Add Crystal Space and Oxidation Utilities to the Documentation

docs/conf.py

@@ -45,7 +45,7 @@
     "html_image",
 ]
 myst_url_schemes = ("http", "https", "mailto")
-jupyter_execute_notebooks = "off"
+nb_execution_mode = "off"
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
@@ -154,7 +154,7 @@
 # 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 = ["_static"]
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
@@ -418,5 +418,8 @@ def __getattr__(cls, name):
     "pymatgen.analysis.structure_prediction",
     "pymatgen.transformations.standard_transformations",
     "tabulate",
+    "mp_api",
+    "mp_api.client",
+    "emmet",
 ]
 sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)

docs/examples.rst

@@ -15,7 +15,6 @@ For workflows that have been used in real examples and in published work, visit
    examples/filter
    examples/validity
    examples/lists
-   examples/neutral_combos
    examples/oxidation_states
    examples/compound_electroneg
    examples/valence_electron_count

docs/examples/doper.ipynb

@@ -11,7 +11,8 @@
     "\n",
     "By default, the top five p-type and n-type candidates are reported. Use the `num_dopants` input to modify the number of outputs.\n",
     "\n",
-    "### Output Format\n",
+    "**Output Format**\n",
+    "\n",
     "The output is a dictionary with keys:\n",
     "- \"n_type_cation\"\n",
     "- \"p_type_cation\"\n",

docs/smact.utils.crystal_space.download_compounds_with_mp_api.rst

@@ -0,0 +1,8 @@
+Crystal Space Materials Project Data Retrieval Module
+===========================
+
+
+.. automodule:: smact.utils.crystal_space.download_compounds_with_mp_api
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/smact.utils.crystal_space.generate_composition_with_smact.rst

@@ -0,0 +1,7 @@
+Crystal Space SMACT Generation Module
+===========================
+
+.. automodule:: smact.utils.crystal_space.generate_composition_with_smact
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/smact.utils.crystal_space.plot_embedding.rst

@@ -0,0 +1,8 @@
+Crystal Space Embedding Module
+===========================
+
+
+.. automodule:: smact.utils.crystal_space.plot_embedding
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/smact.utils.crystal_space.rst

@@ -0,0 +1,14 @@
+SMACT Utilities Crystal Space Module
+===========================
+
+Utility functions associated with our `Faraday Discussions publication 'Mapping Inorganic Crystal Space' <https://doi.org/10.1039/D4FD00063C>`_  using SMACT
+
+
+Submodules
+----------
+
+.. toctree::
+
+    smact.utils.crystal_space.download_compounds_with_mp_api
+    smact.utils.crystal_space.generate_composition_with_smact
+    smact.utils.crystal_space.plot_embedding

docs/smact.utils.oxidation.rst

@@ -0,0 +1,9 @@
+SMACT Utilities Oxidation Module
+=====================================
+
+Miscellaneous utilities for creating SMACT compatible oxidation states list
+
+.. automodule:: smact.utils.oxidation
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/smact.utils.rst

@@ -9,7 +9,5 @@ Submodules
 .. toctree::
 
     smact.utils.composition
-    smact.utils.band_gap_simple
-    smact.utils.download_compounds_with_mp_api
-    smact.utils.generate_composition_with_smact
-    smact.utils.plot_embeddings
+    smact.utils.crystal_space
+    smact.utils.oxidation

docs/tutorials/crystal_space.ipynb

@@ -44,7 +44,7 @@
     "\n",
     "First, we'll create binary chemical compositions using the SMACT filter. The SMACT filter is a smart tool that helps us select compositions based on important chemical rules, such as oxidation states and electronegativity.\n",
     "\n",
-    "To generate these compositions, we'll use a function called [`generate_composition_with_smact`](../smact/utils/generate_composition_with_smact.py). This function allows us to enumerate all possible binary compositions and filter them based on the SMACT rules. \n",
+    "To generate these compositions, we'll use a function called [`generate_composition_with_smact`](../../smact/utils/crystal_space/generate_composition_with_smact.py). This function allows us to enumerate all possible binary compositions and filter them based on the SMACT rules. \n",
     "\n",
     "### Key parameters:\n",
     "- `num_elements`: Number of elements in the composition (e.g., 2 for binary).\n",
@@ -127,7 +127,7 @@
    "source": [
     "Next, we download data from the `Materials Project api` using the `download_mp_data` function. This function allows us to download data for a given number of elements and maximum stoichiometry. The data includes the chemical formula, energy, and other properties of the compounds.\n",
     "\n",
-    "[`download_mp_data`](../smact/utils/download_compounds_with_mp_api.py) function takes in the following parameters:\n",
+    "[`download_mp_data`](../../smact/utils/crystal_space/download_compounds_with_mp_api.py) function takes in the following parameters:\n",
     "\n",
     "### Key parameters:\n",
     "- `mp_api_key`: your Materials Project API key\n",

docs/tutorials/crystal_space_visualisation.ipynb

@@ -11,7 +11,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "(prerequisite: [crystal_space_with_smact.ipynb](./crystal_space_with_smact.ipynb))\n",
+    "(prerequisite: [crystal_space.ipynb](./crystal_space.ipynb))\n",
     "\n",
     "In this tutorial, we will use the dimension reduction techniques to visualise a large crystal space. We will use the following techniques:\n",
     "\n",