fix on read the docs

.readthedocs.yaml

@@ -0,0 +1,17 @@
+# Read the Docs configuration file.
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details.
+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.12"
+
+sphinx:
+  configuration: docs/conf.py
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .

README.md

@@ -7,7 +7,7 @@ Welcome to the LOICA (Logical Operators for Integrated Cell Algorithms) reposito
 
 
 ![PyPI](https://img.shields.io/pypi/v/loica)
-[![Documentation Status](https://readthedocs.org/projects/loica/badge/?version=latest)](https://loica.readthedocs.io/en/latest/?badge=latest)
+[![Documentation Status](https://readthedocs.org/projects/loica/badge/?version=latest)](https://loica.readthedocs.io/en/latest/)
 ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/loica)
 ![PyPI - License](https://img.shields.io/pypi/l/loica)
 
@@ -43,7 +43,7 @@ For more details please refer to our [Wiki](https://github.com/RudgeLab/LOICA/wi
 
 ## Documentation
 
- Please visit our documentation with API reference at Read the Docs [loica.rtfd.io](https://loica.rtfd.io)
+ Please visit our documentation with API reference at Read the Docs: [loica.readthedocs.io](https://loica.readthedocs.io/en/latest/).
 
 ## Tutorials
 

docs/conf.py

@@ -36,7 +36,7 @@
 ]
 
 # See https://sphinx-autoapi.readthedocs.io/en/latest/reference/config.html
-autoapi_dirs = ['../loica']
+autoapi_dirs = ['../src/loica']
 # autoapi_options = ['members', 'undoc-members', 'show-inheritance',
 #                   'show-module-summary', 'special-members']
 autoapi_type = 'python'
@@ -67,4 +67,5 @@
 # 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 = ['_static']
+# html_static_path can be enabled when custom static assets are added.
+html_static_path = []

docs/index.rst

@@ -9,12 +9,8 @@ Welcome to LOICA's documentation!
 
 .. toctree::
    :maxdepth: 2
-   
+
    introduction
-
-   ============
-Introduction
-============
 
 Welcome to the LOICA (Logical Operators for Integrated Cell Algorithms) repository, our Python package for designing, modeling and characterizing genetic networks.
 

docs/requirements.txt

@@ -1,4 +1,5 @@
-# these are fixed in accordance with rtd recommendations: https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html#pinning-dependencies
-sphinx==4.4.0
-sphinx_rtd_theme==1.0.0
-sphinx-autoapi==1.8.4
+# These pins follow Read the Docs' reproducible-build recommendations while
+# staying compatible with the current Read the Docs build image.
+sphinx==7.4.7
+sphinx_rtd_theme==2.0.0
+sphinx-autoapi==3.6.0

src/loica/geneproduct.py

@@ -14,7 +14,7 @@ class GeneProduct:
         Initial concentration of the gene product in Molar
     degradation_rate : int | float
         Degradation rate of the gene product
-    type_ : str, optional
+    type\_ : str, optional
         Molecular type of the gene product, could be 'PRO' or 'RNA'
     uri : str, optional
         SynBioHub URI

src/loica/sample.py

@@ -18,10 +18,10 @@ class Sample:
     strain : str
         Name of the strain in the sample
 
-     Methods
+    Methods
     -------
-    add_supplement(supplement, concentration)
-        stablishes the concentration of Supplement
+    set_supplement(supplement, concentration, profile=None)
+        Sets the concentration profile for a supplement.
     """
     def __init__(self, 
             genetic_network=None,