Updating docs

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/api_reference.rst

@@ -0,0 +1,13 @@
+API Reference
+-------------
+
+The following documents provide a detailed reference to the functions and modules in `evofr`.
+
+.. toctree::
+   :maxdepth: 1
+
+   source/evofr.data
+   source/evofr.models
+   source/evofr.infer
+   source/evofr.posterior
+   source/evofr.plotting

docs/conf.py

@@ -1,6 +1,7 @@
 import pathlib
 import sys
 from datetime import datetime
+
 import evofr
 
 # -- Path setup --------------------------------------------------------------
@@ -23,10 +24,13 @@
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
     "sphinx.ext.napoleon",
+    "sphinx_rtd_theme",
+    "nbsphinx",
+    "sphinx.ext.mathjax",
 ]
 
 templates_path = ["_templates"]
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
@@ -38,6 +42,8 @@
 autodoc_typehints = "description"
 add_module_names = False
 
+nbsphinx_execute = "never"
+
 # Napolean settings
 napoleon_google_docstring = True
 napoleon_numpy_docstring = True

docs/index.rst

@@ -1,23 +1,51 @@
+.. evofr documentation master file, created by
+   sphinx-quickstart on [date you ran the command].
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
 Welcome to evofr's documentation!
 =================================
 
-.. automodule:: evofr
-   :members:
+.. image:: https://github.com/blab/evofr/actions/workflows/ci.yaml/badge.svg
+    :target: https://github.com/blab/evofr/actions/workflows/ci.yaml
 
-.. toctree::
-   :maxdepth: 1
+Overview
+--------
+
+`evofr` is a Python package designed for evolutionary forecasting of genetic variants. 
+This project provides tools aimed at modeling and predicting the evolution and prevalence of genetic variants over time. 
+The package integrates various data handling, modeling, and plotting capabilities, making it a useful toolkit for researchers in the field of genetic epidemiology and evolutionary dynamics.
+
+Installation
+------------
+
+You can install the latest release of `evofr` directly using pip:
+
+.. code-block:: bash
+
+    pip install evofr
 
-   source/evofr.data.rst
-   source/evofr.models.rst
-   source/evofr.infer.rst
-   source/evofr.posterior.rst
-   source/evofr.plotting.rst
+For those looking to contribute or modify the package, it can be built locally with:
 
+.. code-block:: bash
+
+    poetry build
+    pip install path-to-wheel>
 
 
 Indices and tables
-==================
+------------------
 
 * :ref:`genindex`
 * :ref:`modindex`
 * :ref:`search`
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents
+
+   installation
+   api_reference
+   mlr_quickstart
+
+=================================

docs/installation.rst

@@ -0,0 +1,67 @@
+Installation Guide
+==================
+
+This page provides detailed instructions on how to install `evofr`, a Python package for evolutionary forecasting of genetic variants.
+
+Installing with pip
+-------------------
+
+The easiest way to install the latest version of `evofr` is via pip. This method will automatically handle all dependencies, including JAX and Numpyro:
+
+.. code-block:: bash
+
+    pip install evofr
+
+Installing from Source
+----------------------
+
+For those who prefer to install `evofr` from the source or want to contribute to the development, follow these steps:
+
+.. code-block:: bash
+
+    git clone https://github.com/blab/evofr.git
+    cd evofr
+    pip install .
+
+Installing from Source Using Poetry
+-----------------------------------
+
+Poetry is a tool for dependency management and packaging in Python. To use Poetry to install `evofr` from the source, follow these instructions:
+
+.. code-block:: bash
+
+    git clone https://github.com/blab/evofr.git
+    cd evofr
+    poetry install
+
+This command will create a virtual environment and install all dependencies defined in `pyproject.toml`. To activate the virtual environment created by Poetry, you can use:
+
+.. code-block:: bash
+
+    poetry shell
+
+Alternatively, to run commands within the virtual environment without activating it, use `poetry run`:
+
+.. code-block:: bash
+
+    poetry run python -m mymodule
+
+For more information on using Poetry, visit the `Poetry documentation <https://python-poetry.org/docs/>`_.
+
+Environment Setup
+-----------------
+
+It is often beneficial to set up a virtual environment for Python projects to manage dependencies separately from the system-wide installations:
+
+.. code-block:: bash
+
+    python -m venv evofr-env
+    source evofr-env/bin/activate
+    pip install evofr
+
+This method is especially recommended when working on development or managing multiple Python packages.
+
+Additional Installation Help
+----------------------------
+
+If you encounter any issues during the installation, particularly related to JAX, please consult the `JAX installation guide <https://jax.readthedocs.io/en/latest/installation.html>`_ for detailed instructions and troubleshooting tips.

docs/mlr_quickstart.rst

@@ -0,0 +1,8 @@
+Getting starting with Evofr
+--------------------------
+
+.. toctree::
+   :maxdepth: 2
+   :caption Test
+
+   notebooks/example_mlr.ipynb

evofr/infer/MCMC_handler.py

@@ -60,7 +60,7 @@ def fit(
         num_samples:
             number of samples to be returned in MCMC.
 
-        **mcmc_kwargs:
+        mcmc_kwargs:
             additional arguments to be passed to MCMC algorithms.
         """
         self.mcmc = MCMC(