Isolate dox on specific directory

docs/Makefile

+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = PYTHONPATH=.. /idiap/group/torch5spro/nightlies/externals/v2/linux-x86_64/pyenv/bin/sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest
+
+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 "  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 "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	-rm -rf $(BUILDDIR)/*
+
+html:
+	$(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/GridTk.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/GridTk.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/GridTk"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/GridTk"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(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:
+	$(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."
+
+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."
+
+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."

docs/conf.py

+# -*- coding: utf-8 -*-
+#
+# Torch5spro documentation build configuration file, created by
+# sphinx-quickstart on Mon Mar 21 18:07:34 2011.
+#
+# 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, 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('.'))
+
+# -- 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.todo',
+  'sphinx.ext.coverage',
+  'sphinx.ext.pngmath',
+  'sphinx.ext.ifconfig',
+  'sphinx.ext.autodoc',
+  'sphinx.ext.autosummary',
+  'sphinx.ext.doctest',
+  ]
+
+# The viewcode extension appeared only on Sphinx >= 1.0.0
+import sphinx
+if sphinx.__version__ >= "1.0":
+  extensions.append('sphinx.ext.viewcode')
+
+# If we are on OSX, the 'dvipng' path maybe different
+dvipng_osx = '/opt/local/libexec/texlive/binaries/dvipng'
+if os.path.exists(dvipng_osx): pngmath_dvipng = dvipng_osx
+
+# 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 = u'GridTk'
+import time
+copyright = u'%s, Idiap Research Institute' % time.strftime('%Y')
+
+# 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 = '0.1'
+# The full version, including alpha/beta/rc tags.
+release = 'beta'
+
+# 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 = []
+
+# 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 = []
+
+
+# -- 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 = {}
+
+# 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']
+
+# 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 = 'gridtkdoc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+# The paper size ('letter' or 'a4').
+#latex_paper_size = 'letter'
+
+# The font size ('10pt', '11pt' or '12pt').
+#latex_font_size = '10pt'
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+  ('index', 'gridtk.tex', u'Grid TookKit Documentation',
+   u'Idiap Research Institute', '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
+
+# Additional stuff for the LaTeX preamble.
+#latex_preamble = ''
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+# Included after all input documents
+rst_epilog = """
+.. Some variables
+.. |project| replace:: GridTk
+.. |torchweb| replace:: http://www.idiap.ch/software/torch5spro
+.. |current-year| date:: %Y
+"""
+
+# -- Options for manual page output --------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index', 'torch5spro', u'GridTk Documentation',
+     [u'Idiap Research Institute'], 1)
+]
+
+# Skips selected members in auto-generated documentation. Unfortunately, old
+# versions of Boost.Python will note generate a __self__ member for static
+# methods and that screws-up Sphinx processing
+def skip_member(app, what, name, obj, skip, options):
+  # We don't use this technique if the version of Sphinx is relatively new
+  if sphinx.__version__ >= "1.0": return False
+
+  # Else, we have to remove objects that do not have a __self__ attribute set
+  import types
+  if isinstance(obj, types.BuiltinFunctionType) and \
+    not hasattr(obj, '__self__') and what == 'class':
+      app.warn("Skipping %s %s (no __self__)" % (what, name))
+      return True
+
+  return False
+
+def setup(app):
+  app.connect('autodoc-skip-member', skip_member)

docs/index.rst

+.. GridTk documentation master file, created by
+   sphinx-quickstart on Thu Aug 25 15:51:27 2011.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to GridTk's documentation!
+==================================
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+
+   manual
+   program
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+

readme.rst → docs/manual.rst

@@ -32,7 +32,7 @@ To interact with the Job Manager we use the `jman` utility. Make sure to have
 your shell environment setup to reach it w/o requiring to type-in the full
 path. The first task you may need to pursue is to submit jobs. Here is how:
 
-.. code-block:: shell
+.. code-block:: sh
 
   $ jman torch -- dbmanage.py --help
   Submitted (torch'd) 6151645 @all.q (0 seconds ago) -S /usr/bin/python /idiap/group/torch5spro/nightlies/last/bin/shell.py -- dbmanage.py --help
@@ -55,7 +55,7 @@ Once the job has been submitted you will noticed a database file (by default
 called `.jobmanager.db`) has been created in the current working directory. It
 contains the information for the job you just submitted:
 
-.. code-block:: shell
+.. code-block:: sh
 
   $ jman list
   job-id   queue  age                         arguments                       
@@ -74,7 +74,7 @@ it is monitoring. Finished jobs will be reported to the screen and removed from
 the job manager database and placed on a second database (actually two)
 containing jobs that failed and jobs that succeeded.
 
-.. code-block:: shell
+.. code-block:: sh
   
   $ jman refresh
   These jobs require attention:
@@ -93,7 +93,7 @@ requires attention. If jobs fail, they are copied to a database named
 `failure.db` in the current directory. Otherwise, they are copied to
 `success.db`. You can inspect the job log files like this:
 
-.. code-block:: shell
+.. code-block:: sh
 
   $ jman explain failure.db
   Job 6151645 @all.q (34 minutes ago) -S /usr/bin/python /idiap/group/torch5spro/nightlies/last/bin/shell.py -- dbmanage.py --help
@@ -117,7 +117,7 @@ If you are convinced the job did not work because of external conditions (e.g.
 temporary network outage), you may re-submit it, *exactly* like it was
 submitted the first time:
 
-.. code-block:: shell
+.. code-block:: sh
 
   $ jman resubmit --clean failure.db
   Re-submitted job 6151663 @all.q (1 second ago) -S /usr/bin/python /idiap/group/torch5spro/nightlies/last/bin/shell.py -- dbmanage.py --help
@@ -136,7 +136,7 @@ The job in question will not work no matter how many times we re-submit it. It
 is not a temporary error. In these circumstances, I may just want to clean the
 job and do something else. The job manager is here for you again:
 
-.. code-block:: shell
+.. code-block:: sh
 
   $ jman cleanup --remove-job failure.db
   Cleaning-up logs for job 6151663 @all.q (5 minutes ago) -S /usr/bin/python /idiap/group/torch5spro/nightlies/last/bin/shell.py -- dbmanage.py --help
@@ -147,34 +147,3 @@ job and do something else. The job manager is here for you again:
 Inspection on the current directory will now show you everything concerning the
 said job is gone.
 
-Programatically submit and query for jobs
------------------------------------------
-
-The Job Manager is part of the `gridtk` framework, which is a python library to
-help submitting, tracking and querying SGE. Here is quick example on how to use
-the `gridtk` framework:
-
-.. code-block:: python
-
-  # This variable points to the torch5spro root directory you want to use
-  TORCH = '/idiap/group/torch5spro/nightlies/last'
-
-  from gridtk.manager import JobManager
-
-  # This helps constructing the command line with bracket'ed by Torch
-  from gridtk.tools import make_torch_wrapper
-
-  man = JobManager()
-  command = ['dbmange.py', '--help']
-  command, kwargs = make_torch_wrapper(TORCH, False, command, kwargs)
-
-  # For more options look do help(gridtk.qsub)
-  job = man.submit(command, cwd=True, stdout='logs', name='testjob')
-
-You can do, programatically, everything you can do with the job manager just
-browse the help messages and the `jman` script for more information.
-
-.. note::
-
-  To be able to import the `gridtk` library, you must have it on your
-  PYTHONPATH.

docs/program.rst

+.. vim: set fileencoding=utf-8 :
+.. Andre Anjos <andre.anjos@idiap.ch>
+.. Thu 25 Aug 2011 15:58:21 CEST 
+
+=======================
+ The GridTk User Guide
+=======================
+
+The `gridtk` framework is a python library to help submitting, tracking and
+querying SGE. Here is quick example on how to use the `gridtk` framework:
+
+.. code-block:: python
+
+  # This variable points to the torch5spro root directory you want to use
+  TORCH = '/idiap/group/torch5spro/nightlies/last'
+
+  from gridtk.manager import JobManager
+
+  # This helps constructing the command line with bracket'ed by Torch
+  from gridtk.tools import make_torch_wrapper
+
+  man = JobManager()
+  command = ['dbmange.py', '--help']
+  command, kwargs = make_torch_wrapper(TORCH, False, command, kwargs)
+
+  # For more options look do help(gridtk.qsub)
+  job = man.submit(command, cwd=True, stdout='logs', name='testjob')
+
+You can do, programatically, everything you can do with the job manager just
+browse the help messages and the `jman` script for more information.
+
+.. note::
+
+  To be able to import the `gridtk` library, you must have it on your
+  PYTHONPATH.
+
+Reference Manual
+----------------
+
+API to the Job Manager
+======================
+
+.. automodule:: gridtk.manager
+  :members:
+
+Middleware
+==========
+
+.. automodule:: gridtk.tools
+  :members:
+
+Low-level Utilities
+===================
+
+.. automodule:: gridtk.setshell
+  :members: