Fix empty list in reports

bluepysnap/frame_report.py

@@ -23,6 +23,7 @@
 from libsonata import ElementReportReader
 
 from bluepysnap.exceptions import BluepySnapError
+from bluepysnap.utils import fix_libsonata_empty_list
 
 L = logging.getLogger(__name__)
 
@@ -211,6 +212,8 @@ def nodes(self):
 
     def _resolve(self, group):
         """Transform a group into a node_id array."""
+        if group == []:
+            return fix_libsonata_empty_list()
         return self.nodes.ids(group=group)
 
 

bluepysnap/spike_report.py

@@ -24,6 +24,7 @@
 import numpy as np
 
 from bluepysnap.exceptions import BluepySnapError
+from bluepysnap.utils import fix_libsonata_empty_list
 
 
 def _get_reader(spike_report):
@@ -84,6 +85,8 @@ def nodes(self):
 
     def _resolve_nodes(self, group):
         """Transform a node group into a node_id array."""
+        if group == []:
+            return fix_libsonata_empty_list()
         return self.nodes.ids(group=group)
 
     def get(self, group=None, t_start=None, t_stop=None):

bluepysnap/utils.py

@@ -46,6 +46,14 @@ def ensure_list(v):
         return [v]
 
 
+def fix_libsonata_empty_list():
+    """Temporary solution to return empty list from libsonata report readers `.get` functions.
+
+    see: https://github.com/BlueBrain/libsonata/issues/84
+    """
+    return np.array([-2])
+
+
 def add_dynamic_prefix(properties):
     """Add the dynamic prefix to a list of properties."""
     return [DYNAMICS_PREFIX + name for name in list(properties)]

tests/test_frame_report.py

@@ -142,6 +142,8 @@ def test_nodes_invalid_population(self):
     def test_get(self):
         pdt.assert_frame_equal(self.test_obj.get(), self.df)
 
+        pdt.assert_frame_equal(self.test_obj.get([]),  pd.DataFrame())
+
         pdt.assert_frame_equal(self.test_obj.get(2), self.df.loc[:, [2]])
 
         pdt.assert_frame_equal(self.test_obj.get([2, 0]), self.df.loc[:, [0, 2]])

tests/test_spike_report.py

@@ -105,7 +105,7 @@ def test__resolve_nodes(self):
     def test_get(self):
         pdt.assert_series_equal(self.test_obj.get(),
                                 _create_series([2, 0, 1, 2, 0], [0.1, 0.2, 0.3, 0.7, 1.3]))
-
+        pdt.assert_series_equal(self.test_obj.get([]), _create_series([], []))
         npt.assert_allclose(self.test_obj.get(2), np.array([0.1, 0.7]))
         npt.assert_allclose(self.test_obj.get(0, t_start=1.), [1.3])
         npt.assert_allclose(self.test_obj.get(0, t_stop=1.), [0.2])

tests/test_utils.py

@@ -29,6 +29,10 @@ def test_ensure_list():
     assert test_module.ensure_list('abc') == ['abc']
 
 
+def test_fix_libsonata_empty_list():
+    npt.assert_array_equal(test_module.fix_libsonata_empty_list(), np.array([-2]))
+
+
 def test_add_dynamic_prefix():
     assert test_module.add_dynamic_prefix(["a", "b"]) == [DYNAMICS_PREFIX+"a", DYNAMICS_PREFIX+"b"]