bug fixing

README.md

@@ -1,4 +1,4 @@
-![logo](logo.svg)
+![logo](logo.png)
 
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ipqa-research/ugropy/main)
 [![License](https://img.shields.io/badge/License-MIT-blue.svg)](https://tldrlegal.com/license/mit-license)
@@ -21,26 +21,26 @@ molecules that `ugropy` fails solving the subgroups of a model is very helpful.
 `ugropy` is tested for `Python` 3.10, 3.11 and 3.12 on Linux, Windows and Mac
 OS.
 
-## Try ugropy now
+# Try ugropy now
 You can try ugropy from its
 [Binder](https://mybinder.org/v2/gh/ipqa-research/ugropy/main). Open the
 binder.ipynb file to explore the basic features.
 
-## Models supported v2.0.5
+# Models supported v2.0.5
 - Classic liquid-vapor UNIFAC
 - Predictive Soave-Redlich-Kwong (PSRK)
 - Joback
 
-## Writers
+# Writers
 `ugropy` allows you to convert the obtained functional groups or estimated
 properties to the input format required by the following thermodynamic
 libraries:
 
-- [Clapeyron.jl](github.com/ClapeyronThermo/Clapeyron.jl)
+- [Clapeyron.jl](https://github.com/ClapeyronThermo/Clapeyron.jl)
 - [Thermo](https://github.com/CalebBell/thermo)
 
 
-## Example of use
+# Example of use
 You can check the full tutorial
 [here](https://ipqa-research.github.io/ugropy/tutorial/tutorial.html).
 

docs/requirements.txt

@@ -3,6 +3,7 @@ setuptools
 Sphinx
 sphinx_rtd_theme
 
+myst-parser
 nbsphinx
 sphinx_copybutton
 sphinxcontrib-bibtex

docs/source/conf.py

@@ -1,15 +1,9 @@
-# Configuration file for the Sphinx documentation builder.
-#
-# For the full list of built-in configuration values, see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
-
-# -- Project information -----------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 import os
 import pathlib
 import sys
 import toml
 
+
 CURRENT_PATH = pathlib.Path(os.path.abspath(os.path.dirname(__file__)))
 UGROPY_PATH = CURRENT_PATH.parent.parent
 
@@ -31,6 +25,7 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
 extensions = [
+    "myst_parser",
     "sphinx.ext.autodoc",
     "sphinx.ext.coverage",
     "sphinx.ext.mathjax",
@@ -53,6 +48,7 @@
 
 bibtex_bibfiles = ["refs.bib"]
 
+add_module_names = False
 # =============================================================================
 # NUMPY DOC
 # =============================================================================
@@ -65,7 +61,10 @@
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = ".rst"
+source_suffix = {
+    ".rst": "restructuredtext",
+    ".md": "markdown",
+}
 
 # The master toctree document.
 master_doc = "index"

docs/source/index.rst

@@ -3,7 +3,8 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-.. include:: README.rst
+.. include:: ../../README.md
+   :parser: myst_parser.sphinx_
 
 .. toctree::
    :maxdepth: 2
@@ -12,12 +13,10 @@
    tutorial/tutorial
    modules
 
-References
-==========
+.. toctree::
+   :maxdepth: 1
 
-.. bibliography::
-   :style: unsrt
-   :cited:
+   references.rst
 
 
 Indices and tables