Update documentation

.buildinfo

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+# 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: d683d1f5691da2c4a19f6c17d431aa8b
+tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/cog_plot.rst.txt

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+cog\_plot package
+=================
+
+Submodules
+----------
+
+cog\_plot.colors module
+-----------------------
+
+.. automodule:: cog_plot.colors
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+cog\_plot.plotters module
+-------------------------
+
+.. automodule:: cog_plot.plotters
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: cog_plot
+   :members:
+   :undoc-members:
+   :show-inheritance:

_sources/colors.rst.txt

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+Colors Module
+=============
+
+.. automodule:: cog_plot.colors
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. autosummary::
+   :toctree: generated/
+
+   DEFAULT_COLORS

_sources/generated/cog_plot.colors.DEFAULT_COLORS.rst.txt

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+cog\_plot.colors.DEFAULT\_COLORS
+================================
+
+.. currentmodule:: cog_plot.colors
+
+.. autodata:: DEFAULT_COLORS

_sources/generated/cog_plot.plot_matrix.rst.txt

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+cog\_plot.plot\_matrix
+======================
+
+.. currentmodule:: cog_plot
+
+.. autofunction:: plot_matrix

_sources/generated/cog_plot.plot_time_series.rst.txt

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+cog\_plot.plot\_time\_series
+============================
+
+.. currentmodule:: cog_plot
+
+.. autofunction:: plot_time_series

_sources/generated/cog_plot.plotters.plot_matrix.rst.txt

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+cog\_plot.plotters.plot\_matrix
+===============================
+
+.. currentmodule:: cog_plot.plotters
+
+.. autofunction:: plot_matrix

_sources/generated/cog_plot.plotters.plot_rasters.rst.txt

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+cog\_plot.plotters.plot\_rasters
+================================
+
+.. currentmodule:: cog_plot.plotters
+
+.. autofunction:: plot_rasters

_sources/generated/cog_plot.plotters.plot_time_series.rst.txt

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+cog\_plot.plotters.plot\_time\_series
+=====================================
+
+.. currentmodule:: cog_plot.plotters
+
+.. autofunction:: plot_time_series

_sources/index.rst.txt

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+.. cog_plot documentation master file, created by
+   sphinx-quickstart on Tue Aug 27 10:05:38 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+cog_plot documentation
+======================
+
+.. raw:: html
+
+   <div style="width: 100%; display: flex; justify-content: space-between; align-items: center;">
+     <img src="../img/cogitate_logo.png" alt="Left Logo" width="200">
+     <h1 style="text-align: center; flex-grow: 1;">cog_lib</h1>
+     <img src="../img/templeton_logo.png" alt="Right Logo" width="200">
+   </div>
+
+This repository contains a package called ``cog_plot`` containing functions to generate the default plot types used in the cogitate papers.
+
+It can generate three types of plots:
+
+- Time series plot with statistical significance (``plot_time_series``)
+- Matrices with statistical significance, such as time-frequency decomposition or temporal generalization (``plot_matrix``)
+- Single trial data using a raster plot and a time series plot of the evoked response (``plot_raster``)
+
+Setup guide:
+============
+
+The package can be installed via pip, like so:
+
+.. code-block:: bash
+
+   pip install https://github.com/Cogitate-consortium/cog_plot
+
+Support
+============
+
+This repository is meant mostly for internal use by the cogitate project. But if you find it useful, don't hesitate to contact us.
+
+## Questions?
+
+If you have any questions, feel free to open an issue or contact the maintainers ([email protected]).
+
+Acknowledgments
+===============
+
+We would like to thank all the COGITATE consortium members:
+
+.. raw:: html
+
+   <div style="display: flex; flex-wrap: wrap; justify-content: space-around;">
+      <div style="text-align: center;">
+         <a href="https://www.arc-cogitate.com/our-team" target="_blank">
+            <img src="../img/IEEG DP Authors.png" alt="COGITATE team">
+         </a>
+      </div>
+   </div>
+
+.. image:: ../img/templeton_logo.png
+   :width: 200
+   :align: right
+
+This research was supported by Templeton World Charity Foundation (`TWCF0389 <https://doi.org/10.54224/20389>`_) and the Max Planck Society. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of TWCF.
+
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   plot_matrix <generated/cog_plot.plotters.plot_matrix>
+   plot_rasters <generated/cog_plot.plotters.plot_rasters>
+   plot_time_series <generated/cog_plot.plotters.plot_time_series>
+   colors

_sources/modules.rst.txt

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+cog_plot
+========
+
+.. toctree::
+   :maxdepth: 4
+
+   cog_plot

_sources/plotters.rst.txt

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+Plotters Module
+===============
+
+.. automodule:: cog_plot.plotters
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. autosummary::
+   :toctree: generated/
+
+   plot_time_series
+   plot_matrix
+   plot_rasters

_static/_sphinx_javascript_frameworks_compat.js

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+/* 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;
+}