add main / models.py to docs (#27)

* add main / models.py to docs

* use font awesome

* remove todo

* add link to packmol

docs/source/conf.py

@@ -52,19 +52,21 @@
         {
             "name": "GitHub",
             "url": "https://github.com/basf/mlipx",
-            "html": """
-                <svg stroke="currentColor" fill="currentColor" stroke-width="0" viewBox="0 0 16 16">
-                    <path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"></path>
-                </svg>
-            """,  # noqa: E501
-            "class": "",
+            "html": "",
+            "class": "fa-brands fa-github fa-2x",
         },
     ],
     "source_repository": "https://github.com/basf/mlipx/",
     "source_branch": "main",
     "source_directory": "docs/source/",
+    "navigation_with_keys": True,
 }
 
+# font-awesome logos
+html_css_files = [
+    "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0/css/brands.min.css",
+]
+
 # -- Options for hoverxref extension -----------------------------------------
 # https://sphinx-hoverxref.readthedocs.io/en/latest/
 

docs/source/glossary.rst

@@ -46,7 +46,7 @@ Glossary
             }
 
     packmol
-        Packmol is a software package used for building initial configurations for molecular dynamics or Monte Carlo simulations. It can generate a random collection of molecules using the specified density and composition. TODO add cite
+        Packmol is a software package used for building initial configurations for molecular dynamics or Monte Carlo simulations. It can generate a random collection of molecules using the specified density and composition. More information can be found at https://m3g.github.io/packmol/ .
 
     rdkit2ase
         A package for converting RDKit molecules to ASE atoms.

docs/source/recipes/phase_diagram.rst

@@ -25,3 +25,14 @@ You can run the following command to instantiate a test directory:
 This test uses the following Nodes together with your provided model in the :term:`models.py` file:
 
 * :term:`PhaseDiagram`
+
+.. dropdown:: Content of :code:`main.py`
+
+   .. literalinclude:: ../../../examples/phase_diagram/main.py
+      :language: Python
+
+
+.. dropdown:: Content of :code:`models.py`
+
+   .. literalinclude:: ../../../examples/phase_diagram/models.py
+      :language: Python

docs/source/recipes/pourbaix_diagram.rst

@@ -27,3 +27,14 @@ Pourbaix Diagram
 This test uses the following Nodes together with your provided model in the :term:`models.py` file:
 
 * :term:`PourbaixDiagram`
+
+.. dropdown:: Content of :code:`main.py`
+
+   .. literalinclude:: ../../../examples/pourbaix_diagram/main.py
+      :language: Python
+
+
+.. dropdown:: Content of :code:`models.py`
+
+   .. literalinclude:: ../../../examples/pourbaix_diagram/models.py
+      :language: Python

docs/source/recipes/vibrational_analysis.rst

@@ -31,3 +31,14 @@ Then run the following commands to reproduce and inspect the results:
 This test uses the following Nodes together with your provided model in the :term:`models.py` file:
 
 * :term:`VibrationalAnalysis`
+
+.. dropdown:: Content of :code:`main.py`
+
+   .. literalinclude:: ../../../examples/vibrational_analysis/main.py
+      :language: Python
+
+
+.. dropdown:: Content of :code:`models.py`
+
+   .. literalinclude:: ../../../examples/vibrational_analysis/models.py
+      :language: Python