From 3971d5efb0bc48ccd35123e564b3ddc16178b7c2 Mon Sep 17 00:00:00 2001
From: balajtimate <balajtimate@gmail.com>
Date: Fri, 15 Nov 2024 12:26:23 +0100
Subject: [PATCH] docs: update index, restructure API docs

---
 docs/guides/examples.rst     |  9 +++++++
 docs/guides/installation.rst | 46 ++++++++++++++++++++++++++----------
 docs/index.rst               | 13 +++-------
 docs/indices_and_tables.rst  |  8 +++++++
 4 files changed, 53 insertions(+), 23 deletions(-)
 create mode 100644 docs/indices_and_tables.rst

diff --git a/docs/guides/examples.rst b/docs/guides/examples.rst
index a3be423..9f2ad42 100644
--- a/docs/guides/examples.rst
+++ b/docs/guides/examples.rst
@@ -84,4 +84,13 @@ Here is a sample output for the paired-ended library:
       }
    }
 
+Results
+-------
+
 For more details on the output structure, refer to the :code:`Results` model in the API documentation.
+
+- :code:`library_stats`: Read length statistics results, including the minimum, maximum, mean, median and mode.
+- :code:`library_source`: Library source inference results, with the short name and NCBI taxonomy ID of the source organism.
+- :code:`library_type`: Library type inference results, single- or paired-end. In case of paired-end samples, the mate designation.
+- :code:`read_orientation`: Read orientation inference results, based on the fragment library types notation from `Salmon <https://salmon.readthedocs.io/en/latest/library_type.html>`_.
+- :code:`read_layout`: Read layout inference results, including the 3'-adapter sequence and the poly(A) fraction. 
\ No newline at end of file
diff --git a/docs/guides/installation.rst b/docs/guides/installation.rst
index c71ea5f..d734156 100644
--- a/docs/guides/installation.rst
+++ b/docs/guides/installation.rst
@@ -1,28 +1,48 @@
 Installation
 ============
 
-This section describes how to install `HTSinfer` using Conda.
+This section describes how to install `HTSinfer`.
 
-Clone the Repository and Install Dependencies
----------------------------------------------
+Install using Conda
+-------------------
 
-To install `HTSinfer`, first clone the repository and install the dependencies via `Conda <https://docs.conda.io/en/latest/miniconda.html>`_:
+The easiest and quickest installation method is via `Mamba <https://mamba.readthedocs.io/en/latest/installation.html>`_ or `Conda <https://docs.conda.io/en/latest/miniconda.html>`_.
+`HTSinfer` is available as part of the `Bioconda <https://anaconda.org/bioconda/htsinfer>`_ channel.
+
+To create a new Conda environment with `HTSinfer` and its dependencies installed, run:
+
+.. code-block:: bash
+
+   mamba create --name htsinfer bioconda::htsinfer
+
+
+Then, activate the `htsinfer` Conda environment with:
+
+.. code-block:: bash
+
+   conda activate htsinfer
+
+
+To install `HTSinfer` in your current environment, run:
+
+.. code-block:: bash
+
+   mamba install bioconda::htsinfer
+
+Install from GitHub
+-------------------
+
+If you would like to contribute to the development of `HTSinfer`, or wishing to use unreleased versions, you can install `HTSinfer` from the `GitHub <https://github.com/zavolanlab/htsinfer>`_.
+First clone the repository and install the dependencies via `Conda <https://docs.conda.io/en/latest/miniconda.html>`_:
 
 .. code-block:: bash
 
    git clone https://github.com/zavolanlab/htsinfer.git
    cd htsinfer
-   conda env create --file environment.yml
+   mamba env create --file environment.yml
    # Alternatively, to install with development dependencies,
    # run the following instead
-   conda env create --file environment-dev.ymls
-
-.. note::
-
-   Creating the environment may take some time. It is strongly recommended to install `Mamba <https://mamba.readthedocs.io/en/latest/installation.html>`_ and replace :code:`conda` with :code:`mamba` in the previous commands for faster installation.
-
-Activate the Conda Environment
-------------------------------
+   mamba env create --file environment-dev.ymls
 
 After the installation is complete, activate the :code:`htsinfer` Conda environment with:
 
diff --git a/docs/index.rst b/docs/index.rst
index 1b241c6..404304e 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -15,10 +15,8 @@ This documentation will guide you through installation and usage. It also contai
 
    Home <self>
 
-Documentation
--------------
-
 .. toctree::
+   :caption: Documentation
    :maxdepth: 1
 
    guides/installation
@@ -26,14 +24,9 @@ Documentation
    guides/examples
 
 .. toctree::
-   :caption: API Overview
+   :caption: API overview
    :maxdepth: 1
 
    modules/modules
-
-Indices and tables
-------------------
-
-* :ref:`genindex`
-* :ref:`modindex`
+   indices_and_tables
 
diff --git a/docs/indices_and_tables.rst b/docs/indices_and_tables.rst
new file mode 100644
index 0000000..63d1b81
--- /dev/null
+++ b/docs/indices_and_tables.rst
@@ -0,0 +1,8 @@
+Indices and tables
+------------------
+
+.. toctree::
+   :maxdepth: 1
+
+   genindex
+   modindex
\ No newline at end of file