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Commit f28f0e7c authored by André Anjos's avatar André Anjos :speech_balloon:
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Isolate dox on specific directory

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# 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 ...@@ -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 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: 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 $ 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 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 ...@@ -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 called `.jobmanager.db`) has been created in the current working directory. It
contains the information for the job you just submitted: contains the information for the job you just submitted:
.. code-block:: shell .. code-block:: sh
$ jman list $ jman list
job-id queue age arguments job-id queue age arguments
...@@ -74,7 +74,7 @@ it is monitoring. Finished jobs will be reported to the screen and removed from ...@@ -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) the job manager database and placed on a second database (actually two)
containing jobs that failed and jobs that succeeded. containing jobs that failed and jobs that succeeded.
.. code-block:: shell .. code-block:: sh
$ jman refresh $ jman refresh
These jobs require attention: These jobs require attention:
...@@ -93,7 +93,7 @@ requires attention. If jobs fail, they are copied to a database named ...@@ -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 `failure.db` in the current directory. Otherwise, they are copied to
`success.db`. You can inspect the job log files like this: `success.db`. You can inspect the job log files like this:
.. code-block:: shell .. code-block:: sh
$ jman explain failure.db $ 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 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. ...@@ -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 temporary network outage), you may re-submit it, *exactly* like it was
submitted the first time: submitted the first time:
.. code-block:: shell .. code-block:: sh
$ jman resubmit --clean failure.db $ 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 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 ...@@ -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 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: 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 $ 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 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: ...@@ -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 Inspection on the current directory will now show you everything concerning the
said job is gone. 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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