always cast atoms.arrays to numpy (#162)

* always cast `atoms.arrays` to numpy

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

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* remove comment

* update test

* [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 = "0.4.2"
+version = "0.4.3"
 description = "ASE Interface for the H5MD format."
 authors = ["zincwarecode <[email protected]>"]
 license = "Apache-2.0"

tests/format/test_info_array_calc.py

@@ -9,7 +9,7 @@
 
 # Define assertion functions for different data types
 def assert_equal(actual, expected):
-    assert actual == expected
+    npt.assert_equal(actual, expected)
 
 
 def assert_allclose(actual, expected):

tests/test_arrays_str.py

@@ -0,0 +1,18 @@
+import numpy as np
+import numpy.testing as npt
+import rdkit2ase
+
+import znh5md
+
+
+def test_pdb_repeat(tmp_path):
+    water = rdkit2ase.smiles2conformers(smiles="O", numConfs=1)[0]
+    water.arrays["atomtypes"] = np.array(["H", "O", "H"])
+    assert isinstance(water.arrays["atomtypes"], np.ndarray)
+
+    io = znh5md.IO(tmp_path / "test.h5")
+    io.append(water)
+
+    atoms = io[0]
+    assert isinstance(atoms.arrays["atomtypes"], np.ndarray)
+    npt.assert_array_equal(atoms.arrays["atomtypes"], water.arrays["atomtypes"])

tests/test_znh5md.py

@@ -2,7 +2,7 @@
 
 
 def test_version():
-    assert znh5md.__version__ == "0.4.2"
+    assert znh5md.__version__ == "0.4.3"
 
 
 def test_creator(tmp_path):

znh5md/interface/read.py

@@ -1,5 +1,6 @@
 import json
 import typing as t
+import warnings
 
 import ase
 import numpy as np
@@ -114,7 +115,14 @@ def handle_origin_data(self, name: str, data: list, origin: ORIGIN_TYPE) -> None
     elif origin == "info":
         self.info[name] = data
     elif origin == "arrays":
-        self.arrays[name] = data
+        try:
+            self.arrays[name] = np.array(data)
+        except ValueError:
+            warnings.warn(
+                f"Could not convert data to array for '{name}'. "
+                "Storing as list instead."
+            )
+            self.arrays[name] = data
     elif origin == "atoms":
         raise ValueError(f"Origin 'atoms' is not allowed for {name}")
     else: