Added plot_directive and mathmpl extensions

doc/sphinxext/apigen.py

@@ -0,0 +1,427 @@
+"""Attempt to generate templates for module reference with Sphinx
+
+XXX - we exclude extension modules
+
+To include extension modules, first identify them as valid in the
+``_uri2path`` method, then handle them in the ``_parse_module`` script.
+
+We get functions and classes by parsing the text of .py files.
+Alternatively we could import the modules for discovery, and we'd have
+to do that for extension modules.  This would involve changing the
+``_parse_module`` method to work via import and introspection, and
+might involve changing ``discover_modules`` (which determines which
+files are modules, and therefore which module URIs will be passed to
+``_parse_module``).
+
+NOTE: this is a modified version of a script originally shipped with the
+PyMVPA project, which we've adapted for NIPY use.  PyMVPA is an MIT-licensed
+project."""
+
+# Stdlib imports
+import os
+import re
+
+# Functions and classes
+class ApiDocWriter(object):
+    ''' Class for automatic detection and parsing of API docs
+    to Sphinx-parsable reST format'''
+
+    # only separating first two levels
+    rst_section_levels = ['*', '=', '-', '~', '^']
+
+    def __init__(self,
+                 package_name,
+                 rst_extension='.rst',
+                 package_skip_patterns=None,
+                 module_skip_patterns=None,
+                 ):
+        ''' Initialize package for parsing
+
+        Parameters
+        ----------
+        package_name : string
+            Name of the top-level package.  *package_name* must be the
+            name of an importable package
+        rst_extension : string, optional
+            Extension for reST files, default '.rst'
+        package_skip_patterns : None or sequence of {strings, regexps}
+            Sequence of strings giving URIs of packages to be excluded
+            Operates on the package path, starting at (including) the
+            first dot in the package path, after *package_name* - so,
+            if *package_name* is ``sphinx``, then ``sphinx.util`` will
+            result in ``.util`` being passed for earching by these
+            regexps.  If is None, gives default. Default is:
+            ['\.tests$']
+        module_skip_patterns : None or sequence
+            Sequence of strings giving URIs of modules to be excluded
+            Operates on the module name including preceding URI path,
+            back to the first dot after *package_name*.  For example
+            ``sphinx.util.console`` results in the string to search of
+            ``.util.console``
+            If is None, gives default. Default is:
+            ['\.setup$', '\._']
+        '''
+        if package_skip_patterns is None:
+            package_skip_patterns = ['\\.tests$']
+        if module_skip_patterns is None:
+            module_skip_patterns = ['\\.setup$', '\\._']
+        self.package_name = package_name
+        self.rst_extension = rst_extension
+        self.package_skip_patterns = package_skip_patterns
+        self.module_skip_patterns = module_skip_patterns
+
+    def get_package_name(self):
+        return self._package_name
+
+    def set_package_name(self, package_name):
+        ''' Set package_name
+
+        >>> docwriter = ApiDocWriter('sphinx')
+        >>> import sphinx
+        >>> docwriter.root_path == sphinx.__path__[0]
+        True
+        >>> docwriter.package_name = 'docutils'
+        >>> import docutils
+        >>> docwriter.root_path == docutils.__path__[0]
+        True
+        '''
+        # It's also possible to imagine caching the module parsing here
+        self._package_name = package_name
+        self.root_module = __import__(package_name)
+        self.root_path = self.root_module.__path__[0]
+        self.written_modules = None
+
+    package_name = property(get_package_name, set_package_name, None,
+                            'get/set package_name')
+
+    def _get_object_name(self, line):
+        ''' Get second token in line
+        >>> docwriter = ApiDocWriter('sphinx')
+        >>> docwriter._get_object_name("  def func():  ")
+        'func'
+        >>> docwriter._get_object_name("  class Klass(object):  ")
+        'Klass'
+        >>> docwriter._get_object_name("  class Klass:  ")
+        'Klass'
+        '''
+        name = line.split()[1].split('(')[0].strip()
+        # in case we have classes which are not derived from object
+        # ie. old style classes
+        return name.rstrip(':')
+
+    def _uri2path(self, uri):
+        ''' Convert uri to absolute filepath
+
+        Parameters
+        ----------
+        uri : string
+            URI of python module to return path for
+
+        Returns
+        -------
+        path : None or string
+            Returns None if there is no valid path for this URI
+            Otherwise returns absolute file system path for URI
+
+        Examples
+        --------
+        >>> docwriter = ApiDocWriter('sphinx')
+        >>> import sphinx
+        >>> modpath = sphinx.__path__[0]
+        >>> res = docwriter._uri2path('sphinx.builder')
+        >>> res == os.path.join(modpath, 'builder.py')
+        True
+        >>> res = docwriter._uri2path('sphinx')
+        >>> res == os.path.join(modpath, '__init__.py')
+        True
+        >>> docwriter._uri2path('sphinx.does_not_exist')
+
+        '''
+        if uri == self.package_name:
+            return os.path.join(self.root_path, '__init__.py')
+        path = uri.replace('.', os.path.sep)
+        path = path.replace(self.package_name + os.path.sep, '')
+        path = os.path.join(self.root_path, path)
+        # XXX maybe check for extensions as well?
+        if os.path.exists(path + '.py'): # file
+            path += '.py'
+        elif os.path.exists(os.path.join(path, '__init__.py')):
+            path = os.path.join(path, '__init__.py')
+        else:
+            return None
+        return path
+
+    def _path2uri(self, dirpath):
+        ''' Convert directory path to uri '''
+        relpath = dirpath.replace(self.root_path, self.package_name)
+        if relpath.startswith(os.path.sep):
+            relpath = relpath[1:]
+        return relpath.replace(os.path.sep, '.')
+
+    def _parse_module(self, uri):
+        ''' Parse module defined in *uri* '''
+        filename = self._uri2path(uri)
+        if filename is None:
+            # nothing that we could handle here.
+            return ([],[])
+        f = open(filename, 'rt')
+        functions, classes = self._parse_lines(f)
+        f.close()
+        return functions, classes
+    
+    def _parse_lines(self, linesource):
+        ''' Parse lines of text for functions and classes '''
+        functions = []
+        classes = []
+        for line in linesource:
+            if line.startswith('def ') and line.count('('):
+                # exclude private stuff
+                name = self._get_object_name(line)
+                if not name.startswith('_'):
+                    functions.append(name)
+            elif line.startswith('class '):
+                # exclude private stuff
+                name = self._get_object_name(line)
+                if not name.startswith('_'):
+                    classes.append(name)
+            else:
+                pass
+        functions.sort()
+        classes.sort()
+        return functions, classes
+
+    def generate_api_doc(self, uri):
+        '''Make autodoc documentation template string for a module
+
+        Parameters
+        ----------
+        uri : string
+            python location of module - e.g 'sphinx.builder'
+
+        Returns
+        -------
+        S : string
+            Contents of API doc
+        '''
+        # get the names of all classes and functions
+        functions, classes = self._parse_module(uri)
+        if not len(functions) and not len(classes):
+            print 'WARNING: Empty -',uri  # dbg
+            return ''
+
+        # Make a shorter version of the uri that omits the package name for
+        # titles 
+        uri_short = re.sub(r'^%s\.' % self.package_name,'',uri)
+        
+        ad = '.. AUTO-GENERATED FILE -- DO NOT EDIT!\n\n'
+
+        chap_title = uri_short
+        ad += (chap_title+'\n'+ self.rst_section_levels[1] * len(chap_title)
+               + '\n\n')
+
+        # Set the chapter title to read 'module' for all modules except for the
+        # main packages
+        if '.' in uri:
+            title = 'Module: :mod:`' + uri_short + '`'
+        else:
+            title = ':mod:`' + uri_short + '`'
+        ad += title + '\n' + self.rst_section_levels[2] * len(title)
+
+        if len(classes):
+            ad += '\nInheritance diagram for ``%s``:\n\n' % uri
+            ad += '.. inheritance-diagram:: %s \n' % uri
+            ad += '   :parts: 3\n'
+
+        ad += '\n.. automodule:: ' + uri + '\n'
+        ad += '\n.. currentmodule:: ' + uri + '\n'
+        multi_class = len(classes) > 1
+        multi_fx = len(functions) > 1
+        if multi_class:
+            ad += '\n' + 'Classes' + '\n' + \
+                  self.rst_section_levels[2] * 7 + '\n'
+        elif len(classes) and multi_fx:
+            ad += '\n' + 'Class' + '\n' + \
+                  self.rst_section_levels[2] * 5 + '\n'
+        for c in classes:
+            ad += '\n:class:`' + c + '`\n' \
+                  + self.rst_section_levels[multi_class + 2 ] * \
+                  (len(c)+9) + '\n\n'
+            ad += '\n.. autoclass:: ' + c + '\n'
+            # must NOT exclude from index to keep cross-refs working
+            ad += '  :members:\n' \
+                  '  :undoc-members:\n' \
+                  '  :show-inheritance:\n' \
+                  '  :inherited-members:\n' \
+                  '\n' \
+                  '  .. automethod:: __init__\n'
+        if multi_fx:
+            ad += '\n' + 'Functions' + '\n' + \
+                  self.rst_section_levels[2] * 9 + '\n\n'
+        elif len(functions) and multi_class:
+            ad += '\n' + 'Function' + '\n' + \
+                  self.rst_section_levels[2] * 8 + '\n\n'
+        for f in functions:
+            # must NOT exclude from index to keep cross-refs working
+            ad += '\n.. autofunction:: ' + uri + '.' + f + '\n\n'
+        return ad
+
+    def _survives_exclude(self, matchstr, match_type):
+        ''' Returns True if *matchstr* does not match patterns
+
+        ``self.package_name`` removed from front of string if present
+
+        Examples
+        --------
+        >>> dw = ApiDocWriter('sphinx')
+        >>> dw._survives_exclude('sphinx.okpkg', 'package')
+        True
+        >>> dw.package_skip_patterns.append('^\\.badpkg$')
+        >>> dw._survives_exclude('sphinx.badpkg', 'package')
+        False
+        >>> dw._survives_exclude('sphinx.badpkg', 'module')
+        True
+        >>> dw._survives_exclude('sphinx.badmod', 'module')
+        True
+        >>> dw.module_skip_patterns.append('^\\.badmod$')
+        >>> dw._survives_exclude('sphinx.badmod', 'module')
+        False
+        '''
+        if match_type == 'module':
+            patterns = self.module_skip_patterns
+        elif match_type == 'package':
+            patterns = self.package_skip_patterns
+        else:
+            raise ValueError('Cannot interpret match type "%s"' 
+                             % match_type)
+        # Match to URI without package name
+        L = len(self.package_name)
+        if matchstr[:L] == self.package_name:
+            matchstr = matchstr[L:]
+        for pat in patterns:
+            try:
+                pat.search
+            except AttributeError:
+                pat = re.compile(pat)
+            if pat.search(matchstr):
+                return False
+        return True
+
+    def discover_modules(self):
+        ''' Return module sequence discovered from ``self.package_name`` 
+
+
+        Parameters
+        ----------
+        None
+
+        Returns
+        -------
+        mods : sequence
+            Sequence of module names within ``self.package_name``
+
+        Examples
+        --------
+        >>> dw = ApiDocWriter('sphinx')
+        >>> mods = dw.discover_modules()
+        >>> 'sphinx.util' in mods
+        True
+        >>> dw.package_skip_patterns.append('\.util$')
+        >>> 'sphinx.util' in dw.discover_modules()
+        False
+        >>> 
+        '''
+        modules = [self.package_name]
+        # raw directory parsing
+        for dirpath, dirnames, filenames in os.walk(self.root_path):
+            # Check directory names for packages
+            root_uri = self._path2uri(os.path.join(self.root_path,
+                                                   dirpath))
+            for dirname in dirnames[:]: # copy list - we modify inplace
+                package_uri = '.'.join((root_uri, dirname))
+                if (self._uri2path(package_uri) and
+                    self._survives_exclude(package_uri, 'package')):
+                    modules.append(package_uri)
+                else:
+                    dirnames.remove(dirname)
+            # Check filenames for modules
+            for filename in filenames:
+                module_name = filename[:-3]
+                module_uri = '.'.join((root_uri, module_name))
+                if (self._uri2path(module_uri) and
+                    self._survives_exclude(module_uri, 'module')):
+                    modules.append(module_uri)
+        return sorted(modules)
+    
+    def write_modules_api(self, modules,outdir):
+        # write the list
+        written_modules = []
+        for m in modules:
+            api_str = self.generate_api_doc(m)
+            if not api_str:
+                continue
+            # write out to file
+            outfile = os.path.join(outdir,
+                                   m + self.rst_extension)
+            fileobj = open(outfile, 'wt')
+            fileobj.write(api_str)
+            fileobj.close()
+            written_modules.append(m)
+        self.written_modules = written_modules
+
+    def write_api_docs(self, outdir):
+        """Generate API reST files.
+
+        Parameters
+        ----------
+        outdir : string
+            Directory name in which to store files
+            We create automatic filenames for each module
+            
+        Returns
+        -------
+        None
+
+        Notes
+        -----
+        Sets self.written_modules to list of written modules
+        """
+        if not os.path.exists(outdir):
+            os.mkdir(outdir)
+        # compose list of modules
+        modules = self.discover_modules()
+        self.write_modules_api(modules,outdir)
+        
+    def write_index(self, outdir, froot='gen', relative_to=None):
+        """Make a reST API index file from written files
+
+        Parameters
+        ----------
+        path : string
+            Filename to write index to
+        outdir : string
+            Directory to which to write generated index file
+        froot : string, optional
+            root (filename without extension) of filename to write to
+            Defaults to 'gen'.  We add ``self.rst_extension``.
+        relative_to : string
+            path to which written filenames are relative.  This
+            component of the written file path will be removed from
+            outdir, in the generated index.  Default is None, meaning,
+            leave path as it is.
+        """
+        if self.written_modules is None:
+            raise ValueError('No modules written')
+        # Get full filename path
+        path = os.path.join(outdir, froot+self.rst_extension)
+        # Path written into index is relative to rootpath
+        if relative_to is not None:
+            relpath = outdir.replace(relative_to + os.path.sep, '')
+        else:
+            relpath = outdir
+        idx = open(path,'wt')
+        w = idx.write
+        w('.. AUTO-GENERATED FILE -- DO NOT EDIT!\n\n')
+        w('.. toctree::\n\n')
+        for f in self.written_modules:
+            w('   %s\n' % os.path.join(relpath,f))
+        idx.close()