[DOC] Initial documentation setup

.gitignore

@@ -10,3 +10,4 @@ dist/*
 localtest
 .pytest_cache/
 __pycache__/
+_build/

README.rst

@@ -0,0 +1,82 @@
+peakdet: A toolbox for physiological peak detection analyses
+============================================================
+
+This package is designed for use in the reproducible processing and analysis of
+physiological data, like those collected from respiratory belts, pulse
+photoplethysmography, or electrocardiogram (ECG/EKG) monitors.
+
+.. image:: https://travis-ci.org/rmarkello/peakdet.svg?branch=master
+   :target: https://travis-ci.org/rmarkello/peakdet
+.. image:: https://codecov.io/gh/rmarkello/peakdet/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/rmarkello/peakdet
+.. image:: https://readthedocs.org/projects/peakdet/badge/?version=latest
+   :target: http://peakdet.readthedocs.io/en/latest
+.. image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg
+   :target: https://www.gnu.org/licenses/gpl-3.0
+
+.. _overview:
+
+Overview
+--------
+
+Physiological data are messy and prone to artifact (e.g.,) movement in
+respiration and pulse, ectopic beats in ECG). Despite leaps and bounds in
+recent algorithms for processing these data there still exists a need for
+manual inspection to ensure such artifacts have been appropriately removed.
+Because of this manual intervention step, understanding exactly what happened
+to go from "raw" data to processed, "analysis-ready" data can often be
+difficult or impossible. This toolbox aims to provide a set of tools that will
+work with a variety of input data to reproducibly generate manually-corrected,
+analysis-ready physiological data.
+
+.. _development:
+
+Development and getting involved
+--------------------------------
+
+This package has been largely developed in the spare time of a single graduate
+student (`@rmarkello <https://github.com/rmarkello>`_) with help from some
+incredible `contributors <https://github.com/rmarkello/peakdet/graphs/
+contributors>`_. While it would be |sparkles| amazing |sparkles| if anyone else
+finds it helpful, given the limited time constraints of graduate school, the
+current package is not currently accepting requests for new features.
+
+However, if you're interested in getting involved in the project, we're
+thrilled to welcome new contributors! You should start by reading our
+`contributing guidelines <https://github.com/rmarkello/peakdet/blob/master/
+CONTRIBUTING.md>`_ and `code of conduct <https://github.com/rmarkello/peakdet/
+blob/master/CODE_OF_CONDUCT.md>`_. Once you're done with that, take a look at
+our `issues <https://github.com/rmarkello/peakdet/issues>`_ to see if there's
+anything you might like to work on. Alternatively, if you've found a bug, are
+experiencing a problem, or have a question, create a new issue with some
+information about it!
+
+.. _acknowledgments:
+
+Acknowledgments
+---------------
+
+While this package was initially created in 2016, some of the behind-the-scenes
+functions in the project were translated from the `PhysIO <https://github.com/
+translationalneuromodeling/tapas/tree/master/PhysIO>`_ MATLAB toolbox. As such,
+if you use this code it would be good to (1) provide a link back to the
+``peakdet`` repostiory with the version of the code used, and (2) cite `their
+paper <http://www.sciencedirect.com/science/article/pii/S016502701630259X>`_:
+
+.. [1] Kasper, L., Bollmann, S., Diaconescu, A. O., Hutton, C., Heinzle, J.,
+   Iglesias, S., ... & Stephan, K. E. (2017). The PhysIO toolbox for modeling
+   physiological noise in fMRI data. Journal of Neuroscience Methods, 276,
+   56-72.
+
+.. _licensing:
+
+License Information
+-------------------
+
+This codebase is licensed under the GNU General Public License version 3.
+The full license can be found in the `LICENSE <https://github.com/rmarkello/
+peakdet/blob/master/LICENSE>`_ file in the ``peakdet`` distribution.
+
+All trademarks referenced herein are property of their respective holders.
+
+.. |sparkles| replace:: ✨

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = peakdet
+SOURCEDIR     = .
+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)

docs/api.rst

@@ -0,0 +1,33 @@
+.. _api_ref:
+
+.. currentmodule:: peakdet
+
+API
+===
+
+Physiological data
+------------------
+
+.. autoclass:: peakdet.Physio
+
+Loading data
+------------
+
+.. autofunction:: peakdet.load_physio
+.. autofunction:: peakdet.load_history
+.. autofunction:: peakdet.load_rtpeaks
+
+Processing data
+---------------
+
+.. autofunction:: peakdet.interpolate_physio
+.. autofunction:: peakdet.filter_physio
+.. autofunction:: peakdet.peakfind_physio
+.. autofunction:: peakdet.edit_physio
+.. autofunction:: peakdet.plot_physio
+
+Saving data
+-----------
+
+.. autofunction:: peakdet.save_physio
+.. autofunction:: peakdet.save_history

docs/conf.py

@@ -0,0 +1,105 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+
+# -- 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
+
+# -- Project information -----------------------------------------------------
+
+# Add project name, copyright holder, and author(s)
+project = 'peakdet'
+copyright = '2018, peakdet developers'
+author = 'Ross Markello'
+
+# Import project to get version info
+sys.path.insert(0, os.path.abspath(os.path.pardir))
+import peakdet  # noqa
+# The short X.Y version
+version = peakdet.__version__
+# The full version, including alpha/beta/rc tags
+release = peakdet.__version__
+
+
+# -- General configuration ---------------------------------------------------
+
+# 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.autosummary',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.viewcode',
+]
+
+# Generate the API documentation when building
+autosummary_generate = True
+numpydoc_show_class_members = False
+autoclass_content = "class"
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+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 = ['_build', 'Thumbs.db', '.DS_Store']
+
+# 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.
+import sphinx_rtd_theme  # noqa
+html_theme = 'sphinx_rtd_theme'
+html_show_sourcelink = False
+
+# 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']
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'peakdetdoc'
+
+
+# -- Extension configuration -------------------------------------------------
+intersphinx_mapping = {
+    'matplotlib': ('https://matplotlib.org', None),
+    'numpy': ('https://docs.scipy.org/doc/numpy', None),
+    'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
+    'sklearn': ('http://scikit-learn.org/stable', None),
+}

docs/index.rst

@@ -0,0 +1,11 @@
+.. include:: ../README.rst
+
+Contents
+--------
+
+.. toctree::
+   :maxdepth: 1
+
+   installation
+   usage
+   api

docs/installation.rst

@@ -0,0 +1,19 @@
+.. _installation_setup:
+
+Installation and setup
+======================
+
+.. _basic_installation:
+
+Basic installation
+--------------------
+
+This package requires Python >= 3.6. Assuming you have the correct version of
+Python installed, you can install ``peakdet`` by opening a terminal and running
+the following:
+
+.. code-block:: bash
+
+   git clone https://github.com/rmarkello/peakdet.git
+   cd peakdet
+   python setup.py install

docs/requirements.txt

@@ -0,0 +1,4 @@
+-r ../requirements.txt
+sphinx>=1.2
+sphinx_rtd_theme
+

docs/usage.rst

@@ -0,0 +1,11 @@
+.. _usage:
+
+Using peakdet
+=============
+
+The API of ``peakdet`` is under active development, so it's not quite stable
+enough for example usage instructions. Try taking a look at the :ref:`api_ref`
+to get an idea about the available functions and methods. If you're *super
+eager* to get started, try `opening an issue <https://github.com/rmarkello/
+peakdet/issues>`_  to let the developers know there's external interest in these
+sorts of things. Otherwise, check back soon!

peakdet/info.py

@@ -9,8 +9,8 @@
 DESCRIPTION = """\
 A toolbox for reproducible physiological data analysis\
 """
-LONG_DESCRIPTION = 'README.md'
-LONG_DESCRIPTION_CONTENT_TYPE = 'text/markdown'
+LONG_DESCRIPTION = 'README.rst'
+LONG_DESCRIPTION_CONTENT_TYPE = 'text/x-rst'
 URL = 'https://github.com/rmarkello/{name}'.format(name=NAME)
 DOWNLOAD_URL = ('http://github.com/rmarkello/{name}/archive/{ver}.tar.gz'
                 .format(name=NAME, ver=__version__))
@@ -29,8 +29,16 @@
 ]
 
 EXTRAS_REQUIRES = {
+    'doc': [
+        'sphinx>=1.2',
+        'sphinx_rtd_theme'
+    ]
 }
 
+EXTRAS_REQUIRES['all'] = list(
+    set([v for deps in EXTRAS_REQUIRES.values() for v in deps])
+)
+
 PACKAGE_DATA = {
     'peakdet.tests': [
         'data/*'

setup.cfg

@@ -1,5 +1,5 @@
 [metadata]
-description-file = README.md
+description-file = README.rst
 
 [flake8]
 ignore = E402