Commit f28f0e7c authored by André Anjos's avatar André Anjos 💬

Isolate dox on specific directory

parent a30c63aa
# 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."
# -*- 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)
.. 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`
......@@ -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.
.. 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:
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