Merge pull request #334 from WMD-group/documentation_fix

Fix documentation and tutorial notebooks ahead of new release
WMD-group · Nov 25, 2024 · 8bc5fc1 · 8bc5fc1
2 parents ba5e986 + ad2d0b8
commit 8bc5fc1
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Showing 14 changed files with 5,919 additions and 43 deletions.
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -203,7 +203,7 @@ stack-data==0.6.3
     # via ipython
 tabulate==0.9.0
     # via jupyter-cache
-tornado==6.4.1
+tornado==6.4.2
     # via
     #   ipykernel
     #   jupyter-client

diff --git a/docs/tutorials.rst b/docs/tutorials.rst
@@ -8,8 +8,9 @@ Tutorials are intended as a more complete example of `smact` being applied in re
 .. toctree::
    :maxdepth: 1
 
-   tutorials/crystal_space
-   tutorials/crystal_space_visualisation
-   tutorials/smact_validity_of_GNoMe
    tutorials/smact_generation_of_solar_oxides
    tutorials/oxidation_states
+   tutorials/smact_validity_of_GNoMe
+   tutorials/crystal_space
+   tutorials/crystal_space_visualisation
+   tutorials/filtering_icsd_oxidation_states.ipynb
diff --git a/docs/tutorials/crystal_space.ipynb b/docs/tutorials/crystal_space.ipynb
@@ -58,7 +58,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/WMD-group/SMACT/blob/docs_updates/docs/tutorials/crystal_space.ipynb)"
+    "[![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/WMD-group/SMACT/blob/master/docs/tutorials/crystal_space.ipynb)"
    ]
   },
   {

diff --git a/docs/tutorials/crystal_space_visualisation.ipynb b/docs/tutorials/crystal_space_visualisation.ipynb
@@ -47,7 +47,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/WMD-group/SMACT/blob/docs_updates/docs/tutorials/crystal_space_visualisation.ipynb)"
+    "[![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/WMD-group/SMACT/blob/master/docs/tutorials/crystal_space_visualisation.ipynb)"
    ]
   },
   {