bluecellulab 2.5.0__py3-none-any.whl → 2.6.38__py3-none-any.whl

bluecellulab/synapse/synapse_factory.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -114,10 +114,14 @@ class SynapseFactory:
         section: NeuronSection = cell.get_psection(section_id=isec).hsection
 
         # old circuits don't have it, it needs to be computed via synlocation_to_segx
-        if ("afferent_section_pos" in syn_description and
-                not np.isnan(syn_description["afferent_section_pos"])):
+        if (SynapseProperty.AFFERENT_SECTION_POS in syn_description and
+                not np.isnan(syn_description[SynapseProperty.AFFERENT_SECTION_POS])):
             # position is pre computed in SONATA
-            location = syn_description["afferent_section_pos"]
+            location = syn_description[SynapseProperty.AFFERENT_SECTION_POS]
+            if location == 0.0:
+                location = 0.0000001
+            elif location >= 1.0:
+                location = 0.9999999
         else:
             ipt = syn_description[SynapseProperty.POST_SEGMENT_ID]
             syn_offset = syn_description[SynapseProperty.POST_SEGMENT_OFFSET]

bluecellulab/synapse/synapse_types.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

bluecellulab/tools.py

@@ -1,4 +1,4 @@
-# Copyright 2012-2024 Blue Brain Project / EPFL
+# Copyright 2023-2024 Blue Brain Project / EPFL
 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -25,7 +25,8 @@ import numpy as np
 import bluecellulab
 from bluecellulab.circuit.circuit_access import EmodelProperties
 from bluecellulab.exceptions import UnsteadyCellError
-from bluecellulab.utils import CaptureOutput, IsolatedProcess
+from bluecellulab.simulation.parallel import IsolatedProcess
+from bluecellulab.utils import CaptureOutput
 
 logger = logging.getLogger(__name__)
 
@@ -151,9 +152,9 @@ def holding_current(
 ) -> Tuple[float, float]:
     """Calculate the holding current necessary for a given holding voltage."""
     cell_id = bluecellulab.circuit.node_id.create_cell_id(cell_id)
-    ssim = bluecellulab.SSim(circuit_path)
+    circuit_sim = bluecellulab.CircuitSimulation(circuit_path)
 
-    cell_kwargs = ssim.fetch_cell_kwargs(cell_id)
+    cell_kwargs = circuit_sim.fetch_cell_kwargs(cell_id)
     with IsolatedProcess() as runner:
         i_hold, v_control = runner.apply(
             holding_current_subprocess, [v_hold, enable_ttx, cell_kwargs]
@@ -290,8 +291,7 @@ def detect_spike_step_subprocess(
 
     time = cell.get_time()
     voltage = cell.get_soma_voltage()
-    time_step = time[np.where((time > inj_start) & (time < inj_stop))]
-    voltage_step = voltage[np.where((time_step > inj_start) & (time_step < inj_stop))]
+    voltage_step = voltage[np.where((time > inj_start) & (time < inj_stop))]
     spike_detected = detect_spike(voltage_step)
 
     cell.delete()
@@ -317,8 +317,11 @@ def search_threshold_current(
     inj_stop: float,
     min_current: float,
     max_current: float,
+    current_precision: float = 0.01,
 ):
     """Search current necessary to reach threshold."""
+    if abs(max_current - min_current) < current_precision:
+        return max_current
     med_current = min_current + abs(min_current - max_current) / 2
     logger.info("Med current %d" % med_current)
 
@@ -328,18 +331,18 @@ def search_threshold_current(
     )
     logger.info("Spike threshold detection at: %f nA" % med_current)
 
-    if abs(max_current - min_current) < .01:
-        return max_current
-    elif spike_detected:
+    if spike_detected:
         return search_threshold_current(template_name, morphology_path,
                                         template_format, emodel_properties,
                                         hyp_level, inj_start, inj_stop,
-                                        min_current, med_current)
+                                        min_current, med_current,
+                                        current_precision)
     else:
         return search_threshold_current(template_name, morphology_path,
                                         template_format, emodel_properties,
                                         hyp_level, inj_start, inj_stop,
-                                        med_current, max_current)
+                                        med_current, max_current,
+                                        current_precision)
 
 
 def check_empty_topology() -> bool:

bluecellulab/utils.py

@@ -1,19 +1,21 @@
 """Utility functions used within BlueCellulab."""
+
 from __future__ import annotations
 import contextlib
 import io
 import json
-from multiprocessing.pool import Pool
 
 import numpy as np
 
 
 def run_once(func):
     """A decorator to ensure a function is only called once."""
+
     def wrapper(*args, **kwargs):
         if not wrapper.has_run:
             wrapper.has_run = True
             return func(*args, **kwargs)
+
     wrapper.has_run = False
     return wrapper
 
@@ -32,29 +34,25 @@ class CaptureOutput(list):
 
 class NumpyEncoder(json.JSONEncoder):
     def default(self, obj):
-        if isinstance(obj, (np.int_, np.intc, np.intp, np.int8,
-                            np.int16, np.int32, np.int64, np.uint8,
-                            np.uint16, np.uint32, np.uint64)):
+        if isinstance(
+            obj,
+            (
+                np.int_,
+                np.intc,
+                np.intp,
+                np.int8,
+                np.int16,
+                np.int32,
+                np.int64,
+                np.uint8,
+                np.uint16,
+                np.uint32,
+                np.uint64,
+            ),
+        ):
             return int(obj)
-        elif isinstance(obj, (np.float_, np.float16, np.float32,
-                              np.float64)):
+        elif isinstance(obj, (np.float_, np.float16, np.float32, np.float64)):
             return float(obj)
         elif isinstance(obj, np.ndarray):
             return obj.tolist()
         return json.JSONEncoder.default(self, obj)
-
-
-class IsolatedProcess(Pool):
-    """Multiprocessing Pool that restricts a worker to run max 1 process.
-
-    Use this when running isolated NEURON simulations. Running 2 NEURON
-    simulations on a single process is to be avoided.
-    """
-    def __init__(self, processes: int | None = 1):
-        """Initialize the IsolatedProcess pool.
-
-        Args:
-            processes: The number of processes to use for running the stimuli.
-            If set to None, then the number returned by os.cpu_count() is used.
-        """
-        super().__init__(processes=processes, maxtasksperchild=1)

{bluecellulab-2.5.0.dist-info → bluecellulab-2.6.38.dist-info}/LICENSE

@@ -1,10 +1,3 @@
-BlueCellulab is licensed under the Apache License, unless noted otherwise, 
-e.g., for external dependencies such as MOD or morphology files.
-For MOD files for which the original source is available on ModelDB, 
-any specific licenses on mentioned on ModelDB, or the generic License of ModelDB apply.
-The licenses of the morphology files used in this repository are available on: https://zenodo.org/record/5909613
-
-
                                  Apache License
                            Version 2.0, January 2004
                         http://www.apache.org/licenses/

{bluecellulab-2.5.0.dist-info → bluecellulab-2.6.38.dist-info}/METADATA

@@ -1,11 +1,12 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: bluecellulab
-Version: 2.5.0
-Summary: The Pythonic Blue Brain simulator access
-Home-page: https://github.com/BlueBrain/BlueCelluLab
+Version: 2.6.38
+Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0
-Keywords: computational neuroscience,simulation,analysis,parameters,Blue Brain Project
+Project-URL: Homepage, https://github.com/openbraininstitute/BlueCelluLab
+Project-URL: Documentation, https://bluecellulab.readthedocs.io/
+Keywords: computational neuroscience,simulation,analysis,SONATA,neural networks,neuron,Blue Brain Project
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console
 Classifier: License :: OSI Approved :: Apache Software License
@@ -13,18 +14,19 @@ Classifier: Operating System :: POSIX
 Classifier: Topic :: Scientific/Engineering
 Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Utilities
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: AUTHORS.txt
-Requires-Dist: NEURON <9.0.0,>=8.0.2
-Requires-Dist: numpy <2.0.0,>=1.8.0
-Requires-Dist: matplotlib <4.0.0,>=3.0.0
-Requires-Dist: pandas <3.0.0,>=1.0.0
-Requires-Dist: bluepysnap <4.0.0,>=3.0.0
-Requires-Dist: pydantic <3.0.0,>=2.5.2
-Requires-Dist: typing-extensions >=4.8.0
-Requires-Dist: networkx >=3.1
+Requires-Dist: NEURON<9.0.0,>=8.0.2
+Requires-Dist: numpy<2.0.0,>=1.8.0
+Requires-Dist: matplotlib<4.0.0,>=3.0.0
+Requires-Dist: pandas<3.0.0,>=1.0.0
+Requires-Dist: bluepysnap<4.0.0,>=3.0.0
+Requires-Dist: pydantic<3.0.0,>=2.5.2
+Requires-Dist: typing-extensions>=4.8.0
+Requires-Dist: networkx>=3.1
+Requires-Dist: h5py>=3.8.0
 
 |banner|
 
@@ -44,9 +46,10 @@ BlueCelluLab
 +----------------+------------+
 | Gitter         | |gitter|   |
 +----------------+------------+
-| Citation       | |zenodo|   |
+| Paper          | |joss|     |
++----------------+------------+
+| Zenodo         | |zenodo|   |
 +----------------+------------+
-
 
 The Blue Brain Cellular Laboratory is designed for simulations and experiments on individual cells or groups of cells.
 Suitable use cases for BlueCelluLab include:
@@ -66,29 +69,34 @@ Suitable use cases for BlueCelluLab include:
 Citation
 ========
 
-When you use this BlueCelluLab software for your research, we ask you to cite the following reference(this includes poster presentations):
+When using the BlueCelluLab software for your research, please cite the following paper (including for poster presentations): `BlueCelluLab: Biologically Detailed Neural Network Experimentation API <https://doi.org/10.21105/joss.07026>`_
 
 .. code-block::
 
-    @software{bluecellulab_zenodo,
-      author       = {Van Geit, Werner and Tuncel, Anil and Gevaert, Mike and Torben-Nielsen, Benjamin and Muller, Eilif},
-      title        = {BlueCelluLab},
-      month        = jul,
-      year         = 2023,
-      publisher    = {Zenodo},
-      doi          = {10.5281/zenodo.8113483},
-      url          = {https://doi.org/10.5281/zenodo.8113483}
+    @article{Tuncel2024,
+        doi = {10.21105/joss.07026},
+        url = {https://doi.org/10.21105/joss.07026},
+        year = {2024},
+        publisher = {The Open Journal},
+        volume = {9},
+        number = {100},
+        pages = {7026},
+        author = {Anıl Tuncel and Werner Van Geit and Mike Gevaert and Benjamin Torben-Nielsen and Darshan Mandge and İlkan Kılıç and Aurélien Jaquier and Eilif Muller and Lida Kanari and Henry Markram},
+        title = {BlueCelluLab: Biologically Detailed Neural Network Experimentation API},
+        journal = {Journal of Open Source Software}
     }
 
+If you need to cite a specific version, please use the DOI provided by `Zenodo <https://zenodo.org/records/8113483>`_, which you can access via the "Cite this repository" button at the top of the repository page.
+
 Support
 =======
 
-We are providing support on `Gitter <https://gitter.im/BlueBrain/BlueCelluLab>`_. We suggest you create tickets on the `Github issue tracker <https://github.com/BlueBrain/BlueCelluLab/issues>`_ in case you encounter problems while using the software or if you have some suggestions.
+We are providing support on `Gitter <https://gitter.im/openbraininstitute/BlueCelluLab>`_. We suggest you create tickets on the `Github issue tracker <https://github.com/openbraininstitute/BlueCelluLab/issues>`_ in case you encounter problems while using the software or if you have some suggestions.
 
 Main dependencies
 =================
 
-* `Python 3.8+ <https://www.python.org/downloads/release/python-380/>`_
+* `Python 3.9+ <https://www.python.org/downloads/release/python-390/>`_
 * `Neuron 8.0.2+ <https://pypi.org/project/NEURON/>`_
 
 Installation
@@ -119,13 +127,13 @@ The following example shows how to create a cell, add a stimulus and run a simul
     time, voltage = cell.get_time(), cell.get_soma_voltage()
     # plotting time and voltage ...
 
-.. image:: https://raw.githubusercontent.com/BlueBrain/BlueCelluLab/main/docs/images/voltage-readme.png
+.. image:: https://raw.githubusercontent.com/openbraininstitute/BlueCelluLab/main/docs/images/voltage-readme.png
    :alt: Voltage plot
 
 Tutorial
 ========
 
-A more detailed explanation on how to use BlueCelluLab, as well as other examples can be found on the `examples page <https://github.com/BlueBrain/BlueCelluLab/blob/main/examples/README.rst>`_.
+A more detailed explanation on how to use BlueCelluLab, as well as other examples can be found on the `examples page <https://github.com/openbraininstitute/BlueCelluLab/blob/main/examples/README.rst>`_.
 
 API Documentation
 =================
@@ -144,6 +152,11 @@ 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/openbraininstitute/BlueCelluLab/blob/main/CONTRIBUTING.rst>`_ for guidelines on how to contribute.
+
 Funding & Acknowledgements
 ==========================
 
@@ -152,7 +165,8 @@ The development and maintenance of this code is supported by funding to the Blue
 Copyright
 =========
 
-Copyright (c) 2023 Blue Brain Project/EPFL
+Copyright (c) 2023-2024 Blue Brain Project/EPFL
+Copyright (c) 2025 Open Brain Institute
 
 This work is licensed under `Apache 2.0 <https://www.apache.org/licenses/LICENSE-2.0.html>`_
 
@@ -162,10 +176,10 @@ The licenses of the morphology files used in this repository are available on: h
 
 
 .. |license| image:: https://img.shields.io/badge/License-Apache%202.0-blue.svg
-                :target: https://github.com/BlueBrain/BlueCelluLab/blob/main/LICENSE
+                :target: https://github.com/openbraininstitute/BlueCelluLab/blob/main/LICENSE
 
-.. |tests| image:: https://github.com/BlueBrain/BlueCelluLab/actions/workflows/test.yml/badge.svg?branch=main
-   :target: https://github.com/BlueBrain/BlueCelluLab/actions/workflows/test.yml
+.. |tests| image:: https://github.com/openbraininstitute/BlueCelluLab/actions/workflows/test.yml/badge.svg?branch=main
+   :target: https://github.com/openbraininstitute/BlueCelluLab/actions/workflows/test.yml
    :alt: CI
 
 .. |pypi| image:: https://img.shields.io/pypi/v/bluecellulab.svg
@@ -176,13 +190,17 @@ The licenses of the morphology files used in this repository are available on: h
                :target: https://bluecellulab.readthedocs.io/
                :alt: latest documentation
 
-.. |coverage| image:: https://codecov.io/github/BlueBrain/BlueCelluLab/coverage.svg?branch=main
-                   :target: https://codecov.io/gh/BlueBrain/bluecellulab
+.. |coverage| image:: https://codecov.io/github/openbraininstitute/BlueCelluLab/coverage.svg?branch=main
+                   :target: https://codecov.io/gh/openbraininstitute/bluecellulab
                    :alt: coverage
 
 .. |gitter| image:: https://badges.gitter.im/Join%20Chat.svg
-                 :target: https://gitter.im/BlueBrain/BlueCelluLab
-                 :alt: Join the chat at https://gitter.im/BlueBrain/BlueCelluLab
+                 :target: https://gitter.im/openbraininstitute/BlueCelluLab
+                 :alt: Join the chat at https://gitter.im/openbraininstitute/BlueCelluLab
+
+.. |joss| image:: https://joss.theoj.org/papers/effd553ca48734a2966d9d7ace3b05ff/status.svg
+                :target: https://joss.theoj.org/papers/effd553ca48734a2966d9d7ace3b05ff
+                :alt: JOSS
 
 .. |zenodo| image:: https://zenodo.org/badge/640805129.svg
                  :target: https://zenodo.org/badge/latestdoi/640805129
@@ -195,4 +213,4 @@ The licenses of the morphology files used in this repository are available on: h
     to skip content after the marker 'substitutions'.
 
 .. substitutions
-.. |banner| image:: https://raw.githubusercontent.com/BlueBrain/BlueCelluLab/main/docs/source/logo/BlueCelluLabBanner.jpg
+.. |banner| image:: https://raw.githubusercontent.com/openbraininstitute/BlueCelluLab/main/docs/source/logo/BlueCelluLabBanner.jpg

bluecellulab-2.6.38.dist-info/RECORD

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