fix RuntimeErrror (#27)

* fix RuntimeErrror

* lint

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "znh5md"
-version = "0.1.0"
+version = "0.1.1"
 description = "High Performance Interface for H5MD Trajectories"
 authors = ["zincwarecode <[email protected]>"]
 license = "Apache-2.0"

tests/test_ASEH5MD.py

@@ -1,6 +1,8 @@
 import os
 
 import ase
+import pytest
+from ase.calculators.calculator import PropertyNotImplementedError
 
 import znh5md
 
@@ -19,8 +21,12 @@ def test_get_atoms_list(example_h5):
     assert isinstance(atoms[0], ase.Atoms)
 
 
-def test_get_slice(tmp_path, atoms_list):
+@pytest.mark.parametrize("remove_calc", [True, False])
+def test_get_slice(tmp_path, atoms_list, remove_calc):
     os.chdir(tmp_path)
+    if remove_calc:
+        for atoms in atoms_list:
+            atoms.calc = None
 
     db = znh5md.io.DataWriter(filename="db.h5")
     db.initialize_database_groups()
@@ -39,3 +45,27 @@ def test_get_slice(tmp_path, atoms_list):
     traj[1:2] == atoms_list[1:2]
 
     assert len(traj.position) == 21
+
+
+@pytest.mark.parametrize("remove_calc", [True, False])
+def test_request_missing_properties(tmp_path, atoms_list, remove_calc):
+    os.chdir(tmp_path)
+    if remove_calc:
+        for atoms in atoms_list:
+            atoms.calc = None
+
+    db = znh5md.io.DataWriter(filename="db.h5")
+    db.initialize_database_groups()
+
+    if remove_calc:
+        with pytest.raises(RuntimeError):
+            for chunk in znh5md.io.AtomsReader(atoms_list).yield_chunks(
+                group_names=["stress"]
+            ):
+                db.add_chunk_data(**chunk)
+    else:
+        with pytest.raises(PropertyNotImplementedError):
+            for chunk in znh5md.io.AtomsReader(atoms_list).yield_chunks(
+                group_names=["stress"]
+            ):
+                db.add_chunk_data(**chunk)

tests/test_znh5md.py

@@ -5,7 +5,7 @@
 
 
 def test_version():
-    assert znh5md.__version__ == "0.1.0"
+    assert znh5md.__version__ == "0.1.1"
 
 
 def test_shape(example_h5):

znh5md/io/reader.py

@@ -33,7 +33,7 @@ def _get_box(self, atoms: list[ase.Atoms]) -> np.ndarray:
         return np.array([x.get_cell() for x in atoms])
 
     def yield_chunks(
-        self, group_name: list = None
+        self, group_names: list = None
     ) -> typing.Iterator[typing.Dict[str, ExplicitStepTimeChunk]]:
         start_index = 0
         stop_index = 0
@@ -55,7 +55,7 @@ def yield_chunks(
                 "box": self._get_box,
             }
 
-            for name in group_name or functions:
+            for name in group_names or functions:
                 if name not in functions:
                     raise ValueError(f"Value {name} not supported")
 
@@ -66,8 +66,8 @@ def yield_chunks(
                         step=np.arange(start_index, start_index + len(value)),
                         time=np.arange(start_index, start_index + len(value)),
                     )
-                except PropertyNotImplementedError as err:
-                    if group_name is not None:
+                except (PropertyNotImplementedError, RuntimeError) as err:
+                    if group_names is not None:
                         # if the property was specifcally selected, raise the error
                         raise err
                     else: