MIT-LCP · cx1111 · Feb 11, 2018 · Jan 2, 2018 · Jan 2, 2018 · Jan 2, 2018
diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,5 @@
 # For private use
-private_tests.ipynb
+private-tests.ipynb
 notes.md
 
 # Byte-compiled / optimized / DLL files

diff --git a/README.rst b/README.rst
diff --git a/demoimg.png → demo-img.png b/demoimg.png → demo-img.png
diff --git a/demo.ipynb b/demo.ipynb
diff --git a/devtests.ipynb b/devtests.ipynb
diff --git a/docs/Makefile b/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    = wfdb
+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)
diff --git a/wfdb/readwrite/__init__.py → docs/_static/.gitkeep b/wfdb/readwrite/__init__.py → docs/_static/.gitkeep
diff --git a/docs/_templates/.gitkeep b/docs/_templates/.gitkeep
diff --git a/docs/conf.py b/docs/conf.py
@@ -0,0 +1,170 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# wfdb documentation build configuration file, created by
+# sphinx-quickstart on Tue Jan  2 13:19:02 2018.
+#
+# 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.
+
+# 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('.'))
+
+
+# -- 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']
+
+# 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'
+
+# General information about the project.
+project = 'wfdb'
+copyright = '2018, MIT Lab for Computational Physiology'
+author = 'Chen Xie, Julien Dubiel'
+
+import wfdb
+# 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 = wfdb.__version__
+# The full version, including alpha/beta/rc tags.
+release = wfdb.__version__
+
+# 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 patterns also effect to 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'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- 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.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+html_sidebars = {
+    '**': [
+        'relations.html',  # needs 'show_related': True theme option to display
+        'searchbox.html',
+    ]
+}
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'wfdbdoc'
+
+
+# -- 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, 'wfdb.tex', 'wfdb Documentation',
+     'Chen Xie, Julien Dubiel', '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, 'wfdb', 'wfdb 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, 'wfdb', 'wfdb Documentation',
+     author, 'wfdb', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+
diff --git a/docs/index.rst b/docs/index.rst
@@ -0,0 +1,79 @@
+wfdb
+====
+
+Introduction
+------------
+
+The native Python waveform-database (WFDB) package. A library of tools
+for reading, writing, and processing WFDB signals and annotations.
+
+Core components of this package are based on the original WFDB
+specifications. This package does not contain the exact same
+functionality as the original WFDB package. It aims to implement as many
+of its core features as possible, with user-friendly APIs. Additional
+useful physiological signal-processing tools are added over time.
+
+
+Development
+-----------
+
+The development repository is hosted at: https://github.com/MIT-LCP/wfdb-python
+
+The package is to be expanded with physiological signal-processing tools, and general improvements. Development is made for Python 2.7 and 3.5+ only.
+
+
+API Reference
+--------------
+
+The exact API of all accessible functions and classes, as given by the docstrings, grouped by subpackage:
+
+.. toctree::
+   :maxdepth: 2
+
+   io
+   plot
+   processing
+
+
+Core Components
+---------------
+
+A subset of the above components are accessible by directly importing the base package.
+
+.. toctree::
+   :maxdepth: 2
+
+   wfdb
+
+
+Other Content
+-------------
+.. toctree::
+   :maxdepth: 2
+
+   installation
+   wfdb-specifications
+
+
+Indices and tables
+------------------
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+
+Authors
+-------
+
+`Chen Xie`_
+
+`Julien Dubiel`_
+
+
+.. _PEP8: https://www.python.org/dev/peps/pep-0008/
+.. _docstrings: https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt
+.. _existing tests: https://github.com/MIT-LCP/wfdb-python/tree/master/tests
+
+.. _Chen Xie: https://github.com/cx1111/
+.. _Julien Dubiel: https://github.com/Dubrzr/
diff --git a/docs/installation.rst b/docs/installation.rst
@@ -0,0 +1,10 @@
+Installation
+------------
+
+The distribution is hosted on pypi at: https://pypi.python.org/pypi/wfdb/. To directly install the package from pypi without needing to explicitly download content, run from your terminal::
+
+    $ pip install wfdb
+
+The development version is hosted at: https://github.com/MIT-LCP/wfdb-python. This repository also contains demo scripts and example data. To install the development version, clone or download the repository, navigate to the base directory, and run::
+
+    $ pip install .
diff --git a/docs/io.rst b/docs/io.rst
@@ -0,0 +1,35 @@
+io
+===
+
+The input/output subpackage contains classes used to represent WFDB
+objects, and functions to read, write, and download WFDB files.
+
+
+WFDB Records
+---------------
+
+.. automodule:: wfdb.io
+    :members: rdrecord, rdsamp, wrsamp
+
+.. autoclass:: wfdb.io.Record
+    :members: wrsamp, adc, dac
+
+.. autoclass:: wfdb.io.MultiRecord
+    :members: multi_to_single
+
+
+WFDB Anotations
+---------------
+
+.. automodule:: wfdb.io
+    :members: rdann, wrann, show_ann_labels, show_ann_classes
+
+.. autoclass:: wfdb.io.Annotation
+    :members: wrann
+
+
+Downloading
+-----------
+
+.. automodule:: wfdb.io
+    :members: get_dbs, get_record_list, dl_database, dl_files
diff --git a/docs/plot.rst b/docs/plot.rst
@@ -0,0 +1,5 @@
+plot
+----
+
+.. automodule:: wfdb.plot
+    :members: plot_items, plot_wfdb, plot_all_records
diff --git a/docs/processing.rst b/docs/processing.rst
@@ -0,0 +1,41 @@
+processing
+==========
+
+The processing subpackage contains signal-processing tools.
+
+
+Basic Utility
+-------------
+
+Basic signal processing functions
+
+.. automodule:: wfdb.processing
+    :members: resample_ann, resample_sig, resample_singlechan,
+              resample_multichan, normalize_bound, get_filter_gain
+
+Heart Rate
+----------
+
+.. automodule:: wfdb.processing
+    :members: compute_hr
+
+
+Peaks
+-----
+
+.. automodule:: wfdb.processing
+    :members: find_peaks, find_local_peaks, correct_peaks
+
+
+QRS Detectors
+-------------
+
+.. automodule:: wfdb.processing
+    :members: XQRS, xqrs_detect, gqrs_detect
+
+
+Annotation Evaluators
+---------------------
+
+.. automodule:: wfdb.processing
+    :members: Comparitor, compare_annotations
diff --git a/docs/wfdb-specifications.rst b/docs/wfdb-specifications.rst
@@ -0,0 +1,16 @@
+WFDB Specifications
+-------------------
+
+The wfdb-python package is built according to the specifications of the original WFDB package.
+
+* `WFDB Software Package`_
+* `WFDB Applications Guide`_
+* `WFDB Header Specifications`_
+* `WFDB Signal Specifications`_
+* `WFDB Annotation Specifications`_
+
+.. _WFDB Software Package: http://physionet.org/physiotools/wfdb.shtml
+.. _WFDB Applications Guide: http://physionet.org/physiotools/wag/
+.. _WFDB Header Specifications: https://physionet.org/physiotools/wag/header-5.htm
+.. _WFDB Signal Specifications: https://physionet.org/physiotools/wag/signal-5.htm
+.. _WFDB Annotation Specifications: https://physionet.org/physiotools/wag/annot-5.htm