bluecellulab 1.8.5__tar.gz → 2.0.0__tar.gz

{bluecellulab-1.8.5 → bluecellulab-2.0.0}/CHANGELOG.rst

@@ -1,6 +1,11 @@
 Changelog
 ==========
 
+2.0.0
+---------
+
+* update to BluePySnap 3.0.0
+
 1.3
 ---------
 

{bluecellulab-1.8.5 → bluecellulab-2.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 1.8.5
+Version: 2.0.0
 Summary: The Pythonic Blue Brain simulator access
 Home-page: https://github.com/BlueBrain/BlueCelluLab
 Author: Blue Brain Project, EPFL

{bluecellulab-1.8.5 → bluecellulab-2.0.0}/bluecellulab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 1.8.5
+Version: 2.0.0
 Summary: The Pythonic Blue Brain simulator access
 Home-page: https://github.com/BlueBrain/BlueCelluLab
 Author: Blue Brain Project, EPFL

{bluecellulab-1.8.5 → bluecellulab-2.0.0}/bluecellulab.egg-info/requires.txt

@@ -2,7 +2,7 @@ NEURON<9.0.0,>=8.0.2
 numpy<2.0.0,>=1.8.0
 matplotlib<4.0.0,>=3.0.0
 pandas<3.0.0,>=1.0.0
-bluepysnap<3.0.0,>=2.0.0
+bluepysnap<4.0.0,>=3.0.0
 pydantic<3.0.0,>=2.5.2
 typing-extensions>=4.8.0
 networkx>=3.1

{bluecellulab-1.8.5 → bluecellulab-2.0.0}/setup.py

@@ -38,7 +38,7 @@ setuptools.setup(
         "numpy>=1.8.0,<2.0.0",
         "matplotlib>=3.0.0,<4.0.0",
         "pandas>=1.0.0,<3.0.0",
-        "bluepysnap>=2.0.0,<3.0.0",
+        "bluepysnap>=3.0.0,<4.0.0",
         "pydantic>=2.5.2,<3.0.0",
         "typing-extensions>=4.8.0",
         "networkx>=3.1"

{bluecellulab-1.8.5 → bluecellulab-2.0.0}/tests/test_bglib.py

@@ -11,7 +11,7 @@ class TestBGLibBaseClass1:
 
     """Test BGLib base class"""
 
-    def setup(self):
+    def setup_method(self):
         """Setup"""
         self.taper_cell = bluecellulab.Cell(
             "%s/examples/tapertest_cells/taper_cell.hoc" % script_dir,
@@ -20,7 +20,7 @@ class TestBGLibBaseClass1:
             "%s/examples/tapertest_cells/notaper_cell.hoc" % script_dir,
             "%s/examples/tapertest_cells" % script_dir)
 
-    def teardown(self):
+    def teardown_method(self):
         """Teardown"""
         del self.taper_cell
         del self.notaper_cell

{bluecellulab-1.8.5 → bluecellulab-2.0.0}/tests/test_cell/test_core.py

@@ -58,14 +58,14 @@ def test_shorten_and_hash_string():
 class TestCellBaseClass1:
     """First Cell test class"""
 
-    def setup(self):
+    def setup_method(self):
         """Setup"""
         self.cell = bluecellulab.Cell(
             "%s/examples/cell_example1/test_cell.hoc" % str(parent_dir),
             "%s/examples/cell_example1" % str(parent_dir))
         assert isinstance(self.cell, bluecellulab.Cell)
 
-    def teardown(self):
+    def teardown_method(self):
         """Teardown"""
         del self.cell
 
@@ -198,14 +198,14 @@ class TestCellBaseClassVClamp:
 
     """First Cell test class"""
 
-    def setup(self):
+    def setup_method(self):
         """Setup"""
         self.cell = bluecellulab.Cell(
             "%s/examples/cell_example1/test_cell.hoc" % str(parent_dir),
             "%s/examples/cell_example1" % str(parent_dir))
         assert (isinstance(self.cell, bluecellulab.Cell))
 
-    def teardown(self):
+    def teardown_method(self):
         """Teardown"""
         del self.cell
 
@@ -263,7 +263,7 @@ class TestCellBaseClassVClamp:
 
 class TestCellSpikes:
 
-    def setup(self):
+    def setup_method(self):
         self.cell = bluecellulab.Cell(
             f"{parent_dir}/examples/cell_example1/test_cell.hoc",
             f"{parent_dir}/examples/cell_example1")
@@ -317,7 +317,7 @@ def test_add_dendrogram():
 class TestCellV6:
     """Test class for testing Cell object functionalities with v6 template."""
 
-    def setup(self):
+    def setup_method(self):
         """Setup."""
         emodel_properties = EmodelProperties(
             threshold_current=1.1433533430099487,
@@ -406,7 +406,7 @@ def test_add_synapse_replay():
 @pytest.mark.v6
 class TestWithinCircuit:
 
-    def setup(self):
+    def setup_method(self):
         """Setup method called before each test method."""
         sonata_sim_path = (
             parent_dir

{bluecellulab-1.8.5 → bluecellulab-2.0.0}/tests/test_cell/test_sonata_proxy.py

@@ -22,7 +22,7 @@ hipp_circuit_with_projections = (
 
 class TestSonataProxy:
 
-    def setup(self):
+    def setup_method(self):
         circuit_access = SonataCircuitAccess(str(hipp_circuit_with_projections))
         cell_id = CellId("hippocampus_neurons", 1)
         self.sonata_proxy = SonataProxy(cell_id, circuit_access)

{bluecellulab-1.8.5 → bluecellulab-2.0.0}/tests/test_circuit/test_circuit_access.py

@@ -44,7 +44,7 @@ def test_sonata_circuit_access_file_not_found():
 
 
 class TestSonataCircuitAccess:
-    def setup(self):
+    def setup_method(self):
         self.circuit_access = SonataCircuitAccess(hipp_circuit_with_projections)
 
     def test_available_cell_properties(self):

{bluecellulab-1.8.5 → bluecellulab-2.0.0}/tests/test_circuit/test_simulation_access.py

@@ -43,7 +43,7 @@ def test_sample_array():
 
 class TestSonataSimulationAccess:
 
-    def setup(self):
+    def setup_method(self):
         self.simulation_access = SonataSimulationAccess(str(hipp_simulation_with_projections))
 
     @staticmethod

{bluecellulab-1.8.5 → bluecellulab-2.0.0}/tests/test_synapse/test_synapse_factory.py

@@ -22,7 +22,7 @@ parent_dir = Path(__file__).resolve().parent.parent
 @pytest.mark.v6
 class TestSynapseFactory:
 
-    def setup(self):
+    def setup_method(self):
         emodel_properties = EmodelProperties(
             threshold_current=1.1433533430099487,
             holding_current=1.4146618843078613,