Use libsonata for getting the framereport file name (#172)

* require libsonata>=0.1.16

CHANGELOG.rst

@@ -28,6 +28,7 @@ Breaking Changes
 - The NodeStorage & EdgeStorage classes were removed
 - point_neuron is no longer supported
 - Some column data types in the nodes and edges DataFrames returned by the `get()` method may be `float` or `int` instead of `object`.
+- require ``libsonata>=0.1.16``
 
 Version v0.13.1
 ---------------

bluepysnap/frame_report.py

@@ -16,7 +16,6 @@
 # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 """Frame report access."""
 import logging
-from pathlib import Path
 
 import numpy as np
 import pandas as pd
@@ -29,23 +28,13 @@
 
 L = logging.getLogger(__name__)
 
-REPORT_EXTENSION = ".h5"
-
 
 def _collect_population_reports(frame_report, cls):
     return {
         population: cls(frame_report, population) for population in frame_report.population_names
     }
 
 
-def _get_reader(reader_report, cls):
-    path = reader_report.simulation.output.output_dir
-    # TODO: change to use reader_report.to_libsonata.file_name when fixed in libsonata
-    file_name = reader_report.config.get("file_name", reader_report.name) + REPORT_EXTENSION
-    path = str(Path(path, file_name))
-    return cls(path)
-
-
 class PopulationFrameReport:
     """Access to PopulationFrameReport data."""
 
@@ -66,7 +55,7 @@ def __init__(self, frame_report, population_name):
     @staticmethod
     def _get_reader(frame_report, population_name):
         """Access to the population compartment reader."""
-        return _get_reader(frame_report, ElementReportReader)[population_name]
+        return ElementReportReader(frame_report.to_libsonata.file_name)[population_name]
 
     @property
     def name(self):
@@ -202,7 +191,7 @@ def __init__(self, simulation, report_name):
     @cached_property
     def _frame_reader(self):
         """Access to the compartment report reader."""
-        return _get_reader(self, ElementReportReader)
+        return ElementReportReader(self.to_libsonata.file_name)
 
     @property
     def to_libsonata(self):

setup.py

@@ -46,7 +46,7 @@ def __init__(self, *args, **kwargs):
         "cached_property>=1.0",
         "h5py>=3.0.1,<4.0.0",
         "jsonschema>=4.0.0,<5.0.0",
-        "libsonata>=0.1.13,<1.0.0",
+        "libsonata>=0.1.16,<1.0.0",
         "morphio>=3.0.0,<4.0.0",
         "morph-tool>=2.4.3,<3.0.0",
         "neurom>=1.6",

tests/data/simulation_config.json

@@ -42,6 +42,7 @@
       "variable_name": "m",
       "sections": "soma",
       "type": "compartment",
+      "file_name": "soma_report",
       "start_time": 0,
       "end_time": 1000.0,
       "dt": 0.01,

tests/test_frame_report.py

@@ -28,6 +28,7 @@ def test_config(self):
             "variable_name": "m",
             "sections": "soma",
             "type": "compartment",
+            "file_name": "soma_report",
             "start_time": 0,
             "end_time": 1000.0,
             "dt": 0.01,