bluecellulab 2.3.1__tar.gz → 2.3.2__tar.gz

{bluecellulab-2.3.1 → bluecellulab-2.3.2}/.github/workflows/release.yml

@@ -8,6 +8,8 @@ on:
 jobs:
   call-test-workflow:
     uses: BlueBrain/BlueCelluLab/.github/workflows/test.yml@main
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   build-and-publish:
     name: Build, publish on PyPI and make a GitHub release

{bluecellulab-2.3.1 → bluecellulab-2.3.2}/.github/workflows/test.yml

@@ -4,7 +4,10 @@ on:
     pull_request:
     # allows this workflow to be reusable (e.g. by the build workflow)
     workflow_call:
-
+      secrets:
+        CODECOV_TOKEN:
+          description: The token to upload coverage to codecov
+          required: true
 
 jobs:
   tests:

{bluecellulab-2.3.1 → bluecellulab-2.3.2}/CHANGELOG.rst

@@ -1,6 +1,16 @@
 Changelog
 ==========
 
+2.4.0
+------
+
+* Add StimulusFactory enabling Python generated Stimulus creation
+* Stimulus creation through StimulusFactory is decoupled from the Cell object
+* Cell.add_step and Cell.add_ramp use StimulusFactory
+* Move stimuli module to stimulus/circuit_stimulus_definitions
+* [DOCS] Add list of stimuli page that describe, generate and plot the stimuli
+* Add jupyter notebook displaying how to inject the StimulusFactory Stimulus into Cell
+
 2.3.0
 -------
 

{bluecellulab-2.3.1 → bluecellulab-2.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.3.1
+Version: 2.3.2
 Summary: The Pythonic Blue Brain simulator access
 Home-page: https://github.com/BlueBrain/BlueCelluLab
 Author: Blue Brain Project, EPFL

{bluecellulab-2.3.1 → bluecellulab-2.3.2}/bluecellulab/cell/core.py

@@ -41,7 +41,7 @@ from bluecellulab.exceptions import BluecellulabError
 from bluecellulab.importer import load_hoc_and_mod_files
 from bluecellulab.neuron_interpreter import eval_neuron
 from bluecellulab.rngsettings import RNGSettings
-from bluecellulab.stimuli import SynapseReplay
+from bluecellulab.stimulus.circuit_stimulus_definitions import SynapseReplay
 from bluecellulab.synapse import SynapseFactory, Synapse
 from bluecellulab.synapse.synapse_types import SynapseID
 from bluecellulab.type_aliases import HocObjectType, NeuronSection

{bluecellulab-2.3.1 → bluecellulab-2.3.2}/bluecellulab/cell/injector.py

@@ -12,7 +12,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """Contains injection functionality for the cell."""
-
+from __future__ import annotations
 import math
 import warnings
 import logging
@@ -27,7 +27,7 @@ from bluecellulab.cell.stimuli_generator import (
     get_relative_shotnoise_params,
 )
 from bluecellulab.exceptions import BluecellulabError
-from bluecellulab.stimuli import (
+from bluecellulab.stimulus.circuit_stimulus_definitions import (
     ClampMode,
     Hyperpolarizing,
     Noise,
@@ -36,7 +36,8 @@ from bluecellulab.stimuli import (
     RelativeOrnsteinUhlenbeck,
     RelativeShotNoise,
 )
-from bluecellulab.type_aliases import HocObjectType
+from bluecellulab.stimulus.factory import StimulusFactory
+from bluecellulab.type_aliases import NeuronSection
 
 
 logger = logging.getLogger(__name__)
@@ -69,36 +70,62 @@ class InjectableMixin:
         self.persistent.append(tstim)
         return tstim
 
-    def add_step(self, start_time, stop_time, level, section=None, segx=0.5):
-        """Add a step current injection."""
-        if section is None:
-            section = self.soma
-
-        tstim = neuron.h.TStim(segx, sec=section)
-        duration = stop_time - start_time
-        tstim.pulse(start_time, duration, level)
-        self.persistent.append(tstim)
-        return tstim
+    def add_step(
+        self,
+        start_time: float,
+        stop_time: float,
+        level: float,
+        section: NeuronSection | None = None,
+        segx: float = 0.5,
+        dt: float = 0.025
+    ) -> tuple[np.ndarray, np.ndarray]:
+        """Add a step current injection.
 
-    def add_ramp(self, start_time, stop_time, start_level, stop_level,
-                 section=None, segx=0.5):
-        """Add a ramp current injection."""
-        if section is None:
-            section = self.soma
+        Args:
+            start_time: Start time of the step injection in seconds.
+            stop_time: Stop time of the step injection in seconds.
+            level: Current level to inject in nanoamperes (nA).
+            section: The section to inject current into.
+                Defaults to the soma section.
+            segx: The fractional location within the section to inject.
+                Defaults to 0.5 (center of the section).
+
+        Returns:
+            Tuple of time and current data.
+        """
+        stim = StimulusFactory(dt=dt).step(start_time, stop_time, level)
+        t_content, i_content = stim.time, stim.current
+        self.inject_current_waveform(t_content, i_content, section, segx)
+        return (t_content, i_content)
 
-        tstim = neuron.h.TStim(segx, sec=section)
+    def add_ramp(
+        self,
+        start_time: float,
+        stop_time: float,
+        start_level: float,
+        stop_level: float,
+        section: NeuronSection | None = None,
+        segx: float = 0.5,
+        dt: float = 0.025
+    ) -> tuple[np.ndarray, np.ndarray]:
+        """Add a ramp current injection.
 
-        tstim.ramp(
-            0.0,
-            start_time,
-            start_level,
-            stop_level,
-            stop_time - start_time,
-            0.0,
-            0.0)
+        Args:
+            start_time: Start time of the ramp injection in seconds.
+            stop_time: Stop time of the ramp injection in seconds.
+            start_level: Current level at the start of the ramp in nanoamperes (nA).
+            stop_level: Current level at the end of the ramp in nanoamperes (nA).
+            section: The section to inject current into (optional). Defaults to soma.
+            segx: The fractional location within the section to inject (optional).
+
+        Returns:
+            A tuple of numpy arrays containing time and current data.
+        """
+        stim = StimulusFactory(dt=dt).ramp(start_time, stop_time, start_level, stop_level)
+        t_content, i_content = stim.time, stim.current
+        self.inject_current_waveform(t_content, i_content, section, segx)
 
-        self.persistent.append(tstim)
-        return tstim
+        return t_content, i_content
 
     def add_voltage_clamp(
             self, stop_time, level, rs=None, section=None, segx=0.5,
@@ -395,32 +422,22 @@ class InjectableMixin:
         else:
             return self.inject_current_clamp_signal(section, segx, tvec, svec)
 
-    def inject_current_waveform(self, t_content, i_content, section=None,
-                                segx=0.5):
-        """Inject a custom current to the cell."""
-        start_time = t_content[0]
-        stop_time = t_content[-1]
-        time = neuron.h.Vector()
-        currents = neuron.h.Vector()
-        time = time.from_python(t_content)
-        currents = currents.from_python(i_content)
-
+    def inject_current_waveform(self, t_content, i_content, section=None, segx=0.5):
+        """Inject a custom current waveform into the cell."""
         if section is None:
             section = self.soma
+
+        time_vector = neuron.h.Vector().from_python(t_content)
+        current_vector = neuron.h.Vector().from_python(i_content)
+
         pulse = neuron.h.IClamp(segx, sec=section)
-        self.persistent.append(pulse)
-        self.persistent.append(time)
-        self.persistent.append(currents)
-        setattr(pulse, 'del', start_time)
-        pulse.dur = stop_time - start_time
-        currents.play(pulse._ref_amp, time)
-        return currents
-
-    @deprecated("Use inject_current_waveform instead.")
-    def injectCurrentWaveform(self, t_content, i_content, section=None,
-                              segx=0.5):
-        """Inject a current in the cell."""
-        return self.inject_current_waveform(t_content, i_content, section, segx)
+        self.persistent.extend([pulse, time_vector, current_vector])
+
+        pulse.delay = t_content[0]
+        pulse.dur = t_content[-1] - t_content[0]
+        current_vector.play(pulse._ref_amp, time_vector)
+
+        return current_vector
 
     @deprecated("Use add_sin_current instead.")
     def addSineCurrentInject(self, start_time, stop_time, freq,
@@ -435,7 +452,7 @@ class InjectableMixin:
         t_content = np.arange(start_time, stop_time, dt)
         i_content = [amplitude * math.sin(freq * (x - start_time) * (
             2 * math.pi)) + mid_level for x in t_content]
-        self.injectCurrentWaveform(t_content, i_content)
+        self.inject_current_waveform(t_content, i_content)
         return (t_content, i_content)
 
     def add_sin_current(self, amp, start_time, duration, frequency,
@@ -454,9 +471,9 @@ class InjectableMixin:
         tau: float,
         gmax: float,
         e: float,
-        section: HocObjectType,
+        section: NeuronSection,
         segx=0.5,
-    ) -> HocObjectType:
+    ) -> NeuronSection:
         """Add an AlphaSynapse NEURON point process stimulus to the cell."""
         syn = neuron.h.AlphaSynapse(segx, sec=section)
         syn.onset = onset

{bluecellulab-2.3.1 → bluecellulab-2.3.2}/bluecellulab/circuit/config/bluepy_simulation_config.py

@@ -25,7 +25,7 @@ if BLUEPY_AVAILABLE:
     from bluepy.utils import open_utf8
 
 from bluecellulab.circuit.config.sections import Conditions, ConnectionOverrides
-from bluecellulab.stimuli import Stimulus
+from bluecellulab.stimulus.circuit_stimulus_definitions import Stimulus
 
 
 class BluepySimulationConfig:

{bluecellulab-2.3.1 → bluecellulab-2.3.2}/bluecellulab/circuit/config/definition.py

@@ -18,7 +18,7 @@ from typing import Optional, Protocol
 
 
 from bluecellulab.circuit.config.sections import Conditions, ConnectionOverrides
-from bluecellulab.stimuli import Stimulus
+from bluecellulab.stimulus.circuit_stimulus_definitions import Stimulus
 
 
 class SimulationConfig(Protocol):

{bluecellulab-2.3.1 → bluecellulab-2.3.2}/bluecellulab/circuit/config/sonata_simulation_config.py

@@ -17,7 +17,7 @@ from pathlib import Path
 from typing import Optional
 
 from bluecellulab.circuit.config.sections import Conditions, ConnectionOverrides
-from bluecellulab.stimuli import Stimulus
+from bluecellulab.stimulus.circuit_stimulus_definitions import Stimulus
 
 from bluepysnap import Simulation as SnapSimulation
 

{bluecellulab-2.3.1 → bluecellulab-2.3.2}/bluecellulab/ssim.py

@@ -40,8 +40,8 @@ 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.stimuli import Noise, OrnsteinUhlenbeck, RelativeOrnsteinUhlenbeck, RelativeShotNoise, ShotNoise
-import bluecellulab.stimuli as stimuli
+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,
@@ -298,40 +298,40 @@ class SSim:
             for cell_id in self.cells:
                 if cell_id not in gids_of_target:
                     continue
-                if isinstance(stimulus, stimuli.Noise):
+                if isinstance(stimulus, circuit_stimulus_definitions.Noise):
                     if add_noise_stimuli:
                         self.cells[cell_id].add_replay_noise(
                             stimulus, noisestim_count=noisestim_count)
-                elif isinstance(stimulus, stimuli.Hyperpolarizing):
+                elif isinstance(stimulus, circuit_stimulus_definitions.Hyperpolarizing):
                     if add_hyperpolarizing_stimuli:
                         self.cells[cell_id].add_replay_hypamp(stimulus)
-                elif isinstance(stimulus, stimuli.Pulse):
+                elif isinstance(stimulus, circuit_stimulus_definitions.Pulse):
                     if add_pulse_stimuli:
                         self.cells[cell_id].add_pulse(stimulus)
-                elif isinstance(stimulus, stimuli.RelativeLinear):
+                elif isinstance(stimulus, circuit_stimulus_definitions.RelativeLinear):
                     if add_relativelinear_stimuli:
                         self.cells[cell_id].add_replay_relativelinear(stimulus)
-                elif isinstance(stimulus, stimuli.ShotNoise):
+                elif isinstance(stimulus, circuit_stimulus_definitions.ShotNoise):
                     if add_shotnoise_stimuli:
                         self.cells[cell_id].add_replay_shotnoise(
                             self.cells[cell_id].soma, 0.5, stimulus,
                             shotnoise_stim_count=shotnoise_stim_count)
-                elif isinstance(stimulus, stimuli.RelativeShotNoise):
+                elif isinstance(stimulus, circuit_stimulus_definitions.RelativeShotNoise):
                     if add_shotnoise_stimuli:
                         self.cells[cell_id].add_replay_relative_shotnoise(
                             self.cells[cell_id].soma, 0.5, stimulus,
                             shotnoise_stim_count=shotnoise_stim_count)
-                elif isinstance(stimulus, stimuli.OrnsteinUhlenbeck):
+                elif isinstance(stimulus, circuit_stimulus_definitions.OrnsteinUhlenbeck):
                     if add_ornstein_uhlenbeck_stimuli:
                         self.cells[cell_id].add_ornstein_uhlenbeck(
                             self.cells[cell_id].soma, 0.5, stimulus,
                             stim_count=ornstein_uhlenbeck_stim_count)
-                elif isinstance(stimulus, stimuli.RelativeOrnsteinUhlenbeck):
+                elif isinstance(stimulus, circuit_stimulus_definitions.RelativeOrnsteinUhlenbeck):
                     if add_ornstein_uhlenbeck_stimuli:
                         self.cells[cell_id].add_relative_ornstein_uhlenbeck(
                             self.cells[cell_id].soma, 0.5, stimulus,
                             stim_count=ornstein_uhlenbeck_stim_count)
-                elif isinstance(stimulus, stimuli.SynapseReplay):  # sonata only
+                elif isinstance(stimulus, circuit_stimulus_definitions.SynapseReplay):  # sonata only
                     if self.circuit_access.target_contains_cell(
                         stimulus.target, cell_id
                     ):

bluecellulab-2.3.2/bluecellulab/stimulus/__init__.py

@@ -0,0 +1 @@
+from .factory import StimulusFactory

bluecellulab-2.3.1/bluecellulab/stimuli.py → bluecellulab-2.3.2/bluecellulab/stimulus/circuit_stimulus_definitions.py

@@ -11,7 +11,11 @@
 # 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.
+"""Defines the expected data structures associated with the stimulus defined in
+simulation configs.
 
+Run-time validates the data via Pydantic.
+"""
 from __future__ import annotations
 
 from enum import Enum

bluecellulab-2.3.2/bluecellulab/stimulus/factory.py

@@ -0,0 +1,254 @@
+from __future__ import annotations
+from abc import ABC, abstractmethod
+import matplotlib.pyplot as plt
+import numpy as np
+
+
+class Stimulus(ABC):
+    def __init__(self, dt: float) -> None:
+        self.dt = dt
+
+    @property
+    @abstractmethod
+    def time(self) -> np.ndarray:
+        """Time values of the stimulus."""
+        ...
+
+    @property
+    @abstractmethod
+    def current(self) -> np.ndarray:
+        """Current values of the stimulus."""
+        ...
+
+    def __len__(self) -> int:
+        return len(self.time)
+
+    @property
+    def stimulus_time(self) -> float:
+        return len(self) * self.dt
+
+    def __repr__(self) -> str:
+        return f"{self.__class__.__name__}(dt={self.dt})"
+
+    def plot(self, ax=None, **kwargs):
+        if ax is None:
+            ax = plt.gca()
+        ax.plot(self.time, self.current, **kwargs)
+        ax.set_xlabel("Time (ms)")
+        ax.set_ylabel("Current (nA)")
+        ax.set_title(self.__class__.__name__)
+        return ax
+
+    def plot_during_simulation(self, duration: float, ax=None, **kwargs):
+        if ax is None:
+            ax = plt.gca()
+        # Create an array for the entire duration
+        full_time = np.arange(0, duration, self.dt)
+        full_current = np.zeros_like(full_time)
+
+        # Replace the corresponding values with self.time and self.current
+        indices = (self.time / self.dt).astype(int)
+        full_current[indices] = self.current
+
+        ax.plot(full_time, full_current, **kwargs)
+        ax.set_xlabel("Time (ms)")
+        ax.set_ylabel("Current (nA)")
+        ax.set_title(self.__class__.__name__)
+        ax.set_xlim(0, duration)
+        return ax
+
+    def __add__(self, other: Stimulus) -> CombinedStimulus:
+        """Override + operator to concatenate Stimulus objects."""
+        if self.dt != other.dt:
+            raise ValueError("Stimulus objects must have the same dt to be concatenated")
+        # shift other time
+        other_time = other.time + self.time[-1] + self.dt
+        combined_time = np.concatenate([self.time, other_time])
+        # Concatenate the current arrays
+        combined_current = np.concatenate([self.current, other.current])
+        return CombinedStimulus(self.dt, combined_time, combined_current)
+
+
+class CombinedStimulus(Stimulus):
+    """Represents the Stimulus created by combining multiple stimuli."""
+    def __init__(self, dt: float, time: np.ndarray, current: np.ndarray) -> None:
+        super().__init__(dt)
+        self._time = time
+        self._current = current
+
+    @property
+    def time(self) -> np.ndarray:
+        return self._time
+
+    @property
+    def current(self) -> np.ndarray:
+        return self._current
+
+
+class EmptyStimulus(Stimulus):
+    """Represents empty stimulus (all zeros) that has no impact on the cell.
+
+    This is required by some Stimuli that expect the cell to rest.
+    """
+    def __init__(self, dt: float, duration: float) -> None:
+        super().__init__(dt)
+        self.duration = duration
+
+    @property
+    def time(self) -> np.ndarray:
+        return np.arange(0.0, self.duration, self.dt)
+
+    @property
+    def current(self) -> np.ndarray:
+        return np.zeros_like(self.time)
+
+
+class Step(Stimulus):
+    def __init__(self, dt: float, start: float, end: float, amplitude: float) -> None:
+        super().__init__(dt)
+        self.start = start
+        self.end = end
+        self.amplitude = amplitude
+
+    @classmethod
+    def threshold_based(
+        cls,
+        dt: float,
+        threshold_current: float,
+        threshold_percentage: float,
+        start: float,
+        end: float,
+        post_wait: float,
+    ) -> CombinedStimulus:
+        amplitude = threshold_current * threshold_percentage / 100
+        res = cls(dt, start, end, amplitude) + EmptyStimulus(dt, duration=post_wait)
+        return res
+
+    @property
+    def time(self) -> np.ndarray:
+        return np.arange(self.start, self.end, self.dt)
+
+    @property
+    def current(self) -> np.ndarray:
+        return np.full_like(self.time, self.amplitude)
+
+
+class Ramp(Stimulus):
+    def __init__(
+        self,
+        dt: float,
+        start: float,
+        end: float,
+        amplitude_start: float,
+        amplitude_end: float,
+    ) -> None:
+        super().__init__(dt)
+        self.start = start
+        self.end = end
+        self.amplitude_start = amplitude_start
+        self.amplitude_end = amplitude_end
+
+    @property
+    def time(self) -> np.ndarray:
+        return np.arange(self.start, self.end, self.dt)
+
+    @property
+    def current(self) -> np.ndarray:
+        return np.linspace(self.amplitude_start, self.amplitude_end, len(self.time))
+
+
+class StimulusFactory:
+    def __init__(self, dt: float):
+        self.dt = dt
+
+    def step(self, start: float, end: float, amplitude: float) -> Stimulus:
+        return Step(self.dt, start, end, amplitude)
+
+    def ramp(
+        self, start: float, end: float, amplitude_start: float, amplitude_end: float
+    ) -> Stimulus:
+        return Ramp(self.dt, start, end, amplitude_start, amplitude_end)
+
+    def ap_waveform(
+        self,
+        threshold_current: float,
+        threshold_percentage: float = 220.0,
+        start: float = 250.0,
+        end: float = 300.0,
+        post_wait: float = 250.0,
+    ) -> Stimulus:
+        """Returns the APWaveform Stimulus object, a type of Step stimulus.
+
+        Args:
+            threshold_current: The threshold current of the Cell.
+            threshold_percentage: Percentage of desired threshold_current amplification.
+            start: The start time of the step.
+            end: The end time of the step.
+            post_wait: The time to wait after the end of the step.
+        """
+        return Step.threshold_based(
+            self.dt, threshold_current, threshold_percentage, start, end, post_wait
+        )
+
+    def idrest(
+        self,
+        threshold_current: float,
+        threshold_percentage: float = 200.0,
+        start: float = 250.0,
+        end: float = 1600.0,
+        post_wait: float = 250.0,
+    ) -> Stimulus:
+        """Returns the IDRest Stimulus object, a type of Step stimulus.
+
+        Args:
+            threshold_current: The threshold current of the Cell.
+            threshold_percentage: Percentage of desired threshold_current amplification.
+            start: The start time of the step.
+            end: The end time of the step.
+            post_wait: The time to wait after the end of the step.
+        """
+        return Step.threshold_based(
+            self.dt, threshold_current, threshold_percentage, start, end, post_wait
+        )
+
+    def iv(
+        self,
+        threshold_current: float,
+        threshold_percentage: float = -40.0,
+        start: float = 250.0,
+        end: float = 3250.0,
+        post_wait: float = 250.0,
+    ) -> Stimulus:
+        """Returns the IV Stimulus object, a type of Step stimulus.
+
+        Args:
+            threshold_current: The threshold current of the Cell.
+            threshold_percentage: Percentage of desired threshold_current amplification.
+            start: The start time of the step.
+            end: The end time of the step.
+            post_wait: The time to wait after the end of the step.
+        """
+        return Step.threshold_based(
+            self.dt, threshold_current, threshold_percentage, start, end, post_wait
+        )
+
+    def fire_pattern(
+        self,
+        threshold_current: float,
+        threshold_percentage: float = 200.0,
+        start: float = 250.0,
+        end: float = 3850.0,
+        post_wait: float = 250.0,
+    ) -> Stimulus:
+        """Returns the FirePattern Stimulus object, a type of Step stimulus.
+
+        Args:
+            threshold_current: The threshold current of the Cell.
+            threshold_percentage: Percentage of desired threshold_current amplification.
+            start: The start time of the step.
+            end: The end time of the step.
+            post_wait: The time to wait after the end of the step.
+        """
+        return Step.threshold_based(
+            self.dt, threshold_current, threshold_percentage, start, end, post_wait
+        )

{bluecellulab-2.3.1 → bluecellulab-2.3.2}/bluecellulab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.3.1
+Version: 2.3.2
 Summary: The Pythonic Blue Brain simulator access
 Home-page: https://github.com/BlueBrain/BlueCelluLab
 Author: Blue Brain Project, EPFL

{bluecellulab-2.3.1 → bluecellulab-2.3.2}/bluecellulab.egg-info/SOURCES.txt

@@ -28,7 +28,6 @@ bluecellulab/psection.py
 bluecellulab/psegment.py
 bluecellulab/rngsettings.py
 bluecellulab/ssim.py
-bluecellulab/stimuli.py
 bluecellulab/tools.py
 bluecellulab/type_aliases.py
 bluecellulab/utils.py
@@ -75,6 +74,9 @@ bluecellulab/hoc/fileUtils.hoc
 bluecellulab/simulation/__init__.py
 bluecellulab/simulation/neuron_globals.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
@@ -87,6 +89,7 @@ docs/source/changelog.rst
 docs/source/compiling-mechanisms.rst
 docs/source/conf.py
 docs/source/index.rst
+docs/source/list_of_stim.rst
 docs/source/_static/.gitkeep
 docs/source/logo/BlueCelluLabBanner.jpg
 examples/README.rst
@@ -155,6 +158,7 @@ examples/4-epsp/hippocampus_mechanisms/kmb.mod
 examples/4-epsp/hippocampus_mechanisms/na3n.mod
 examples/4-epsp/hoc/cell_seed2_0.hoc
 examples/4-epsp/morphology/011017HP2.asc
+examples/5-stimuli/stimuli.ipynb
 examples/mechanisms/Ca.mod
 examples/mechanisms/CaDynamics_DC0.mod
 examples/mechanisms/CaDynamics_E2.mod
@@ -196,7 +200,6 @@ tests/test_psection.py
 tests/test_rngsettings.py
 tests/test_ssim.py
 tests/test_ssim_sonata.py
-tests/test_stimuli.py
 tests/test_tools.py
 tests/test_ttx.py
 tests/test_utils.py
@@ -410,6 +413,9 @@ tests/test_circuit/test_validate.py
 tests/test_simulation/__init__.py
 tests/test_simulation/test_neuron_globals.py
 tests/test_simulation/test_simulation.py
+tests/test_stimulus/__init__.py
+tests/test_stimulus/test_circuit_stimulus_definitions.py
+tests/test_stimulus/test_factory.py
 tests/test_synapse/__init__.py
 tests/test_synapse/test-synapse-series.json
 tests/test_synapse/test_synapse.py

{bluecellulab-2.3.1 → bluecellulab-2.3.2}/docs/requirements_docs.txt

@@ -1,3 +1,4 @@
 sphinx>=7.0.1
 sphinx-bluebrain-theme>=0.4.1
 sphinx_autodoc_typehints>=1.23.2
+seaborn>=0.13.2