Add quantem.atoms: 3D atomic model analysis and atom tracing from volumes

src/quantem/__init__.py

@@ -12,5 +12,7 @@
 from quantem import diffraction as diffraction
 from quantem import spectroscopy as spectroscopy
 from quantem import diffractive_imaging as diffractive_imaging
+from quantem import tomography as tomography
+from quantem import atoms as atoms
 
 __version__ = version("quantem")

src/quantem/atoms/__init__.py

@@ -0,0 +1,9 @@
+from quantem.atoms.atomic_model import AtomicModel as AtomicModel
+from quantem.atoms.templates import (
+    PolyhedralTemplate as PolyhedralTemplate,
+    TEMPLATE_NAMES as TEMPLATE_NAMES,
+    get_template as get_template,
+    template_from_crystal as template_from_crystal,
+)
+from quantem.atoms.matching import match_template as match_template
+from quantem.atoms.visualization import PLOT_REGISTRY as PLOT_REGISTRY