Migrate Help site from Docusaurus to Sphinx + sphinx_rtd_theme

.gitignore

@@ -7,3 +7,4 @@
 
 e2e/npm-debug.log
 
+src/Help/venv/

.readthedocs.yaml

@@ -1,13 +1,13 @@
 version: 2
+
 build:
   os: "ubuntu-22.04"
   tools:
-    nodejs: "18"
-  jobs:
-    install:
-      - cd src/Help && npm install
-    build:
-      html:
-        - cd src/Help && npm run build
-        - mkdir --parents $READTHEDOCS_OUTPUT/html/
-        - cp --recursive src/Help/build/* $READTHEDOCS_OUTPUT/html/
+    python: "3.11"
+
+sphinx:
+  configuration: src/Help/conf.py
+
+python:
+  install:
+    - requirements: src/Help/requirements.txt

src/Help/_build/gettext/_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;
+}

src/Help/_build/gettext/contributing-data-to-the-atlas/creating-sources.pot

@@ -0,0 +1,33 @@
+# SOME DESCRIPTIVE TITLE.
+# Copyright (C) 2026, ICIPE
+# This file is distributed under the same license as the Vector Atlas Help package.
+# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
+#
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: Vector Atlas Help \n"
+"Report-Msgid-Bugs-To: \n"
+"POT-Creation-Date: 2026-08-26 12:50+0300\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
+"Language-Team: LANGUAGE <LL@li.org>\n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#: ../../contributing-data-to-the-atlas/creating-sources.md:1
+msgid "Creating sources"
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/creating-sources.md:3
+msgid "To create a source you need the `uploader` role. Navigate to the `More > Add Source` option in the navigation menu. Fill in the details for a source and click `Submit`. Use the `Reset` button to clear the form."
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/creating-sources.md:5
+msgid "![Add source](add-source.png)"
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/creating-sources.md:5
+msgid "Add source"
+msgstr ""

src/Help/_build/gettext/contributing-data-to-the-atlas/reviewing-data.pot

@@ -0,0 +1,65 @@
+# SOME DESCRIPTIVE TITLE.
+# Copyright (C) 2026, ICIPE
+# This file is distributed under the same license as the Vector Atlas Help package.
+# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
+#
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: Vector Atlas Help \n"
+"Report-Msgid-Bugs-To: \n"
+"POT-Creation-Date: 2026-08-26 12:50+0300\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
+"Language-Team: LANGUAGE <LL@li.org>\n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#: ../../contributing-data-to-the-atlas/reviewing-data.md:1
+msgid "Reviewing data"
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/reviewing-data.md:3
+msgid "When data has been successfully uploaded, the system will send an email to all users with the `reviewer` role, containing a link to the review page:"
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/reviewing-data.md:5
+msgid "![Review page](review.png)"
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/reviewing-data.md:5
+msgid "Review page"
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/reviewing-data.md:7
+msgid "To see the data uploaded, click the `DOWNLOAD DATA` button. This will download the data as a csv file."
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/reviewing-data.md:9
+msgid "To leave any comments on the data for the uploader to address, type them into the `Review Comments` box and click `REQUEST CHANGES`. This will send an email to the uploader and all other reviewers with the comments. It will also change the status of the dataset to 'In review':"
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/reviewing-data.md:11
+msgid "![Review page In review](reviewed.png)"
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/reviewing-data.md:11
+msgid "Review page In review"
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/reviewing-data.md:13
+msgid "To approve data, click on the `APPROVE DATA` button. This will send an email to the uploader and all other reviewers, saying that you have approved the data."
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/reviewing-data.md:15
+msgid "Two approvals are needed to fully approve data - once two reviewers have approved, the data will be made public, and the review page will be updated:"
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/reviewing-data.md:17
+msgid "![Review page Approved](approved.png)"
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/reviewing-data.md:17
+msgid "Review page Approved"
+msgstr ""

src/Help/_build/gettext/contributing-data-to-the-atlas/signing-up-to-the-site.pot

@@ -0,0 +1,97 @@
+# SOME DESCRIPTIVE TITLE.
+# Copyright (C) 2026, ICIPE
+# This file is distributed under the same license as the Vector Atlas Help package.
+# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
+#
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: Vector Atlas Help \n"
+"Report-Msgid-Bugs-To: \n"
+"POT-Creation-Date: 2026-08-26 12:50+0300\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
+"Language-Team: LANGUAGE <LL@li.org>\n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#: ../../contributing-data-to-the-atlas/signing-up-to-the-site.md:1
+msgid "Signing up to the site"
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/signing-up-to-the-site.md:3
+msgid "Most operations do not require a log in as the data is intended to be open. The time that a log in is required is when contributing data to the site, this means we can assign roles to users who are uploaders, those who are reviewers and those who are editors for the site."
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/signing-up-to-the-site.md:5
+msgid "To sign up to the site, click on the `Login` button in the top right of the navigation menu."
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/signing-up-to-the-site.md:7
+msgid "![log in](login.png)"
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/signing-up-to-the-site.md:7
+msgid "log in"
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/signing-up-to-the-site.md:9
+msgid "This will redirect you to the Vector Atlas' authentication provider, Auth0. Click on the `Sign up` option below the \"Continue\" button."
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/signing-up-to-the-site.md:11
+msgid "![sign up](sign-up.png)"
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/signing-up-to-the-site.md:11
+msgid "sign up"
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/signing-up-to-the-site.md:13
+msgid "Enter your email, create a password and click `Continue`. This will register you for the site and redirect you to the homepage but you won't have any roles by this point."
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/signing-up-to-the-site.md:15
+msgid "You will receive an email from Auth0 asking you to verify your email address by clicking on a button in the email. Once this verification is done then the system team can assign roles."
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/signing-up-to-the-site.md:17
+msgid "To request new roles, go to the `Settings` page in the user menu."
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/signing-up-to-the-site.md:19
+msgid "![user settings](user-settings.png)"
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/signing-up-to-the-site.md:19
+msgid "user settings"
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/signing-up-to-the-site.md:21
+msgid "On the user settings page click on the `Request additional roles` button to open the roles form. Select the roles that you require; uploader to upload data or model overlays, reviewer to review data before it is published, editor to edit news and species information, admin to be a site admin."
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/signing-up-to-the-site.md:23
+msgid "Enter a reason for the request and then click submit request, this will then email the admins with your requested roles, Auth0 id and the reason for the request. They should then respond directly to you."
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/signing-up-to-the-site.md:25
+msgid "![role request](role-request.png)"
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/signing-up-to-the-site.md:25
+msgid "role request"
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/signing-up-to-the-site.md:27
+msgid "Equally, you don't need to know the roles you need ahead of time. The system will display an unauthorised message is you try to perform an operation that you don't have the right role for. For example, if you navigate to the Data Hub page and select `Upload Model` then you will get the message that you are not an uploader and be directed to the user settings page."
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/signing-up-to-the-site.md:29
+msgid "![not an uploader](not-an-uploader.png)"
+msgstr ""
+
+#: ../../contributing-data-to-the-atlas/signing-up-to-the-site.md:29
+msgid "not an uploader"
+msgstr ""