add sphinx skeleton

impute_jass/doc/Makefile

+# 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

impute_jass/doc/make.bat

+@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/doc/source/_autosummary/impute_jass.imputation_launcher.rst

+impute\_jass.imputation\_launcher
+=================================
+
+.. automodule:: impute_jass.imputation_launcher
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Classes
+
+   .. autosummary::
+   
+      ImputationLauncher
+   
+   
+
+   
+   
+   
\ No newline at end of file

impute_jass/doc/source/_autosummary/impute_jass.ld_matrix.rst

+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/doc/source/_autosummary/impute_jass.stat_models.rst

+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/doc/source/_autosummary/impute_jass.windows.rst

+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

impute_jass/doc/source/conf.py

+# -*- 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

impute_jass/doc/source/index.rst

+.. 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

impute_jass/impute_jass/__init__.py

+"""
+
+.. 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

impute_jass/setup.py

@@ -17,5 +17,4 @@ setup(name='impute_jass',
             'impute_jass = impute_jass.__main__:main'
           ]
       }
-
       )