Clarify text and names

micro_manager/snapshot/dataset.py

@@ -40,7 +40,7 @@ def collect_output_files(
         file_list : list
             List of files to be combined.
         dataset_length : int
-            Number of snapshots.
+            Global number of snapshots.
         """
         # Create a output file
         main_file = h5py.File(os.path.join(dir_name, "snapshot_data.hdf5"), "w")
@@ -109,11 +109,11 @@ def write_output_to_hdf(
         macro_data : dict
             Dict of macro simulation input.
         micro_data : dict | None
-            Dict of micro simulation output.
+            Dict of micro simulation output. If None, only the macro data is written.
         idx: int
             Local index of the current snapshot.
         length : int
-            Number of snapshots.
+            Local number of snapshots.
         """
         parameter_file = h5py.File(file_path, "a")
         if micro_data is None:
@@ -178,7 +178,7 @@ def read_hdf(self, file_path: str, data_names: dict, start: int, end: int) -> li
             output.append(current_data)
         return output
 
-    def get_length(self, file_path: str) -> int:
+    def get_parameter_space_size(self, file_path: str) -> int:
         """
         Get the length of the parameter space from the HDF5 file.
 

micro_manager/snapshot/snapshot.py

@@ -6,9 +6,6 @@
 - solve
 - initialize
 
-This file is directly executable as it consists of a main() function. Upon execution, an object of the class SnapshotComputation is created using a given JSON file,
-the solve method is called.
-
 Detailed documentation: https://precice.org/tooling-micro-manager-overview.html
 """
 
@@ -153,7 +150,7 @@ def initialize(self) -> None:
         - Distribute the parameter data equally if the snapshot creation is executed in parallel.
         - Read macro parameter from parameter file.
         - Create output subdirectory and file paths to store output.
-        - Import micro simulation class.
+        - Import micro simulation.
         """
 
         # Create subdirectory to store output files in
@@ -164,7 +161,9 @@ def initialize(self) -> None:
         # Create object responsible for reading parameters and writing simulation output
         self._data_storage = ReadWriteHDF(self._logger)
 
-        self._parameter_space_size = self._data_storage.get_length(self._parameter_file)
+        self._parameter_space_size = self._data_storage.get_parameter_space_size(
+            self._parameter_file
+        )
         # Read macro parameters from the parameter file
         # Decompose parameters if the snapshot creation is executed in parallel
         if self._is_parallel:
@@ -258,7 +257,7 @@ def _solve_micro_simulation(self, micro_sims_input: dict) -> dict | None:
         Returns
         -------
         micro_sims_output : dict | None
-            Dicts in which keys are names of data and the values are the data of the output of the micro
+            Dict in which keys are names of data and the values are the data of the output of the micro
             simulations. The return type is None if the simulation has crashed.
         """
         try:

tests/unit/test_hdf5_functionality.py

@@ -168,6 +168,4 @@ def test_get_parameter_space_length(self):
             "test_parameter.hdf5",
         )
         data_manager = ReadWriteHDF(MagicMock())
-
-        data_manager.get_length(file_name)
-        self.assertEqual(data_manager.get_length(file_name), 1)
+        self.assertEqual(data_manager.get_parameter_space_size(file_name), 1)