try

docs/README.rst

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+PhysioZoo ECG documentation
+===========================
+
+Digital electrocardiography biomarkers to assess cardiac conduction.
+
+Based on the paper 
+S. Gendelman et al., "PhysioZoo ECG: Digital electrocardiography biomarkers to assess cardiac conduction," 2021 Computing in Cardiology (CinC), 2021, pp. 1-4, doi: 10.23919/CinC53138.2021.9662857.
+
+Introduction
+----------------------
+
+The electrocardiogram (ECG) is a standard tool used in medical practice for identifying cardiac pathologies. Because the necessary expertise to interpret this tracing is not readily available in all medical institutions or at all in some large areas of developing countries, there is a need to create a data-driven approach that can automatically capture the information contained in this physiological time series. The primary objective of this package is to identify and implement clinically important digital ECG biomarkers for the purpose of creating a reference toolbox and software for ECG morphological analysis.
+
+Description
+----------------------
+
+Few steps are required to extract the morphological ECG biomarkers, thos steps are impelemented in the PEBM toolbox:
+
+1. ECG Signal Preprocessing - Before computing the ECG morphological biomarkers, prefiltering of the raw ECG time series is performed to remove the baseline wander as well as remove high frequency noise. Specifically, the toolbox include a zero phase second-order infinite impulse response bandpass filter with the passband of 0.67Hz - 100Hz to remove baseline wander and high frequency noise. Also, the toolbox include an optional Notch filter that can be set to 50 or 60Hz to remove the power-line interference.
+
+2. ECG Fiducial Points Detection - The toolbox include the epltd R-peaks algorithem, and the the well-known wavedet algorithm for ECG fiducial points  detection. 
+
+3. Engineering of ECG Biomarkers - Using the fiducial points ECG biomarkers are engineered for individual ECG cycles. When a biomarker cannot be engineered because some fiducial points could not be detected by wavedet then the feature was marked as a NaN. For an ECG channel a total of 14 features are extracted from intervals duration and 8 from waves characteristics to describe the ECG morphology.
+
+.. image:: ../../ecg_wth_bio.png
+  :width: 600
+
+
+4. Summary Statistics - For a specified time window the five summary statistics (median, min, max, Ql and Q3) are computed for all ECG biomarkers.
+
+Installation
+-----------------------
+
+Available on pip, with the command: 
+pip install pebm
+
+pip project: pip install -i https://test.pypi.org/simple/ pecg
+
+Requirements
+-----------------------
+
+Python >= 3.6
+
+numpy == 1.19.4
+
+mne == 0.23.4
+
+scipy == 1.5.2
+
+wfdb == 3.4.0
+
+All the requirements are installed when the toolbox is installed, no need for additional commands.
+
+System Requirements
+------------------------
+
+To run the wavdet fiucial-points detector matlab runtime (MCR) 2021a is requierd. https://www.mathworks.com/products/compiler/matlab-runtime.html
+
+To run the epltd peak detector additional wfdb toolbox is requierd. https://archive.physionet.org/physiotools/wfdb-linux-quick-start.shtml
+
+Documentation
+------------------------
+
+

docs/conf.py

@@ -0,0 +1,205 @@
+# -*- 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 sphinx_rtd_theme
+
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../.."))
+
+# os.path.join('pe')
+print(sys.path)
+
+# -- Project information -----------------------------------------------------
+
+project = "pecg"
+copyright = "2021, Sheina"
+author = "Sheina"
+
+# The short X.Y version
+version = ""
+# The full version, including alpha/beta/rc tags
+release = ""
+
+
+# -- 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.
+
+# This value selects what content will be inserted into the main body of an autoclass directive. The possible values are:
+# "class" Only the class’ docstring is inserted. This is the default. You can still document __init__ as a separate method using automethod or the members option to autoclass.
+# "both" Both the class’ and the __init__ method’s docstring are concatenated and inserted.
+# "init" Only the __init__ method’s docstring is inserted.
+autoclass_content = "both"
+
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.todo",
+    "recommonmark",
+]
+
+# 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"]
+
+# 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 = "en"
+
+# 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 = None
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+# extensions = ['sphinx.ext.autodoc', 'sphinx.ext.napoleon']
+
+html_theme = "sphinx_rtd_theme"
+
+# 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_logo = "logo.png"
+
+html_theme_options = {"logo_only": False}
+
+
+# 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 = "pecgdoc"
+
+
+# -- 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, "pecg.tex", "pecg Documentation", "Author", "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, "pecg", "pecg 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,
+        "pecg",
+        "pecg Documentation",
+        author,
+        "pecg",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ["search.html"]
+
+
+# -- Extension configuration -------------------------------------------------
+
+
+# -- Options for todo extension ----------------------------------------------
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
+
+autodoc_member_order = "bysource"

docs/pecg.ecg.rst

@@ -0,0 +1,28 @@
+pecg.ecg package
+================
+
+pecg.ecg.FiducialPoints
+--------------------------
+
+.. automodule:: pecg.ecg.FiducialPoints
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+pecg.ecg.Biomarkers
+--------------------------
+
+.. automodule:: pecg.ecg.Biomarkers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pecg.ecg
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/pecg.rst

@@ -0,0 +1,25 @@
+pecg package
+============
+
+.. toctree::
+   :maxdepth: 4
+
+   pecg.ecg
+
+
+pecg.Preprocessing
+--------------------------
+
+.. automodule:: pecg.Preprocessing
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pecg
+   :members:
+   :undoc-members:
+   :show-inheritance: