bluecellulab 2.4.1__tar.gz → 2.5.3__tar.gz

{bluecellulab-2.4.1 → bluecellulab-2.5.3}/.github/workflows/release.yml

@@ -36,8 +36,8 @@ jobs:
 
       - name: Build a source tarball and wheel
         run: |
-            pip install wheel
-            python setup.py sdist bdist_wheel
+            pip install build
+            python -m build --sdist --wheel .
 
       - name: Get and store tag from 'Bump version and push tag' step
         if: ${{ !startsWith(github.ref, 'refs/tags/') }}

{bluecellulab-2.4.1 → bluecellulab-2.5.3}/CHANGELOG.rst

@@ -1,6 +1,13 @@
 Changelog
 ==========
 
+2.5.0
+-----
+
+* Breaking Change: sim.run() no longer takes celsius and v_init
+* NeuronGlobals is added to control the global NEURON parameters such as celsius and v_init
+* removed use_random123_stochkv param from re_init_rng
+
 2.4.1
 ------
 

{bluecellulab-2.4.1 → bluecellulab-2.5.3}/Makefile

@@ -1,5 +1,7 @@
 clean:
 	rm -f .coverage
+	rm -f .coverage.*
+	rm -f *.coverage
 	rm -f coverage.xml
 	rm -f *.nrndat
 	rm -f .coverage.*

{bluecellulab-2.4.1 → bluecellulab-2.5.3}/PKG-INFO

@@ -1,11 +1,12 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.4.1
+Version: 2.5.3
 Summary: The Pythonic Blue Brain simulator access
-Home-page: https://github.com/BlueBrain/BlueCelluLab
 Author: Blue Brain Project, EPFL
 License: Apache2.0
-Keywords: computational neuroscience,simulation,analysis,parameters,Blue Brain Project
+Project-URL: Homepage, https://github.com/BlueBrain/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
@@ -17,6 +18,14 @@ Requires-Python: >=3.8
 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
 
 |banner|
 

{bluecellulab-2.4.1 → bluecellulab-2.5.3}/bluecellulab/__init__.py

@@ -8,9 +8,9 @@ except ImportError:
     BLUEPY_AVAILABLE = False
 
 from .importer import *  # NOQA
-from .tools import *  # NOQA
 from .verbosity import *
 from .cell import Cell, create_ball_stick  # NOQA
+from .circuit import EmodelProperties
 from .connection import Connection  # NOQA
 from .plotwindow import PlotWindow  # NOQA
 from .dendrogram import Dendrogram  # NOQA
@@ -19,3 +19,10 @@ from .psegment import PSegment  # NOQA
 from .simulation import Simulation  # NOQA
 from .rngsettings import RNGSettings  # NOQA
 from .ssim import SSim  # NOQA
+
+
+from .simulation.neuron_globals import NeuronGlobals
+
+logger.debug("Loading the hoc files.")
+import_hoc(neuron)
+_ = NeuronGlobals.get_instance()  # initiate the singleton

{bluecellulab-2.4.1 → bluecellulab-2.5.3}/bluecellulab/cell/core.py

@@ -39,7 +39,7 @@ from bluecellulab.circuit import EmodelProperties, SynapseProperty
 from bluecellulab.circuit.node_id import CellId
 from bluecellulab.circuit.simulation_access import get_synapse_replay_spikes
 from bluecellulab.exceptions import BluecellulabError
-from bluecellulab.importer import load_hoc_and_mod_files
+from bluecellulab.importer import load_mod_files
 from bluecellulab.neuron_interpreter import eval_neuron
 from bluecellulab.rngsettings import RNGSettings
 from bluecellulab.stimulus.circuit_stimulus_definitions import SynapseReplay
@@ -73,7 +73,7 @@ class Cell(InjectableMixin, PlottableMixin):
             emodel_properties=template_params.emodel_properties,
         )
 
-    @load_hoc_and_mod_files
+    @load_mod_files
     def __init__(self,
                  template_path: str | Path,
                  morphology_path: str | Path,
@@ -191,29 +191,10 @@ class Cell(InjectableMixin, PlottableMixin):
         """Connect this cell to a circuit via sonata proxy."""
         self.sonata_proxy = sonata_proxy
 
-    def re_init_rng(self, use_random123_stochkv: bool = False) -> None:
+    def re_init_rng(self) -> None:
         """Reinitialize the random number generator for stochastic channels."""
-
         if not self.is_made_passive:
-            if use_random123_stochkv:
-                channel_id = 0
-                for section in self.somatic:
-                    for seg in section:
-                        neuron.h.setdata_StochKv(seg.x, sec=section)
-                        neuron.h.setRNG_StochKv(channel_id, self.cell_id.id)
-                        channel_id += 1
-                for section in self.basal:
-                    for seg in section:
-                        neuron.h.setdata_StochKv(seg.x, sec=section)
-                        neuron.h.setRNG_StochKv(channel_id, self.cell_id.id)
-                        channel_id += 1
-                for section in self.apical:
-                    for seg in section:
-                        neuron.h.setdata_StochKv(seg.x, sec=section)
-                        neuron.h.setRNG_StochKv(channel_id, self.cell_id.id)
-                        channel_id += 1
-            else:
-                self.cell.re_init_rng()
+            self.cell.re_init_rng()
 
     def get_psection(self, section_id: int | str) -> PSection:
         """Return a python section with the specified section id."""

{bluecellulab-2.4.1 → bluecellulab-2.5.3}/bluecellulab/importer.py

@@ -52,8 +52,8 @@ def import_mod_lib(neuron: ModuleType) -> str:
     return res
 
 
-def import_neurodamus(neuron: ModuleType) -> None:
-    """Import neurodamus."""
+def import_hoc(neuron: ModuleType) -> None:
+    """Import hoc dependencies."""
     neuron.h.load_file("stdrun.hoc")  # nrn
     hoc_files = [
         "Cell.hoc",  # ND
@@ -75,17 +75,15 @@ def print_header(neuron: ModuleType, mod_lib_path: str) -> None:
 
 
 @run_once
-def _load_hoc_and_mod_files() -> None:
+def _load_mod_files() -> None:
     """Import hoc and mod files."""
     logger.debug("Loading the mod files.")
     mod_lib_paths = import_mod_lib(neuron)
-    logger.debug("Loading the hoc files.")
-    import_neurodamus(neuron)
     print_header(neuron, mod_lib_paths)
 
 
-def load_hoc_and_mod_files(func):
+def load_mod_files(func):
     def wrapper(*args, **kwargs):
-        _load_hoc_and_mod_files()
+        _load_mod_files()
         return func(*args, **kwargs)
     return wrapper

{bluecellulab-2.4.1 → bluecellulab-2.5.3}/bluecellulab/rngsettings.py

@@ -20,7 +20,7 @@ from typing import Optional
 import neuron
 from bluecellulab.circuit.config.definition import SimulationConfig
 from bluecellulab.exceptions import UndefinedRNGException
-from bluecellulab.importer import load_hoc_and_mod_files
+from bluecellulab.importer import load_mod_files
 
 logger = logging.getLogger(__name__)
 
@@ -37,7 +37,7 @@ class RNGSettings:
             cls._instance = cls()
         return cls._instance
 
-    @load_hoc_and_mod_files
+    @load_mod_files
     def __init__(
         self,
         mode="Random123",

{bluecellulab-2.4.1 → bluecellulab-2.5.3}/bluecellulab/simulation/__init__.py

@@ -3,4 +3,3 @@
 from .simulation import Simulation
 from .neuron_globals import set_global_condition_parameters
 from .neuron_globals import set_minis_single_vesicle_values
-from .neuron_globals import set_tstop_value

{bluecellulab-2.4.1 → bluecellulab-2.5.3}/bluecellulab/simulation/neuron_globals.py

@@ -62,6 +62,37 @@ def set_minis_single_vesicle_values(mech_conditions: MechanismConditions) -> Non
             )
 
 
-def set_tstop_value(tstop: float) -> None:
-    """Set the tstop value required by Tstim noise stimuli."""
-    neuron.h.tstop = tstop
+class NeuronGlobals:
+    _instance = None
+
+    def __init__(self):
+        raise RuntimeError('Call get_instance() instead')
+
+    @classmethod
+    def get_instance(cls):
+        if cls._instance is None:
+            cls._instance = cls.__new__(cls)
+            # Initialize default values
+            cls._instance._temperature = 34.0  # Default temperature
+            cls._instance.v_init = neuron.h.v_init
+            # Set the default values in NEURON
+            neuron.h.celsius = cls._instance._temperature
+        return cls._instance
+
+    @property
+    def temperature(self):
+        return self._temperature
+
+    @temperature.setter
+    def temperature(self, value):
+        self._temperature = value
+        neuron.h.celsius = value
+
+    @property
+    def v_init(self):
+        return self._v_init
+
+    @v_init.setter
+    def v_init(self, value):
+        self._v_init = value
+        neuron.h.v_init = value

{bluecellulab-2.4.1 → bluecellulab-2.5.3}/bluecellulab/simulation/simulation.py

@@ -88,13 +88,11 @@ class Simulation:
             cvode=True,
             cvode_minstep=None,
             cvode_maxstep=None,
-            celsius=34,
-            v_init=-65,
             dt=0.025,
             forward_skip=None,
             forward_skip_value=False,
-            show_progress=None,
-            use_random123_stochkv=False):
+            show_progress=None
+    ):
         """Run the simulation."""
         # if maxtime <= neuron.h.t:
         #     raise Exception("Simulation: need to provide a maxtime (=%f) "
@@ -108,7 +106,6 @@ class Simulation:
             self.progress_dt = maxtime / 100
             self.init_progress_callback()
 
-        neuron.h.celsius = celsius
         neuron.h.tstop = maxtime
 
         cvode_old_status = neuron.h.cvode_active()
@@ -125,11 +122,9 @@ class Simulation:
                                "was set")
             neuron.h.cvode_active(0)
 
-        neuron.h.v_init = v_init
-
         for cell in self.cells:
             with contextlib.suppress(AttributeError):
-                cell.re_init_rng(use_random123_stochkv=use_random123_stochkv)
+                cell.re_init_rng()
         neuron.h.dt = dt
         neuron.h.steps_per_ms = 1.0 / dt
 
@@ -176,6 +171,3 @@ class Simulation:
             neuron.h.cvode_active(cvode_old_status)
 
         logger.debug("Finished simulation.")
-
-    def __del__(self):
-        pass

{bluecellulab-2.4.1 → bluecellulab-2.5.3}/bluecellulab/ssim.py

@@ -39,14 +39,14 @@ from bluecellulab.circuit.config import SimulationConfig
 from bluecellulab.circuit.format import determine_circuit_format, CircuitFormat
 from bluecellulab.circuit.node_id import create_cell_id, create_cell_ids
 from bluecellulab.circuit.simulation_access import BluepySimulationAccess, SimulationAccess, SonataSimulationAccess, _sample_array
-from bluecellulab.importer import load_hoc_and_mod_files
+from bluecellulab.importer import load_mod_files
 from bluecellulab.rngsettings import RNGSettings
+from bluecellulab.simulation.neuron_globals import NeuronGlobals
 from bluecellulab.stimulus.circuit_stimulus_definitions import Noise, OrnsteinUhlenbeck, RelativeOrnsteinUhlenbeck, RelativeShotNoise, ShotNoise
 import bluecellulab.stimulus.circuit_stimulus_definitions as circuit_stimulus_definitions
 from bluecellulab.exceptions import BluecellulabError
 from bluecellulab.simulation import (
     set_global_condition_parameters,
-    set_tstop_value
 )
 from bluecellulab.synapse.synapse_types import SynapseID
 
@@ -56,7 +56,7 @@ logger = logging.getLogger(__name__)
 class SSim:
     """Class that loads a circuit simulation to do cell simulations."""
 
-    @load_hoc_and_mod_files
+    @load_mod_files
     def __init__(
         self,
         simulation_config: str | Path | SimulationConfig,
@@ -106,11 +106,6 @@ class SSim:
 
         self.gids_instantiated = False
 
-        # Make sure tstop is set correctly, because it is used by the
-        # TStim noise stimulus
-        if self.circuit_access.config.duration is not None:
-            set_tstop_value(self.circuit_access.config.duration)
-
         self.spike_threshold = self.circuit_access.config.spike_threshold
         self.spike_location = self.circuit_access.config.spike_location
 
@@ -596,8 +591,10 @@ class SSim:
             forward_skip_value = self.circuit_access.config.forward_skip
         if celsius is None:
             celsius = self.circuit_access.config.celsius
+            NeuronGlobals.get_instance().temperature = celsius
         if v_init is None:
             v_init = self.circuit_access.config.v_init
+            NeuronGlobals.get_instance().v_init = v_init
 
         sim = bluecellulab.Simulation(self.pc)
         for cell_id in self.cells:
@@ -612,8 +609,6 @@ class SSim:
             t_stop,
             cvode=cvode,
             dt=dt,
-            celsius=celsius,
-            v_init=v_init,
             forward_skip=forward_skip,
             forward_skip_value=forward_skip_value,
             show_progress=show_progress)

{bluecellulab-2.4.1 → bluecellulab-2.5.3}/bluecellulab/tools.py

@@ -60,6 +60,8 @@ def calculate_SS_voltage(
     template_format: str,
     emodel_properties: EmodelProperties | None,
     step_level: float,
+    check_for_spiking=False,
+    spike_threshold=-20.0,
 ) -> float:
     """Calculate the steady state voltage at a certain current step."""
     with IsolatedProcess() as runner:
@@ -71,6 +73,8 @@ def calculate_SS_voltage(
                 template_format,
                 emodel_properties,
                 step_level,
+                check_for_spiking,
+                spike_threshold,
             ],
         )
     return SS_voltage
@@ -82,8 +86,8 @@ def calculate_SS_voltage_subprocess(
     template_format: str,
     emodel_properties: EmodelProperties | None,
     step_level: float,
-    check_for_spiking=False,
-    spike_threshold=-20.0,
+    check_for_spiking: bool,
+    spike_threshold: float,
 ) -> float:
     """Subprocess wrapper of calculate_SS_voltage.
 

{bluecellulab-2.4.1 → bluecellulab-2.5.3}/bluecellulab.egg-info/PKG-INFO

@@ -1,11 +1,12 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.4.1
+Version: 2.5.3
 Summary: The Pythonic Blue Brain simulator access
-Home-page: https://github.com/BlueBrain/BlueCelluLab
 Author: Blue Brain Project, EPFL
 License: Apache2.0
-Keywords: computational neuroscience,simulation,analysis,parameters,Blue Brain Project
+Project-URL: Homepage, https://github.com/BlueBrain/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
@@ -17,6 +18,14 @@ Requires-Python: >=3.8
 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
 
 |banner|
 

{bluecellulab-2.4.1 → bluecellulab-2.5.3}/bluecellulab.egg-info/SOURCES.txt

@@ -11,7 +11,6 @@ MANIFEST.in
 Makefile
 README.rst
 pyproject.toml
-setup.py
 tox.ini
 .github/dependabot.yml
 .github/workflows/release.yml