deploy: ee61a93

.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: 47771fc8414f1dd46734ed3e8226f12a
+tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/credit.rst.txt

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+
+
+Credit and inspiration
+======================
+
+Inspired by and derived from https://hpc-carpentry.github.io/hpc-python/
+which is distributed under CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/).

_sources/dependencies.rst.txt

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+
+
+Dependencies
+============
+
+Required
+--------
+
+- Python
+- Numpy
+- Matplotlib
+
+
+Optional
+--------
+
+- Docker

_sources/exercises.rst.txt

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+
+
+Exercises (documentation lesson)
+================================
+
+Before you start
+----------------
+
+- Discuss the exercise idea with the classroom.
+- Distribute exercises among groups of 2-3 persons.
+- Open a GitHub issue and inform the community about the problem and how you
+  plan to solve it. Discuss why we do this.
+- Fork this project.
+- Commit to your fork. In your commit message auto-close the issue you have addressed.
+- Submit a pull request.
+- We then review the pull requests.
+- After the pull requests are merged we verify that documentation updates itself.
+
+
+Basic
+-----
+
+- Document the purpose of this example code.
+- Document how to clone the code.
+- Describe the project tree structure.
+- Write a sentence or two about Zipf's law and link to Wikipedia
+  (coordinate with the group working on the previous exercise).
+- Document how to check the code style with ``pycodestyle``.
+- Give other developers hints on how they can contribute to the documentation.
+- Document how to build the documentation locally
+  (coordinate with the group working on the previous exercise).
+- Add an example output.
+- Add an example plot
+  (coordinate with the group working on the previous exercise).
+- Document where/how to ask for help.
+- Add a math equation somewhere.
+
+
+Advanced
+--------
+
+- Add a test and document how to run it.
+- Add the possibility to auto-document Python code.
+
+
+Meta
+----
+
+- Add new exercises ideas for future workshops (edit this file).

_sources/index.rst.txt

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+.. this is a comment, it is not rendered
+   when adding new *.rst files, reference them here
+   in this index.rst for them to be rendered and added to the
+   table of contents
+
+
+Basics
+==========
+
+.. toctree::
+   :maxdepth: 2
+
+   purpose.rst
+   dependencies.rst
+   usage.rst
+   queries.rst
+   credit.rst

_sources/purpose.rst.txt

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+
+
+Purpose
+=======
+
+Write me ...
+
+
+Basics
+----------
+
+Write me ...

_sources/queries.rst.txt

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+.. |check| raw:: html
+
+    <input checked=""  type="checkbox">
+
+.. |check_| raw:: html
+
+    <input checked=""  disabled="" type="checkbox">
+
+.. |uncheck| raw:: html
+
+    <input type="checkbox">
+
+.. |uncheck_| raw:: html
+
+    <input disabled="" type="checkbox">
+
++-------+--------------------------------+---------------------------------------------------+--------------------------------------------------------------------------------------------------------+------------+
+| Query | Endpoint                       | Description                                       | Returns                                                                                                |   Ready?   |
++=======+================================+===================================================+========================================================================================================+============+
+|   Q1  | getThetasDocById               | Get document-topic distribution of a selected     | ``{"thetas": thetas}``                                                                                 |  |check_|  |
+|       |                                | document in a corpus collection                   |                                                                                                        |            |
++-------+--------------------------------+---------------------------------------------------+--------------------------------------------------------------------------------------------------------+------------+
+|   Q2  | getCorpusMetadataFields        | Get the name of the metadata fields available for |                                                                                                        |            |
+|       |                                | a specific corpus collection (not all corpus have |                                                                                                        |            |
+|       |                                | the same metadata available)                      |                                                                                                        |            |
++-------+--------------------------------+---------------------------------------------------+--------------------------------------------------------------------------------------------------------+------------+
+|   Q3  | getMetadataDocById             | Get metadata of a selected document in a          |                                                                                                        |            |
+|       |                                | corpus collection                                 |                                                                                                        |            |
++-------+--------------------------------+---------------------------------------------------+--------------------------------------------------------------------------------------------------------+------------+
+|   Q4  | getNrDocsColl                  | Get number of documents in a collection           | ``{"ndocs": ndocs}``                                                                                   |  |check_|  |
++-------+--------------------------------+---------------------------------------------------+--------------------------------------------------------------------------------------------------------+------------+
+|   Q5  | getDocsWithThetasLargerThanThr | Get documents that have a proportion of a         | ``[{"id": id1, "doctpc_{model_name}":, doctpc1 }, {"id": id2, "doctpc_{model_name}":, doctpc2}, ...]`` |  |check_|  |
+|       |                                | certain topic larger than a threshold             |                                                                                                        |            |
++-------+--------------------------------+---------------------------------------------------+--------------------------------------------------------------------------------------------------------+------------+
+|   Q6  | getDocsWithHighSimWithDocByid  | Retrieve documents that have a high semantic      | ``[{"id": id1, "score":, score1 }, {"id": id2, "score":, score2 }, ...]``                              | |check_|   |
+|       |                                | relationship with a selected document             |                                                                                                        |            |
++-------+--------------------------------+---------------------------------------------------+--------------------------------------------------------------------------------------------------------+------------+
+|   Q7  | getDocsWithString              | Given a corpus collection, a field, and a         |                                                                                                        | |uncheck_| |
+|       |                                | string, retrieves the documents whose field       |                                                                                                        |            |
+|       |                                | contains such a string                            |                                                                                                        |            |
++-------+--------------------------------+---------------------------------------------------+--------------------------------------------------------------------------------------------------------+------------+
+|   Q8  | getCorpusDocumentList          |                                                   |                                                                                                        |            |
++-------+--------------------------------+---------------------------------------------------+--------------------------------------------------------------------------------------------------------+------------+
+|   Q9  | getTopicsLabels                | Retrieve the label associated to each of the      |                                                                                                        | |uncheck_| |
+|       |                                | topics in a selected model                        |                                                                                                        |            |
++-------+--------------------------------+---------------------------------------------------+--------------------------------------------------------------------------------------------------------+------------+
+|  Q10  | getTopicsChemicalDescription   | Retrieve the chemical description associated      |                                                                                                        | |uncheck_| |
+|       |                                | to each of the topics in a selected model         |                                                                                                        |            |
++-------+--------------------------------+---------------------------------------------------+--------------------------------------------------------------------------------------------------------+------------+
+|  Q11  | getTopicTopDocs                |                                                   |                                                                                                        |            |
++-------+--------------------------------+---------------------------------------------------+--------------------------------------------------------------------------------------------------------+------------+

_sources/usage.rst.txt

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+
+
+Usage
+=====
+
+
+How to clone the code
+---------------------
+
+Write me ...
+
+
+
+Where to find the results
+-------------------------
+
+Write me ...

_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;
+}