Merge pull request #40 from segrelab/landing-page

Add a descriptive landing page to the docs

.github/workflows/publish_docs.yml

@@ -36,7 +36,7 @@ jobs:
 
       - name: Install Dependencies
         run: |
-          pip install sphinx sphinx-autodoc-typehints pandas cobra
+          pip install sphinx sphinx-autodoc-typehints sphinx_rtd_theme pandas cobra
 
       - name: Generate Documentation
         run: |

docs/build/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: e02b0dfd2659bc3356d6c1e30e269d53
+config: 683ed239e83aeb31a6d829fb79ba53e5
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/_sources/cometspy.rst.txt

@@ -0,0 +1,53 @@
+cometspy package
+================
+
+Submodules
+----------
+
+cometspy.comets module
+----------------------
+
+.. automodule:: cometspy.comets
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+cometspy.layout module
+----------------------
+
+.. automodule:: cometspy.layout
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+cometspy.model module
+---------------------
+
+.. automodule:: cometspy.model
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+cometspy.params module
+----------------------
+
+.. automodule:: cometspy.params
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+cometspy.utils module
+---------------------
+
+.. automodule:: cometspy.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: cometspy
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/build/_sources/index.rst.txt

@@ -1,20 +1,93 @@
-.. COMETSpy documentation master file, created by
-   sphinx-quickstart on Wed Aug 16 14:46:05 2023.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
+.. COMETSpy documentation master file, written by Helen Scott, last
+   updated on 2023-08-21.
+   You can adapt this file completely to your liking, but it should at
+   least contain the root `toctree` directive.
 
-Welcome to COMETSpy's documentation!
-====================================
+.. The toctree directive controls what links are in the "Navigation" bar
+   at the top of each page. The "maxdepth" argument determines how many
+   levels deep the links are shown. The "caption" argument determines the
+   title of the "Navigation" bar.
 
 .. toctree::
+   :caption: Package Documentation
    :maxdepth: 2
-   :caption: Contents:
+   :hidden:
 
+   install
+   cometspy
 
 
-Indices and tables
-==================
+.. toctree::
+    :maxdepth: 2
+    :numbered:
+    :caption: Tutorials
+    :hidden:
+
+
+Introduction
+============
+
+What is COMETSpy?
+----------------------------
+COMETS is a software platform for performing **computer simulations of
+metabolism in spatially structured microbial communities**. It is based on
+stoichiometric modeling of the genome-scale metabolic network of
+individual microbial species (using dynamic flux balance analysis), and
+on a discrete approximation of convection-diffusion equations.
+
+.. Images from COMETS imulations here, i.e. colony morpologies
+.. image:: images/comets_results.png
+  :width: 800
+  :alt: Results from COMETS simulations
+
+COMETSpy is a Python package that provides a user-friendly interface to
+COMETS. It allows users to easily set up and run simulations, and to
+analyze the results. COMETSpy is designed to be used in conjunction with
+COMETS. It is not a standalone package, and requires COMETS to be
+installed on the user's computer.
+
+.. Graphic showing the relationship between COMETS and COMETSpy
+.. image:: images/cometspy_workflow.png
+  :width: 800
+  :alt: The COMETSpy/COMETS workflow
+
+How to use this Documentation:
+------------------------------
+
+This documentation is meant to aide users in installing COMETSpy and
+using COMETSpy to run simulations and analyze the results. If you need
+help and do not easily find an answer in this documentation, ask your question
+in a `new issue on GitHub <https://github.com/segrelab/cometspy/issues/new>`_.
+**Any question that you have likely indicates a shortcoming in the documentation,
+which we will want to fix!**
+
+Find the module/class/function that you are interested in using in the
+table of contents on the left or in the following indices, click on the link to
+go to the appropriate documentation:
 
-* :ref:`genindex`
 * :ref:`modindex`
-* :ref:`search`
+* :ref:`genindex`
+
+For a class, the documentation will include a brief description of the class,
+the parameters that the class takes, and a list of all attributes, and examples
+of how to use the class. The documentation will also include a list of all
+the methods that are available for that class.
+
+For a function, including the methods for a class, the documentation will 
+include a description of what the function does, a list of the parameters that
+the function takes and the objects that the function returns, and examples of
+how to use the function.
+
+Cite Us:
+--------
+
+The newest version of COMETS, which was developed as a partnership between
+researchers at `Boston University <https://www.bu.edu/segrelab/>`_,
+`Yale University <https://eeb.yale.edu/people/alvaro-sanchez>`_ and the
+`University of Minnesota <http://www.wrharcombe.org/>`_ is fully described
+in the following paper:
+
+`Dukovski, Bajić, Chacón, Quintin, et al.: A metabolic modeling platform for
+the computation of microbial ecosystems in time and space (COMETS), Nature
+Protocols (2021) https://doi.org/10.1038/s41596-021-00593-3.
+<https://www.nature.com/articles/s41596-021-00593-3>`_

docs/build/_sources/install.rst.txt

@@ -0,0 +1,15 @@
+.. Installation documentation page, written by Helen Scott, last
+   updated on 2023-08-21.
+   You can adapt this file completely to your liking, but it should at
+   least contain the root `toctree` directive.
+
+.. The toctree directive controls what links are in the "Navigation" bar
+   at the top of each page. The "maxdepth" argument determines how many
+   levels deep the links are shown. The "caption" argument determines the
+   title of the "Navigation" bar.
+Installation
+============
+
+How to Install:
+----------------------------
+pip it

docs/build/_sources/modules.rst.txt

@@ -0,0 +1,7 @@
+cometspy
+========
+
+.. toctree::
+   :maxdepth: 4
+
+   cometspy

docs/build/_static/_sphinx_javascript_frameworks_compat.js

@@ -0,0 +1,123 @@
+/* Compatability shim for jQuery and underscores.js.
+ *
+ * Copyright Sphinx contributors
+ * Released under the two clause BSD licence
+ */
+
+/**
+ * small helper function to urldecode strings
+ *
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
+ */
+jQuery.urldecode = function(x) {
+    if (!x) {
+        return x
+    }
+    return decodeURIComponent(x.replace(/\+/g, ' '));
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+    if (typeof s === 'undefined')
+        s = document.location.search;
+    var parts = s.substr(s.indexOf('?') + 1).split('&');
+    var result = {};
+    for (var i = 0; i < parts.length; i++) {
+        var tmp = parts[i].split('=', 2);
+        var key = jQuery.urldecode(tmp[0]);
+        var value = jQuery.urldecode(tmp[1]);
+        if (key in result)
+            result[key].push(value);
+        else
+            result[key] = [value];
+    }
+    return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+    function highlight(node, addItems) {
+        if (node.nodeType === 3) {
+            var val = node.nodeValue;
+            var pos = val.toLowerCase().indexOf(text);
+            if (pos >= 0 &&
+                !jQuery(node.parentNode).hasClass(className) &&
+                !jQuery(node.parentNode).hasClass("nohighlight")) {
+                var span;
+                var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
+                if (isInSVG) {
+                    span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+                } else {
+                    span = document.createElement("span");
+                    span.className = className;
+                }
+                span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+                node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+                    document.createTextNode(val.substr(pos + text.length)),
+                    node.nextSibling));
+                node.nodeValue = val.substr(0, pos);
+                if (isInSVG) {
+                    var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+                    var bbox = node.parentElement.getBBox();
+                    rect.x.baseVal.value = bbox.x;
+                    rect.y.baseVal.value = bbox.y;
+                    rect.width.baseVal.value = bbox.width;
+                    rect.height.baseVal.value = bbox.height;
+                    rect.setAttribute('class', className);
+                    addItems.push({
+                        "parent": node.parentNode,
+                        "target": rect});
+                }
+            }
+        }
+        else if (!jQuery(node).is("button, select, textarea")) {
+            jQuery.each(node.childNodes, function() {
+                highlight(this, addItems);
+            });
+        }
+    }
+    var addItems = [];
+    var result = this.each(function() {
+        highlight(this, addItems);
+    });
+    for (var i = 0; i < addItems.length; ++i) {
+        jQuery(addItems[i].parent).before(addItems[i].target);
+    }
+    return result;
+};
+
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+    jQuery.uaMatch = function(ua) {
+        ua = ua.toLowerCase();
+
+        var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+            /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+            /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+            /(msie) ([\w.]+)/.exec(ua) ||
+            ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+            [];
+
+        return {
+            browser: match[ 1 ] || "",
+            version: match[ 2 ] || "0"
+        };
+    };
+    jQuery.browser = {};
+    jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}