Commit 1adef6b5 authored by Hanna  JULIENNE's avatar Hanna JULIENNE

add sphinx skeleton

parent 658e9bce
# Minimal makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
SPHINXPROJ = Peppa-PIG
SOURCEDIR = source
BUILDDIR = build
# Put it first so that "make" without argument is like "make help".
help:
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
.PHONY: help Makefile
# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file
@ECHO OFF
pushd %~dp0
REM Command file for Sphinx documentation
if "%SPHINXBUILD%" == "" (
set SPHINXBUILD=sphinx-build
)
set SOURCEDIR=source
set BUILDDIR=build
set SPHINXPROJ=Peppa-PIG
if "%1" == "" goto help
%SPHINXBUILD% >NUL 2>NUL
if errorlevel 9009 (
echo.
echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
echo.installed, then set the SPHINXBUILD environment variable to point
echo.to the full path of the 'sphinx-build' executable. Alternatively you
echo.may add the Sphinx directory to PATH.
echo.
echo.If you don't have Sphinx installed, grab it from
echo.http://sphinx-doc.org/
exit /b 1
)
%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
goto end
:help
%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
:end
popd
impute\_jass.imputation\_launcher
=================================
.. automodule:: impute_jass.imputation_launcher
.. rubric:: Classes
.. autosummary::
ImputationLauncher
\ No newline at end of file
impute\_jass.ld\_matrix
=======================
.. automodule:: impute_jass.ld_matrix
.. rubric:: Functions
.. autosummary::
generate_genome_matrices
generate_sparse_matrix
launch_plink_ld
\ No newline at end of file
impute\_jass.stat\_models
=========================
.. automodule:: impute_jass.stat_models
.. rubric:: Functions
.. autosummary::
check_inversion
compute_mu
compute_var
impg_model
var_in_boundaries
\ No newline at end of file
impute\_jass.windows
====================
.. automodule:: impute_jass.windows
.. rubric:: Functions
.. autosummary::
compute_window_and_size
empty_imputed_dataframe
format_result_df
impg_like_imputation
in_region
ld_region_centered_window_imputation
parse_region_position
prepare_zscore_for_imputation
print_progression
realigned_zfiles_on_panel
\ No newline at end of file
# -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config
# -- Path setup --------------------------------------------------------------
# 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.
#
import os
import sys
sys.path.insert(0, os.path.abspath('../..'))
#print(os.path.abspath('../..'))
# -- Project information -----------------------------------------------------
project = 'Peppa-PIG'
copyright = '2018, hjulienne'
author = 'hjulienne'
# The short X.Y version
version = ''
# The full version, including alpha/beta/rc tags
release = '1.0'
# -- 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.coverage',
'sphinx.ext.mathjax',
'sphinx.ext.viewcode',
'sphinx.ext.autosummary'
]
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
# source_suffix = ['.rst', '.md']
source_suffix = '.rst'
# The master toctree document.
master_doc = 'index'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path .
exclude_patterns = []
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
# -- 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 = 'alabaster'
# 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 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']
# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
# The default sidebars (for documents that don't match any pattern) are
# defined by theme itself. Builtin themes are using these templates by
# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
# 'searchbox.html']``.
#
# html_sidebars = {}
# -- Options for HTMLHelp output ---------------------------------------------
# Output file base name for HTML help builder.
htmlhelp_basename = 'Peppa-PIGdoc'
# -- Options for LaTeX output ------------------------------------------------
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
#
# 'papersize': 'letterpaper',
# The font size ('10pt', '11pt' or '12pt').
#
# 'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
#
# 'preamble': '',
# Latex figure (float) alignment
#
# 'figure_align': 'htbp',
}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
(master_doc, 'Peppa-PIG.tex', 'Peppa-PIG Documentation',
'hjulienne', 'manual'),
]
# -- Options for manual page output ------------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
(master_doc, 'peppa-pig', 'Peppa-PIG Documentation',
[author], 1)
]
# -- Options for Texinfo output ----------------------------------------------
# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
(master_doc, 'Peppa-PIG', 'Peppa-PIG Documentation',
author, 'Peppa-PIG', 'One line description of project.',
'Miscellaneous'),
]
# -- Extension configuration -------------------------------------------------i
autoclass_content = "both" # include both class docstring and __init__
autodoc_default_flags = [
# Make sure that any autodoc declarations show the right members
"members",
"inherited-members",
"private-members",
"show-inheritance",
]
autosummary_generate = True # Make _autosummary files and include them
.. Peppa-PIG documentation master file, created by
sphinx-quickstart on Mon Aug 20 16:17:59 2018.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to Peppa-PIG's documentation!
=====================================
.. toctree::
:maxdepth: 2
:caption: Contents:
What is Peppa-PIG ?
===================
Installation
============
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
.. automodule:: impute_jass
:members:
.. autosummary::
:toctree: _autosummary
"""
.. autosummary::
:toctree: _autosummary
imputation_launcher
ld_matrix
stat_models
windows
"""
import impute_jass.ld_matrix as LD
import impute_jass.stat_models as model
import impute_jass.windows
......
......@@ -17,5 +17,4 @@ setup(name='impute_jass',
'impute_jass = impute_jass.__main__:main'
]
}
)
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