docs: update guides

zavolanlab · Oct 21, 2024 · f1b4b4c · f1b4b4c
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diff --git a/docs/_static/custom.css b/docs/_static/custom.css
@@ -0,0 +1,4 @@
+/* Increase font size for toctree elements */
+.toctree-l1 {
+    font-size: 18px;  /* Adjust the size as needed */
+}
diff --git a/docs/conf.py b/docs/conf.py
@@ -88,3 +88,4 @@ def run_apidoc(_):
 
 def setup(app):
     app.connect('builder-inited', run_apidoc)
+    app.add_css_file('custom.css')
diff --git a/docs/guides/examples.rst b/docs/guides/examples.rst
@@ -3,6 +3,7 @@ Examples
 
 HTSinfer provides easy-to-use commands for analyzing single- and paired-ended RNA-Seq libraries.
 
+
 Single-ended Library Example
 ----------------------------
 

diff --git a/docs/guides/installation.rst b/docs/guides/installation.rst
@@ -1,12 +1,12 @@
 Installation
 ============
 
-This section describes how to install HTSinfer using Conda.
+This section describes how to install `HTSinfer` using Conda.
 
 Clone the Repository and Install Dependencies
 ---------------------------------------------
 
-To install HTSinfer, first clone the repository and install the dependencies via `Conda <https://docs.conda.io/en/latest/miniconda.html>`_:
+To install `HTSinfer`, first clone the repository and install the dependencies via `Conda <https://docs.conda.io/en/latest/miniconda.html>`_:
 
 .. code-block:: bash
 
@@ -33,7 +33,7 @@ After the installation is complete, activate the `htsinfer` Conda environment wi
 Verify the Installation (Optional)
 ----------------------------------
 
-If you have installed the development or testing dependencies, you can verify that HTSinfer was installed correctly by executing the tests shipped with the package:
+If you have installed the development or testing dependencies, you can verify that `HTSinfer` was installed correctly by executing the tests shipped with the package:
 
 .. code-block:: bash
 

diff --git a/docs/guides/usage.rst b/docs/guides/usage.rst
@@ -1,6 +1,8 @@
 Usage
 =====
 
+This sections describes the general usage of `HTSinfer`.
+
 General Usage
 -------------
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -3,15 +3,20 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to HTSinfer Documentation!
-==================================
+Welcome to the HTSinfer documentation pages!
+============================================
 
-HTSinfer is a tool for high-throughput sequencing inference.
+`HTSinfer` is a command-line tool that infers metadata from Illumina high-throughput sequencing (HTS) data. 
 
 This documentation will guide you through installation, usage, and the API reference.
 
-HTSinfer Documentation
-----------------------
+.. toctree::
+   :hidden:
+
+   Home <self>
+
+Documentation
+-------------
 
 .. toctree::
    :maxdepth: 1
@@ -21,7 +26,7 @@ HTSinfer Documentation
    guides/examples
 
 .. toctree::
-   :caption: API Documentation
+   :caption: API Overview
    :maxdepth: 1
 
    modules/modules
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Expand Up		@@ -88,3 +88,4 @@ def run_apidoc(_):

		def setup(app):
		app.connect('builder-inited', run_apidoc)
		app.add_css_file('custom.css')
Original file line number	Diff line number	Diff line change
Expand Up		@@ -3,6 +3,7 @@ Examples

		HTSinfer provides easy-to-use commands for analyzing single- and paired-ended RNA-Seq libraries.


		Single-ended Library Example
		----------------------------

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