add rudimentary documentation

add rudimentary documentation

cleanup .readthedocs.yaml

add docs requirements

fix requirements

fix requirements

update

.gitignore

@@ -14,3 +14,5 @@
 .coverage
 
 *.egg-info
+
+docs/_build

README.md

@@ -1,3 +1,5 @@
+[![Documentation Status](https://readthedocs.org/projects/cmdtools/badge/?version=latest)](https://cmdtools.readthedocs.io/en/latest/?badge=latest)
+
 # cmdtools
 
 This Python library implements a suite of tools used and/or developed in the [Computational Molecular Design](https://www.zib.de/numeric/cmd) group of the Zuse Institute Berlin.
@@ -11,5 +13,5 @@ This Python library implements a suite of tools used and/or developed in the [Co
 
 ## Contents
 *  `cmdtools.analysis.pcca`: An implementation of (generalized) PCCA⁺ using the Schur decomposition
-*  `cmdtools.estimation.galerkin`: Estimation of the transfer operator using a Galerkin projection onto Gaussian RBFs 
+*  `cmdtools.estimation.galerkin`: Estimation of the transfer operator using a Galerkin projection onto Gaussian RBFs
 *  `cmdtools.systems`: A collection of dynamical systems

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     = .
+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 +1,26 @@
+API
+================
+
+.. automodule:: cmdtools
+
+analysis
+--------
+.. automodule:: cmdtools.analysis
+.. automodule:: cmdtools.analysis.pcca
+.. automodule:: cmdtools.analysis.optimization
+
+estimation
+----------
+.. automodule:: cmdtools.estimation
+.. automodule:: cmdtools.estimation.galerkin
+.. automodule:: cmdtools.estimation.sqra
+
+systems
+-------
+.. automodule:: cmdtools.systems
+.. automodule:: cmdtools.systems.diffusion
+
+
+utils
+---------------
+.. automodule:: cmdtools.utils

docs/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.
+#
+# import os
+# import sys
+# sys.path.insert(0, '/Users/alex/Documents/code/cmdtools/src/cmdtools')
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'cmdtools'
+copyright = '2020, Author'
+author = 'Author'
+
+
+# -- 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.viewcode',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.todo',
+]
+
+autodoc_default_options = {
+    'members': True,
+    'undoc-members': True,
+}
+
+# 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 = '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']
+
+
+# -- 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 = 'pyramid'
+
+# 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']
+
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for todo extension ----------------------------------------------
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True

docs/index.rst

@@ -0,0 +1,20 @@
+.. cmdtools documentation master file, created by
+   sphinx-quickstart on Mon Jun  8 16:16:30 2020.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to cmdtools's documentation!
+====================================
+
+.. toctree::
+
+   introduction
+   api
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/introduction.rst

@@ -0,0 +1,4 @@
+Introduction
+============
+
+Work in progress

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=.
+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.http://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 @@
+Sphinx >= 3.0

src/cmdtools/estimation/galerkin.py

@@ -22,24 +22,26 @@ def get_membership(timeseries, centers, sigma):
 
 
 def find_bandwidth(timeseries, centers, percentile=50):
-    """Find the bandwidth of the Gaussian based on:
+    """
+    Find the bandwidth of the Gaussian based on:
 
     "Stein Variational Gradient Descent:
     A General Purpose Bayesian Inference Algorithm",
     Qiang Liu and Dilin Wang (2016).
 
-     Based on the value of the percentile is possible to decide the points to
-     take into consideration for the determination of the bandwidth.
+    Based on the value of the percentile is possible to decide the points to
+    take into consideration for the determination of the bandwidth.
 
     Input:
-        timeseries: arr, trajectory, each row is a collection of
-            coordinates at a different timestep
-        centers: arr, centers of the Gaussians, each row has the coordinates
-            of a different center
+        timeseries: arr, trajectory, each row is a collection of \
+                    coordinates at a different timestep
+        centers:    arr, centers of the Gaussians, each row has the \
+                    coordinates of a different center
         percentile: int [0,100], default value = 50
 
-     Output:
-         sigma: float, the  variance of the Gaussian"""
+    Output:
+        sigma: float, the  variance of the Gaussian
+    """
 
     no_centers = np.shape(centers)[0]
     sqdist = distance.cdist(timeseries, centers, distance.sqeuclidean)