I now made it optional to use autosummary and the extra file generation 
with a switch in the command line.


autodoc file generation for each module!
> -------------------------------------------------------
>
> The most important change I made, and which I would like to have 
> integrated in the official software is to the autodoc.py. When the software 
> is generating rst-files automatically all modules of one package get one 
> rst file and so  in my use case only one web page, which is nearly 
> unreadable. So I added the option to generate one file for each module and 
> only have an auto-summary of the modules.
> I also preferred having an auto-summary of the sub packages instead of a 
> toctree, but this could be made optional or discussed. :)
>
> Further improvement could be also one file per class, but maybe that is to 
> detailed.
>
>
>

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# -*- coding: utf-8 -*-
"""
    sphinx.apidoc
    ~~~~~~~~~~~~~

    Parses a directory tree looking for Python modules and packages and creates
    ReST files appropriately to create code documentation with Sphinx.  It also
    creates a modules index (named modules.<suffix>).

    This is derived from the "sphinx-autopackage" script, which is:
    Copyright 2008 Soci?t? des arts technologiques (SAT),
    http://www.sat.qc.ca/

    :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
    :license: BSD, see LICENSE for details.
"""
import os
import sys
import optparse
from os import path

# automodule options
if 'SPHINX_APIDOC_OPTIONS' in os.environ:
    OPTIONS = os.environ['SPHINX_APIDOC_OPTIONS'].split(',')
else:
    OPTIONS = [
        'members',
        'undoc-members',
        # 'inherited-members', # disabled because there's a bug in sphinx
        'show-inheritance',
    ]

INITPY = '__init__.py'


def makename(package, module):
    """Join package and module with a dot."""
    # Both package and module can be None/empty.
    if package:
        name = package
        if module:
            name += '.' + module
    else:
        name = module
    return name


def write_file(name, text, opts):
    """Write the output file for module/package <name>."""
    fname = path.join(opts.destdir, '%s.%s' % (name, opts.suffix))
    if opts.dryrun:
        print 'Would create file %s.' % fname
        return
    if not opts.force and path.isfile(fname):
        print 'File %s already exists, skipping.' % fname
    else:
        print 'Creating file %s.' % fname
        f = open(fname, 'w')
        try:
            f.write(text)
        finally:
            f.close()


def format_heading(level, text):
    """Create a heading of <level> [1, 2 or 3 supported]."""
    underlining = ['=', '-', '~', ][level-1] * len(text)
    return '%s\n%s\n\n' % (text, underlining)


def format_directive(module, package=None):
    """Create the automodule directive and add the options."""
    directive = '.. automodule:: %s\n' % makename(package, module)
    for option in OPTIONS:
        directive += '    :%s:\n' % option
    return directive


def create_module_file(package, module, opts):
    """Build the text of the file and write the file."""
    text = format_heading(1, '%s Module' % module)
    #text += format_heading(2, ':mod:`%s` Module' % module)
    text += format_directive(module, package)
    write_file(makename(package, module), text, opts)


def create_package_file(root, master_package, subroot, py_files, opts, subs):
    """Build the text of the file and write the file."""
    package = path.split(root)[-1]
    text = format_heading(1, '%s Package' % package)
    module_text = format_heading(2, 'Modules')
    module_text += '.. autosummary::\n'
    module_text += '    :toctree:\n\n'

    # add each module in the package
    for py_file in py_files:
        if shall_skip(path.join(root, py_file)):
            continue
        is_package = py_file == INITPY
        py_file = path.splitext(py_file)[0]
        py_path = makename(subroot, py_file)
        if is_package:
            heading = ':mod:`%s` Package' % package
        else:
            module = path.splitext(py_file)[0]
            # if there is just one module, we don't need an extra modul file
            if len(py_files)>1 and opts.module:
                module_root=makename(master_package, subroot)
                create_module_file(module_root,module,opts)
                module_text += '    %s.%s\n' % (module_root, module)
                continue
            heading = ':mod:`%s` Module' % py_file
        text += format_heading(2, heading)
        # Package documentation gets __init__ additionally to the package name
        # though it is not needed. This causes problems in combination with
        # autosummary.
        if py_path=="__init__":
            py_path=""
        text += format_directive(is_package and subroot or py_path,
                                 master_package)
        text += '\n'
    
    module_text+='\n'
    if len(py_files)>1 and opts.module:
        text += module_text
        text += '\n'
    
    # build a list of directories that are packages (contain an INITPY file)
    subs = [sub for sub in subs if path.isfile(path.join(root, sub, INITPY))]
    # if there are some package directories, add a TOC for theses subpackages
    if subs:
        toc_text = format_heading(2, 'Subpackages Tree')
        sum_text = format_heading(2, 'Subpackages Summary')
        sum_text += '.. autosummary::\n\n'
        toc_text += '.. toctree::\n'
        toc_text += '    :maxdepth: %s\n\n' % opts.maxdepth
        for sub in subs:
            sum_text += '    %s.%s\n' % (makename(master_package, subroot), sub)
            toc_text += '    %s.%s\n' % (makename(master_package, subroot), sub)
        toc_text += '\n'
        sum_text += '\n'
        if opts.packagesummary:
            text +=sum_text
        text +=toc_text
    
    write_file(makename(master_package, subroot), text, opts)


def create_modules_toc_file(modules, opts, name='modules'):
    """Create the module's index."""
    text = format_heading(1, '%s' % opts.header)
    text += '.. toctree::\n'
    text += '   :maxdepth: %s\n\n' % opts.maxdepth

    modules.sort()
    prev_module = ''
    for module in modules:
        # look if the module is a subpackage and, if yes, ignore it
        if module.startswith(prev_module + '.'):
            continue
        prev_module = module
        text += '   %s\n' % module

    write_file(name, text, opts)


def shall_skip(module):
    """Check if we want to skip this module."""
    # skip it if there is nothing (or just \n or \r\n) in the file
    return path.getsize(module) <= 2


def recurse_tree(rootpath, excludes, opts):
    """
    Look for every file in the directory tree and create the corresponding
    ReST files.
    """
    # use absolute path for root, as relative paths like '../../foo' cause
    # 'if "/." in root ...' to filter out *all* modules otherwise
    rootpath = path.normpath(path.abspath(rootpath))
    # check if the base directory is a package and get its name
    if INITPY in os.listdir(rootpath):
        root_package = rootpath.split(path.sep)[-1]
    else:
        # otherwise, the base is a directory with packages
        root_package = None

    toplevels = []
    for root, subs, files in os.walk(rootpath):
        if is_excluded(root, excludes):
            del subs[:]
            continue
        # document only Python module files
        py_files = sorted([f for f in files if path.splitext(f)[1] == '.py'])
        is_pkg = INITPY in py_files
        if is_pkg:
            py_files.remove(INITPY)
            py_files.insert(0, INITPY)
        elif root != rootpath:
            # only accept non-package at toplevel
            del subs[:]
            continue
        # remove hidden ('.') and private ('_') directories
        subs[:] = sorted(sub for sub in subs if sub[0] not in ['.', '_'])

        if is_pkg:
            # we are in a package with something to document
            if subs or len(py_files) > 1 or not \
                shall_skip(path.join(root, INITPY)):
                subpackage = root[len(rootpath):].lstrip(path.sep).\
                    replace(path.sep, '.')
                create_package_file(root, root_package, subpackage,
                                    py_files, opts, subs)
                toplevels.append(makename(root_package, subpackage))
        else:
            # if we are at the root level, we don't require it to be a package
            assert root == rootpath and root_package is None
            for py_file in py_files:
                if not shall_skip(path.join(root, py_file)):
                    module = path.splitext(py_file)[0]
                    create_module_file(root, module, opts)
                    toplevels.append(module)

    return toplevels


def normalize_excludes(rootpath, excludes):
    """
    Normalize the excluded directory list:
    * must be either an absolute path or start with rootpath,
    * otherwise it is joined with rootpath
    * with trailing slash
    """
    f_excludes = []
    for exclude in excludes:
        if not path.isabs(exclude) and not exclude.startswith(rootpath):
            exclude = path.join(rootpath, exclude)
        f_excludes.append(path.normpath(exclude) + path.sep)
    return f_excludes


def is_excluded(root, excludes):
    """
    Check if the directory is in the exclude list.

    Note: by having trailing slashes, we avoid common prefix issues, like
          e.g. an exlude "foo" also accidentally excluding "foobar".
    """
    sep = path.sep
    if not root.endswith(sep):
        root += sep
    for exclude in excludes:
        if root.startswith(exclude):
            return True
    return False


def main(argv=sys.argv):
    """
    Parse and check the command line arguments.
    """
    parser = optparse.OptionParser(
        usage="""\
usage: %prog [options] -o <output_path> <module_path> [exclude_paths, ...]

Look recursively in <module_path> for Python modules and packages and create
one reST file with automodule directives per package in the <output_path>.

Note: By default this script will not overwrite already created files.""")

    parser.add_option('-o', '--output-dir', action='store', dest='destdir',
                      help='Directory to place all output', default='')
    parser.add_option('-d', '--maxdepth', action='store', dest='maxdepth',
                      help='Maximum depth of submodules to show in the TOC '
                      '(default: 4)', type='int', default=4)
    parser.add_option('-f', '--force', action='store_true', dest='force',
                      help='Overwrite all files')
    parser.add_option('-n', '--dry-run', action='store_true', dest='dryrun',
                      help='Run the script without creating files')
    parser.add_option('-T', '--no-toc', action='store_true', dest='notoc',
                      help='Don\'t create a table of contents file')
    parser.add_option('-s', '--suffix', action='store', dest='suffix',
                      help='file suffix (default: rst)', default='rst')
    parser.add_option('-F', '--full', action='store_true', dest='full',
                      help='Generate a full project with sphinx-quickstart')
    parser.add_option('-H', '--doc-project', action='store', dest='header',
                      help='Project name (default: root module name)')
    parser.add_option('-A', '--doc-author', action='store', dest='author',
                      type='str',
                      help='Project author(s), used when --full is given')
    parser.add_option('-V', '--doc-version', action='store', dest='version',
                      help='Project version, used when --full is given')
    parser.add_option('-R', '--doc-release', action='store', dest='release',
                      help='Project release, used when --full is given, '
                      'defaults to --doc-version')
    parser.add_option('-M', '--single-module-page', action='store_true', dest='module',
                      help='One extra page for each module')
    parser.add_option('-P', '--package-summary', action='store_true', dest='packagesummary',
                      help='Auto summary of sub packages additionally to toctree')


    (opts, args) = parser.parse_args(argv[1:])

    if not args:
        parser.error('A package path is required.')

    rootpath, excludes = args[0], args[1:]
    if not opts.destdir:
        parser.error('An output directory is required.')
    if opts.header is None:
        opts.header = path.normpath(rootpath).split(path.sep)[-1]
    if opts.suffix.startswith('.'):
        opts.suffix = opts.suffix[1:]
    if not path.isdir(rootpath):
        print >>sys.stderr, '%s is not a directory.' % rootpath
        sys.exit(1)
    if not path.isdir(opts.destdir):
        if not opts.dryrun:
            os.makedirs(opts.destdir)
    if not path.isabs(rootpath):
        rootpath=path.abspath(rootpath)
    excludes = normalize_excludes(rootpath, excludes)
    modules = recurse_tree(rootpath, excludes, opts)
    if opts.full:
        from sphinx import quickstart as qs
        modules.sort()
        prev_module = ''
        text = ''
        for module in modules:
            if module.startswith(prev_module + '.'):
                continue
            prev_module = module
            text += '   %s\n' % module
        d = dict(
            path = opts.destdir,
            sep  = False,
            dot  = '_',
            project = opts.header,
            author = opts.author or 'Author',
            version = opts.version or '',
            release = opts.release or opts.version or '',
            suffix = '.' + opts.suffix,
            master = 'index',
            epub = True,
            ext_autodoc = True,
            ext_viewcode = True,
            makefile = True,
            batchfile = True,
            mastertocmaxdepth = opts.maxdepth,
            mastertoctree = text,
        )
        if not opts.dryrun:
            qs.generate(d, silent=True, overwrite=opts.force)
    elif not opts.notoc:
        create_modules_toc_file(modules, opts)

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