Refactor visualize.py & add config for RTDs

.readthedocs.yaml

@@ -0,0 +1,35 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#   - pdf
+#   - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - requirements: docs/requirements.txt

docs/source/examples/resume.py

@@ -20,7 +20,6 @@
 import lightning as L
 from lightning.pytorch.cli import LightningArgumentParser
 from torch.utils.data import DataLoader
-from aidsorb.data import PCDDataset
 from aidsorb.datamodules import PCDDataModule
 from aidsorb.litmodels import PointLit
 
@@ -78,7 +77,7 @@
 
 # %%
 
-# Set the model for inference (disable grads & evaluation mode).
+# Set the model for inference (disable grads & enable eval mode).
 litmodel.freeze()
 print(f'Model in evaluation mode: {not litmodel.training}')
 

docs/source/tutorial.rst

@@ -2,7 +2,7 @@
 ==========================
 
 .. note::
-    **This tutorial covers the most common use cases of |aidsorb|**. For more
+    **This tutorial covers the most common use cases of AIdsorb**. For more
     advanced usage, you should consult the :doc:`api`.
 
 .. _Introduction:

src/aidsorb/visualize.py

@@ -121,27 +121,26 @@ def draw_pcd(pcd, scheme='cpk', feature_to_color=None, colorscale=None, **kwargs
     """
     _check_shape_vis(pcd)
 
-    points = pcd[:, :3]
-    atoms = pcd[:, 3]
-    elements = get_elements(atoms)
+    atomic_numbers = pcd[:, 3]
+    elements = get_elements(atomic_numbers)
 
     if feature_to_color is None:
-        colors = get_atom_colors(atoms, scheme=scheme)
-        marker = {'size': atoms, 'color': colors}
+        colors = get_atom_colors(atomic_numbers, scheme=scheme)
+        marker = {'size': atomic_numbers, 'color': colors}
     else:
         idx, label = feature_to_color
         colors = pcd[:, idx]
         marker = {
-                'size': atoms, 'color': colors,
+                'size': atomic_numbers, 'color': colors,
                 'colorscale': colorscale,
                 'colorbar': {'thickness': 20, 'title': label}
                 }
 
     fig = go.Figure(
             data=[go.Scatter3d(
-                x=points[:, 0],
-                y=points[:, 1],
-                z=points[:, 2],
+                x=pcd[:, 0],
+                y=pcd[:, 1],
+                z=pcd[:, 2],
                 mode='markers',
                 marker=marker,
                 hovertext=elements