bluecellulab 2.6.19__tar.gz → 2.6.21__tar.gz

bluecellulab-2.6.21/CONTRIBUTING.rst

@@ -0,0 +1,27 @@
+Contributing to BlueCelluLab
+============================
+
+Thank you for taking the time to contribute!
+
+Reporting Bugs and Suggesting Enhancements
+------------------------------------------
+
+1. Search existing `issues <https://github.com/BlueBrain/BlueCelluLab/issues>`_.
+2. Open a new issue with a clear title and detailed description.
+3. Include steps to reproduce, expected and actual behavior for bugs, or the current and expected behavior for enhancements.
+4. Attach any relevant screenshots or files.
+5. If applicable specify the versions of BlueCelluLab, Python and any relevant dependencies.
+
+Pull Requests
+-------------
+
+1. Fork the repository and create a new branch.
+2. Make your changes.
+3. Run `tox -e lint` to check the code format.
+4. Run the tests with `tox -e py3`.
+5. Add unit tests for the new code.
+6. If applicable add type hints and docstrings.
+7. If applicable update the documentation.
+8. Submit a pull request with a clear description.
+
+Thank you for contributing to BlueCelluLab!

{bluecellulab-2.6.19 → bluecellulab-2.6.21}/PKG-INFO

@@ -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 → bluecellulab-2.6.21}/README.rst

@@ -116,6 +116,11 @@ 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 → bluecellulab-2.6.21}/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 → bluecellulab-2.6.21}/bluecellulab.egg-info/PKG-INFO

@@ -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 → bluecellulab-2.6.21}/bluecellulab.egg-info/SOURCES.txt

@@ -6,6 +6,7 @@
 .zenodo.json
 AUTHORS.txt
 CHANGELOG.rst
+CONTRIBUTING.rst
 LICENSE
 MANIFEST.in
 Makefile
@@ -92,6 +93,7 @@ docs/source/api.rst
 docs/source/changelog.rst
 docs/source/compiling-mechanisms.rst
 docs/source/conf.py
+docs/source/contributing.rst
 docs/source/index.rst
 docs/source/list_of_stim.rst
 docs/source/_static/.gitkeep

bluecellulab-2.6.21/docs/source/contributing.rst

@@ -0,0 +1 @@
+.. include:: ../../CONTRIBUTING.rst

{bluecellulab-2.6.19 → bluecellulab-2.6.21}/docs/source/index.rst

@@ -17,5 +17,6 @@
    api.rst
    compiling-mechanisms.rst
    changelog
+   contributing
 
 .. |banner| image:: /logo/BlueCelluLabBanner.jpg