Fix indexing error for 0-dimensional HDF5 datasets

* Refactor ProfileResultHDF5Writer to be more readable
* Raise more informative error if writing to HDF5 fails
* Don't index 0-dimensional datasets (Fixes ICB-DCM#1205)

pypesto/result/profile.py

@@ -183,7 +183,7 @@ class ProfileResult:
     """
 
     def __init__(self):
-        self.list = []
+        self.list: list[list[ProfilerResult]] = []
 
     def append_empty_profile_list(self) -> int:
         """Append an empty profile list to the list of profile lists.

pypesto/store/hdf5.py

@@ -45,7 +45,8 @@ def write_string_array(f: h5py.Group, path: str, strings: Collection) -> None:
     """
     dt = h5py.special_dtype(vlen=str)
     dset = f.create_dataset(path, (len(strings),), dtype=dt)
-    dset[:] = [s.encode('utf8') for s in strings]
+    if len(strings):
+        dset[:] = [s.encode('utf8') for s in strings]
 
 
 def write_float_array(
@@ -69,7 +70,9 @@ def write_float_array(
         dset = f.create_dataset(path, (np.shape(values)), dtype=dtype)
     else:
         dset = f[path]
-    dset[:] = values
+
+    if len(values):
+        dset[:] = values
 
 
 def write_int_array(
@@ -90,4 +93,5 @@ def write_int_array(
         datatype
     """
     dset = f.create_dataset(path, (len(values),), dtype=dtype)
-    dset[:] = values
+    if len(values):
+        dset[:] = values

pypesto/store/save_to_hdf5.py

@@ -8,7 +8,7 @@
 import h5py
 import numpy as np
 
-from ..result import Result, SampleResult
+from ..result import ProfilerResult, Result, SampleResult
 from .hdf5 import write_array, write_float_array
 
 logger = logging.getLogger(__name__)
@@ -234,20 +234,35 @@ def write(self, result: Result, overwrite: bool = False):
                 profile_grp = profiling_grp.require_group(str(profile_id))
                 for parameter_id, parameter_profile in enumerate(profile):
                     result_grp = profile_grp.require_group(str(parameter_id))
+                    self._write_profiler_result(parameter_profile, result_grp)
 
-                    if parameter_profile is None:
-                        result_grp.attrs['IsNone'] = True
-                        continue
-                    result_grp.attrs['IsNone'] = False
-                    for key in parameter_profile.keys():
-                        if isinstance(parameter_profile[key], np.ndarray):
-                            write_float_array(
-                                result_grp, key, parameter_profile[key]
-                            )
-                        elif parameter_profile[key] is not None:
-                            result_grp.attrs[key] = parameter_profile[key]
             f.flush()
 
+    @staticmethod
+    def _write_profiler_result(
+        parameter_profile: Union[ProfilerResult, None], result_grp: h5py.Group
+    ) -> None:
+        """Write a single ProfilerResult to hdf5.
+
+        Writes a single profile for a single parameter to the provided HDF5 group.
+        """
+        if parameter_profile is None:
+            result_grp.attrs['IsNone'] = True
+            return
+
+        result_grp.attrs['IsNone'] = False
+
+        for key, value in parameter_profile.items():
+            try:
+                if isinstance(value, np.ndarray):
+                    write_float_array(result_grp, key, value)
+                elif value is not None:
+                    result_grp.attrs[key] = value
+            except Exception as e:
+                raise ValueError(
+                    f"Error writing {key} ({value}) to {result_grp}."
+                ) from e
+
 
 def write_result(
     result: Result,

setup.cfg

@@ -72,7 +72,7 @@ all =
     %(amici)s
     %(petab)s
     %(all_optimizers)s
-    %(mpi)s
+        %(mpi)s
     %(pymc)s
     %(aesara)s
     %(jax)s