fix IndexError (#88)

* fix IndexError

* test missing properties

* bump version

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "znh5md"
-version = "0.1.8"
+version = "0.1.9"
 description = "High Performance Interface for H5MD Trajectories"
 authors = ["zincwarecode <[email protected]>"]
 license = "Apache-2.0"

tests/conftest.py

@@ -76,6 +76,7 @@ def atoms_list(request) -> list[ase.Atoms]:
             )
             for _ in range(21)
         ]
+
     if getattr(request, "param", "").endswith("vary_pbc"):
         atoms[0].pbc = np.array([True, True, False])
         atoms[1].pbc = np.array([True, False, True])

tests/test_ASEH5MD.py

@@ -70,3 +70,19 @@ def test_request_missing_properties(tmp_path, atoms_list, remove_calc):
                 group_names=["stress"]
             ):
                 db.add_chunk_data(**chunk)
+
+
+@pytest.mark.parametrize("atoms_list", ["vary_size"], indirect=True)
+def test_skip_property(tmp_path, atoms_list):
+    os.chdir(tmp_path)
+
+    db = znh5md.io.DataWriter(filename="db.h5")
+    db.initialize_database_groups()
+
+    atoms_list[-1].arrays.pop("momenta")
+    atoms_list[-1].get_momenta()
+
+    db.add(znh5md.io.AtomsReader(atoms_list))
+
+    traj = znh5md.ASEH5MD("db.h5")
+    assert traj.get_atoms_list() == atoms_list

tests/test_znh5md.py

@@ -5,7 +5,7 @@
 
 
 def test_version():
-    assert znh5md.__version__ == "0.1.8"
+    assert znh5md.__version__ == "0.1.9"
 
 
 def test_shape(example_h5):

znh5md/znh5md/h5ase.py

@@ -17,11 +17,15 @@ def _gather_value(particles_data, key, idx):
 
     Returns None if the key is not present in the data.
     """
-    if key in particles_data:
-        if key in [GRP.species, GRP.position, GRP.velocity, GRP.forces, GRP.momentum]:
-            # use PARTICLES_GRP
-            return rm_nan(particles_data[key][idx])
-        return particles_data[key][idx]
+    try:
+        if key in particles_data:
+            if key in [GRP.species, GRP.position, GRP.velocity, GRP.forces, GRP.momentum]:
+                # use PARTICLES_GRP
+                return rm_nan(particles_data[key][idx])
+            return particles_data[key][idx]
+    except IndexError:
+        # a property might not be available at all frames.
+        pass
     return None