Merge pull request #266 from nlesc-nano/param

BUG: Fix the param columns being incorrectly written to the .hdf5 file

FOX/io/hdf5_utils.py

@@ -126,7 +126,7 @@ def create_hdf5(filename: PathType, armc: ARMC) -> None:
     pd_dict = {
         'aux_error': pd.Series(np.nan, index=aux_error_idx, name='aux_error'),
         'aux_error_mod': pd.Series(np.nan, index=idx, name='aux_error_mod'),
-        'param': armc.param.param[0],
+        'param': armc.param.param,
         'phi': pd.Series(np.nan, index=np.arange(kappa), name='phi'),
     }
     pd_dict2 = {
@@ -811,6 +811,9 @@ def dset_to_df(f: File, key: str) -> Union[pd.DataFrame, List[pd.DataFrame]]:
     else:
         data = f[key][:]
 
+    if key == "/param":
+        data = np.swapaxes(data, 1, 2)
+
     # Return a DataFrame or list of DataFrames
     if data.ndim == 2:
         return pd.DataFrame(data, index=index, columns=columns)

FOX/testing_utils.py

@@ -16,6 +16,7 @@
 
 """
 
+import re
 import warnings
 from types import MappingProxyType
 from os import listdir
@@ -256,8 +257,9 @@ def load_results(workdir, *, result_type=CP2KMM_Result, n=1):  # noqa: E302
     ret = []
     tmp = []
     i = -n
+    file_pattern = re.compile(r"md(\.([0-9]+))?")
     for jobname in sorted(listdir(workdir_path)):
-        if jobname == '__pycache__':
+        if file_pattern.fullmatch(jobname) is None:
             continue
 
         plams_dir = workdir_path / jobname

tests/test_hdf5_utils.py

@@ -235,6 +235,6 @@ def test_from_hdf5():
     assertion.eq(hdf5_dict['aux_error'], out['aux_error']['rdf.0'][0])
     assertion.eq(hdf5_dict['phi'], out['aux_error_mod'].values[:, -1])
     assertion.eq(hdf5_dict['phi'][0], out['phi'].loc[0, 0])
-    np.testing.assert_allclose(hdf5_dict['param'], out['param'].values)
+    np.testing.assert_allclose(hdf5_dict['param'], out['param'][0].T)
     np.testing.assert_allclose(hdf5_dict['rdf.0'], out['rdf.0'][0].values)
     np.testing.assert_array_equal(PARAM_METADATA, out['param_metadata'])