🐛 Fix __version__ undefined at dev setup and Uij transformations

README.md

@@ -121,8 +121,7 @@ The following instructions are currently supported by picometer:
   - fit `plane` to the currect atom / centroid selection;
 - **Evaluation instructions**
   - write out fractional `coordinates` of currently selected centroids or atoms.
-  - write out `displacement` parameters of currently selected centroids or atoms
-    (note: currently does not correctly handle symmetry transformations).
+  - write out `displacement` parameters of currently selected centroids or atoms.
   - measure `distance` between 2 selected objects; if the selection includes
     groups of atoms, measure closes distance to the group of atoms.
   - measure `angle` between 2–3 selected objects: planes, lines, or (ordered) atoms.

picometer/__init__.py

@@ -1,4 +1,8 @@
 # read version from installed package
-from importlib.metadata import version
+from importlib.metadata import PackageNotFoundError, version
 
-__version__ = version("picometer")
+
+try:
+    __version__ = version('picometer')
+except PackageNotFoundError:
+    __version__ = '0+unknown'

picometer/atom.py

@@ -176,7 +176,9 @@ def transform(self, symm_op_code: str) -> 'AtomSet':
             uij = self.fract_uij  # shape: (n_atoms, 3, 3)
             mask = ~np.isnan(uij).all(axis=(1, 2))  # atoms with defined Uij
             if np.any(mask):
-                uij_rot = (s := symm_op.tf) @ uij[mask] @ s.T
+                abc_r = [self.base.a_r, self.base.b_r, self.base.c_r]
+                k = np.diag([1 / a for a in abc_r]) @ symm_op.tf @ np.diag(abc_r)
+                uij_rot = k @ uij[mask] @ k.T
                 data.loc[mask, 'U11'] = uij_rot[:, 0, 0]
                 data.loc[mask, 'U22'] = uij_rot[:, 1, 1]
                 data.loc[mask, 'U33'] = uij_rot[:, 2, 2]