Update eFEL deprecated functions calls

.github/workflows/test.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v2

README.rst

@@ -70,7 +70,7 @@ BluePyEfe: Blue Brain Python E-feature extraction
 Introduction
 ============
 
-BluePyEfe aims at easing the process of reading experimental recordings and extracting 
+BluePyEfe aims at easing the process of reading experimental recordings and extracting
 batches of electrical features from these recordings. To do so, it combines trace reading
 functions and features extraction functions from the `eFel library <https://github.com/BlueBrain/eFEL>`_.
 
@@ -84,7 +84,7 @@ This software is citable using a `DOI generated by Zenodo <https://zenodo.org/re
 Requirements
 ============
 
-* `Python 3.8+ <https://www.python.org/downloads/release/python-380/>`_
+* `Python 3.9+ <https://www.python.org/downloads/release/python-380/>`_
 * `eFEL eFeature Extraction Library <https://github.com/BlueBrain/eFEL>`_ (automatically installed by pip)
 * `Numpy <http://www.numpy.org>`_ (automatically installed by pip)
 * `Scipy <https://www.scipy.org/>`_ (automatically installed by pip)
@@ -112,7 +112,7 @@ The e-features considered in the present package are the one implemented in the
 The present package makes one major assumption: E-features are more meaningful if they are coming from a set of traces rather than a single trace. And they are even more meaningful if these traces come from different cells of the same cellular type.
 This assumption dictates the organisation of the package and has several consequences:
 
-The efeatures extracted through the package will always be averaged over the trace considered. For example, the AP_amplitude will be an average over all the action potentials present in a trace. If you wish to work on an AP by AP basis, please consider using the eFEL library directly. 
+The efeatures extracted through the package will always be averaged over the trace considered. For example, the AP_amplitude will be an average over all the action potentials present in a trace. If you wish to work on an AP by AP basis, please consider using the eFEL library directly.
 
 A large part of the present software is therefore dedicated to averaging the features across set of "equivalent" recordings. To be able to average e-features across different cells in a meaningful way, an equivalence must be established between the traces coming from these different cells. It would not make sense to average the mean firing frequency obtain cell A on a 1s long step protocol with the one obtain for cell B on a ramp protocol that lasts for 500ms. We chose to define recordings as equivalent based on two criteria: (1) They have the same name and (2) they are of the same amplitude when the amplitude is expressed as a percentage of the rheobase of the cell.
 
@@ -130,7 +130,7 @@ Each of these steps are parametrized by a number of settings, therefore we recom
 Coming from the legacy version
 ==============================
 The legacy version (v0.4*) is moved to the legacy branch.
-Changes introduced in v2.0.0 are listed in the `CHANGELOG.rst <CHANGELOG.rst>`_. 
+Changes introduced in v2.0.0 are listed in the `CHANGELOG.rst <CHANGELOG.rst>`_.
 That is the only file you need to look at for the changes as the future changes will also be noted there.
 
 Funding
@@ -139,10 +139,10 @@ This work has been partially funded by the European Union Seventh Framework Prog
 
 
 ..
-    The following image is also defined in the index.rst file, as the relative path is 
+    The following image is also defined in the index.rst file, as the relative path is
     different, depending from where it is sourced.
     The following location is used for the github README
-    The index.rst location is used for the docs README; index.rst also defined an end-marker, 
+    The index.rst location is used for the docs README; index.rst also defined an end-marker,
     to skip content after the marker 'substitutions'.
 
 .. substitutions

bluepyefe/extract.py

@@ -931,7 +931,8 @@ def extract_efeatures(
 
     if efel_settings is None:
         logger.warning(
-            "efel_settings is None. Default settings will be used"
+            "efel_settings is None. Default settings will be used: " +
+            str(DEFAULT_EFEL_SETTINGS)
         )
         efel_settings = DEFAULT_EFEL_SETTINGS.copy()
 

bluepyefe/tools.py

@@ -112,17 +112,7 @@ def set_efel_settings(efeature_settings):
         if setting in ['stim_start', 'stim_end']:
             value = float(value)
 
-        if setting == 'Threshold':
-            efel.setThreshold(value)
-
-        elif isinstance(value, bool) or isinstance(value, int):
-            efel.setIntSetting(setting, int(value))
-
-        elif isinstance(value, (float, list)):
-            efel.setDoubleSetting(setting, value)
-
-        elif isinstance(value, str):
-            efel.setStrSetting(setting, value)
+        efel.set_setting(setting, value)
 
 
 def dict_to_json(data, path):

setup.py

@@ -35,7 +35,7 @@
     "format that can then be used by BluePyOpt for electrical model building "
     "purposes.",
     packages=setuptools.find_packages(exclude=["tests"]),
-    python_requires=">=3.8",
+    python_requires=">=3.9",
     include_package_data=True,
     author="BlueBrain Project, EPFL",
     license="LGPLv3",

tests/test_efel_settings.py

@@ -1,6 +1,7 @@
 """bluepyefe.cell tests"""
 
 import unittest
+import pytest
 
 import bluepyefe.cell
 import bluepyefe.recording
@@ -27,7 +28,7 @@ def setUp(self):
         )
 
     def test_efel_threshold(self):
-        
+
         self.cell.recordings[0].efeatures = {}
 
         self.cell.extract_efeatures(
@@ -69,6 +70,16 @@ def test_efel_threshold(self):
         recording = self.cell.recordings[0]
         self.assertEqual(recording.efeatures["Spikecount"], 0.)
 
+    def test_efel_incorrect_threshold(self):
+
+        self.cell.recordings[0].efeatures = {}
+
+        with pytest.raises(ValueError):
+            self.cell.extract_efeatures(
+                protocol_name="IDRest",
+                efeatures=["Spikecount"],
+                efel_settings={'Threshold': "40."}
+            )
 
 if __name__ == "__main__":
     unittest.main()

tox.ini

@@ -4,10 +4,10 @@ minversion = 4
 
 [gh-actions]
 python =
-    3.8: py3
     3.9: py3
     3.10: py3
     3.11: py3
+    3.12: py3
 
 [testenv]
 envdir =