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Max Burnette
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Merge branch 'master' into add-delete-methods
# Conflicts: # pyclowder/datasets.py
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README.md

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Besides wrapping often used api calls in convenient python calls, we have also added some code to make it easy to
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create new extractors.
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## Setup
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Install pyClowder2 on your system:
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```
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pip install -r requirements.txt
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python setup.py install
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```
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## Example Extractor
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Following is an example of the WordCount extractor. This example will allow the user to specify from the command line

docs/Makefile

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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line.
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SPHINXOPTS =
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SPHINXBUILD = python -msphinx
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SPHINXPROJ = pyClowder
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SOURCEDIR = source
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BUILDDIR = build
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: help Makefile
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/requirements.txt

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enum34==1.1.6
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Sphinx==1.6.2
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pika==0.10.0
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PyYAML==3.11

docs/source/conf.py

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# -*- coding: utf-8 -*-
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#
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# pyClowder documentation build configuration file, created by
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# sphinx-quickstart on Thu Sep 28 15:55:01 2017.
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#
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# This file is execfile()d with the current directory set to its
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# containing dir.
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#
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# Note that not all possible configuration values are present in this
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# autogenerated file.
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#
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# All configuration values have a default; values that are commented out
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# serve to show the default.
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# If extensions (or modules to document with autodoc) are in another directory,
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# add these directories to sys.path here. If the directory is relative to the
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# documentation root, use os.path.abspath to make it absolute, like shown here.
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#
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import os
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import sys
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sys.path.insert(0, os.path.abspath('../..'))
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sys.path.insert(0, os.path.abspath('../../pyclowder'))
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# -- General configuration ------------------------------------------------
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# If your documentation needs a minimal Sphinx version, state it here.
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#
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# needs_sphinx = '1.0'
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = ['sphinx.ext.autodoc',
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'sphinx.ext.doctest',
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'sphinx.ext.intersphinx']
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ['_templates']
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# The suffix(es) of source filenames.
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# You can specify multiple suffix as a list of string:
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#
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# source_suffix = ['.rst', '.md']
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source_suffix = '.rst'
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# The master toctree document.
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master_doc = 'index'
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# General information about the project.
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project = u'pyClowder'
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copyright = u'2017, Max Burnette, Rob Kooper, Luigi Marini'
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author = u'Max Burnette, Rob Kooper, Luigi Marini'
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# The version info for the project you're documenting, acts as replacement for
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# |version| and |release|, also used in various other places throughout the
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# built documents.
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#
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# The short X.Y version.
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version = u'2.0'
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# The full version, including alpha/beta/rc tags.
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release = u'2.0'
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# The language for content autogenerated by Sphinx. Refer to documentation
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# for a list of supported languages.
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#
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# This is also used if you do content translation via gettext catalogs.
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# Usually you set "language" from the command line for these cases.
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language = None
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This patterns also effect to html_static_path and html_extra_path
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exclude_patterns = []
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# The name of the Pygments (syntax highlighting) style to use.
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pygments_style = 'sphinx'
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# If true, `todo` and `todoList` produce output, else they produce nothing.
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todo_include_todos = False
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# -- Options for HTML output ----------------------------------------------
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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#
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html_theme = 'alabaster'
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# Theme options are theme-specific and customize the look and feel of a theme
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# further. For a list of options available for each theme, see the
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# documentation.
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#
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# html_theme_options = {}
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# so a file named "default.css" will overwrite the builtin "default.css".
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html_static_path = ['_static']
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# Custom sidebar templates, must be a dictionary that maps document names
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# to template names.
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#
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# This is required for the alabaster theme
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# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
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html_sidebars = {
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'**': [
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'about.html',
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'navigation.html',
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'relations.html', # needs 'show_related': True theme option to display
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'searchbox.html',
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'donate.html',
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]
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}
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# -- Options for HTMLHelp output ------------------------------------------
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# Output file base name for HTML help builder.
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htmlhelp_basename = 'pyClowderdoc'
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# -- Options for LaTeX output ---------------------------------------------
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latex_elements = {
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# The paper size ('letterpaper' or 'a4paper').
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#
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# 'papersize': 'letterpaper',
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# The font size ('10pt', '11pt' or '12pt').
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#
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# 'pointsize': '10pt',
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# Additional stuff for the LaTeX preamble.
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#
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# 'preamble': '',
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# Latex figure (float) alignment
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#
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# 'figure_align': 'htbp',
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}
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# Grouping the document tree into LaTeX files. List of tuples
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# (source start file, target name, title,
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# author, documentclass [howto, manual, or own class]).
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latex_documents = [
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(master_doc, 'pyClowder.tex', u'pyClowder Documentation',
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u'Max Burnette, Rob Kooper, Luigi Marini', 'manual'),
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]
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# -- Options for manual page output ---------------------------------------
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# One entry per manual page. List of tuples
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# (source start file, name, description, authors, manual section).
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man_pages = [
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(master_doc, 'pyclowder', u'pyClowder Documentation',
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[author], 1)
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]
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# -- Options for Texinfo output -------------------------------------------
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# Grouping the document tree into Texinfo files. List of tuples
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# (source start file, target name, title, author,
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# dir menu entry, description, category)
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texinfo_documents = [
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(master_doc, 'pyClowder', u'pyClowder Documentation',
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author, 'pyClowder', 'One line description of project.',
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'Miscellaneous'),
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]
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# -- Options for Epub output ----------------------------------------------
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# Bibliographic Dublin Core info.
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epub_title = project
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epub_author = author
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epub_publisher = author
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epub_copyright = copyright
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# The unique identifier of the text. This can be a ISBN number
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# or the project homepage.
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#
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# epub_identifier = ''
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# A unique identification for the text.
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#
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# epub_uid = ''
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# A list of files that should not be packed into the epub file.
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epub_exclude_files = ['search.html']
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# Example configuration for intersphinx: refer to the Python standard library.
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intersphinx_mapping = {'https://docs.python.org/': None}

docs/source/index.rst

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.. pyClowder documentation master file, created by
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sphinx-quickstart on Thu Sep 28 15:55:01 2017.
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You can adapt this file completely to your liking, but it should at least
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contain the root `toctree` directive.
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Pyclowder
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=========
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Pyclowder is a Python library to simplify interacting with `Clowder <https://clowder.ncsa.illinois.edu/>`_, an open source
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data management system for research data.
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.. toctree::
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:maxdepth: 2
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:caption: Contents:
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modules
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Indices and tables
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==================
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* :ref:`genindex`
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* :ref:`modindex`
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* :ref:`search`

docs/source/modules.rst

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pyclowder
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=========
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.. toctree::
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:maxdepth: 4
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pyclowder
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docs/source/pyclowder.rst

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PyClowder package
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=================
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Submodules
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----------
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pyclowder.client module
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-----------------------
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.. automodule:: pyclowder.client
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:members:
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:undoc-members:
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:show-inheritance:
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pyclowder.collections module
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----------------------------
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.. automodule:: pyclowder.collections
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:members:
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:undoc-members:
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:show-inheritance:
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pyclowder.connectors module
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---------------------------
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.. automodule:: pyclowder.connectors
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:members:
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:undoc-members:
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:show-inheritance:
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pyclowder.datasets module
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-------------------------
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.. automodule:: pyclowder.datasets
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:members:
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:undoc-members:
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:show-inheritance:
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pyclowder.extractors module
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---------------------------
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.. automodule:: pyclowder.extractors
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:members:
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:undoc-members:
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:show-inheritance:
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pyclowder.files module
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----------------------
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.. automodule:: pyclowder.files
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:members:
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:undoc-members:
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:show-inheritance:
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pyclowder.sections module
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-------------------------
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.. automodule:: pyclowder.sections
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:members:
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:undoc-members:
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:show-inheritance:
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pyclowder.utils module
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----------------------
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.. automodule:: pyclowder.utils
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:members:
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:undoc-members:
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:show-inheritance:
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Module contents
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---------------
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.. automodule:: pyclowder
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:members:
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:undoc-members:
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:show-inheritance:

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