Merge pull request #368 from azneto/master

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

@@ -6,70 +6,70 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
 .highlight .hll { background-color: #ffffcc }
 .highlight { background: #eeffcc; }
 .highlight .c { color: #408090; font-style: italic } /* Comment */
-.highlight .err { border: 1px solid #FF0000 } /* Error */
+.highlight .err { border: 1px solid #F00 } /* Error */
 .highlight .k { color: #007020; font-weight: bold } /* Keyword */
-.highlight .o { color: #666666 } /* Operator */
+.highlight .o { color: #666 } /* Operator */
 .highlight .ch { color: #408090; font-style: italic } /* Comment.Hashbang */
 .highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */
 .highlight .cp { color: #007020 } /* Comment.Preproc */
 .highlight .cpf { color: #408090; font-style: italic } /* Comment.PreprocFile */
 .highlight .c1 { color: #408090; font-style: italic } /* Comment.Single */
-.highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
+.highlight .cs { color: #408090; background-color: #FFF0F0 } /* Comment.Special */
 .highlight .gd { color: #A00000 } /* Generic.Deleted */
 .highlight .ge { font-style: italic } /* Generic.Emph */
 .highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */
-.highlight .gr { color: #FF0000 } /* Generic.Error */
+.highlight .gr { color: #F00 } /* Generic.Error */
 .highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
 .highlight .gi { color: #00A000 } /* Generic.Inserted */
-.highlight .go { color: #333333 } /* Generic.Output */
-.highlight .gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */
+.highlight .go { color: #333 } /* Generic.Output */
+.highlight .gp { color: #C65D09; font-weight: bold } /* Generic.Prompt */
 .highlight .gs { font-weight: bold } /* Generic.Strong */
 .highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
-.highlight .gt { color: #0044DD } /* Generic.Traceback */
+.highlight .gt { color: #04D } /* Generic.Traceback */
 .highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */
 .highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */
 .highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */
 .highlight .kp { color: #007020 } /* Keyword.Pseudo */
 .highlight .kr { color: #007020; font-weight: bold } /* Keyword.Reserved */
 .highlight .kt { color: #902000 } /* Keyword.Type */
 .highlight .m { color: #208050 } /* Literal.Number */
-.highlight .s { color: #4070a0 } /* Literal.String */
-.highlight .na { color: #4070a0 } /* Name.Attribute */
+.highlight .s { color: #4070A0 } /* Literal.String */
+.highlight .na { color: #4070A0 } /* Name.Attribute */
 .highlight .nb { color: #007020 } /* Name.Builtin */
-.highlight .nc { color: #0e84b5; font-weight: bold } /* Name.Class */
-.highlight .no { color: #60add5 } /* Name.Constant */
-.highlight .nd { color: #555555; font-weight: bold } /* Name.Decorator */
-.highlight .ni { color: #d55537; font-weight: bold } /* Name.Entity */
+.highlight .nc { color: #0E84B5; font-weight: bold } /* Name.Class */
+.highlight .no { color: #60ADD5 } /* Name.Constant */
+.highlight .nd { color: #555; font-weight: bold } /* Name.Decorator */
+.highlight .ni { color: #D55537; font-weight: bold } /* Name.Entity */
 .highlight .ne { color: #007020 } /* Name.Exception */
-.highlight .nf { color: #06287e } /* Name.Function */
+.highlight .nf { color: #06287E } /* Name.Function */
 .highlight .nl { color: #002070; font-weight: bold } /* Name.Label */
-.highlight .nn { color: #0e84b5; font-weight: bold } /* Name.Namespace */
+.highlight .nn { color: #0E84B5; font-weight: bold } /* Name.Namespace */
 .highlight .nt { color: #062873; font-weight: bold } /* Name.Tag */
-.highlight .nv { color: #bb60d5 } /* Name.Variable */
+.highlight .nv { color: #BB60D5 } /* Name.Variable */
 .highlight .ow { color: #007020; font-weight: bold } /* Operator.Word */
-.highlight .w { color: #bbbbbb } /* Text.Whitespace */
+.highlight .w { color: #BBB } /* Text.Whitespace */
 .highlight .mb { color: #208050 } /* Literal.Number.Bin */
 .highlight .mf { color: #208050 } /* Literal.Number.Float */
 .highlight .mh { color: #208050 } /* Literal.Number.Hex */
 .highlight .mi { color: #208050 } /* Literal.Number.Integer */
 .highlight .mo { color: #208050 } /* Literal.Number.Oct */
-.highlight .sa { color: #4070a0 } /* Literal.String.Affix */
-.highlight .sb { color: #4070a0 } /* Literal.String.Backtick */
-.highlight .sc { color: #4070a0 } /* Literal.String.Char */
-.highlight .dl { color: #4070a0 } /* Literal.String.Delimiter */
-.highlight .sd { color: #4070a0; font-style: italic } /* Literal.String.Doc */
-.highlight .s2 { color: #4070a0 } /* Literal.String.Double */
-.highlight .se { color: #4070a0; font-weight: bold } /* Literal.String.Escape */
-.highlight .sh { color: #4070a0 } /* Literal.String.Heredoc */
-.highlight .si { color: #70a0d0; font-style: italic } /* Literal.String.Interpol */
-.highlight .sx { color: #c65d09 } /* Literal.String.Other */
+.highlight .sa { color: #4070A0 } /* Literal.String.Affix */
+.highlight .sb { color: #4070A0 } /* Literal.String.Backtick */
+.highlight .sc { color: #4070A0 } /* Literal.String.Char */
+.highlight .dl { color: #4070A0 } /* Literal.String.Delimiter */
+.highlight .sd { color: #4070A0; font-style: italic } /* Literal.String.Doc */
+.highlight .s2 { color: #4070A0 } /* Literal.String.Double */
+.highlight .se { color: #4070A0; font-weight: bold } /* Literal.String.Escape */
+.highlight .sh { color: #4070A0 } /* Literal.String.Heredoc */
+.highlight .si { color: #70A0D0; font-style: italic } /* Literal.String.Interpol */
+.highlight .sx { color: #C65D09 } /* Literal.String.Other */
 .highlight .sr { color: #235388 } /* Literal.String.Regex */
-.highlight .s1 { color: #4070a0 } /* Literal.String.Single */
+.highlight .s1 { color: #4070A0 } /* Literal.String.Single */
 .highlight .ss { color: #517918 } /* Literal.String.Symbol */
 .highlight .bp { color: #007020 } /* Name.Builtin.Pseudo */
-.highlight .fm { color: #06287e } /* Name.Function.Magic */
-.highlight .vc { color: #bb60d5 } /* Name.Variable.Class */
-.highlight .vg { color: #bb60d5 } /* Name.Variable.Global */
-.highlight .vi { color: #bb60d5 } /* Name.Variable.Instance */
-.highlight .vm { color: #bb60d5 } /* Name.Variable.Magic */
+.highlight .fm { color: #06287E } /* Name.Function.Magic */
+.highlight .vc { color: #BB60D5 } /* Name.Variable.Class */
+.highlight .vg { color: #BB60D5 } /* Name.Variable.Global */
+.highlight .vi { color: #BB60D5 } /* Name.Variable.Instance */
+.highlight .vm { color: #BB60D5 } /* Name.Variable.Magic */
 .highlight .il { color: #208050 } /* Literal.Number.Integer.Long */