From ba348da82f1c3e384f6291f4581f7fc8d3954d1d Mon Sep 17 00:00:00 2001
From: Mike Gevaert <michael.gevaert@epfl.ch>
Date: Thu, 1 Feb 2024 14:35:10 +0100
Subject: [PATCH 1/2] work around libsonata refactor

* see https://github.com/BlueBrain/libsonata/pull/345
---
 tests/test_input.py        |  9 ++++++++-
 tests/test_simulation.py   | 14 +++++++++++---
 tests/test_spike_report.py |  8 +++++++-
 3 files changed, 26 insertions(+), 5 deletions(-)

diff --git a/tests/test_input.py b/tests/test_input.py
index 67104770..ad923cca 100644
--- a/tests/test_input.py
+++ b/tests/test_input.py
@@ -40,7 +40,14 @@ def test_get_simulation_inputs():
     assert inputs.keys() == {"spikes_1", "current_clamp_1"}
 
     assert isinstance(inputs["spikes_1"], test_module.SynapseReplay)
-    assert isinstance(inputs["current_clamp_1"], libsonata._libsonata.Linear)
+
+    try:
+        Linear = libsonata._libsonata.Linear
+    except AttributeError:
+        from libsonata._libsonata import SimulationConfig
+        Linear = SimulationConfig.Linear
+
+    assert isinstance(inputs["current_clamp_1"], Linear)
 
     with pytest.raises(BluepySnapError, match="Unexpected type for 'simulation': str"):
         test_module.get_simulation_inputs("fail_me")
diff --git a/tests/test_simulation.py b/tests/test_simulation.py
index 56a2bf99..4f48554d 100644
--- a/tests/test_simulation.py
+++ b/tests/test_simulation.py
@@ -5,7 +5,6 @@
 
 import libsonata
 import pytest
-from libsonata import SonataError
 
 import bluepysnap.simulation as test_module
 from bluepysnap.exceptions import BluepySnapError
@@ -20,6 +19,14 @@
 
 from utils import PICKLED_SIZE_ADJUSTMENT, TEST_DATA_DIR, copy_test_data, edit_config
 
+try:
+    Run = libsonata._libsonata.Run
+    Conditions = libsonata._libsonata.Conditions
+except AttributeError:
+    from libsonata._libsonata import SimulationConfig
+    Run = SimulationConfig.Run
+    Conditions = SimulationConfig.Conditions
+
 
 def test__warn_on_overwritten_node_sets():
     # No warnings if no overwritten
@@ -40,7 +47,8 @@ def test_all():
     assert set(simulation.circuit.nodes) == {"default", "default2"}
     assert set(simulation.circuit.edges) == {"default", "default2"}
 
-    assert isinstance(simulation.run, libsonata._libsonata.Run)
+    assert isinstance(simulation.run, Run)
+
     assert simulation.run.tstop == 1000.0
     assert simulation.run.dt == 0.01
     assert simulation.run.spike_threshold == -15
@@ -51,7 +59,7 @@ def test_all():
     assert simulation.time_units == "ms"
 
     assert simulation.simulator == "CORENEURON"
-    assert isinstance(simulation.conditions, libsonata._libsonata.Conditions)
+    assert isinstance(simulation.conditions, Conditions)
     assert simulation.conditions.celsius == 34.0
     assert simulation.conditions.v_init == -80
 
diff --git a/tests/test_spike_report.py b/tests/test_spike_report.py
index c97c5f09..0cab43fd 100644
--- a/tests/test_spike_report.py
+++ b/tests/test_spike_report.py
@@ -17,6 +17,12 @@
 
 from utils import TEST_DATA_DIR, copy_test_data, edit_config
 
+try:
+    Output = libsonata._libsonata.Output
+except AttributeError:
+    from libsonata._libsonata import SimulationConfig
+    Output = SimulationConfig.Output
+
 
 def _create_series(node_ids, index, name="ids"):
     def _get_index(ids):
@@ -34,7 +40,7 @@ def setup_method(self):
         self.test_obj = test_module.SpikeReport(self.simulation)
 
     def test_config(self):
-        assert isinstance(self.test_obj.config, libsonata._libsonata.Output)
+        assert isinstance(self.test_obj.config, Output)
         assert self.test_obj.config.output_dir == str(TEST_DATA_DIR / "reporting")
         assert self.test_obj.config.log_file == "log_spikes.log"
         assert self.test_obj.config.spikes_file == "spikes.h5"

From 67b7d3aa46749df1cbabf3f142439406cd4c8c52 Mon Sep 17 00:00:00 2001
From: Mike Gevaert <michael.gevaert@epfl.ch>
Date: Fri, 2 Feb 2024 13:49:54 +0100
Subject: [PATCH 2/2] format

---
 tests/test_input.py        | 1 +
 tests/test_simulation.py   | 1 +
 tests/test_spike_report.py | 1 +
 3 files changed, 3 insertions(+)

diff --git a/tests/test_input.py b/tests/test_input.py
index ad923cca..342e1ffd 100644
--- a/tests/test_input.py
+++ b/tests/test_input.py
@@ -45,6 +45,7 @@ def test_get_simulation_inputs():
         Linear = libsonata._libsonata.Linear
     except AttributeError:
         from libsonata._libsonata import SimulationConfig
+
         Linear = SimulationConfig.Linear
 
     assert isinstance(inputs["current_clamp_1"], Linear)
diff --git a/tests/test_simulation.py b/tests/test_simulation.py
index 4f48554d..90a3fa99 100644
--- a/tests/test_simulation.py
+++ b/tests/test_simulation.py
@@ -24,6 +24,7 @@
     Conditions = libsonata._libsonata.Conditions
 except AttributeError:
     from libsonata._libsonata import SimulationConfig
+
     Run = SimulationConfig.Run
     Conditions = SimulationConfig.Conditions
 
diff --git a/tests/test_spike_report.py b/tests/test_spike_report.py
index 0cab43fd..5b59e7c1 100644
--- a/tests/test_spike_report.py
+++ b/tests/test_spike_report.py
@@ -21,6 +21,7 @@
     Output = libsonata._libsonata.Output
 except AttributeError:
     from libsonata._libsonata import SimulationConfig
+
     Output = SimulationConfig.Output