updates documentation

docs/html/.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: 2e35b89f1eca31368046d88025537fca
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 7c6d303bbe9e7306892b50168be5cd9d
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/html/_sources/index_search.rst.txt

@@ -21,8 +21,8 @@ Now, proceding with elasticsearch instalation, run the following commands:
     cd YOURPROJECT
     source bin/activate
     cd src
-    wget https://artifacts.elastic.co/downloads/elasticsearch/elasticsearch-7.17.3-amd64.deb
-    sudo dpkg -i elasticsearch-7.17.3-amd64.deb
+    wget https://artifacts.elastic.co/downloads/elasticsearch/elasticsearch-7.17.26-amd64.deb
+    sudo dpkg -i elasticsearch-7.17.26-amd64.deb
     sudo systemctl daemon-reload
     sudo systemctl enable elasticsearch.service
     sudo systemctl start elasticsearch.service

docs/html/_sources/installation.rst.txt

@@ -30,14 +30,16 @@ Be sure to have the following dependencies installed
 
     sudo apt install zlib1g-dev libbz2-dev liblzma-dev python3-dev
 
-**Python 3.8**
+**Python 3.12**
 
 We strongly recommend creating a new virtualenv for your project
 
 .. code-block:: bash
 
-    virtualenv -p /usr/bin/python3.8 YOURPROJECT
-    cd YOURPROJECT
+    sudo mkdir /var/www/YOURPROJECT
+    sudo chown $USER:$USER /var/www/YOURPROJECT
+    virtualenv -p /usr/bin/python3.12 /var/www/YOURPROJECT
+    cd /var/www/YOURPROJECT
     source bin/activate
 
 **machado**
@@ -60,8 +62,7 @@ Inside YOURPROJECT directory create a Django project with the following command:
 
 .. code-block:: bash
 
-    django-admin startproject WEBPROJECT
-    cd WEBPROJECT
+    django-admin startproject WEBPROJECT .
 
 Then, configure the WEBPROJECT/settings.py file to connect to your Chado database.
 
@@ -109,6 +110,7 @@ You have to run the following command to create django admin tables:
 
     python manage.py migrate
 
+Just ignore the warnings about unapplied migrations.
 Run tests to check the instalation:
 
 .. code-block:: bash
@@ -121,7 +123,6 @@ Now, just run the DJango server to access the web interface:
 
     python manage.py runserver
 
-The API interface will be available at http://localhost:8000/machado/api
 
 
 References

docs/html/_sources/webserver.rst.txt

@@ -33,20 +33,12 @@ take care of this process. It will be necessary to install the following package
 
     sudo apt install libapache2-mod-wsgi-py3
 
-Now symlink the directory of YOURPROJECT to '/var/www/' (tested in Ubuntu 20.04):
-
-.. code-block:: bash
-
-    sudo ln -s /FULL/PATH/TO/YOURPROJECT /var/www/
-
-* Make sure this directory and sub-directories have 755 permissions
-
 Now configure Apache to use the WSGI module.
 Here is the configuration file (/etc/apache2/sites-available/YOURPROJECT.conf)
 
 .. code-block:: bash
 
-    <Directory "/var/www/YOURPROJECT/WEBPROJECT/WEBPROJECT">
+    <Directory "/var/www/YOURPROJECT/WEBPROJECT">
     <Files "wsgi.py">
         Require all granted
     </Files>
@@ -60,8 +52,8 @@ Here is the configuration file (/etc/apache2/sites-available/YOURPROJECT.conf)
 
     WSGIDaemonProcess WEBPROJECT
     WSGIPythonHome /var/www/YOURPROJECT
-    WSGIPythonPath /var/www/YOURPROJECT/WEBPROJECT
-    WSGIScriptAlias /YOURPROJECT /var/www/YOURPROJECT/WEBPROJECT/WEBPROJECT/wsgi.py
+    WSGIPythonPath /var/www/YOURPROJECT
+    WSGIScriptAlias /YOURPROJECT /var/www/YOURPROJECT/WEBPROJECT/wsgi.py
 
 * In this example the whole project is in /var/www/YOURPROJECT, but it's not required to be there.
 * This directory and sub-directories must have 755 permissions

docs/html/_static/basic.css

@@ -1,12 +1,5 @@
 /*
- * basic.css
- * ~~~~~~~~~
- *
  * Sphinx stylesheet -- basic theme.
- *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 
 /* -- main layout ----------------------------------------------------------- */
@@ -115,15 +108,11 @@ img {
 /* -- search page ----------------------------------------------------------- */
 
 ul.search {
-    margin: 10px 0 0 20px;
-    padding: 0;
+    margin-top: 10px;
 }
 
 ul.search li {
-    padding: 5px 0 5px 20px;
-    background-image: url(file.png);
-    background-repeat: no-repeat;
-    background-position: 0 7px;
+    padding: 5px 0;
 }
 
 ul.search li a {

docs/html/_static/doctools.js

@@ -1,12 +1,5 @@
 /*
- * doctools.js
- * ~~~~~~~~~~~
- *
  * Base JavaScript utilities for all Sphinx HTML documentation.
- *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 "use strict";
 

docs/html/_static/language_data.js

@@ -1,19 +1,12 @@
 /*
- * language_data.js
- * ~~~~~~~~~~~~~~~~
- *
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
- *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 
 var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
 
 
-/* Non-minified version is copied as a separate JS file, is available */
+/* Non-minified version is copied as a separate JS file, if available */
 
 /**
  * Porter Stemmer

docs/html/_static/pygments.css

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