adding readthedocs

.readthedocs.yaml

@@ -0,0 +1,20 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 1
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.8
+  install:
+    - requirements: docs/requirements.txt

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+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)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+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.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements.txt

@@ -0,0 +1,6 @@
+Babel==2.9.1
+imagesize==1.3.0
+readme-renderer>=32.0
+sphinx==4.2.0
+sphinx_rtd_theme==1.0.0
+readthedocs-sphinx-search==0.1.1

docs/source/conf.py

@@ -0,0 +1,76 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- 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.
+#
+from os.path import dirname
+import os
+import sys
+
+current_dir = os.getcwd()
+path = dirname(dirname(current_dir))
+sys.path.append(path)
+sys.path.append(os.path.join(path, 'sklearn'))
+sys.path.insert(0, os.path.abspath('../../'))
+sys.path.insert(0, os.path.abspath('sphinxext'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'MontePython'
+copyright = '2022, Montgomery Flora'
+author = 'Montgomery Flora'
+
+# The full version, including alpha/beta/rc tags
+release = '1.1.851-py3.8'
+
+
+# -- 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.coverage', 
+              'sphinx.ext.napoleon',
+               "sphinx.ext.intersphinx",
+                "sphinx.ext.mathjax",
+                "sphinx.ext.viewcode",
+             ]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# 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 = 'Python'
+
+# 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 = []
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+html_tile=project
+
+# on_rtd is whether we are on readthedocs.org, this line of code grabbed from docs.readthedocs.org
+on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
+
+# 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']

docs/source/index.rst

@@ -0,0 +1,40 @@
+.. MontePython documentation master file, created by
+   sphinx-quickstart on Fri Mar 11 21:19:45 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to MontePython's documentation!
+=======================================
+
+Methods for Object-based and Neighborhood Threat Evaluation in Python (MontePython) is a Python module for meteorological-based image segementation, matching, and tracking. This package was originally built for `NOAA's Warn-on-Forecast System <https://www.nssl.noaa.gov/projects/wof/>`_ (WoFS). 
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+Install
+==================
+
+MontePython is not available through PyPi at the moment. To install it, 
+require cloning the environment and then when the parent directory, 
+using the setup.py to install it. 
+
+    git clone https://github.com/WarnOnForecast/MontePython
+
+    python setup.py install
+
+
+Content
+===========
+
+.. toctree::
+   :maxdepth: 2 
+
+   Object Identification <object_id>
+   Object Quality Control <object_qc>
+   Object Matching <object_matching>
+   Object Tracking <object_tracking>
+   Storm Mode Classification <storm_mode>
+
+

docs/source/object_id.rst

@@ -0,0 +1,18 @@
+.. currentmodule:: monte_python
+
+Object Identification
+=========================
+
+.. automodule:: monte_python.object_identification
+    :members:
+
+.. toctree::
+    :maxdepth: 1
+
+.. automodule:: monte_python.EnhancedWatershedSegmenter
+    :members:
+
+.. toctree::
+    :maxdepth: 1    
+
+

docs/source/object_matching.rst

@@ -0,0 +1,11 @@
+.. currentmodule:: monte_python
+
+
+Object Matching
+=========================
+
+.. automodule:: monte_python.object_matching
+    :members:
+
+.. toctree::
+    :maxdepth: 2

docs/source/object_qc.rst

@@ -0,0 +1,12 @@
+.. currentmodule:: monte_python
+
+Object Quality Control
+=========================
+
+
+.. automodule:: monte_python.object_quality_control
+    :members:
+
+.. toctree::
+    :maxdepth: 2
+

docs/source/object_tracking.rst

@@ -0,0 +1,10 @@
+.. currentmodule:: monte_python
+
+Object Tracking
+=========================
+
+.. automodule:: monte_python.object_tracking
+    :members:
+
+.. toctree::
+    :maxdepth: 2

docs/source/storm_mode.rst

@@ -0,0 +1,11 @@
+.. currentmodule:: monte_python
+
+Storm Segmentation and Mode Classification
+==============================================
+
+.. automodule:: monte_python.storm_mode_classification
+    :members:
+
+.. toctree::
+    :maxdepth: 2
+

monte_python/object_identification.py

@@ -24,9 +24,9 @@ def label(input_data, params, method='watershed', return_object_properties=True)
     method [1]_ [2]_ [3]_ [4]_.
 
     .. note :: 
-        The enhanced and iterative watershed algoritms are a powerful tools for image segementation, but 
-        they require significant parameter tuning. We recommend exploring the single
-        threshold method first. 
+       The enhanced and iterative watershed algoritms are a powerful tools for image segementation 
+       ,but they require significant parameter tuning. We recommend exploring the single
+       threshold method first. 
     
     Parameters
     ----------
@@ -369,13 +369,13 @@ def grow_objects(self, previous_region_props, previous_data_to_label, previous_l
         labelled region with new points. BUT remove the point
         so it is not further considered. 
 
-        Args:
+        Parameters
         ------------------
         regionprops, skimage object
         original_data, 2D numpy array of the data to be labelled
         labelled_data, 2D numpy array of labelled regions in original_data
 
-        Returns:
+        Returns
         ---------------
         labelled_array, 2D numpy array of labelled regions 
         """
@@ -408,13 +408,13 @@ def grow_objects_recursive(self,
         labelled region with new points. BUT remove the point
         so it is not further considered. 
 
-        Args:
+        Parameters
         ------------------
         regionprops, skimage object
         original_data, 2D numpy array of the data to be labelled
         labelled_data, 2D numpy array of labelled regions in original_data
 
-        Returns:
+        Returns
         ---------------
         labelled_array, 2D numpy array of labelled regions 
         """

monte_python/object_tracking.py

@@ -282,10 +282,12 @@ def relabel(self, data):
 
     def match(self, data_a, data_b):
         """ Match two set of data valid at a single or multiple times.
-        Args:
+        Parameters
+        -------------
             object_set_a, 2D array or list of 2D arrays, object labels at a single or multiple times
             object_set_b, 2D array or list of 2D arrays, object labels at a single or multiple times
-        Returns:
+        Returns
+        -------------
             Lists of matched labels in set a, matched labels in set b,
             and tuples of y- and x- components of centroid displacement of matched pairs
         """
@@ -327,10 +329,13 @@ def percent_intersection(self, region_a, region_b):
 
     def find_possible_matches(self, data_a, data_b): 
         """ Finds matches based on amount of intersection between data at time = t and time = t+1.
-        Args: 
+        Parameters 
+        -----------
             regionprops_set_a, skimage.measure.regionprops for object_set_a
             regionprops_set_b, skimage.measure.regionprops for object_set_b
-        Returns: 
+            
+        Returns 
+        ----------
             Dictionary of tuples of possible matched object pairs associated with their total interest score 
             Dictionary of y- and x-component of centroid displacement of possible matched object pairs             
         """