bluecellulab 2.6.20__tar.gz → 2.6.22__tar.gz

bluecellulab-2.6.22/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-2.6.20 → bluecellulab-2.6.22}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.6.20
+Version: 2.6.22
 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-2.6.20 → bluecellulab-2.6.22}/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-2.6.20 → bluecellulab-2.6.22}/bluecellulab/cell/injector.py

@@ -360,17 +360,15 @@ class InjectableMixin:
             stimulus: RelativeShotNoise,
             shotnoise_stim_count=0):
         """Add a replay relative shot noise stimulus."""
-        cv_square = stimulus.amp_cv**2
 
         stim_mode = stimulus.mode
         rel_prop = self.relativity_proportion(stim_mode)
 
         mean = stimulus.mean_percent / 100 * rel_prop
         sd = stimulus.sd_percent / 100 * rel_prop
-        var = sd * sd
 
         rate, amp_mean, amp_var = get_relative_shotnoise_params(
-            mean, var, stimulus.decay_time, stimulus.rise_time, cv_square)
+            mean, sd, stimulus.decay_time, stimulus.rise_time, stimulus.relative_skew)
 
         rng = self._get_shotnoise_step_rand(shotnoise_stim_count, stimulus.seed)
         tvec, svec = gen_shotnoise_signal(stimulus.decay_time, stimulus.rise_time, rate, amp_mean,

{bluecellulab-2.6.20 → bluecellulab-2.6.22}/bluecellulab/cell/stimuli_generator.py

@@ -114,17 +114,35 @@ def gen_shotnoise_signal(tau_D, tau_R, rate, amp_mean, amp_var,
     return tvec, P
 
 
-def get_relative_shotnoise_params(mean, var, tau_D, tau_R, cv_square):
+def get_relative_shotnoise_params(mean, sd, tau_D, tau_R, relative_skew):
     """Returns Rate, amp_mean and amp_var parameters."""
     # bi-exponential time to peak [ms]
     t_peak = math.log(tau_D / tau_R) / (1 / tau_R - 1 / tau_D)
     # bi-exponential peak height [1]
-    x_peak = math.exp(-t_peak / tau_D) - math.exp(-t_peak / tau_R)
-
-    rate_ms = (1 + cv_square) / 2 * (mean ** 2 / var) / (tau_D + tau_R)
-    rate = rate_ms * 1000  # rate in 1 / s [Hz]
-    amp_mean = mean * x_peak / rate_ms / (tau_D - tau_R)
-    amp_var = cv_square * amp_mean ** 2
+    F_peak = math.exp(-t_peak / tau_D) - math.exp(-t_peak / tau_R)
+
+    # utility constants
+    Xi = (tau_D - tau_R) / F_peak
+    A = 1 / (tau_D + tau_R)
+    B = 1 / ((tau_D + 2 * tau_R) * (2 * tau_D + tau_R))
+
+    # skewness
+    skew_bnd_min = (8 / 3) * (B / A ** 2) * (sd / mean)
+    skew = (1 + relative_skew) * skew_bnd_min
+    if skew < skew_bnd_min or skew > 2 * skew_bnd_min:
+        raise ValueError("skewness out of bounds")
+
+    # cumulants
+    lambda2_1 = sd ** 2 / mean                     # lambda2 over lambda1
+    lambda3_2 = sd * skew                          # lambda3 over lambda2
+    theta1pk = 2 / (A * Xi) * lambda2_1            # = (1 + k) * theta
+    theta2pk = (3 * A) / (4 * B * Xi) * lambda3_2  # = (2 + k) * theta
+
+    # derived parameters
+    amp_mean = 2 * theta1pk - theta2pk               # mean amplitude [nA or uS]
+    amp_var = amp_mean * (theta2pk - theta1pk)  # variance of amplitude [nA^2 or uS^2]
+    rate_ms = mean / (amp_mean * Xi)                 # event rate in 1 / ms
+    rate = rate_ms * 1000                            # event rate in 1 / s [Hz]
 
     return rate, amp_mean, amp_var
 

{bluecellulab-2.6.20 → bluecellulab-2.6.22}/bluecellulab/stimulus/circuit_stimulus_definitions.py

@@ -170,7 +170,7 @@ class Stimulus:
                 decay_time=stimulus_entry["DecayTime"],
                 mean_percent=stimulus_entry["MeanPercent"],
                 sd_percent=stimulus_entry["SDPercent"],
-                amp_cv=stimulus_entry["AmpCV"],
+                relative_skew=stimulus_entry.get("RelativeSkew", 0.5),
                 seed=stimulus_entry.get("Seed", None),
                 mode=mode,
                 reversal=stimulus_entry.get("Reversal", 0.0)
@@ -269,7 +269,7 @@ class Stimulus:
                 decay_time=stimulus_entry["decay_time"],
                 mean_percent=stimulus_entry["mean_percent"],
                 sd_percent=stimulus_entry["sd_percent"],
-                amp_cv=stimulus_entry["amp_cv"],
+                relative_skew=stimulus_entry.get("RelativeSkew", 0.5),
                 seed=stimulus_entry.get("random_seed", None),
                 mode=ClampMode(stimulus_entry.get("input_type", "current_clamp").lower()),
                 reversal=stimulus_entry.get("reversal", 0.0)
@@ -365,7 +365,7 @@ class RelativeShotNoise(Stimulus):
     decay_time: float
     mean_percent: float
     sd_percent: float
-    amp_cv: float
+    relative_skew: float = 0.5
     dt: float = 0.25
     seed: Optional[int] = None
     mode: ClampMode = ClampMode.CURRENT
@@ -378,6 +378,13 @@ class RelativeShotNoise(Stimulus):
             raise ValueError("decay_time must be greater than rise_time")
         return v
 
+    @field_validator("relative_skew")
+    @classmethod
+    def relative_skew_in_range(cls, v):
+        if v < 0.0 or v > 1.0:
+            raise ValueError("relative skewness must be in [0,1]")
+        return v
+
 
 @dataclass(frozen=True, config=dict(extra="forbid"))
 class OrnsteinUhlenbeck(Stimulus):

{bluecellulab-2.6.20 → bluecellulab-2.6.22}/bluecellulab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.6.20
+Version: 2.6.22
 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-2.6.20 → bluecellulab-2.6.22}/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-2.6.20 → bluecellulab-2.6.22}/docs/source/conf.py

@@ -19,6 +19,10 @@ autosummary_mock_imports = [  # these modules are not publicly available
     'bluepy_configfile'
 ]
 
+suppress_warnings = [
+    'autosummary.import_cycle',
+]
+
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 

bluecellulab-2.6.22/docs/source/contributing.rst

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

{bluecellulab-2.6.20 → bluecellulab-2.6.22}/docs/source/index.rst

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

{bluecellulab-2.6.20 → bluecellulab-2.6.22}/tox.ini

@@ -44,7 +44,7 @@ commands =
     ruff check . --select F541,F401 --per-file-ignores="__init__.py:F401"
     pycodestyle {[base]name} --ignore=E501,W504,W503
     pycodestyle tests --ignore=E501,W504,W503,E741
-    mypy . --ignore-missing-imports --disable-error-code=call-overload  # remove once pandas-stubs makes a release after 1.5.3.230321 
+    mypy . --ignore-missing-imports --disable-error-code=call-overload  # remove once pandas-stubs makes a release after 1.5.3.230321
     docformatter --check bluecellulab -r
 
 [testenv:examples]