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• bioservices-master
  • src
    • bioservices
      • omicsdi.py
      • pubchem.py
      • chembl.py
      • kegg.py
      • unichem.py
      • ena.py
      • util.py
      • mygeneinfo.py
      • attic
        • geneprof.py
        • miriam.py
        • README.txt
        • biomodels.py
      • mapping
        • mapping.py
        • mappers.py
        • __init__.py
      • chebi.py
      • biomart.py
      • quickgo.py
      • wikipathway.py
      • muscle.py
      • biodbnet.py
      • ensembl.py
      • xmltools.py
      • picr.py
      • eva.py
      • pathwaycommons.py
      • pfam.py
      • panther.py
      • arrayexpress.py
      • reactome.py
      • services.py
      • intact.py
      • apps
        • peptides.py
        • fasta.py
        • download_fasta.py
        • __init__.py
      • biomodels.py
      • pdbe.py
      • chembldb.py
      • clinvitae.py
      • eutils.py
      • dev
        • __init__.py
      • biocarta.py
      • omnipath.py
      • biogrid.py
      • _compat.py
      • uniprot.py
      • __init__.py
      • bigg.py
      • pride.py
      • psicquic.py
      • settings.py
      • pdb.py
      • chemspider.py
      • ncbiblast.py
      • hgnc.py
      • seqret.py
      • rhea.py
      • dbfetch.py
      • rnaseq_ebi.py
  • Makefile
  • examples
    • plot_kegg_relations.py
    • README.txt
  • LICENSE
  • test
    • test_quickgo.py
    • test_pathwaycommons.py
    • test_eva.py
    • test_pubchem.py
    • test_picr.py
    • test_kegg.py
    • test_panther.py
    • test_clinvitae.py
    • attic
      • _test_miriam.py
      • _test_geneprof.py
    • test_arrayexpress.py
    • test_uniprot.py
    • test_xmltools.py
    • test_dbfetch.py
    • test_eutils.py
    • test_bigg.py
    • test_apps_download.py
    • test_rhea.py
    • test_ensembl.py
    • test_unichem.py
    • test_wikipathway.py
    • test_rnaseq_ebi.py
    • test_biodbnet.py
    • test_pdb.py
    • test_ncbiblast.py
    • test_chemspider.py
    • test_pfam.py
    • test_seqret.py
    • test_services.py
    • test_biocarta.py
    • __init__.py
    • test_biomart.py
    • test_apps_fasta.py
    • test_pdbe.py
    • test_biogrid.py
    • test_mygeneinfo.py
    • pytest.ini
    • settings.py
    • test_muscle.py
    • test_ena.py
    • test_hgnc.py
    • test_psicquic.py
    • test_omicsdi.py
    • test_intact_complex.py
    • test_chebi.py
    • test_biomodels.py
    • test_apps_peptides.py
    • test_reactome.py
    • test_chembl.py
    • test_omnipath.py
    • test_pride.py
  • .readthedocs.yml
  • README.rst
  • notebooks
    • EUtils.ipynb
    • introduction
      • Overview.ipynb
    • ENA
      • ENA.ipynb
  • setup.py
  • requirements-dev.txt
  • setup.cfg
  • HISTORY.rst
  • .travis.yml
  • requirements.txt
  • .gitignore
  • MANIFEST.in
  • doc
    • notebooks.rst
    • faqs.rst
    • Makefile
    • source
      • _static
        • copybutton.js
    • make.bat
    • biopython.rst
    • developers.rst
    • protein.rst
    • ChangeLog.rst
    • convertor_tutorial.rst
    • pymol.rst
    • contributors.rst
    • notebooks
      • Gene_Mapping.ipynb
      • Entrez_EUtils.ipynb
      • NCBIBlast.ipynb
      • MUSCLE.ipynb
      • ChEMBL.ipynb
      • BioModels.ipynb
      • KEGG.ipynb
      • UniProt.ipynb
      • Ensembl.ipynb
      • BioMart.ipynb
    • biomodels.rst
    • applications.rst
    • galaxy
      • tool_conf.xml
      • uniprot.xml
      • uniprot.py
    • geneprof_tutorial.rst
    • compound_tutorial.rst
    • tutorials.rst
    • quickstart.rst
    • references.rst
    • index.rst
    • conf.py
    • galaxy.rst
    • biomart.rst
    • _static
      • copybutton.js
    • external_references.rst
    • kegg_tutorial.rst

# -*- coding: utf-8 -*-
#
# documentation build configuration file, created by
# sphinx-quickstart on Wed Aug 10 16:58:13 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
import sphinx

sys.path.insert(0, os.path.abspath('sphinxext'))

import sphinx_gallery
# 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.

pkg_name = "bioservices"

# This is for ReadTheDoc
import matplotlib
matplotlib.use('Agg')

on_rtd = os.environ.get("READTHEDOCS", None) == "True"



import pkg_resources
version = pkg_resources.require(pkg_name)[0].version
release = version
author = "Thomas Cokelaer, Lea M. Harder, Jordi Serra-Musach, \nDennis Pultz"
title = "BioServices"
copyright = author + ", 2012-2020"
project = pkg_name

import easydev
from easydev import get_path_sphinx_themes


# -- 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.imgmath'  # only available for sphinx >= 1.4
                  if sphinx.version_info[:2] >= (1, 4)
                  else 'sphinx.ext.pngmath'),
    'sphinx.ext.coverage',
    'sphinx.ext.doctest',
    'sphinx.ext.intersphinx',
    'sphinx.ext.todo',
    'sphinx.ext.ifconfig',
    'sphinx.ext.viewcode',
    "numpydoc.numpydoc",
    'matplotlib.sphinxext.plot_directive',
    'sphinx.ext.autosummary',
    'sphinx_gallery.gen_gallery',
    ]
# note that the numpy directives is buggy. Example: class and init are not recognised as two entities for the autoclass_content=both here below


todo_include_todos=True
jscopybutton_path = "copybutton.js"
autoclass_content = 'both'

# 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 = project
copyright = copyright

# 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 = 'Current version: ' + str(version)
# The full version, including alpha/beta/rc tags.
release = release

# 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 documents that shouldn't be included in the build.
#unused_docs = []


# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_trees = ['build']
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 = False

# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
show_authors = True

# 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 = ["bioservices."]

# -- sphinx gallery ------------------------------------------------------------

# By default, examples are not built locally. You can set plot_gallery to True
# to force their creation. Note that it requires singularity or dot to be
# installed. Fixes https://github.com/biokit/bioconvert/issues/153

plot_gallery = False

#sphinx_gallery_conf = {
#    "doc_module": "bioservices",
#    'backreferences_dir': os.path.join("modules", "generated"),
#    #"examples_dirs": "examples",
#    #"gallery_dirs": "auto_examples",
#}

# Get rid of spurious warnings due to some interaction between
# autosummary and numpydoc. See
# https://github.com/phn/pytpm/issues/3#issuecomment-12133978 for more
# details
numpydoc_show_class_members = False


# solution from nilearn
def touch_example_backreferences(app, what, name, obj, options, lines):
    # generate empty examples files, so that we don't get
    # inclusion errors if there are no examples for a class / module
    examples_path = os.path.join(app.srcdir, "modules", "generated",
                                 "%s.examples" % name)
    if not os.path.exists(examples_path):
        # touch file
        os.makedirs(os.path.dirname(examples_path), exist_ok=True)
        open(examples_path, 'w').close()


# Add the 'copybutton' javascript, to hide/show the prompt in code
# examples
def setup(app):
    app.add_javascript('copybutton.js')
    app.connect('autodoc-process-docstring', touch_example_backreferences)

# -- Options for HTML output ---------------------------------------------------

# The theme to use for HTML and HTML Help pages.  Major themes that come with
# Sphinx are currently 'default' and 'sphinxdoc'.
html_theme = 'standard'
on_rtd = os.environ.get("READTHEDOCS", None) == True
if not on_rtd:
    import sphinx_rtd_theme
    html_theme = 'sphinx_rtd_theme'
    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
else:
    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.
# the user theme contains the otpions 'homepage', which is populated here
#html_theme_options = {'homepage': init_sphinx.url}
# Add any paths that contain custom themes here, relative to this directory.
html_theme_path = [get_path_sphinx_themes()]



# 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".

# the copybutton.js must be copied there:
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_index = 'index.html'

#Custom sidebar templates, maps page names to templates.
html_sidebars = {
                    'index': [ 'indexsidebar.html'], 
                    'contents':'indexsidebar.html',
}
# Additional templates that should be rendered to pages, maps page names to
# template names.
#html_additional_pages = {   'index': 'index.html'}


# If false, no module index is generated.
html_use_modindex = 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
html_copy_source = 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 = 'doc'


# -- Options for LaTeX output --------------------------------------------------

# NOT in original quickstart
pngmath_use_preview = True

# 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', 'main.tex', title,
   author, 'manual'),
]

latex_elements = { 'inputenc': '\\usepackage[utf8]{inputenc}' }
#latex_elements["latex_paper_size"] = "a4"
# 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', project, project,
     [author], 1)
]


# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {'http://docs.python.org/': None}