Bump dependencies

GazzolaLab · Jan 6, 2025 · 82cac9d · 82cac9d
1 parent a17dcb5
commit 82cac9d
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Showing 4 changed files with 1,112 additions and 641 deletions.
diff --git a/src/miv_simulator/interface/network.py b/src/miv_simulator/interface/network.py
@@ -91,7 +91,8 @@ def launch(self):
                         30,
                         sum(config.cell_distributions[population].values()),
                     ),
-                    "write_size": sum(config.cell_distributions[population].values()) // 32,
+                    "write_size": sum(config.cell_distributions[population].values())
+                    // 32,
                     "chunk_size": _lp(
                         0,
                         5e5,
@@ -143,7 +144,8 @@ def launch(self):
                         20,
                         sum(config.cell_distributions[population].values()),
                     ),
-                    "write_size": sum(config.cell_distributions[population].values()) // 32,
+                    "write_size": sum(config.cell_distributions[population].values())
+                    // 32,
                     "chunk_size": _lp(
                         0,
                         5e5,

diff --git a/src/miv_simulator/stimulus.py b/src/miv_simulator/stimulus.py
@@ -201,7 +201,6 @@ def get_equilibration(env: AbstractEnv) -> Tuple[ndarray, int]:
             / env.stimulus_config["Temporal Resolution"]
         )
         from scipy.signal.windows import hann
-
 
         equilibrate_hann = hann(2 * equilibrate_len)[:equilibrate_len]
         equilibrate = (equilibrate_hann, equilibrate_len)

diff --git a/src/miv_simulator/utils/io.py b/src/miv_simulator/utils/io.py
@@ -1155,7 +1155,7 @@ def import_synapse_attributes(
     ):
         forest_dset_path = f"/Populations/{population}/Trees"
         forest_syns_dset_path = f"/Populations/{population}/Synapse Attributes"
-        
+
         with h5py.File(self.cells_filepath, "a") as f_dst:
             with h5py.File(forest_file, "r") as f_src:
                 copy_dataset(f_src, f_dst, forest_dset_path)
@@ -1174,5 +1174,7 @@ def copy_stim_coordinates(self):
         with h5py.File(self.cells_filepath, "a") as f:
             if "/Populations/STIM" not in f:
                 return
-            f.copy("/Populations/STIM/Generated Coordinates", "/Populations/STIM/Coordinates")
-
+            f.copy(
+                "/Populations/STIM/Generated Coordinates",
+                "/Populations/STIM/Coordinates",
+            )