release

.gitignore

-SSBtoolkit-Tutorial1-DEV.ipynb
-SSBtoolkit-Tutorial2-DEV.ipynb
-SSBtoolkit-Tutorial3A-DEV.ipynb
-SSBtoolkit-Tutorial4-OXTR-DEV.ipynb
-src/lib/__pycache__/
-src/lib/autogrid_reference_files/
-src/lib/autogrids/
-src/lib/ssbtoolkit_BK.py
-.ipynb_checkpoints/
-debugging.txt

docs/_build/html/.buildinfo

 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: b647779c966b74360299afc589cf109b
+config: b18c64a1de10b91df8b26059330c35f6
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/html/_sources/apidocs.rst.txt

 API Documentation
 =================
+.. automodule:: Binding
+   :members:
+
+.. automodule:: Simulation
+   :members:
 
-.. automodule:: ssbtoolkit
+.. automodule:: Utils
    :members:

docs/_build/html/_sources/index.rst.txt

@@ -46,6 +46,51 @@ protocols.
    apidocs
    faq
 
+\
+
+\ 
+
+Availability and License
+========================
+The source code is freely available at https://github.com/rribeiro-sci/SSBtoolkit under
+the Apache 2.0 license. Tutorial notebooks containing minimal working examples can be found at https://github.com/rribeiro-sci/SSBtoolkit.
+
+\
+
+\ 
+
+Developed by
+============
+.. image:: https://res.cloudinary.com/djz27k5hg/image/upload/v1637333672/logos/Juelich_logo_100px_ecv2hy.png
+  :width: 200
+
+\
+
+\ 
+
+Funded by
+=========
+.. image:: https://res.cloudinary.com/djz27k5hg/image/upload/v1637657234/logos/HBP_horizontal_logo_qtcyzn.png
+  :width: 200
+  :alt: Alternative text
+  
+Citation |DOI for Citing ssbtoolkit|
+====================================
+
+pyGOMoDo is research software. If you make use of pyGOMoDo in scientific
+publications, please cite it. The BibTeX reference is
+
+::
+
+    @article{ribeiro_ssb_2022,
+        title={{SSB} toolkit: from molecular structure to subcellular signaling pathways.},
+        author={Ribeiro, Rui Pedro and Gossen, Jonas and Rossetti, Giulia and Giorgetti, Alejandro},
+        publisher={bioRxiv},
+        url={https://www.biorxiv.org/content/10.1101/2022.11.08.515595v1},
+        doi={10.1101/2022.11.08.515595},
+        year={2022}
+    }
+
 
 Indices and tables
 ==================
@@ -53,3 +98,7 @@ Indices and tables
 * :ref:`genindex`
 * :ref:`modindex`
 * :ref:`search`
+
+
+.. |DOI for Citing ssbtoolkit| image:: https://img.shields.io/badge/DOI-10.1016%2Fj.bpj.2015.08.015-blue.svg
+   :target: https://github.com/rribeiro-sci/SSBtoolkit
\ No newline at end of file

docs/_build/html/_static/custom.css

+.wy-side-nav-search, .wy-nav-top {
+    background: #EFEFEF;
+
+}
+/* Text inside search */
+.wy-side-nav-search input[type=text] {
+    color: #000000;
+}
+
+
+/* Home button */
+.wy-side-nav-search > a {
+    color: #555753;
+    font-size: 25px;
+}
\ No newline at end of file

docs/_build/html/_static/documentation_options.js

 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: 'v1',
+    VERSION: 'v1.0.1',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

docs/_build/html/about.html

@@ -4,7 +4,7 @@
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   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>What is the SSBtoolkit? &mdash; SSBtoolkit v1 documentation</title>
+  <title>What is the SSBtoolkit? &mdash; SSBtoolkit v1.0.1 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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docs/_build/html/faq.html

@@ -4,7 +4,7 @@
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   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Frequently Asked Questions &mdash; SSBtoolkit v1 documentation</title>
+  <title>Frequently Asked Questions &mdash; SSBtoolkit v1.0.1 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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