bluecellulab 2.6.19__py3-none-any.whl → 2.6.21__py3-none-any.whl

bluecellulab/circuit_simulation.py

@@ -26,6 +26,7 @@ import numpy as np
 import pandas as pd
 from pydantic.types import NonNegativeInt
 from typing_extensions import deprecated
+from typing import Optional
 
 import bluecellulab
 from bluecellulab.cell import CellDict
@@ -116,6 +117,8 @@ class CircuitSimulation:
         self.spike_threshold = self.circuit_access.config.spike_threshold
         self.spike_location = self.circuit_access.config.spike_location
 
+        self.projections: list[str] = []
+
         condition_parameters = self.circuit_access.config.condition_parameters()
         set_global_condition_parameters(condition_parameters)
 
@@ -239,18 +242,17 @@ class CircuitSimulation:
                                         "pre_spike_trains")
 
         if add_projections is True:
-            projections = self.circuit_access.config.get_all_projection_names()
+            self.projections = self.circuit_access.config.get_all_projection_names()
         elif add_projections is False:
-            projections = []
+            self.projections = []
         else:
-            projections = add_projections
+            self.projections = add_projections
 
         self._add_cells(cell_ids)
         if add_synapses:
             self._add_synapses(
                 pre_gids=pre_gids,
-                add_minis=add_minis,
-                projections=projections)
+                add_minis=add_minis)
         if add_replay or interconnect_cells or pre_spike_trains:
             if add_replay and not add_synapses:
                 raise BluecellulabError("add_replay option can not be used if "
@@ -357,18 +359,17 @@ class CircuitSimulation:
                 ornstein_uhlenbeck_stim_count += 1
 
     def _add_synapses(
-            self, pre_gids=None, add_minis=False, projections=None):
+            self, pre_gids=None, add_minis=False):
         """Instantiate all the synapses."""
         for cell_id in self.cells:
             self._add_cell_synapses(
                 cell_id, pre_gids=pre_gids,
-                add_minis=add_minis,
-                projections=projections)
+                add_minis=add_minis)
 
     def _add_cell_synapses(
-        self, cell_id: CellId, pre_gids=None, add_minis=False, projections=None
+        self, cell_id: CellId, pre_gids=None, add_minis=False
     ) -> None:
-        syn_descriptions = self.get_syn_descriptions(cell_id, projections=projections)
+        syn_descriptions = self.get_syn_descriptions(cell_id)
 
         if pre_gids is not None:
             if self.circuit_format == CircuitFormat.SONATA:
@@ -423,12 +424,10 @@ class CircuitSimulation:
         )
         return syn_descriptions[filtered_rows]
 
-    def get_syn_descriptions(
-        self, cell_id: int | tuple[str, int], projections=None
-    ) -> pd.DataFrame:
+    def get_syn_descriptions(self, cell_id: int | tuple[str, int]) -> pd.DataFrame:
         """Get synapse descriptions dataframe."""
         cell_id = create_cell_id(cell_id)
-        return self.circuit_access.extract_synapses(cell_id, projections=projections)
+        return self.circuit_access.extract_synapses(cell_id, projections=self.projections)
 
     @staticmethod
     def merge_pre_spike_trains(*train_dicts) -> dict[CellId, np.ndarray]:

{bluecellulab-2.6.19.dist-info → bluecellulab-2.6.21.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.6.19
+Version: 2.6.21
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0
@@ -146,6 +146,11 @@ Testing is set up using `tox`:
     tox -e py3  # runs the tests
     tox -e lint  # runs the format checks
 
+Contributing
+============
+
+We welcome contributions to BlueCelluLab! Please see the `CONTRIBUTING.rst <https://github.com/BlueBrain/BlueCelluLab/blob/main/CONTRIBUTING.rst>`_ for guidelines on how to contribute.
+
 Funding & Acknowledgements
 ==========================
 

{bluecellulab-2.6.19.dist-info → bluecellulab-2.6.21.dist-info}/RECORD

@@ -1,5 +1,5 @@
 bluecellulab/__init__.py,sha256=JvigOm_7WDjVAodm4R_TyRzj7vd9hmEbvLJDUVtgeqo,899
-bluecellulab/circuit_simulation.py,sha256=GLy_O5onhiSa-RajorDHlgP1rkFxjUONB4G6B4upyg0,33672
+bluecellulab/circuit_simulation.py,sha256=cLCA97WKjhlEitD4CUad9n4pH4KF7Iw68w1bZH512yw,33587
 bluecellulab/connection.py,sha256=volV2YKtmqAF7MOEJar5ldF1ARAo7k2vF9MB1NXybUY,4640
 bluecellulab/dendrogram.py,sha256=w0vvv0Q169DolTX1j9dAZIvHIl4H258gAjQ1xQaNiGk,6427
 bluecellulab/exceptions.py,sha256=KIxF7s_7gPVJ07TiQ-Z1D8de7ylV74gNMhzl0339CVM,2379
@@ -62,9 +62,9 @@ bluecellulab/stimulus/factory.py,sha256=XDbnqCuMCh1RdZLKvlRucMj3wkXDqy6mEda_Oh6Y
 bluecellulab/synapse/__init__.py,sha256=RW8XoAMXOvK7OG1nHl_q8jSEKLj9ZN4oWf2nY9HAwuk,192
 bluecellulab/synapse/synapse_factory.py,sha256=3y15LlaBoNJiU2KUeTkh70pyU5OYf6xQIMSBmmMPMak,6987
 bluecellulab/synapse/synapse_types.py,sha256=4gne-hve2vq1Lau-LAVPsfLjffVYqAYBW3kCfC7_600,16871
-bluecellulab-2.6.19.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.6.19.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
-bluecellulab-2.6.19.dist-info/METADATA,sha256=IEr-rd-kfUVgbtQtMun0hl4zAWn7IRGySnn041OYpzQ,7054
-bluecellulab-2.6.19.dist-info/WHEEL,sha256=y4mX-SOX4fYIkonsAGA5N0Oy-8_gI4FXw5HNI1xqvWg,91
-bluecellulab-2.6.19.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.6.19.dist-info/RECORD,,
+bluecellulab-2.6.21.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.6.21.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
+bluecellulab-2.6.21.dist-info/METADATA,sha256=LKVNoBDRhEGl3HqRRq3YDgfkJ3nFDzoP6I5mZ0A2yo8,7267
+bluecellulab-2.6.21.dist-info/WHEEL,sha256=Z4pYXqR_rTB7OWNDYFOm1qRk0RX6GFP2o8LgvP453Hk,91
+bluecellulab-2.6.21.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.6.21.dist-info/RECORD,,

{bluecellulab-2.6.19.dist-info → bluecellulab-2.6.21.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (70.2.0)
+Generator: setuptools (70.3.0)
 Root-Is-Purelib: true
 Tag: py3-none-any