bugfix finalize

tests/test_single_obs_key.py

@@ -15,7 +15,7 @@ def test_single_entry_info(tmp_path):
     io.extend([water for _ in range(5)])
     assert len(io) == 6
     assert len(list(io)) == 6
-    # assert len(io[:]) == 6
+    assert len(io[:]) == 6
 
 def test_single_entry_arrays(tmp_path):
     # Test a special case where only the first config has the key
@@ -28,7 +28,7 @@ def test_single_entry_arrays(tmp_path):
     io.extend([water for _ in range(5)])
     assert len(io) == 6
     assert len(list(io)) == 6
-    # assert len(io[:]) == 6
+    assert len(io[:]) == 6
 
 
 def test_single_entry_calc(tmp_path):
@@ -42,4 +42,4 @@ def test_single_entry_calc(tmp_path):
     io.extend([water for _ in range(5)])
     assert len(io) == 6
     assert len(list(io)) == 6
-    # assert len(io[:]) == 6
+    assert len(io[:]) == 6

znh5md/interface/io.py

@@ -103,7 +103,8 @@ def __getitem__(
             # FileNotFoundError is an OSError, but we want to handle it
             #  separately from the OSError h5py raises
             raise
-        except OSError:
+        except OSError as err:
+            print(err)
             raise IndexError("Index out of range")
 
     def extend(self, frames: list[ase.Atoms]) -> None:

znh5md/interface/read.py

@@ -181,8 +181,13 @@ def getitem(
         if f"/observables/{self.particles_group}" in f:
             observables = f[f"/observables/{self.particles_group}"]
             process_observables(self, frames, observables, index)
+
+    print(len(frames))
+    print(particles)
+    print(is_single_item)
 
-    return list(frames) if not is_single_item else frames[0]
+    # return list(frames) if not is_single_item else frames[0]
+    return frames
 
 
 def process_species_group(self, frames: Frames, particles, index) -> None:
@@ -341,10 +346,12 @@ def process_observables(self, frames: Frames, observables, index) -> None:
                     update_frames(
                         frames, grp_name, grp["value"][index], origin, self.use_ase_calc
                     )
-            except (OSError, IndexError):
+            except (OSError, IndexError) as err:
+                print(err)
                 # ??? why is this not triggering?
                 pass  # Handle backfilling for invalid values
-        except KeyError:
+        except KeyError as err:
+            print(err)
             raise KeyError(
                 f"Key '{grp_name}' does not seem to be a valid H5MD group"
                 " - missing 'value' dataset."

znh5md/serialization/base.py

@@ -2,6 +2,7 @@
 import functools
 import json
 import typing as t
+import contextlib
 
 import ase
 import h5py
@@ -247,19 +248,23 @@ def __getitem__(self, idx: int) -> ase.Atoms:
         for key in self.arrays:
             if isinstance(self.arrays[key][idx], _MISSING):
                 continue
-            if key == "velocities":
-                atoms.set_velocities(self.arrays[key][idx])
-            else:
-                atoms.arrays[key] = self.arrays[key][idx]
+            with contextlib.suppress(KeyError):
+                if key == "velocities":
+                    atoms.set_velocities(self.arrays[key][idx])
+                else:
+                    atoms.arrays[key] = self.arrays[key][idx]
 
         for key in self.info:
             if not isinstance(self.info[key][idx], _MISSING):
-                atoms.info[key] = self.info[key][idx]
+                with contextlib.suppress(KeyError):
+                    atoms.info[key] = self.info[key][idx]
         for key in self.calc:
             if not isinstance(self.calc[key][idx], _MISSING):
-                if atoms.calc is None:
-                    atoms.calc = SinglePointCalculator(atoms)
-                atoms.calc.results[key] = self.calc[key][idx]
+                with contextlib.suppress(KeyError):
+                    value = self.calc[key][idx]
+                    if atoms.calc is None:
+                        atoms.calc = SinglePointCalculator(atoms)
+                    atoms.calc.results[key] = value
 
         return atoms