Initial sphinx documentation.

doc/Readme.md

@@ -0,0 +1,6 @@
+#### jobmanager documentation
+To compile the documentation, run
+
+    python setup.py build_sphinx
+
+

doc/conf.py

@@ -0,0 +1,314 @@
+# -*- coding: utf-8 -*-
+#
+# project documentation build configuration file, created by
+# sphinx-quickstart on Sat Feb 22 09:35:49 2014.
+#
+# 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
+
+# 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('.'))
+
+
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.abspath(
+                    os.path.dirname(__file__)), '../')))
+
+sys.path.append(os.path.abspath('_extensions'))
+
+# include examples
+
+sys.path.append(os.path.abspath(os.path.dirname(__file__)+"/../examples"))
+
+
+# There should be a file "setup.py" that has the property "version"
+from setup import author, authors, description, name, version, year
+projectname = name
+projectdescription = description
+
+
+# -- 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.doctest',
+#    'sphinx.ext.coverage',
+#    'sphinx.ext.pngmath',
+#    'sphinx.ext.viewcode',
+#]
+
+
+extensions = [
+#              'matplotlib.sphinxext.mathmpl',
+#              'matplotlib.sphinxext.only_directives',
+#              'matplotlib.sphinxext.plot_directive',
+#               'ipython_directive',
+              'sphinx.ext.intersphinx',
+              'sphinx.ext.autodoc',
+#              'sphinx.ext.doctest',
+#              'ipython_console_highlighting',
+#               'sphinx.ext.pngmath',
+              'sphinx.ext.mathjax',
+#              'sphinx.ext.todo',
+#             'inheritance_diagram',
+#              'hidden_code_block',
+              'sphinx.ext.autosummary',
+#              'sphinx.ext.viewcode',
+              'numpydoc',
+              ]
+
+
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+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 = projectname
+copyright = year+", "+author
+
+# 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.
+# The full version, including alpha/beta/rc tags.
+release = version
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#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 = ['_build']
+
+# 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 = 'default'
+
+# 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
+
+
+# -- 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 = 'default'
+
+# 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 = {"stickysidebar": True}
+
+# 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
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = projectname+'doc'
+
+
+# -- 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': '',
+}
+
+# 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 = [
+  ('index', projectname+'.tex', projectname+' Documentation',
+   author, '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 = [
+    ('index', projectname, projectname+' Documentation',
+     authors, 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 = [
+  ('index', projectname, projectname+u' Documentation',
+   author, projectname,
+   projectdescription,
+   'Numeric'),
+]
+
+# 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
+
+# -----------------------------------------------------------------------------
+# intersphinx
+# -----------------------------------------------------------------------------
+_python_doc_base = 'http://docs.python.org/2.7'
+intersphinx_mapping = {
+    _python_doc_base: None,
+    'http://docs.scipy.org/doc/numpy': None,
+    'http://docs.scipy.org/doc/scipy/reference': None,
+}
+

doc/description.txt

@@ -0,0 +1 @@
+Easy distributed computing based on the python class SyncManager for remote communication and python module multiprocessing for local parallelism.

doc/index.rst

@@ -0,0 +1,87 @@
+jobmanager documentation
+========================
+
+
+Content
+-------
+.. toctree::
+   :maxdepth: 4
+   
+   index
+    
+For an alphabetically sorted list of all modules, classes, and 
+methods, see :ref:`genindex`.
+
+
+Main module
+-----------
+.. automodule:: jobmanager
+
+
+Progress monitoring
+-------------------
+.. automodule:: jobmanager.progress
+   :members:
+
+
+User Convenience
+-----------------
+Decorators
+~~~~~~~~~~
+.. automodule:: jobmanager.decorators
+   :members:
+   
+   
+ODE wrapper
+~~~~~~~~~~~
+.. automodule:: jobmanager.ode_wrapper
+   :members:
+
+
+Core modules
+------------
+jobmanager
+~~~~~~~~~~
+clients
+~~~~~~~
+.. automodule:: jobmanager.jobmanager
+   :members:
+
+clients
+~~~~~~~
+.. automodule:: jobmanager.clients
+   :members:
+
+
+servers
+~~~~~~~
+.. automodule:: jobmanager.servers
+   :members:
+
+
+persistentData
+~~~~~~~~~~~~~~
+.. automodule:: jobmanager.persistentData
+   :members:
+
+
+
+Examples
+--------
+
+simple example
+~~~~~~~~~~~~~~
+.. automodule:: simple_example
+Download: :download:`../examples/simple_example.py`.
+
+.. literalinclude:: ../examples/simple_example.py
+
+
+decorators
+~~~~~~~~~~
+.. automodule:: wrapper_example
+Download: :download:`../examples/wrapper_example.py`.
+
+.. literalinclude:: ../examples/wrapper_example.py
+
+

examples/wrapper_example.py

@@ -1,8 +1,11 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-""" How to wrap or decorate a function with a progress bar.
-"""
 from __future__ import division, print_function
+""" How to wrap or decorate a function with a progress bar.
+
+
+"""
+
 
 from os.path import split, dirname, abspath
 import sys

jobmanager/__init__.py

@@ -1,5 +1,28 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
+"""
+.. include:: ../doc/description.txt
+
+.. currentmodule:: jobmanager.jobmanager
+
+Scheduling across different processes/machines is implemented in the
+core modules :mod:`jobmanager.jobmanager`, :mod:`jobmanager.servers`,
+and :mod:`jobmanager.clients`.
+
+.. autosummary:: 
+    JobManager_Client
+    JobManager_Server
+
+.. figure::  ../doc/artwork/server_client_communication.png
+   :align:   center
+
+
+Progress classes are implemented in the :mod:`jobmanager.progress`
+submodule. Intuitive access to progress bars is facilitated with
+decorators (:mod:`jobmanager.decorators`).
+
+"""
+
 import warnings
 
 from .jm_version import __version__

jobmanager/decorators.py

@@ -10,7 +10,7 @@ import warnings
 from . import progress
 from .jobmanager import getCountKwargs, validCountKwargs
 
-__all__ = ["ProgressBar", "ProgressBarOverrideCount"]
+#__all__ = ["ProgressBar", "ProgressBarOverrideCount"]
 
 
 class ProgressBar(object):

setup.py

@@ -1,11 +1,20 @@
 #!/usr/bin/env python
+# -*- coding: utf-8 -*-
 # To create a distribution package for pip or easy-install:
 # python setup.py sdist
 from setuptools import setup, find_packages, Command
 from os.path import join, dirname, realpath
 from warnings import warn
 
+author = u"Richard Hartmann"
+authors = [author, u"Paul Müller"]
 name = 'jobmanager'
+description = 'Python job manager for parallel computing.'
+year = "2015"
+
+DIR = realpath(dirname(__file__))
+
+longdescription = open(join(DIR, "doc/description.txt"), "r").read().strip()
 
 class PyTest(Command):
     user_options = []
@@ -33,18 +42,15 @@ except:
 
 setup(
     name=name,
-    author='Richard Hartmann',
+    author=author,
-    #author_email='richard.hartmann...',
+    authors=authors,
     url='https://github.com/cimatosa/jobmanager',
     version=version,
     packages=[name],
     package_dir={name: name},
     license="MIT",
-    description='Python job manager for parallel computing.',
+    description=description,
-    long_description="""easy distributed computing based on the python
+    long_description=longdescription,
-class SyncManager for remote communication
-and python module multiprocessing for local
-parallelism.""",
     install_requires=["sqlitedict>=1.2.0", "NumPy>=1.5.1"],
     tests_require=["psutil"],
     keywords=["multiprocessing", "queue", "parallel", "distributed", "computing",