Crystal lattice and co.

.github/workflows/test.yml

@@ -44,8 +44,8 @@ concurrency:
 # Set the environment variables to be used in all jobs defined in this workflow
 env:
   CI_BRANCH: ${{ github.head_ref || github.ref_name }}
-  PY_VERSIONS: '3.11 3.13'
-  PIXI_ENVS: 'py-311-env py-313-env'
+  PY_VERSIONS: '3.12 3.14'
+  PIXI_ENVS: 'py-312-env py-314-env'
 
 jobs:
   # Job 1: Set up environment variables
@@ -149,7 +149,7 @@ jobs:
             echo
             echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
 
-            env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.11 -> py-311-env
+            env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.12 -> py-312-env
 
             echo "Building wheel in environment: $env"
             pixi run --environment $env dist-build

docs/docs/api-reference/index.md

@@ -7,9 +7,20 @@ icon: material/code-braces-box
 This section contains the reference detailing the functions and modules
 available in EasyImaging.
 
-- [Measurement](measurement/measurement.md) - Loads and inspects
+- [measurement](measurement/measurement.md) - Loads and inspects
   measurement data.
-- [regions_of_interest](regions_of_interest/index.md) - This module
-  contains all types of Regions Of Interests (ROIs) available:
+- [regions_of_interest](regions_of_interest/index.md) - The module
+  containing all types of Regions Of Interests (ROIs) available:
   - [RectangleROI](regions_of_interest/rectangle_roi.md) - A rectangular
     ROI. The most basic and common type of ROI
+- [sample_model](sample_model/index.md) - The module containing the
+  classes and functions related to creating a model of the sample:
+  - [Lattice](sample_model/lattice.md) - The crystallographic unit cell
+    of the sample model.
+  - [AtomSite](sample_model/atom_site.md) - The atomic sites of a
+    crystallographic lattice.
+  - [Atoms](sample_model/atoms.md) - The atomic species occupying an
+    atomic site.
+  - [crystals](sample_model/crystals.md) - A module containing
+    convenience functions to easily create and occupy common
+    crystallographic lattices.

docs/docs/api-reference/sample_model/atom_site.md

@@ -0,0 +1 @@
+::: easyimaging.sample_model.AtomSite

docs/docs/api-reference/sample_model/atoms.md

@@ -0,0 +1,23 @@
+::: easyimaging.sample_model.atoms.Atom
+
+    options:
+      heading_level: 2
+
+::: easyimaging.sample_model.atoms.Atoms
+
+    options:
+      heading_level: 2
+
+The full list of pre-defined
+[`Atom`][easyimaging.sample_model.atoms.Atom] instances in the
+[`Atoms`][easyimaging.sample_model.atoms.Atoms] enum is listed below.
+<br> Isotopes with `nan` values indicate the natually occuring abundant
+isotope.
+
+```python exec="true"
+from easyimaging.sample_model import Atoms
+import pandas as pd
+names = [f'**{atom.name}**' for atom in list(Atoms)]
+pretty_table = pd.DataFrame(list(Atoms), index=names).drop('enum_id', axis=1)
+print(pretty_table.rename_axis('name').to_markdown())
+```

docs/docs/api-reference/sample_model/crystals.md

@@ -0,0 +1,4 @@
+::: easyimaging.sample_model.crystals
+
+    options:
+      group_by_category: false

docs/docs/api-reference/sample_model/index.md

@@ -0,0 +1,16 @@
+---
+icon: material/puzzle
+---
+
+# :fontawesome-solid-puzzle-piece: Sample Model
+
+This module contains all the objects which makes up the model of the
+physical sample.
+
+- [Lattice](lattice.md) - The crystallographic unit cell of the sample
+  model.
+- [AtomSite](atom_site.md) - The atomic sites of a crystallographic
+  lattice.
+- [Atoms](atoms.md) - The atomic species occupying an atomic site.
+- [crystals](crystals.md) - A module containing convenience functions to
+  easily create and occupy common crystallographic lattices.

docs/docs/api-reference/sample_model/lattice.md

@@ -0,0 +1 @@
+::: easyimaging.sample_model.Lattice

docs/docs/assets/stylesheets/extra.css

@@ -364,36 +364,3 @@ h1 .label-experiment {
 .label-experiment:hover {
   color: white !important;
 }
-
-/*
- * FontAwesome 5 icon fix for Jupyter widget toolbars (ipympl / plopp)
- * This is a temporary workaround until this is fixed on Plopps side
- *
- * Comment on the issue from Claude:
- * embed-amd.js injects FA5 SVG-framework CSS inline, which intentionally sets
- * content:"" on all icon classes (expecting FA5 JS to replace elements with SVGs).
- * Since FA5 JS conflicts with RequireJS (breaking widget rendering), we instead:
- *   1. Load FA5 webfonts via <link> in overrides/main.html so the font file is available.
- *   2. Use !important below to override the content:"" with the correct FA5 Solid glyphs.
- */
-.fa::before {
-  font-family: "Font Awesome 5 Free" !important;
-  font-weight: 900 !important;
-}
-.fa-home::before         { content: "\f015" !important; }
-.fa-save::before         { content: "\f0c7" !important; }
-.fa-camera::before       { content: "\f030" !important; }
-.fa-cube::before         { content: "\f1b2" !important; }
-.fa-arrows-alt::before   { content: "\f0b2" !important; }
-.fa-arrows::before       { content: "\f0b2" !important; }  /* FA5 equivalent: arrows-alt */
-.fa-times::before        { content: "\f00d" !important; }
-.fa-plus::before         { content: "\f067" !important; }
-.fa-minus::before        { content: "\f068" !important; }
-.fa-search-plus::before  { content: "\f00e" !important; }
-.fa-crosshairs::before   { content: "\f05b" !important; }
-.fa-arrow-left::before   { content: "\f060" !important; }
-.fa-arrow-right::before  { content: "\f061" !important; }
-.fa-expand::before       { content: "\f065" !important; }
-.fa-compress::before     { content: "\f066" !important; }
-/* fa-arrows-v was removed in FA5; map to arrows-alt-v (\f338) */
-.fa-arrows-v::before     { content: "\f338" !important; }