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Fix documentation and tutorial notebooks ahead of new release #334

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merged 11 commits into from
Nov 25, 2024
Merged

Fix documentation and tutorial notebooks ahead of new release #334

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348c5bb
Update smact installation
AntObi Nov 21, 2024
481a425
Add visualisation and strict dependencies
AntObi Nov 22, 2024
863af11
Update colab notebook link
AntObi Nov 22, 2024
0704b1a
Update requirements
AntObi Nov 25, 2024
d5a3f46
Relabel old ICSD ox states to 2016 ICSD
AntObi Nov 25, 2024
191fb29
Fix parse_spec to handle X+/X-
AntObi Nov 25, 2024
709709b
Accurately label pymatgen structure prediction ox states
AntObi Nov 25, 2024
bcd97d5
Provide option to get the occurence df sorted
AntObi Nov 25, 2024
f7f173f
Update tutorial.rst
AntObi Nov 25, 2024
0be8971
Add tutorial notebook for using CISD oxidation state filter
AntObi Nov 25, 2024
ad2d0b8
Fix vulnerability
AntObi Nov 25, 2024
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2 changes: 1 addition & 1 deletion docs/requirements.txt
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Expand Up @@ -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
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7 changes: 4 additions & 3 deletions docs/tutorials.rst
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Expand Up @@ -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
2 changes: 1 addition & 1 deletion docs/tutorials/crystal_space.ipynb
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Expand Up @@ -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)"
]
},
{
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2 changes: 1 addition & 1 deletion docs/tutorials/crystal_space_visualisation.ipynb
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Expand Up @@ -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)"
]
},
{
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