From acba20309de487dfdaf339abcc0a21a2e1cdf6a6 Mon Sep 17 00:00:00 2001
From: balajtimate <balajtimate@gmail.com>
Date: Mon, 21 Oct 2024 15:20:17 +0200
Subject: [PATCH] docs: add usage and examples pages

---
 docs/conf.py                 | 13 ++++++++++---
 docs/guides/examples.rst     |  2 ++
 docs/guides/installation.rst |  4 ++--
 docs/guides/usage.rst        |  2 ++
 docs/index.rst               | 19 +++++++------------
 5 files changed, 23 insertions(+), 17 deletions(-)
 create mode 100644 docs/guides/examples.rst
 create mode 100644 docs/guides/usage.rst

diff --git a/docs/conf.py b/docs/conf.py
index af28a87..b663050 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -17,7 +17,7 @@
 
 from sphinx.ext import apidoc
 
-sys.path.insert(0, os.path.abspath('..'))
+sys.path.insert(0, os.path.abspath('../htsinfer'))
 
 
 # -- Project information -----------------------------------------------------
@@ -46,7 +46,14 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'api/yourpackage.rst']
+exclude_patterns = [
+    '_build',
+    'api/yourpackage.rst',
+    'setup.py',
+    'Thumbs.db',
+    '.DS_Store',
+    '.eggs'
+]
 
 # Default doc to search for
 master_doc = 'index'
@@ -61,7 +68,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = []
+html_static_path = ['_static']
 
 
 # -- Automation -------------------------------------------------------------
diff --git a/docs/guides/examples.rst b/docs/guides/examples.rst
new file mode 100644
index 0000000..7d4d0aa
--- /dev/null
+++ b/docs/guides/examples.rst
@@ -0,0 +1,2 @@
+Examples
+========
\ No newline at end of file
diff --git a/docs/guides/installation.rst b/docs/guides/installation.rst
index 63ca4e7..5712d5e 100644
--- a/docs/guides/installation.rst
+++ b/docs/guides/installation.rst
@@ -1,5 +1,5 @@
-Installation Guide
-==================
+Installation
+============
 
 This section describes how to install HTSinfer using Conda.
 
diff --git a/docs/guides/usage.rst b/docs/guides/usage.rst
new file mode 100644
index 0000000..9fa12ad
--- /dev/null
+++ b/docs/guides/usage.rst
@@ -0,0 +1,2 @@
+Usage
+=====
\ No newline at end of file
diff --git a/docs/index.rst b/docs/index.rst
index 5f99c23..52351df 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -11,28 +11,23 @@ HTSinfer is a tool for high-throughput sequencing inference.
 This documentation will guide you through installation, usage, and the API reference.
 
 HTSinfer Documentation
-=======================
+----------------------
 
 .. toctree::
-   :caption: Contents
+   :maxdepth: 1
 
    guides/installation
-
-HTSinfer API docs
-=================
+   guides/usage
+   guides/examples
 
 .. toctree::
-   :caption: Modules
+   :caption: API Documentation
+   :maxdepth: 1
 
    modules/modules
 
-.. toctree::
-   :caption: Index
-
-   indices
-
 Indices and tables
-==================
+------------------
 
 * :ref:`genindex`
 * :ref:`modindex`