bluecellulab 2.6.28__tar.gz → 2.6.30__tar.gz

{bluecellulab-2.6.28 → bluecellulab-2.6.30}/.compile_mod.sh

@@ -1,6 +1,6 @@
 #!/bin/sh
 
-# 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-2.6.30/CITATION.cff

@@ -0,0 +1,29 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+title: "BlueCelluLab"
+doi: 10.5281/zenodo.8113483
+url: https://zenodo.org/doi/10.5281/zenodo.8113483
+abstract: "The Blue Brain Cellular Laboratory is designed for simulations and experiments on individual cells or groups of cells. Use cases for which bluecellulab is well suited include: scripting and statistics across single or pairs of cells, light-weight detailed reporting on a few state variables post-simulation, development of synaptic plasticity rules, dynamics validations of e.g. synaptic properties, automation of in-silico whole-cell patching experiments, debugging both scientifically and computationally."
+authors:
+  - family-names: "Tuncel"
+    given-names: "Anil"
+  - family-names: "Van Geit"
+    given-names: "Werner"
+  - family-names: "Gevaert"
+    given-names: "Mike"
+  - family-names: "Torben-Nielsen"
+    given-names: "Benjamin"
+  - family-names: "Mandge"
+    given-names: "Darshan"
+  - family-names: "Kilic"
+    given-names: "Ilkan"
+  - family-names: "Jaquier"
+    given-names: "Aurélien"
+  - family-names: "Muller"
+    given-names: "Eilif"
+  - family-names: "Kanari"
+    given-names: "Lida"
+  - family-names: "Markram"
+    given-names: "Henry"
+date-released: 2020-03-01
+publisher: "Zenodo"

{bluecellulab-2.6.28 → bluecellulab-2.6.30}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.6.28
+Version: 2.6.30
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0
@@ -73,7 +73,7 @@ When you use this BlueCelluLab software for your research, we ask you to cite th
 .. code-block::
 
     @software{bluecellulab_zenodo,
-      author       = {Van Geit, Werner and Tuncel, Anil and Gevaert, Mike and Torben-Nielsen, Benjamin and Muller, Eilif},
+      author       = {Tuncel, Anil and Van Geit, Werner and Gevaert, Mike and Torben-Nielsen, Benjamin and Mandge, Darshan and Kilic, Ilkan and Jaquier, Aurélien and Muller, Eilif and Kanari, Lida and Markram, Henry},
       title        = {BlueCelluLab},
       month        = jul,
       year         = 2023,
@@ -159,7 +159,7 @@ 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
 
 This work is licensed under `Apache 2.0 <https://www.apache.org/licenses/LICENSE-2.0.html>`_
 

{bluecellulab-2.6.28 → bluecellulab-2.6.30}/README.rst

@@ -43,7 +43,7 @@ When you use this BlueCelluLab software for your research, we ask you to cite th
 .. code-block::
 
     @software{bluecellulab_zenodo,
-      author       = {Van Geit, Werner and Tuncel, Anil and Gevaert, Mike and Torben-Nielsen, Benjamin and Muller, Eilif},
+      author       = {Tuncel, Anil and Van Geit, Werner and Gevaert, Mike and Torben-Nielsen, Benjamin and Mandge, Darshan and Kilic, Ilkan and Jaquier, Aurélien and Muller, Eilif and Kanari, Lida and Markram, Henry},
       title        = {BlueCelluLab},
       month        = jul,
       year         = 2023,
@@ -129,7 +129,7 @@ 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
 
 This work is licensed under `Apache 2.0 <https://www.apache.org/licenses/LICENSE-2.0.html>`_
 

{bluecellulab-2.6.28 → bluecellulab-2.6.30}/bluecellulab/cell/cell_dict.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/cell/core.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/cell/injector.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/cell/plotting.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/cell/random.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/cell/section_distance.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/cell/serialized_sections.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/cell/sonata_proxy.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/cell/stimuli_generator.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/cell/template.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/circuit/circuit_access/bluepy_circuit_access.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/circuit/circuit_access/definition.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/circuit/circuit_access/sonata_circuit_access.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/circuit/config/bluepy_simulation_config.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/circuit/config/definition.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/circuit/config/sections.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/circuit/config/sonata_simulation_config.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/circuit/format.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/circuit/iotools.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/circuit/node_id.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/circuit/simulation_access.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/circuit/synapse_properties.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/circuit/validate.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/circuit_simulation.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/connection.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/dendrogram.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/exceptions.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/importer.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/neuron_interpreter.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/plotwindow.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/psection.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/psegment.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/rngsettings.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/simulation/neuron_globals.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/simulation/simulation.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-2.6.28 → bluecellulab-2.6.30}/bluecellulab/stimulus/circuit_stimulus_definitions.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-2.6.28 → bluecellulab-2.6.30}/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.

{bluecellulab-2.6.28 → bluecellulab-2.6.30}/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-2.6.28 → bluecellulab-2.6.30}/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.

{bluecellulab-2.6.28 → bluecellulab-2.6.30}/bluecellulab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.6.28
+Version: 2.6.30
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0
@@ -73,7 +73,7 @@ When you use this BlueCelluLab software for your research, we ask you to cite th
 .. code-block::
 
     @software{bluecellulab_zenodo,
-      author       = {Van Geit, Werner and Tuncel, Anil and Gevaert, Mike and Torben-Nielsen, Benjamin and Muller, Eilif},
+      author       = {Tuncel, Anil and Van Geit, Werner and Gevaert, Mike and Torben-Nielsen, Benjamin and Mandge, Darshan and Kilic, Ilkan and Jaquier, Aurélien and Muller, Eilif and Kanari, Lida and Markram, Henry},
       title        = {BlueCelluLab},
       month        = jul,
       year         = 2023,
@@ -159,7 +159,7 @@ 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
 
 This work is licensed under `Apache 2.0 <https://www.apache.org/licenses/LICENSE-2.0.html>`_
 

bluecellulab-2.6.30/bluecellulab.egg-info/SOURCES.txt

@@ -0,0 +1,101 @@
+.compile_mod.sh
+.gitattributes
+.gitignore
+.gitlab-ci.yml
+.readthedocs.yml
+.zenodo.json
+AUTHORS.txt
+CHANGELOG.rst
+CITATION.cff
+CONTRIBUTING.rst
+LICENSE
+MANIFEST.in
+Makefile
+README.rst
+pyproject.toml
+tox.ini
+.github/dependabot.yml
+.github/workflows/release.yml
+.github/workflows/test.yml
+bluecellulab/__init__.py
+bluecellulab/circuit_simulation.py
+bluecellulab/connection.py
+bluecellulab/dendrogram.py
+bluecellulab/exceptions.py
+bluecellulab/graph.py
+bluecellulab/importer.py
+bluecellulab/neuron_interpreter.py
+bluecellulab/plotwindow.py
+bluecellulab/psection.py
+bluecellulab/psegment.py
+bluecellulab/rngsettings.py
+bluecellulab/tools.py
+bluecellulab/type_aliases.py
+bluecellulab/utils.py
+bluecellulab/verbosity.py
+bluecellulab.egg-info/PKG-INFO
+bluecellulab.egg-info/SOURCES.txt
+bluecellulab.egg-info/dependency_links.txt
+bluecellulab.egg-info/requires.txt
+bluecellulab.egg-info/top_level.txt
+bluecellulab/analysis/__init__.py
+bluecellulab/analysis/inject_sequence.py
+bluecellulab/cell/__init__.py
+bluecellulab/cell/cell_dict.py
+bluecellulab/cell/core.py
+bluecellulab/cell/injector.py
+bluecellulab/cell/plotting.py
+bluecellulab/cell/random.py
+bluecellulab/cell/recording.py
+bluecellulab/cell/section_distance.py
+bluecellulab/cell/serialized_sections.py
+bluecellulab/cell/sonata_proxy.py
+bluecellulab/cell/stimuli_generator.py
+bluecellulab/cell/template.py
+bluecellulab/cell/ballstick/__init__.py
+bluecellulab/cell/ballstick/emodel.hoc
+bluecellulab/cell/ballstick/morphology.asc
+bluecellulab/circuit/__init__.py
+bluecellulab/circuit/format.py
+bluecellulab/circuit/iotools.py
+bluecellulab/circuit/node_id.py
+bluecellulab/circuit/simulation_access.py
+bluecellulab/circuit/synapse_properties.py
+bluecellulab/circuit/validate.py
+bluecellulab/circuit/circuit_access/__init__.py
+bluecellulab/circuit/circuit_access/bluepy_circuit_access.py
+bluecellulab/circuit/circuit_access/definition.py
+bluecellulab/circuit/circuit_access/sonata_circuit_access.py
+bluecellulab/circuit/config/__init__.py
+bluecellulab/circuit/config/bluepy_simulation_config.py
+bluecellulab/circuit/config/definition.py
+bluecellulab/circuit/config/sections.py
+bluecellulab/circuit/config/sonata_simulation_config.py
+bluecellulab/hoc/Cell.hoc
+bluecellulab/hoc/RNGSettings.hoc
+bluecellulab/hoc/TDistFunc.hoc
+bluecellulab/hoc/TStim.hoc
+bluecellulab/hoc/fileUtils.hoc
+bluecellulab/simulation/__init__.py
+bluecellulab/simulation/neuron_globals.py
+bluecellulab/simulation/parallel.py
+bluecellulab/simulation/simulation.py
+bluecellulab/stimulus/__init__.py
+bluecellulab/stimulus/circuit_stimulus_definitions.py
+bluecellulab/stimulus/factory.py
+bluecellulab/synapse/__init__.py
+bluecellulab/synapse/synapse_factory.py
+bluecellulab/synapse/synapse_types.py
+docs/Makefile
+docs/make.bat
+docs/requirements_docs.txt
+docs/images/voltage-readme.png
+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
+docs/source/logo/BlueCelluLabBanner.jpg

{bluecellulab-2.6.28 → bluecellulab-2.6.30}/tox.ini

@@ -27,7 +27,7 @@ setenv =
 commands =
     make clean
     ./.compile_mod.sh . tests/mechanisms
-    pytest {[testenv]coverage_options} tests --numprocesses=auto --timeout=600 -vsx --forked
+    pytest {[testenv]coverage_options} tests --ignore=tests/bluecellulab-bb5-tests/ --numprocesses=auto --timeout=600 -vsx --forked
     coverage report --show-missing
     coverage xml
 

bluecellulab-2.6.28/bluecellulab-bb5-tests/.compile_mod.sh

@@ -1,26 +0,0 @@
-#!/bin/sh
-
-# Copyright 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.
-# You may obtain a copy of the License at
-
-#     http://www.apache.org/licenses/LICENSE-2.0
-
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-set -e
-
-INSTALL_DIR=$1
-MOD_DIR=$2
-
-cd ${INSTALL_DIR}
-
-echo "Building mod files"
-rm -rf x86_64
-nrnivmodl ${MOD_DIR} >nrnivmodl.log 2>&1

bluecellulab-2.6.28/bluecellulab-bb5-tests/.gitignore

@@ -1,11 +0,0 @@
-*.nrndat
-bin
-lib
-share
-.pytest_cache
-.tox-info.json
-.tox
-.neurodamus
-__pycache__
-x86_64
-nrnivmodl.log

bluecellulab-2.6.28/bluecellulab-bb5-tests/Makefile

@@ -1,26 +0,0 @@
-# Variables
-PIP_INDEX_URL := https://pypi.python.org/simple
-NEURON_MODULE_OPTIONS := '-nogui'
-TESTS_DIR := tests
-MECHANISMS_DIR := ./../tests/mechanisms/
-PYTEST_OPTS := --numprocesses=auto --timeout=600 -vsx --forked
-
-# Default rule (similar to 'testenv' in tox)
-default: install_deps compile_mod run_lint run_tests
-
-# Rule for installing dependencies (similar to 'deps' in tox)
-install_deps:
-	python -m pip install --index-url $(PIP_INDEX_URL) -r test_requirements.txt
-
-# Rule for compiling mod (similar to the first 'commands' in tox)
-compile_mod:
-	chmod +x ./.compile_mod.sh
-	./.compile_mod.sh . $(MECHANISMS_DIR)
-
-# Rule for running tests (similar to the second 'commands' in tox)
-run_tests:
-	NEURON_MODULE_OPTIONS=$(NEURON_MODULE_OPTIONS) pytest $(TESTS_DIR) $(PYTEST_OPTS)
-
-run_lint:
-	ruff check $(TESTS_DIR)
-	mypy $(TESTS_DIR) --ignore-missing-imports

bluecellulab-2.6.28/bluecellulab-bb5-tests/README.md

@@ -1,60 +0,0 @@
-# bluecellulab-bb5-tests
-
-## Description
-
-This folder contains tests for bluecellulab on the large circuits located on bb5. Please note that these tests are not directly usable as they are, due to dependencies.
-
-## How to run locally
-
-Simply clone the repository, install tox and type `tox` in the root directory of the repository.
-
-## Continous Integration
-
-This module will continue to be part of the continuous integration (CI) pipeline on GitLab until the end of the year. The scheduled CI tasks will run the tests for this module periodically until 2024.12.31. After this date, the tests will no longer be included in the CI pipeline.
-
-## Mechanisms
-
-The mechanisms for these tests have been merged into the [tests/mechanisms/](./../tests/mechanisms/) folder. Here is the list of mechanisms used for these tests. The original list is provided below, and files marked with an asterisk (*) were added to the tests folder as they were not already present:
-- `Ca.mod`
-- `CaDynamics_DC0.mod`
-- `CaDynamics_E2.mod`
-- `Ca_HVA.mod`
-- `Ca_HVA2.mod`
-- `Ca_LVAst.mod`
-- `DetAMPANMDA.mod`
-- `DetGABAAB.mod`
-- `GluSynapse.mod`
-- *`IN_Ih_Halnes2011.mod`
-- *`IN_iT.mod`
-- `Ih.mod`
-- `Im.mod`
-- `K_Pst.mod`
-- `K_Tst.mod`
-- `KdShu2007.mod`
-- `NaTa_t.mod`
-- `NaTg.mod`
-- `NaTs2_t.mod`
-- `Nap_Et2.mod`
-- `ProbAMPANMDA_EMS.mod`
-- `ProbGABAAB_EMS.mod`
-- *`RC_IT_Des92.mod`
-- `SK_E2.mod`
-- `SKv3_1.mod`
-- `StochKv.mod`
-- `StochKv3.mod`
-- *`TC_HH.mod`
-- *`TC_ITGHK_Des98.mod`
-- *`TC_Ih_Bud97.mod`
-- *`TC_Ih_CaMod.mod`
-- *`TC_Kleak.mod`
-- *`TC_Naleak.mod`
-- *`TC_Nap_Et2.mod`
-- *`TC_cadecay.mod`
-- *`TC_iA.mod`
-- *`TC_iL.mod`
-- *`TC_kir_Con15.mod`
-- `TTXDynamicsSwitch.mod`
-- `VecStim.mod`
-- `gap.mod`
-- *`ican.mod`
-- `netstim_inhpoisson.mod`