound
-    def add_compound(self, value): self.compound.append(value)
-    def insert_compound(self, index, value): self.compound[index] = value
-    def get_version(self): return self.version
-    def set_version(self, version): self.version = version
-    def hasContent_(self):
-        if (
-            self.compound is not None
-            ):
-            return True
-        else:
-            return False
-    def build(self, node_):
-        attrs = node_.attributes
-        self.buildAttributes(attrs)
-        for child_ in node_.childNodes:
-            nodeName_ = child_.nodeName.split(':')[-1]
-            self.buildChildren(child_, nodeName_)
-    def buildAttributes(self, attrs):
-        if attrs.get('version'):
-            self.version = attrs.get('version').value
-    def buildChildren(self, child_, nodeName_):
-        if child_.nodeType == Node.ELEMENT_NODE and \
-            nodeName_ == 'compound':
-            obj_ = CompoundType.factory()
-            obj_.build(child_)
-            self.compound.append(obj_)
-# end class DoxygenType
-
-
-class CompoundType(GeneratedsSuper):
-    subclass = None
-    superclass = None
-    def __init__(self, kind=None, refid=None, name=None, member=None):
-        self.kind = kind
-        self.refid = refid
-        self.name = name
-        if member is None:
-            self.member = []
-        else:
-            self.member = member
-    def factory(*args_, **kwargs_):
-        if CompoundType.subclass:
-            return CompoundType.subclass(*args_, **kwargs_)
-        else:
-            return CompoundType(*args_, **kwargs_)
-    factory = staticmethod(factory)
-    def get_name(self): return self.name
-    def set_name(self, name): self.name = name
-    def get_member(self): return self.member
-    def set_member(self, member): self.member = member
-    def add_member(self, value): self.member.append(value)
-    def insert_member(self, index, value): self.member[index] = value
-    def get_kind(self): return self.kind
-    def set_kind(self, kind): self.kind = kind
-    def get_refid(self): return self.refid
-    def set_refid(self, refid): self.refid = refid
-    def build(self, node_):
-        attrs = node_.attributes
-        self.buildAttributes(attrs)
-        for child_ in node_.childNodes:
-            nodeName_ = child_.nodeName.split(':')[-1]
-            self.buildChildren(child_, nodeName_)
-    def buildAttributes(self, attrs):
-        if attrs.get('kind'):
-            self.kind = attrs.get('kind').value
-        if attrs.get('refid'):
-            self.refid = attrs.get('refid').value
-    def buildChildren(self, child_, nodeName_):
-        if child_.nodeType == Node.ELEMENT_NODE and \
-            nodeName_ == 'name':
-            name_ = ''
-            for text__content_ in child_.childNodes:
-                name_ += text__content_.nodeValue
-            self.name = name_
-        elif child_.nodeType == Node.ELEMENT_NODE and \
-            nodeName_ == 'member':
-            obj_ = MemberType.factory()
-            obj_.build(child_)
-            self.member.append(obj_)
-# end class CompoundType
-
-
-class MemberType(GeneratedsSuper):
-    subclass = None
-    superclass = None
-    def __init__(self, kind=None, refid=None, name=None):
-        self.kind = kind
-        self.refid = refid
-        self.name = name
-    def factory(*args_, **kwargs_):
-        if MemberType.subclass:
-            return MemberType.subclass(*args_, **kwargs_)
-        else:
-            return MemberType(*args_, **kwargs_)
-    factory = staticmethod(factory)
-    def get_name(self): return self.name
-    def set_name(self, name): self.name = name
-    def get_kind(self): return self.kind
-    def set_kind(self, kind): self.kind = kind
-    def get_refid(self): return self.refid
-    def set_refid(self, refid): self.refid = refid
-    def hasContent_(self):
-        if (
-            self.name is not None
-            ):
-            return True
-        else:
-            return False
-    def build(self, node_):
-        attrs = node_.attributes
-        self.buildAttributes(attrs)
-        for child_ in node_.childNodes:
-            nodeName_ = child_.nodeName.split(':')[-1]
-            self.buildChildren(child_, nodeName_)
-    def buildAttributes(self, attrs):
-        if attrs.get('kind'):
-            self.kind = attrs.get('kind').value
-        if attrs.get('refid'):
-            self.refid = attrs.get('refid').value
-    def buildChildren(self, child_, nodeName_):
-        if child_.nodeType == Node.ELEMENT_NODE and \
-            nodeName_ == 'name':
-            name_ = ''
-            for text__content_ in child_.childNodes:
-                name_ += text__content_.nodeValue
-            self.name = name_
-# end class MemberType
-
-
-USAGE_TEXT = """
-Usage: python <Parser>.py [ -s ] <in_xml_file>
-Options:
-    -s        Use the SAX parser, not the minidom parser.
-"""
-
-def usage():
-    print(USAGE_TEXT)
-    sys.exit(1)
-
-
-def parse(inFileName):
-    doc = minidom.parse(inFileName)
-    rootNode = doc.documentElement
-    rootObj = DoxygenType.factory()
-    rootObj.build(rootNode)
-    # Enable Python to collect the space used by the DOM.
-    doc = None
-    sys.stdout.write('<?xml version="1.0" ?>\n')
-    rootObj.export(sys.stdout, 0, name_="doxygenindex",
-        namespacedef_='')
-    return rootObj
-
-
-def parseString(inString):
-    doc = minidom.parseString(inString)
-    rootNode = doc.documentElement
-    rootObj = DoxygenType.factory()
-    rootObj.build(rootNode)
-    # Enable Python to collect the space used by the DOM.
-    doc = None
-    sys.stdout.write('<?xml version="1.0" ?>\n')
-    rootObj.export(sys.stdout, 0, name_="doxygenindex",
-        namespacedef_='')
-    return rootObj
-
-
-def parseLiteral(inFileName):
-    doc = minidom.parse(inFileName)
-    rootNode = doc.documentElement
-    rootObj = DoxygenType.factory()
-    rootObj.build(rootNode)
-    # Enable Python to collect the space used by the DOM.
-    doc = None
-    sys.stdout.write('from index import *\n\n')
-    sys.stdout.write('rootObj = doxygenindex(\n')
-    rootObj.exportLiteral(sys.stdout, 0, name_="doxygenindex")
-    sys.stdout.write(')\n')
-    return rootObj
-
-
-def main():
-    args = sys.argv[1:]
-    if len(args) == 1:
-        parse(args[0])
-    else:
-        usage()
-
-
-
-
-if __name__ == '__main__':
-    main()
-    #import pdb
-    #pdb.run('main()')
-

doc/breathe/process.py

@@ -1,87 +0,0 @@
-
-AUTOCFG_TEMPLATE = r"""
-PROJECT_NAME     = "{project_name}"
-OUTPUT_DIRECTORY = {output_dir}
-GENERATE_LATEX   = NO
-GENERATE_MAN     = NO
-GENERATE_RTF     = NO
-CASE_SENSE_NAMES = NO
-INPUT            = {input}
-ENABLE_PREPROCESSING = YES
-QUIET            = YES
-JAVADOC_AUTOBRIEF = YES
-JAVADOC_AUTOBRIEF = NO
-GENERATE_HTML = NO
-GENERATE_XML = YES
-ALIASES = "rst=\verbatim embed:rst"
-ALIASES += "endrst=\endverbatim"
-""".strip()
-
-
-class ProjectData(object):
-    "Simple handler for the files and project_info for each project"
-
-    def __init__(self, auto_project_info, files):
-
-        self.auto_project_info = auto_project_info
-        self.files = files
-
-
-class AutoDoxygenProcessHandle(object):
-
-    def __init__(self, path_handler, run_process, write_file, project_info_factory):
-
-        self.path_handler = path_handler
-        self.run_process = run_process
-        self.write_file = write_file
-        self.project_info_factory = project_info_factory
-
-    def generate_xml(self, app):
-
-        project_files = {}
-
-        # First collect together all the files which need to be doxygen processed for each project
-        for project_name, file_structure in app.config.breathe_projects_source.items():
-
-            folder = file_structure[0]
-            contents = file_structure[1]
-
-            auto_project_info = self.project_info_factory.create_auto_project_info(
-                project_name, folder)
-
-            project_files[project_name] = ProjectData(auto_project_info, contents)
-
-        # Iterate over the projects and generate doxygen xml output for the files for each one into
-        # a directory in the Sphinx build area
-        for project_name, data in project_files.items():
-
-            project_path = self.process(data.auto_project_info, data.files)
-
-            project_info = data.auto_project_info.create_project_info(project_path)
-
-            self.project_info_factory.store_project_info_for_auto(project_name, project_info)
-
-    def process(self, auto_project_info, files):
-
-        name = auto_project_info.name()
-        cfgfile = "%s.cfg" % name
-
-        full_paths = map(lambda x: auto_project_info.abs_path_to_source_file(x), files)
-
-        cfg = AUTOCFG_TEMPLATE.format(
-            project_name=name,
-            output_dir=name,
-            input=" ".join(full_paths)
-            )
-
-        build_dir = self.path_handler.join(
-            auto_project_info.build_dir(),
-            "breathe",
-            "doxygen"
-            )
-
-        self.write_file(build_dir, cfgfile, cfg)
-
-        self.run_process(['doxygen', cfgfile], cwd=build_dir)
-
-        return self.path_handler.join(build_dir, name, "xml")

doc/breathe/project.py

@@ -1,306 +0,0 @@
-
-from .exception import BreatheError
-
-import os
-
-
-class ProjectError(BreatheError):
-    pass
-
-
-class NoDefaultProjectError(ProjectError):
-    pass
-
-
-class AutoProjectInfo(object):
-    """Created as a temporary step in the automatic xml generation process"""
-
-    def __init__(
-            self,
-            name,
-            source_path,
-            build_dir,
-            reference,
-            source_dir,
-            config_dir,
-            domain_by_extension,
-            domain_by_file_pattern,
-            match
-            ):
-
-        self._name = name
-        self._source_path = source_path
-        self._build_dir = build_dir
-        self._reference = reference
-        self._source_dir = source_dir
-        self._config_dir = config_dir
-        self._domain_by_extension = domain_by_extension
-        self._domain_by_file_pattern = domain_by_file_pattern
-        self._match = match
-
-    def name(self):
-        return self._name
-
-    def build_dir(self):
-        return self._build_dir
-
-    def abs_path_to_source_file(self, file_):
-        """
-        Returns full path to the provide file assuming that the provided path is relative to the
-        projects conf.py directory as specified in the breathe_projects_source config variable.
-        """
-
-        # os.path.join does the appropriate handling if _source_path is an absolute path
-        return os.path.join(self._config_dir, self._source_path, file_)
-
-    def create_project_info(self, project_path):
-        """Creates a proper ProjectInfo object based on the information in this AutoProjectInfo"""
-
-        return ProjectInfo(
-            self._name,
-            project_path,
-            self._source_path,
-            self._reference,
-            self._source_dir,
-            self._config_dir,
-            self._domain_by_extension,
-            self._domain_by_file_pattern,
-            self._match
-            )
-
-
-class ProjectInfo(object):
-
-    def __init__(
-            self,
-            name,
-            path,
-            source_path,
-            reference,
-            source_dir,
-            config_dir,
-            domain_by_extension,
-            domain_by_file_pattern,
-            match
-            ):
-
-        self._name = name
-        self._project_path = path
-        self._source_path = source_path
-        self._reference = reference
-        self._source_dir = source_dir
-        self._config_dir = config_dir
-        self._domain_by_extension = domain_by_extension
-        self._domain_by_file_pattern = domain_by_file_pattern
-        self._match = match
-
-    def name(self):
-        return self._name
-
-    def project_path(self):
-        return self._project_path
-
-    def source_path(self):
-        return self._source_path
-
-    def relative_path_to_xml_file(self, file_):
-        """
-        Returns relative path from Sphinx documentation top-level source directory to the specified
-        file assuming that the specified file is a path relative to the doxygen xml output
-        directory.
-        """
-
-        # os.path.join does the appropriate handling if _project_path is an absolute path
-        full_xml_project_path = os.path.join(self._config_dir, self._project_path, file_)
-
-        return os.path.relpath(
-            full_xml_project_path,
-            self._source_dir
-        )
-
-    def sphinx_abs_path_to_file(self, file_):
-        """
-        Prepends os.path.sep to the value returned by relative_path_to_file.
-
-        This is to match Sphinx's concept of an absolute path which starts from the top-level source
-        directory of the project.
-        """
-        return os.path.sep + self.relative_path_to_xml_file(file_)
-
-    def reference(self):
-        return self._reference
-
-    def domain_for_file(self, file_):
-
-        domain = ""
-        extension = file_.split(".")[-1]
-
-        try:
-            domain = self._domain_by_extension[extension]
-        except KeyError:
-            pass
-
-        for pattern, pattern_domain in self._domain_by_file_pattern.items():
-            if self._match(file_, pattern):
-                domain = pattern_domain
-
-        return domain
-
-
-class ProjectInfoFactory(object):
-
-    def __init__(self, source_dir, build_dir, config_dir, match):
-
-        self.source_dir = source_dir
-        self.build_dir = build_dir
-        self.config_dir = config_dir
-        self.match = match
-
-        self.projects = {}
-        self.default_project = None
-        self.domain_by_extension = {}
-        self.domain_by_file_pattern = {}
-
-        self.project_count = 0
-        self.project_info_store = {}
-        self.project_info_for_auto_store = {}
-        self.auto_project_info_store = {}
-
-    def update(
-            self,
-            projects,
-            default_project,
-            domain_by_extension,
-            domain_by_file_pattern,
-            projects_source,
-            build_dir
-            ):
-
-        self.projects = projects
-        self.default_project = default_project
-        self.domain_by_extension = domain_by_extension
-        self.domain_by_file_pattern = domain_by_file_pattern
-        self.projects_source = projects_source
-
-        # If the breathe config values has a non-empty value for build_dir then use that otherwise
-        # stick with the default
-        if build_dir:
-            self.build_dir = build_dir
-
-    def default_path(self):
-
-        if not self.default_project:
-            raise NoDefaultProjectError(
-                "No breathe_default_project config setting to fall back on "
-                "for directive with no 'project' or 'path' specified."
-            )
-
-        try:
-            return self.projects[self.default_project]
-        except KeyError:
-            raise ProjectError(
-                ("breathe_default_project value '%s' does not seem to be a valid key for the "
-                 "breathe_projects dictionary") % self.default_project
-            )
-
-    def create_project_info(self, options):
-
-        name = ""
-
-        if "project" in options:
-            try:
-                path = self.projects[options["project"]]
-                name = options["project"]
-            except KeyError:
-                raise ProjectError("Unable to find project '%s' in breathe_projects dictionary"
-                                   % options["project"])
-
-        elif "path" in options:
-            path = options["path"]
-
-        else:
-            path = self.default_path()
-
-        try:
-            return self.project_info_store[path]
-        except KeyError:
-
-            reference = name
-
-            if not name:
-                name = "project%s" % self.project_count
-                reference = path
-                self.project_count += 1
-
-            project_info = ProjectInfo(
-                name,
-                path,
-                "NoSourcePath",
-                reference,
-                self.source_dir,
-                self.config_dir,
-                self.domain_by_extension,
-                self.domain_by_file_pattern,
-                self.match
-            )
-
-            self.project_info_store[path] = project_info
-
-            return project_info
-
-    def store_project_info_for_auto(self, name, project_info):
-        """Stores the project info by name for later extraction by the auto directives.
-
-        Stored separately to the non-auto project info objects as they should never overlap.
-        """
-
-        self.project_info_for_auto_store[name] = project_info
-
-    def retrieve_project_info_for_auto(self, options):
-        """Retrieves the project info by name for later extraction by the auto directives.
-
-        Looks for the 'project' entry in the options dictionary. This is a less than ideal API but
-        it is designed to match the use of 'create_project_info' above for which it makes much more
-        sense.
-        """
-
-        name = options.get('project', self.default_project)
-
-        if name is None:
-            raise NoDefaultProjectError(
-                "No breathe_default_project config setting to fall back on "
-                "for directive with no 'project' or 'path' specified."
-            )
-
-        return self.project_info_for_auto_store[name]
-
-    def create_auto_project_info(self, name, source_path):
-
-        key = source_path
-
-        try:
-            return self.auto_project_info_store[key]
-        except KeyError:
-
-            reference = name
-
-            if not name:
-                name = "project%s" % self.project_count
-                reference = source_path
-                self.project_count += 1
-
-            auto_project_info = AutoProjectInfo(
-                name,
-                source_path,
-                self.build_dir,
-                reference,
-                self.source_dir,
-                self.config_dir,
-                self.domain_by_extension,
-                self.domain_by_file_pattern,
-                self.match
-            )
-
-            self.auto_project_info_store[key] = auto_project_info
-
-            return auto_project_info

doc/breathe/renderer/rst/__init__.py

@@ -1,2 +0,0 @@
-
-

doc/breathe/renderer/rst/doxygen/__init__.py

@@ -1,383 +0,0 @@
-
-from .base import Renderer, RenderContext
-from . import index as indexrenderer
-from . import compound as compoundrenderer
-
-from docutils import nodes
-import textwrap
-
-class RstContentCreator(object):
-
-    def __init__(self, list_type, dedent):
-
-        self.list_type = list_type
-        self.dedent = dedent
-
-    def __call__(self, text):
-
-        # Remove the first line which is "embed:rst[:leading-asterisk]"
-        text = "\n".join(text.split(u"\n")[1:])
-
-        # Remove starting whitespace
-        text = self.dedent(text)
-
-        # Inspired by autodoc.py in Sphinx
-        result = self.list_type()
-        for line in text.split("\n"):
-            result.append(line, "<breathe>")
-
-        return result
-
-class UnicodeRenderer(Renderer):
-
-    def render(self):
-
-        # Skip any nodes that are pure whitespace
-        # Probably need a better way to do this as currently we're only doing
-        # it skip whitespace between higher-level nodes, but this will also
-        # skip any pure whitespace entries in actual content nodes
-        #
-        # We counter that second issue slightly by allowing through single white spaces
-        #
-        if self.data_object.strip():
-            return [self.node_factory.Text(self.data_object)]
-        elif self.data_object == unicode(" "):
-            return [self.node_factory.Text(self.data_object)]
-        else:
-            return []
-
-class NullRenderer(Renderer):
-
-    def __init__(self):
-        pass
-
-    def render(self):
-        return []
-
-
-class DoxygenToRstRendererFactory(object):
-
-    def __init__(
-            self,
-            node_type,
-            renderers,
-            renderer_factory_creator,
-            node_factory,
-            project_info,
-            state,
-            document,
-            rst_content_creator,
-            filter_,
-            target_handler,
-            domain_directive_factory
-            ):
-
-        self.node_type = node_type
-        self.node_factory = node_factory
-        self.project_info = project_info
-        self.renderers = renderers
-        self.renderer_factory_creator = renderer_factory_creator
-        self.state = state
-        self.document = document
-        self.rst_content_creator = rst_content_creator
-        self.filter_ = filter_
-        self.target_handler = target_handler
-        self.domain_directive_factory = domain_directive_factory
-
-    def create_renderer(
-            self,
-            context
-            ):
-
-        parent_data_object = context.node_stack[1]
-        data_object = context.node_stack[0]
-
-        if not self.filter_.allow(context.node_stack):
-            return NullRenderer()
-
-        child_renderer_factory = self.renderer_factory_creator.create_child_factory(
-                self.project_info,
-                data_object,
-                self
-                )
-
-        try:
-            node_type = data_object.node_type
-        except AttributeError as e:
-
-            # Horrible hack to silence errors on filtering unicode objects
-            # until we fix the parsing
-            if type(data_object) == unicode:
-                node_type = "unicode"
-            else:
-                raise e
-
-        Renderer = self.renderers[node_type]
-
-        common_args = [
-                self.project_info,
-                context,
-                child_renderer_factory,
-                self.node_factory,
-                self.state,
-                self.document,
-                self.target_handler,
-                self.domain_directive_factory
-                ]
-
-        if node_type == "docmarkup":
-
-            creator = self.node_factory.inline
-            if data_object.type_ == "emphasis":
-                creator = self.node_factory.emphasis
-            elif data_object.type_ == "computeroutput":
-                creator = self.node_factory.literal
-            elif data_object.type_ == "bold":
-                creator = self.node_factory.strong
-            elif data_object.type_ == "superscript":
-                creator = self.node_factory.superscript
-            elif data_object.type_ == "subscript":
-                creator = self.node_factory.subscript
-            elif data_object.type_ == "center":
-                print("Warning: does not currently handle 'center' text display")
-            elif data_object.type_ == "small":
-                print("Warning: does not currently handle 'small' text display")
-
-            return Renderer(
-                    creator,
-                    *common_args
-                    )
-
-        if node_type == "verbatim":
-
-            return Renderer(
-                    self.rst_content_creator,
-                    *common_args
-                    )
-
-        if node_type == "compound":
-
-            kind = data_object.kind
-            if kind in ["file", "dir", "page", "example", "group"]:
-                return Renderer(indexrenderer.FileRenderer, *common_args)
-
-            class_ = indexrenderer.CompoundTypeSubRenderer
-
-            # For compound node types Renderer is CreateCompoundTypeSubRenderer
-            # as defined below. This could be cleaner
-            return Renderer(
-                    class_,
-                    *common_args
-                    )
-
-        if node_type == "memberdef":
-
-            if data_object.kind in ("function", "slot") or (data_object.kind == 'friend' and data_object.argsstring):
-                Renderer = compoundrenderer.FuncMemberDefTypeSubRenderer
-            elif data_object.kind == "enum":
-                Renderer = compoundrenderer.EnumMemberDefTypeSubRenderer
-            elif data_object.kind == "typedef":
-                Renderer = compoundrenderer.TypedefMemberDefTypeSubRenderer
-            elif data_object.kind == "variable":
-                Renderer = compoundrenderer.VariableMemberDefTypeSubRenderer
-            elif data_object.kind == "define":
-                Renderer = compoundrenderer.DefineMemberDefTypeSubRenderer
-
-        if node_type == "param":
-            return Renderer(
-                    parent_data_object.node_type != "templateparamlist", 
-                    *common_args
-                    )
-
-        if node_type == "docsimplesect":
-            if data_object.kind == "par":
-                Renderer = compoundrenderer.ParDocSimpleSectTypeSubRenderer
-
-        return Renderer(
-                *common_args
-                )
-
-class CreateCompoundTypeSubRenderer(object):
-
-    def __init__(self, parser_factory):
-
-        self.parser_factory = parser_factory
-
-    def __call__(self, class_, project_info, *args):
-
-        compound_parser = self.parser_factory.create_compound_parser(project_info)
-        return class_(compound_parser, project_info, *args)
-
-
-class CreateRefTypeSubRenderer(object):
-
-    def __init__(self, parser_factory):
-
-        self.parser_factory = parser_factory
-
-    def __call__(self, project_info, *args):
-
-        compound_parser = self.parser_factory.create_compound_parser(project_info)
-        return compoundrenderer.RefTypeSubRenderer(compound_parser, project_info, *args)
-
-
-class DoxygenToRstRendererFactoryCreator(object):
-
-    def __init__(
-            self,
-            node_factory,
-            parser_factory,
-            domain_directive_factory,
-            rst_content_creator,
-            project_info
-            ):
-
-        self.node_factory = node_factory
-        self.parser_factory = parser_factory
-        self.domain_directive_factory = domain_directive_factory
-        self.rst_content_creator = rst_content_creator
-        self.project_info = project_info
-
-    def create_factory(self, node_stack, state, document, filter_, target_handler):
-
-        data_object = node_stack[0]
-
-        renderers = {
-            "doxygen" : indexrenderer.DoxygenTypeSubRenderer,
-            "compound" : CreateCompoundTypeSubRenderer(self.parser_factory),
-            "doxygendef" : compoundrenderer.DoxygenTypeSubRenderer,
-            "compounddef" : compoundrenderer.CompoundDefTypeSubRenderer,
-            "sectiondef" : compoundrenderer.SectionDefTypeSubRenderer,
-            "memberdef" : compoundrenderer.MemberDefTypeSubRenderer,
-            "enumvalue" : compoundrenderer.EnumvalueTypeSubRenderer,
-            "linkedtext" : compoundrenderer.LinkedTextTypeSubRenderer,
-            "description" : compoundrenderer.DescriptionTypeSubRenderer,
-            "param" : compoundrenderer.ParamTypeSubRenderer,
-            "docreftext" : compoundrenderer.DocRefTextTypeSubRenderer,
-            "docheading" : compoundrenderer.DocHeadingTypeSubRenderer,
-            "docpara" : compoundrenderer.DocParaTypeSubRenderer,
-            "docmarkup" : compoundrenderer.DocMarkupTypeSubRenderer,
-            "docparamlist" : compoundrenderer.DocParamListTypeSubRenderer,
-            "docparamlistitem" : compoundrenderer.DocParamListItemSubRenderer,
-            "docparamnamelist" : compoundrenderer.DocParamNameListSubRenderer,
-            "docparamname" : compoundrenderer.DocParamNameSubRenderer,
-            "docsect1" : compoundrenderer.DocSect1TypeSubRenderer,
-            "docsimplesect" : compoundrenderer.DocSimpleSectTypeSubRenderer,
-            "doctitle" : compoundrenderer.DocTitleTypeSubRenderer,
-            "docformula" : compoundrenderer.DocForumlaTypeSubRenderer,
-            "docimage" : compoundrenderer.DocImageTypeSubRenderer,
-            "docurllink" : compoundrenderer.DocURLLinkSubRenderer,
-            "listing" : compoundrenderer.ListingTypeSubRenderer,
-            "codeline" : compoundrenderer.CodeLineTypeSubRenderer,
-            "highlight" : compoundrenderer.HighlightTypeSubRenderer,
-            "templateparamlist" : compoundrenderer.TemplateParamListRenderer,
-            "inc" : compoundrenderer.IncTypeSubRenderer,
-            "ref" : CreateRefTypeSubRenderer(self.parser_factory),
-            "verbatim" : compoundrenderer.VerbatimTypeSubRenderer,
-            "mixedcontainer" : compoundrenderer.MixedContainerRenderer,
-            "unicode" : UnicodeRenderer,
-            "doclist": compoundrenderer.DocListTypeSubRenderer,
-            "doclistitem": compoundrenderer.DocListItemTypeSubRenderer,
-            }
-
-        try:
-            node_type = data_object.node_type
-        except AttributeError as e:
-
-            # Horrible hack to silence errors on filtering unicode objects
-            # until we fix the parsing
-            if type(data_object) == unicode:
-                node_type = "unicode"
-            else:
-                raise e
-
-        return DoxygenToRstRendererFactory(
-                "root",
-                renderers,
-                self,
-                self.node_factory,
-                self.project_info,
-                state,
-                document,
-                self.rst_content_creator,
-                filter_,
-                target_handler,
-                self.domain_directive_factory
-                )
-
-    def create_child_factory( self, project_info, data_object, parent_renderer_factory ):
-
-        try:
-            node_type = data_object.node_type
-        except AttributeError as e:
-
-            # Horrible hack to silence errors on filtering unicode objects
-            # until we fix the parsing
-            if type(data_object) == unicode:
-                node_type = "unicode"
-            else:
-                raise e
-
-        return DoxygenToRstRendererFactory(
-                    node_type,
-                    parent_renderer_factory.renderers,
-                    self,
-                    self.node_factory,
-                    parent_renderer_factory.project_info,
-                    parent_renderer_factory.state,
-                    parent_renderer_factory.document,
-                    self.rst_content_creator,
-                    parent_renderer_factory.filter_,
-                    parent_renderer_factory.target_handler,
-                    parent_renderer_factory.domain_directive_factory
-                    )
-
-
-# FactoryFactoryFactory. Ridiculous but necessary.
-class DoxygenToRstRendererFactoryCreatorConstructor(object):
-
-    def __init__(
-            self,
-            node_factory,
-            parser_factory,
-            domain_directive_factory,
-            rst_content_creator
-            ):
-
-        self.node_factory = node_factory
-        self.parser_factory = parser_factory
-        self.domain_directive_factory = domain_directive_factory
-        self.rst_content_creator = rst_content_creator
-
-    def create_factory_creator(self, project_info, document, options, target_handler):
-
-        return DoxygenToRstRendererFactoryCreator(
-                self.node_factory,
-                self.parser_factory,
-                self.domain_directive_factory,
-                self.rst_content_creator,
-                project_info,
-                )
-
-
-def format_parser_error(name, error, filename, state, lineno, do_unicode_warning):
-
-    warning = '%s: Unable to parse xml file "%s". ' % (name, filename)
-    explanation = 'Reported error: %s. ' % error
-
-    unicode_explanation_text = ""
-    unicode_explanation = []
-    if do_unicode_warning:
-        unicode_explanation_text = textwrap.dedent("""
-        Parsing errors are often due to unicode errors associated with the encoding of the original
-        source files. Doxygen propagates invalid characters from the input source files to the
-        output xml.""").strip().replace("\n", " ")
-        unicode_explanation = [nodes.paragraph("", "", nodes.Text(unicode_explanation_text))]
-
-    return [nodes.warning("",
-                nodes.paragraph("", "", nodes.Text(warning)),
-                nodes.paragraph("", "", nodes.Text(explanation)),
-                *unicode_explanation
-                ),
-            state.document.reporter.warning(warning + explanation + unicode_explanation_text, line=lineno)
-            ]

doc/breathe/renderer/rst/doxygen/base.py

@@ -1,127 +0,0 @@
-
-class Renderer(object):
-
-    def __init__(self,
-            project_info,
-            context,
-            renderer_factory,
-            node_factory,
-            state,
-            document,
-            target_handler,
-            domain_directive_factory,
-            ):
-
-        self.project_info = project_info
-        self.context = context
-        self.data_object = context.node_stack[0]
-        self.renderer_factory = renderer_factory
-        self.node_factory = node_factory
-        self.state = state
-        self.document = document
-        self.target_handler = target_handler
-        self.domain_directive_factory = domain_directive_factory
-
-        if self.context.domain == '':
-            self.context.domain = self.get_domain()
-
-    def get_domain(self):
-        """Returns the domain for the current node."""
-
-        def get_filename(node):
-            """Returns the name of a file where the declaration represented by node is located."""
-            try:
-                return node.location.file
-            except AttributeError:
-                return None
-
-        node_stack = self.context.node_stack
-        node = node_stack[0]
-        # An enumvalue node doesn't have location, so use its parent node for detecting the domain instead.
-        if type(node) == unicode or node.node_type == "enumvalue":
-            node = node_stack[1]
-        filename = get_filename(node)
-        if not filename and node.node_type == "compound":
-            file_data = self.compound_parser.parse(node.refid)
-            filename = get_filename(file_data.compounddef)
-        return self.project_info.domain_for_file(filename) if filename else ''
-
-    def get_fully_qualified_name(self):
-
-        names = []
-        node_stack = self.context.node_stack
-        node = node_stack[0]
-        if node.node_type == 'enumvalue':
-            names.append(node.name)
-            # Skip the name of the containing enum because it is not a part of the fully qualified name.
-            node_stack = node_stack[2:]
-
-        # If the node is a namespace, use its name because namespaces are skipped in the main loop.
-        if node.node_type == 'compound' and node.kind == 'namespace':
-            names.append(node.name)
-
-        for node in node_stack:
-            if node.node_type == 'ref' and len(names) == 0:
-                return node.valueOf_
-            if (node.node_type == 'compound' and node.kind not in ['file', 'namespace']) or \
-                node.node_type == 'memberdef':
-                # We skip the 'file' entries because the file name doesn't form part of the
-                # qualified name for the identifier. We skip the 'namespace' entries because if we
-                # find an object through the namespace 'compound' entry in the index.xml then we'll
-                # also have the 'compounddef' entry in our node stack and we'll get it from that. We
-                # need the 'compounddef' entry because if we find the object through the 'file'
-                # entry in the index.xml file then we need to get the namespace name from somewhere
-                names.insert(0, node.name)
-            if (node.node_type == 'compounddef' and node.kind == 'namespace'):
-                # Nested namespaces include their parent namespace(s) in compoundname. ie,
-                # compoundname is 'foo::bar' instead of just 'bar' for namespace 'bar' nested in
-                # namespace 'foo'. We need full compoundname because node_stack doesn't necessarily
-                # include parent namespaces and we stop here in case it does.
-                names.insert(0, node.compoundname)
-                break
-
-        return '::'.join(names)
-
-    def create_template_node(self, decl):
-        """Creates a node for the ``template <...>`` part of the declaration."""
-        if not decl.templateparamlist:
-            return None
-        context = self.context.create_child_context(decl.templateparamlist)
-        renderer = self.renderer_factory.create_renderer(context)
-        nodes = [self.node_factory.Text("template <")]
-        nodes.extend(renderer.render())
-        nodes.append(self.node_factory.Text(">"))
-        signode = self.node_factory.desc_signature()
-        signode.extend(nodes)
-        return signode
-
-    def run_domain_directive(self, kind, names):
-        domain_directive = self.renderer_factory.domain_directive_factory.create(
-            self.context.domain, [kind, names] + self.context.directive_args[2:])
-
-        # Translate Breathe's no-link option into the standard noindex option.
-        if 'no-link' in self.context.directive_args[2]:
-            domain_directive.options['noindex'] = True
-        nodes = domain_directive.run()
-
-        # Filter out outer class names if we are rendering a member as a part of a class content.
-        signode = nodes[1].children[0]
-        if len(names) > 0 and self.context.child:
-            signode.children = [n for n in signode.children if not n.tagname == 'desc_addname']
-        return nodes
-
-
-class RenderContext(object):
-
-    def __init__(self, node_stack, mask_factory, directive_args, domain='', child=False):
-        self.node_stack = node_stack
-        self.mask_factory = mask_factory
-        self.directive_args = directive_args
-        self.domain = domain
-        self.child = child
-
-    def create_child_context(self, data_object):
-
-        node_stack = self.node_stack[:]
-        node_stack.insert(0, self.mask_factory.mask(data_object))
-        return RenderContext(node_stack, self.mask_factory, self.directive_args, self.domain, True)

doc/breathe/renderer/rst/doxygen/index.py

@@ -1,115 +0,0 @@
-
-from .base import Renderer
-
-class DoxygenTypeSubRenderer(Renderer):
-
-    def render(self):
-
-        nodelist = []
-
-        # Process all the compound children
-        for compound in self.data_object.get_compound():
-            context = self.context.create_child_context(compound)
-            compound_renderer = self.renderer_factory.create_renderer(context)
-            nodelist.extend(compound_renderer.render())
-
-        return nodelist
-
-
-class CompoundRenderer(Renderer):
-    """Base class for CompoundTypeSubRenderer and RefTypeSubRenderer."""
-
-    def __init__(self, compound_parser, render_empty_node, *args):
-        self.compound_parser = compound_parser
-        self.render_empty_node = render_empty_node
-        Renderer.__init__(self, *args)
-
-    def create_doxygen_target(self):
-        """Can be overridden to create a target node which uses the doxygen refid information
-        which can be used for creating links between internal doxygen elements.
-
-        The default implementation should suffice most of the time.
-        """
-
-        refid = "%s%s" % (self.project_info.name(), self.data_object.refid)
-        return self.target_handler.create_target(refid)
-
-    def render_signature(self, file_data, doxygen_target):
-        # Defer to domains specific directive.
-        name, kind = self.get_node_info(file_data)
-        self.context.directive_args[1] = [self.get_fully_qualified_name()]
-        nodes = self.run_domain_directive(kind, self.context.directive_args[1])
-        node = nodes[1]
-        signode, contentnode = node.children
-
-        # The cpp domain in Sphinx doesn't support structs at the moment, so change the text from "class "
-        # to the correct kind which can be "class " or "struct ".
-        signode[0] = self.node_factory.desc_annotation(kind + ' ', kind + ' ')
-
-        # Check if there is template information and format it as desired
-        template_signode = self.create_template_node(file_data.compounddef)
-        if template_signode:
-            node.insert(0, template_signode)
-        node.children[0].insert(0, doxygen_target)
-        return nodes, contentnode
-
-    def render(self):
-
-        # Read in the corresponding xml file and process
-        file_data = self.compound_parser.parse(self.data_object.refid)
-
-        parent_context = self.context.create_child_context(file_data)
-        data_renderer = self.renderer_factory.create_renderer(parent_context)
-        rendered_data = data_renderer.render()
-
-        if not rendered_data and not self.render_empty_node:
-            return []
-
-        file_data = parent_context.node_stack[0]
-        new_context = parent_context.create_child_context(file_data.compounddef)
-
-        nodes, contentnode = self.render_signature(file_data, self.create_doxygen_target())
-
-        if file_data.compounddef.includes:
-            for include in file_data.compounddef.includes:
-                context = new_context.create_child_context(include)
-                renderer = self.renderer_factory.create_renderer(context)
-                contentnode.extend(renderer.render())
-
-        contentnode.extend(rendered_data)
-        return nodes
-
-
-class CompoundTypeSubRenderer(CompoundRenderer):
-
-    def __init__(self, compound_parser, *args):
-        CompoundRenderer.__init__(self, compound_parser, True, *args)
-
-    def get_node_info(self, file_data):
-        return self.data_object.name, self.data_object.kind
-
-
-class FileRenderer(CompoundTypeSubRenderer):
-
-    def render_signature(self, file_data, doxygen_target):
-        # Build targets for linking
-        targets = []
-        targets.extend(doxygen_target)
-
-        title_signode = self.node_factory.desc_signature()
-        title_signode.extend(targets)
-
-        # Set up the title
-        name, kind = self.get_node_info(file_data)
-        title_signode.append(self.node_factory.emphasis(text=kind))
-        title_signode.append(self.node_factory.Text(" "))
-        title_signode.append(self.node_factory.desc_name(text=name))
-
-        contentnode = self.node_factory.desc_content()
-
-        node = self.node_factory.desc()
-        node.document = self.state.document
-        node['objtype'] = kind
-        node.append(title_signode)
-        node.append(contentnode)
-        return [node], contentnode

doc/breathe/renderer/rst/doxygen/mask.py

@@ -1,62 +0,0 @@
-"""
-Masks
-=====
-
-Masks are related to filters. Filters can block the processing of particular parts of the xml
-hierarchy but they can only work on node level. If the part of the xml hierarchy that you want to
-filter out is read in as an instance of one of the classes in parser/doxygen/*.py then you can use
-the filters. However, if you want to filter out an attribute from one of the nodes (and some of the
-xml child nodes are read in as attributes on their parents) then you can't use a filter.
-
-We introduce the Mask's to fulfil this need. The masks are designed to be applied to a particular
-node type and to limit the access to particular attributes on the node. For example, then
-NoParameterNamesMask wraps a node a returns all its standard attributes but returns None for the
-'declname' and 'defname' attributes.
-
-Currently the Mask functionality is only used for the text signature rendering for doing function
-matching.
-
-"""
-
-class NoParameterNamesMask(object):
-
-    def __init__(self, data_object):
-        self.data_object = data_object
-
-    def __getattr__(self, attr):
-
-        if attr in ['declname', 'defname', 'defval']:
-            return None
-
-        return getattr(self.data_object, attr)
-
-class MaskFactory(object):
-
-    def __init__(self, lookup):
-        self.lookup = lookup
-
-    def mask(self, data_object):
-
-        try:
-            node_type = data_object.node_type
-        except AttributeError as e:
-
-            # Horrible hack to silence errors on filtering unicode objects
-            # until we fix the parsing
-            if type(data_object) == unicode:
-                node_type = "unicode"
-            else:
-                raise e
-
-        if node_type in self.lookup:
-            Mask = self.lookup[node_type]
-            return Mask(data_object)
-
-        return data_object
-
-
-class NullMaskFactory(object):
-
-    def mask(self, data_object):
-        return data_object
-

doc/breathe/renderer/rst/doxygen/target.py

@@ -1,40 +0,0 @@
-
-class TargetHandler(object):
-
-    def __init__(self, project_info, node_factory, document):
-
-        self.project_info = project_info
-        self.node_factory = node_factory
-        self.document = document
-
-    def create_target(self, id_):
-        """Creates a target node and registers it with the document and returns it in a list"""
-
-        target = self.node_factory.target(ids=[id_], names=[id_])
-
-        try:
-            self.document.note_explicit_target(target)
-        except Exception:
-            # TODO: We should really return a docutils warning node here
-            print("Warning: Duplicate target detected: %s" % id_)
-
-        return [target]
-
-class NullTargetHandler(object):
-
-    def create_target(self, refid):
-        return []
-
-class TargetHandlerFactory(object):
-
-    def __init__(self, node_factory):
-
-        self.node_factory = node_factory
-
-    def create_target_handler(self, options, project_info, document):
-
-        if options.has_key("no-link"):
-            return NullTargetHandler()
-
-        return TargetHandler(project_info, self.node_factory, document)
-

doc/doxygen/xml/.gitignore

@@ -1,4 +0,0 @@
-# Ignore everything in this directory
-*
-# Except this file
-!.gitignore

doc/source/DMS.rst

@@ -1,158 +0,0 @@
-*********************************************
-The OBItools3 Data Management System (OBIDMS)
-*********************************************
-
-A complete DNA Metabarcoding experiment rely on several kinds of data.
-
-	- The sequence data resulting of the PCR products sequencing,
-	- The description of the samples including all their metadata,
-	- One or several refence database used for the taxonomical annotation
-	- One or several taxonomies.
-
-Up to now each of these categories of data were stored in separate
-files an nothing obliged to keep them together.
-
-
-The `Data Management System` (DMS) of OBITools3 can be considered
-as a basic database system.
-
-
-OBIDMS UML
-==========
-
-.. image:: ./UML/OBIDMS_UML.png
-
-:download:`html version of the OBIDMS UML file <UML/ObiDMS_UML.class.violet.html>`
-
-
-An OBIDMS directory consists of :
-	* OBIDMS column files
-	* OBIDMS release files
-	* OBIDMS dictionary files
-	* one OBIDMS history file
-
-
-OBIDMS column files
-===================
-
-Each OBIDMS column file contains :
-	* a header of a size equal to a multiple of PAGESIZE (PAGESIZE being equal to 4096 bytes
-	  on most systems) containing metadata
-	* one column of data with the same OBIType
-
-
-Header
-------
-
-The header of an OBIDMS column contains :
-
-	* Endian byte order
-	* Header size (PAGESIZE multiple)
-	*
-	* File status : Open/Closed
-	* Owner : PID of the process that created the file and is the only one allowed to modify it if it is open
-	* Number of lines (total or without the header?)
-	* OBIType
-	* Date of creation
-	* Version of the file
-	* Eventual comments
-
-
-Data
-----
-
-A column of data with the same OBIType.
-
-
-Mandatory columns
------------------
-
-Some columns must exist in an OBIDMS directory :
-    * sequence identifiers column (type *OBIStr_t*)
-
-
-File name
----------
-
-Each file is named with the attribute associated to the data it contains, and the number of
-its version, separated by an ``@``, and with the extension ``.odc``.
-
-Example : ``count@3.odc``
-
-
-Modifications
--------------
-
-An OBIDMS column file can only be modified by the process that created it, if its status is set to Open. Those informations are
-contained in the `header <#header>`_.
-
-When a process wants to modify an OBIDMS column file that is closed, it must first clone it. Cloning creates a new version of the
-file that belongs to the process, i.e., only that process can modify that file, as long as its status is set to Open. Once the process
-has finished writing the new version of the column file, it sets the column file's status to Closed, and the file can never be modified
-again.
-
-That means that one column is stored in one file (if there is only one version)
-or more (if there are several versions), and that there is one file per version.
-
-
-Versioning
-----------
-
-The first version of a column file is numbered 0, and each new version increments that
-number by 1.
-
-The number of the latest version of an OBIDMS column is stored in an `OBIDMS release file <formats.html#obidms-release-files>`_.
-
-
-OBIDMS release files
-====================
-
-Each OBIDMS column is associated with an OBIDMS release file that contains the number of the latest
-version of the column.
-
-File name
----------
-
-OBIDMS release files are named with the attribute associated to the data contained in the column, and
-have the extension ``.odr``.
-
-Example : ``count.odr``
-
-
-OBIDMS views
-============
-
-An OBIDMS view consists of a list of OBIDMS columns and lines. A view includes one version
-of each mandatory column. Only one version of each column is included. All the columns of
-one view contain the same number of lines in the same order.
-
-
-OBIDMS history file
-===================
-
-An OBIDMS history file consists of an ordered list of views and commands, those commands leading
-from one view to the next one.
-
-This history can be represented in the form of a ?? showing all the
-operations ever done in the OBIDMS directory and the views in between them :
-
-.. image:: ./images/history.png
-    :width: 150 px
-    :align: center
-
-OBIType header file
-========================
-
-.. doxygenfile:: obitypes.h
-
-
-OBIIntColumn header file
-========================
-
-.. doxygenfile:: obiintcolumn.h
-
-
-OBIColumn header file
-=====================
-
-.. doxygenfile:: obicolumn.h

doc/source/UML/OBITypes_UML.class.violet.html

@@ -1,832 +0,0 @@
-<HTML>
-<HEAD>
-<META name="description"
-	content="Violet UML Editor cross format document" />
-<META name="keywords" content="Violet, UML" />
-<META charset="UTF-8" />
-<SCRIPT type="text/javascript">
-	function switchVisibility() {
-		var obj = document.getElementById("content");
-		obj.style.display = (obj.style.display == "block") ? "none" : "block";
-	}
-</SCRIPT>
-</HEAD>
-<BODY>
-	This file was generated with Violet UML Editor 2.1.0.
-	&nbsp;&nbsp;(&nbsp;<A href=# onclick="switchVisibility()">View Source</A>&nbsp;/&nbsp;<A href="http://sourceforge.net/projects/violet/files/violetumleditor/" target="_blank">Download Violet</A>&nbsp;)
-	<BR />
-	<BR />
-	<SCRIPT id="content" type="text/xml"><![CDATA[<ClassDiagramGraph id="1">
-  <nodes id="2">
-    <ClassNode id="3">
-      <children id="4"/>
-      <location class="Point2D.Double" id="5" x="520.0" y="30.0"/>
-      <id id="6" value="a6688f6e-9346-46c6-9cf5-4fa6148f613f"/>
-      <revision>1</revision>
-      <backgroundColor id="7">
-        <red>255</red>
-        <green>255</green>
-        <blue>255</blue>
-        <alpha>255</alpha>
-      </backgroundColor>
-      <borderColor id="8">
-        <red>0</red>
-        <green>0</green>
-        <blue>0</blue>
-        <alpha>255</alpha>
-      </borderColor>
-      <textColor reference="8"/>
-      <name id="9" justification="1" size="3" underlined="false">
-        <text>OBIType_t
-</text>
-      </name>
-      <attributes id="10" justification="0" size="4" underlined="false">
-        <text></text>
-      </attributes>
-      <methods id="11" justification="0" size="4" underlined="false">
-        <text></text>
-      </methods>
-    </ClassNode>
-    <ClassNode id="12">
-      <children id="13"/>
-      <location class="Point2D.Double" id="14" x="780.0" y="100.0"/>
-      <id id="15" value="7edd4f08-c5e5-4e41-bc05-8b357cb5e629"/>
-      <revision>1</revision>
-      <backgroundColor reference="7"/>
-      <borderColor reference="8"/>
-      <textColor reference="8"/>
-      <name id="16" justification="1" size="3" underlined="false">
-        <text>OBIContainer_t</text>
-      </name>
-      <attributes id="17" justification="0" size="4" underlined="false">
-        <text></text>
-      </attributes>
-      <methods id="18" justification="0" size="4" underlined="false">
-        <text></text>
-      </methods>
-    </ClassNode>
-    <ClassNode id="19">
-      <children id="20"/>
-      <location class="Point2D.Double" id="21" x="330.0" y="110.0"/>
-      <id id="22" value="dbb15831-2f0b-4e97-83e7-5ecdda6d6075"/>
-      <revision>1</revision>
-      <backgroundColor reference="7"/>
-      <borderColor reference="8"/>
-      <textColor reference="8"/>
-      <name id="23" justification="1" size="3" underlined="false">
-        <text>OBIElementary_t</text>
-      </name>
-      <attributes id="24" justification="0" size="4" underlined="false">
-        <text></text>
-      </attributes>
-      <methods id="25" justification="0" size="4" underlined="false">
-        <text></text>
-      </methods>
-    </ClassNode>
-    <ClassNode id="26">
-      <children id="27"/>
-      <location class="Point2D.Double" id="28" x="670.0" y="240.0"/>
-      <id id="29" value="9693da23-1b47-4bf3-9544-86390a533713"/>
-      <revision>1</revision>
-      <backgroundColor reference="7"/>
-      <borderColor reference="8"/>
-      <textColor reference="8"/>
-      <name id="30" justification="1" size="3" underlined="false">
-        <text>OBIList_t</text>
-      </name>
-      <attributes id="31" justification="0" size="4" underlined="false">
-        <text></text>
-      </attributes>
-      <methods id="32" justification="0" size="4" underlined="false">
-        <text></text>
-      </methods>
-    </ClassNode>
-    <ClassNode id="33">
-      <children id="34"/>
-      <location class="Point2D.Double" id="35" x="780.0" y="240.0"/>
-      <id id="36" value="b2f4d561-0c10-4443-b8f6-d3628ab9bcfe"/>
-      <revision>1</revision>
-      <backgroundColor reference="7"/>
-      <borderColor reference="8"/>
-      <textColor reference="8"/>
-      <name id="37" justification="1" size="3" underlined="false">
-        <text>OBISet_t</text>
-      </name>
-      <attributes id="38" justification="0" size="4" underlined="false">
-        <text></text>
-      </attributes>
-      <methods id="39" justification="0" size="4" underlined="false">
-        <text></text>
-      </methods>
-    </ClassNode>
-    <ClassNode id="40">
-      <children id="41"/>
-      <location class="Point2D.Double" id="42" x="890.0" y="240.0"/>
-      <id id="43" value="8cc209c6-18c7-4a90-a5d4-ab7246638b2f"/>
-      <revision>1</revision>
-      <backgroundColor reference="7"/>
-      <borderColor reference="8"/>
-      <textColor reference="8"/>
-      <name id="44" justification="1" size="3" underlined="false">
-        <text>OBIDictionnary_t</text>
-      </name>
-      <attributes id="45" justification="0" size="4" underlined="false">
-        <text></text>
-      </attributes>
-      <methods id="46" justification="0" size="4" underlined="false">
-        <text></text>
-      </methods>
-    </ClassNode>
-    <ClassNode id="47">
-      <children id="48"/>
-      <location class="Point2D.Double" id="49" x="170.0" y="220.0"/>
-      <id id="50" value="cb77086b-7535-49dc-ab33-b58d16eec496"/>
-      <revision>1</revision>
-      <backgroundColor reference="7"/>
-      <borderColor reference="8"/>
-      <textColor reference="8"/>
-      <name id="51" justification="1" size="3" underlined="false">
-        <text>OBIAtomic_t</text>
-      </name>
-      <attributes id="52" justification="0" size="4" underlined="false">
-        <text></text>
-      </attributes>
-      <methods id="53" justification="0" size="4" underlined="false">
-        <text></text>
-      </methods>
-    </ClassNode>
-    <ClassNode id="54">
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doc/source/conf.py

@@ -1,298 +0,0 @@
-# -*- coding: utf-8 -*-
-#
-# OBITools3 documentation build configuration file, created by
-# sphinx-quickstart on Mon May  4 14:36:57 2015.
-#
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-
-import sys
-import os
-import shlex
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('.'))
-
-# -- General configuration ------------------------------------------------
-
-# If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
-    'sphinx.ext.pngmath',
-    'sphinx.ext.ifconfig',
-    'sphinx.ext.viewcode',
-    'breathe',
-]
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-# source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
-
-# The encoding of source files.
-#source_encoding = 'utf-8-sig'
-
-# The master toctree document.
-master_doc = 'index'
-
-# General information about the project.
-project = u'OBITools3'
-copyright = u'2015, Céline Mercier, Eric Coissac, Frédéric Boyer'
-author = u'Céline Mercier, Eric Coissac, Frédéric Boyer'
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-version = '0.0'
-# The full version, including alpha/beta/rc tags.
-release = '0.0.0'
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = None
-
-# There are two options for replacing |today|: either, you set today to some
-# non-false value, then it is used:
-#today = ''
-# Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-exclude_patterns = []
-
-# The reST default role (used for this markup: `text`) to use for all
-# documents.
-#default_role = None
-
-# If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
-
-# If true, the current module name will be prepended to all description
-# unit titles (such as .. function::).
-#add_module_names = True
-
-# If true, sectionauthor and moduleauthor directives will be shown in the
-# output. They are ignored by default.
-#show_authors = False
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
-# A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
-
-# If true, keep warnings as "system message" paragraphs in the built documents.
-#keep_warnings = False
-
-# If true, `todo` and `todoList` produce output, else they produce nothing.
-todo_include_todos = True
-
-
-# -- Options for HTML output ----------------------------------------------
-
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-html_theme = 'bizstyle'
-
-# Theme options are theme-specific and customize the look and feel of a theme
-# further.  For a list of options available for each theme, see the
-# documentation.
-#html_theme_options = {}
-
-# Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
-
-# The name for this set of Sphinx documents.  If None, it defaults to
-# "<project> v<release> documentation".
-#html_title = None
-
-# A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
-
-# The name of an image file (relative to this directory) to place at the top
-# of the sidebar.
-#html_logo = None
-
-# The name of an image file (within the static path) to use as favicon of the
-# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
-# pixels large.
-#html_favicon = None
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-
-# Add any extra paths that contain custom files (such as robots.txt or
-# .htaccess) here, relative to this directory. These files are copied
-# directly to the root of the documentation.
-#html_extra_path = []
-
-# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
-# using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
-
-# If true, SmartyPants will be used to convert quotes and dashes to
-# typographically correct entities.
-#html_use_smartypants = True
-
-# Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
-
-# Additional templates that should be rendered to pages, maps page names to
-# template names.
-#html_additional_pages = {}
-
-# If false, no module index is generated.
-#html_domain_indices = True
-
-# If false, no index is generated.
-#html_use_index = True
-
-# If true, the index is split into individual pages for each letter.
-#html_split_index = False
-
-# If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
-
-# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
-
-# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
-
-# If true, an OpenSearch description file will be output, and all pages will
-# contain a <link> tag referring to it.  The value of this option must be the
-# base URL from which the finished HTML is served.
-#html_use_opensearch = ''
-
-# This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
-
-# Language to be used for generating the HTML full-text search index.
-# Sphinx supports the following languages:
-#   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
-#   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
-#html_search_language = 'en'
-
-# A dictionary with options for the search language support, empty by default.
-# Now only 'ja' uses this config value
-#html_search_options = {'type': 'default'}
-
-# The name of a javascript file (relative to the configuration directory) that
-# implements a search results scorer. If empty, the default will be used.
-#html_search_scorer = 'scorer.js'
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'OBITools3doc'
-
-# -- Options for LaTeX output ---------------------------------------------
-
-latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
-
-# Latex figure (float) alignment
-#'figure_align': 'htbp',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title,
-#  author, documentclass [howto, manual, or own class]).
-latex_documents = [
-  (master_doc, 'OBITools3.tex', u'OBITools3 Documentation',
-   u'Céline Mercier, Eric Coissac, Frédéric Boyer', 'manual'),
-]
-
-# The name of an image file (relative to this directory) to place at the top of
-# the title page.
-#latex_logo = None
-
-# For "manual" documents, if this is true, then toplevel headings are parts,
-# not chapters.
-#latex_use_parts = False
-
-# If true, show page references after internal links.
-#latex_show_pagerefs = False
-
-# If true, show URL addresses after external links.
-#latex_show_urls = False
-
-# Documents to append as an appendix to all manuals.
-#latex_appendices = []
-
-# If false, no module index is generated.
-#latex_domain_indices = True
-
-
-# -- Options for manual page output ---------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'obitools3', u'OBITools3 Documentation',
-     [author], 1)
-]
-
-# If true, show URL addresses after external links.
-#man_show_urls = False
-
-
-# -- Options for Texinfo output -------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-#  dir menu entry, description, category)
-texinfo_documents = [
-  (master_doc, 'OBITools3', u'OBITools3 Documentation',
-   author, 'OBITools3', 'One line description of project.',
-   'Miscellaneous'),
-]
-
-# Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
-
-# If false, no module index is generated.
-#texinfo_domain_indices = True
-
-# How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
-
-# If true, do not generate a @detailmenu in the "Top" node's menu.
-#texinfo_no_detailmenu = False
-
-#Breathe configuration
-sys.path.append( "../breathe/" )
-breathe_projects = { "OBITools3": "../doxygen/xml/" }
-breathe_default_project = "OBITools3"
-