bugfix for json / list in info data (#145)

* bugfix for json / list in info data

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

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---------

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

tests/test_data_types.py

@@ -1,4 +1,6 @@
 import ase.build
+import ase.io
+import numpy.testing as npt
 import pytest
 
 import znh5md
@@ -39,9 +41,70 @@ def test_int_info_data(tmp_path):
 
 
 def test_dict_data(tmp_path):
-    io = znh5md.IO(tmp_path / "test.h5")
     molecule = ase.build.molecule("H2O")
     molecule.info["test"] = {"a": 1, "b": 2}
 
+    # Write to extxyz format
+    extxyz_path = tmp_path / "molecule.extxyz"
+    ase.io.write(extxyz_path, molecule, format="extxyz")
+
+    # Read from extxyz format
+    molecule = ase.io.read(extxyz_path, format="extxyz")
+
+    io = znh5md.IO(tmp_path / "test.h5")
     io.append(molecule)
+    molecule.info["test"] = {"a": 1, "b": 2, "c": 3}
+    io.append(molecule)
+    molecule.info["b"] = {"a": 1, "b": 2, "c": 3, "d": 4}
+    io.append(molecule)
+
+    assert io[0].info["test"] == {"a": 1, "b": 2}
+    assert io[1].info["test"] == {"a": 1, "b": 2, "c": 3}
+    assert io[2].info["b"] == {"a": 1, "b": 2, "c": 3, "d": 4}
+
+
+def test_list_data(tmp_path):
+    molecule = ase.build.molecule("H2O")
+    molecule.info["test"] = [1, 2]
+
+    # Write to extxyz format
+    extxyz_path = tmp_path / "molecule.extxyz"
+    ase.io.write(extxyz_path, molecule, format="extxyz")
+
+    # Read from extxyz format
+    molecule = ase.io.read(extxyz_path, format="extxyz")
+    npt.assert_array_equal(molecule.info["test"], [1, 2])
+
+    io = znh5md.IO(tmp_path / "test.h5")
+    io.append(molecule)
+    molecule.info["test"] = [1, 2, 3]
+    io.append(molecule)
+    molecule.info["b"] = [1, 2, 3, 4]
+    io.append(molecule)
+
+    npt.assert_array_equal(io[0].info["test"], [1, 2])
+    npt.assert_array_equal(io[1].info["test"], [1, 2, 3])
+    npt.assert_array_equal(io[2].info["b"], [1, 2, 3, 4])
+
+
+def test_multiple_molecules_with_diff_length_dicts(tmp_path):
+    molecules = [
+        ase.build.molecule("H2O"),
+        ase.build.molecule("CH4"),
+    ]
+
+    # Assign different length dicts to molecule info
+    molecules[0].info["test"] = {"a": 1, "b": 2}
+    molecules[1].info["test"] = {"a": 1}
+
+    extxyz_path = tmp_path / "molecules.extxyz"
+    ase.io.write(extxyz_path, molecules, format="extxyz")
+
+    read_molecules = ase.io.read(extxyz_path, index=":", format="extxyz")
+
+    io = znh5md.IO(tmp_path / "test.h5")
+    for mol in read_molecules:
+        io.append(mol)
+
     assert io[0].info["test"] == {"a": 1, "b": 2}
+    assert io[1].info["test"] == {"a": 1}

znh5md/format.py

@@ -298,7 +298,7 @@ def _combine_dicts(dicts: List[Dict[str, np.ndarray]]) -> Dict[str, np.ndarray]:
         data = []
         for d in dicts:
             if key in d:
-                data.append(d[key])
+                data.append(np.array(d[key]))
             else:
                 dims = dicts[0][key].ndim
                 # Create an array with the appropriate number of dimensions.

znh5md/io.py

@@ -17,6 +17,7 @@
 
 import znh5md.format as fmt
 from znh5md import utils
+from znh5md.config import STRING_FILL_VALUE
 
 __version__ = importlib.metadata.version("znh5md")
 
@@ -204,7 +205,12 @@ def _extract_additional_data(self, f, index, arrays_data, calc_data, info_data):
                             ].attrs.get("ZNH5MD_TYPE")
                             == "json"
                         ):
-                            info_data[key] = [json.loads(x) for x in data]
+                            info_data[key] = [
+                                json.loads(x)
+                                if x != STRING_FILL_VALUE
+                                else STRING_FILL_VALUE
+                                for x in data
+                            ]
                         else:
                             info_data[key] = data
                     except IndexError:

znh5md/utils.py

@@ -5,7 +5,7 @@
 
 from znh5md.config import NUMERIC_FILL_VALUE, STRING_FILL_VALUE
 
-NUMPY_STRING_DTYPE = np.dtype("S512")
+NUMPY_STRING_DTYPE = np.dtype("S4096")  # TODO this has to be tested!
 
 
 def concatenate_varying_shape_arrays(arrays: list[np.ndarray]) -> np.ndarray: