Update deps: efel5*, pytest 8, python38+ vcs: #minor (#103)

* allow efel 5.* * pytest remove nose style setup func * replace Spikecount->spike_count * drop py37 * formatting * format tests dir * fix error in feature names
BlueBrain · Feb 7, 2024 · 3f7ef23 · 3f7ef23
1 parent 95afd0e
commit 3f7ef23
Show file tree

Hide file tree

Showing 15 changed files with 116 additions and 113 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v2

diff --git a/README.rst b/README.rst
@@ -102,7 +102,7 @@ Dependencies
 
 The main dependencies of EModelRunner are::
 
-    Python3.7+
+    Python3.8+
     Matplotlib
     Numpy
     Neurom
@@ -117,7 +117,7 @@ pre-installed versions.
 Python
 ------
 
-Modern Linux systems will have Python 2.7 or 3 installed. Make sure that your python version is 3.7 or higher.
+Modern Linux systems will have Python installed. Make sure that your python version is 3.8 or higher.
 
 Make sure you're using a recent version of pip. It's best to run ::
 

diff --git a/emodelrunner/factsheets/units.py b/emodelrunner/factsheets/units.py
@@ -1,4 +1,5 @@
 """Contains the units of the features used in factsheets."""
+
 from types import MappingProxyType
 from efel.units import _units as efel_units
 

diff --git a/emodelrunner/load.py b/emodelrunner/load.py
@@ -176,12 +176,12 @@ def load_unoptimized_parameters(params_path, v_init, celsius):
             dist_param_names = definition["parameters"]
         else:
             dist_param_names = None
-        distributions[
-            distribution
-        ] = ephys.parameterscalers.NrnSegmentSomaDistanceScaler(
-            name=distribution,
-            distribution=definition["fun"],
-            dist_param_names=dist_param_names,
+        distributions[distribution] = (
+            ephys.parameterscalers.NrnSegmentSomaDistanceScaler(
+                name=distribution,
+                distribution=definition["fun"],
+                dist_param_names=dist_param_names,
+            )
         )
 
     params_definitions = definitions["parameters"]

diff --git a/emodelrunner/protocols/reader.py b/emodelrunner/protocols/reader.py
@@ -102,17 +102,17 @@ def _parse_step_and_ramp(
     def _parse_sscx_threshold_detection(self, protocol_definition, recordings, prefix):
         """Parses the sscx threshold detection protocol into self.protocols_dict."""
         if protocol_definition["type"] == "RatSSCxThresholdDetectionProtocol":
-            self.protocols_dict[
-                "ThresholdDetection"
-            ] = sscx_protocols.RatSSCxThresholdDetectionProtocol(
-                "IDRest",
-                step_protocol_template=read_step_protocol(
-                    "Threshold",
-                    sscx_protocols,
-                    protocol_definition["step_template"],
-                    recordings,
-                ),
-                prefix=prefix,
+            self.protocols_dict["ThresholdDetection"] = (
+                sscx_protocols.RatSSCxThresholdDetectionProtocol(
+                    "IDRest",
+                    step_protocol_template=read_step_protocol(
+                        "Threshold",
+                        sscx_protocols,
+                        protocol_definition["step_template"],
+                        recordings,
+                    ),
+                    prefix=prefix,
+                )
             )
 
     def _parse_thalamus_threshold_detection(
@@ -121,30 +121,30 @@ def _parse_thalamus_threshold_detection(
         """Parses the thalamus threshold detection protocol into self.protocols_dict."""
         if protocol_definition["type"] == "RatSSCxThresholdDetectionProtocol":
             if protocol_name == "ThresholdDetection_dep":
-                self.protocols_dict[
-                    "ThresholdDetection_dep"
-                ] = thalamus_protocols.RatSSCxThresholdDetectionProtocol(
-                    "ThresholdDetection_dep",
-                    step_protocol_template=read_step_protocol(
+                self.protocols_dict["ThresholdDetection_dep"] = (
+                    thalamus_protocols.RatSSCxThresholdDetectionProtocol(
                         "ThresholdDetection_dep",
-                        thalamus_protocols,
-                        protocol_definition["step_template"],
-                        recordings,
-                    ),
-                    prefix=prefix,
+                        step_protocol_template=read_step_protocol(
+                            "ThresholdDetection_dep",
+                            thalamus_protocols,
+                            protocol_definition["step_template"],
+                            recordings,
+                        ),
+                        prefix=prefix,
+                    )
                 )
             elif protocol_name == "ThresholdDetection_hyp":
-                self.protocols_dict[
-                    "ThresholdDetection_hyp"
-                ] = thalamus_protocols.RatSSCxThresholdDetectionProtocol(
-                    "ThresholdDetection_hyp",
-                    step_protocol_template=read_step_protocol(
+                self.protocols_dict["ThresholdDetection_hyp"] = (
+                    thalamus_protocols.RatSSCxThresholdDetectionProtocol(
                         "ThresholdDetection_hyp",
-                        thalamus_protocols,
-                        protocol_definition["step_template"],
-                        recordings,
-                    ),
-                    prefix=prefix,
+                        step_protocol_template=read_step_protocol(
+                            "ThresholdDetection_hyp",
+                            thalamus_protocols,
+                            protocol_definition["step_template"],
+                            recordings,
+                        ),
+                        prefix=prefix,
+                    )
                 )
 
     def _parse_vecstim_netstim(
@@ -162,14 +162,18 @@ def _parse_vecstim_netstim(
 
     def _parse_sscx_main(self, protocol_definitions, prefix):
         """Parses the main sscx protocol into self.protocols_dict."""
-        self.protocols_dict[
-            "RinHoldcurrent"
-        ] = sscx_protocols.RatSSCxRinHoldcurrentProtocol(
-            "RinHoldCurrent",
-            rin_protocol_template=self.protocols_dict["Rin"],
-            holdi_precision=protocol_definitions["RinHoldcurrent"]["holdi_precision"],
-            holdi_max_depth=protocol_definitions["RinHoldcurrent"]["holdi_max_depth"],
-            prefix=prefix,
+        self.protocols_dict["RinHoldcurrent"] = (
+            sscx_protocols.RatSSCxRinHoldcurrentProtocol(
+                "RinHoldCurrent",
+                rin_protocol_template=self.protocols_dict["Rin"],
+                holdi_precision=protocol_definitions["RinHoldcurrent"][
+                    "holdi_precision"
+                ],
+                holdi_max_depth=protocol_definitions["RinHoldcurrent"][
+                    "holdi_max_depth"
+                ],
+                prefix=prefix,
+            )
         )
 
         other_protocols = []
@@ -196,43 +200,43 @@ def _parse_sscx_main(self, protocol_definitions, prefix):
     def _parse_thalamus_main(self, protocol_definitions, prefix):
         """Parses the main thalamus protocol into self.protocols_dict."""
         try:  # Only low-threshold bursting cells have thin protocol
-            self.protocols_dict[
-                "RinHoldcurrent_dep"
-            ] = thalamus_protocols.RatSSCxRinHoldcurrentProtocol(
-                "RinHoldcurrent_dep",
-                rin_protocol_template=self.protocols_dict["Rin_dep"],
-                holdi_estimate_multiplier=protocol_definitions["RinHoldcurrent_dep"][
+            self.protocols_dict["RinHoldcurrent_dep"] = (
+                thalamus_protocols.RatSSCxRinHoldcurrentProtocol(
+                    "RinHoldcurrent_dep",
+                    rin_protocol_template=self.protocols_dict["Rin_dep"],
+                    holdi_estimate_multiplier=protocol_definitions[
+                        "RinHoldcurrent_dep"
+                    ]["holdi_estimate_multiplier"],
+                    holdi_precision=protocol_definitions["RinHoldcurrent_dep"][
+                        "holdi_precision"
+                    ],
+                    holdi_max_depth=protocol_definitions["RinHoldcurrent_dep"][
+                        "holdi_max_depth"
+                    ],
+                    prefix=prefix,
+                )
+            )
+            rinhold_protocol_dep = self.protocols_dict["RinHoldcurrent_dep"]
+            thdetect_protocol_dep = self.protocols_dict["ThresholdDetection_dep"]
+        except KeyError:
+            rinhold_protocol_dep = None
+            thdetect_protocol_dep = None
+
+        self.protocols_dict["RinHoldcurrent_hyp"] = (
+            thalamus_protocols.RatSSCxRinHoldcurrentProtocol(
+                "RinHoldcurrent_hyp",
+                rin_protocol_template=self.protocols_dict["Rin_hyp"],
+                holdi_estimate_multiplier=protocol_definitions["RinHoldcurrent_hyp"][
                     "holdi_estimate_multiplier"
                 ],
-                holdi_precision=protocol_definitions["RinHoldcurrent_dep"][
+                holdi_precision=protocol_definitions["RinHoldcurrent_hyp"][
                     "holdi_precision"
                 ],
-                holdi_max_depth=protocol_definitions["RinHoldcurrent_dep"][
+                holdi_max_depth=protocol_definitions["RinHoldcurrent_hyp"][
                     "holdi_max_depth"
                 ],
                 prefix=prefix,
             )
-            rinhold_protocol_dep = self.protocols_dict["RinHoldcurrent_dep"]
-            thdetect_protocol_dep = self.protocols_dict["ThresholdDetection_dep"]
-        except KeyError:
-            rinhold_protocol_dep = None
-            thdetect_protocol_dep = None
-
-        self.protocols_dict[
-            "RinHoldcurrent_hyp"
-        ] = thalamus_protocols.RatSSCxRinHoldcurrentProtocol(
-            "RinHoldcurrent_hyp",
-            rin_protocol_template=self.protocols_dict["Rin_hyp"],
-            holdi_estimate_multiplier=protocol_definitions["RinHoldcurrent_hyp"][
-                "holdi_estimate_multiplier"
-            ],
-            holdi_precision=protocol_definitions["RinHoldcurrent_hyp"][
-                "holdi_precision"
-            ],
-            holdi_max_depth=protocol_definitions["RinHoldcurrent_hyp"][
-                "holdi_max_depth"
-            ],
-            prefix=prefix,
         )
 
         other_protocols = [

diff --git a/emodelrunner/protocols/sscx_protocols.py b/emodelrunner/protocols/sscx_protocols.py
@@ -657,8 +657,8 @@ def detect_spike(
         response = protocol.run(cell_model, param_values, sim=sim)
 
         feature = ephys.efeatures.eFELFeature(
-            name="ThresholdDetection.Spikecount",
-            efel_feature_name="Spikecount",
+            name="ThresholdDetection.spike_count",
+            efel_feature_name="spike_count",
             recording_names={"": self.prefix + "ThresholdDetection.soma.v"},
             stim_start=protocol.stim_start,
             stim_end=protocol.stim_end,
@@ -792,9 +792,11 @@ def __init__(
         """
         super().__init__(
             name,
-            stimuli=step_stimuli + [holding_stimulus]
-            if holding_stimulus is not None
-            else step_stimuli,
+            stimuli=(
+                step_stimuli + [holding_stimulus]
+                if holding_stimulus is not None
+                else step_stimuli
+            ),
             recordings=recordings,
             cvode_active=cvode_active,
         )
@@ -1099,9 +1101,11 @@ def __init__(
         """
         super().__init__(
             name,
-            stimuli=[ramp_stimulus, holding_stimulus]
-            if holding_stimulus is not None
-            else [ramp_stimulus],
+            stimuli=(
+                [ramp_stimulus, holding_stimulus]
+                if holding_stimulus is not None
+                else [ramp_stimulus]
+            ),
             recordings=recordings,
             cvode_active=cvode_active,
         )

diff --git a/emodelrunner/protocols/thalamus_protocols.py b/emodelrunner/protocols/thalamus_protocols.py
@@ -690,8 +690,8 @@ def detect_spike(
 
         if self.name.endswith("_dep"):
             feature = ephys.efeatures.eFELFeature(
-                name="ThresholdDetection_dep.Spikecount",
-                efel_feature_name="Spikecount_stimint",
+                name="ThresholdDetection_dep.spike_count",
+                efel_feature_name="spike_count_stimint",
                 recording_names={"": self.prefix + "ThresholdDetection_dep.soma.v"},
                 stim_start=protocol.step_delay,
                 stim_end=protocol.step_delay + protocol.step_duration,
@@ -701,8 +701,8 @@ def detect_spike(
 
         elif self.name.endswith("_hyp"):
             feature = ephys.efeatures.eFELFeature(
-                name="ThresholdDetection_hyp.Spikecount",
-                efel_feature_name="Spikecount_stimint",
+                name="ThresholdDetection_hyp.spike_count",
+                efel_feature_name="spike_count_stimint",
                 recording_names={"": self.prefix + "ThresholdDetection_hyp.soma.v"},
                 stim_start=protocol.step_delay,
                 stim_end=protocol.step_delay + protocol.step_duration,

diff --git a/examples/sscx_sample_dir/config/features/cADpyr_L4PC.json b/examples/sscx_sample_dir/config/features/cADpyr_L4PC.json
@@ -1,7 +1,7 @@
 {
   "bAP": {
     "soma.v": [
-      {"feature": "Spikecount", "val": [1.0, 0.01]}
+      {"feature": "spike_count", "val": [1.0, 0.01]}
     ], 
     "dend1.v": [
       {"feature": "maximum_voltage_from_voltagebase", "val": [81.329833, 7.018952], "weight": 1, "__comment": "Stuart and Sakmann 1994"}
@@ -94,7 +94,7 @@
   "RMP": {
     "soma.v": [
       {"feature": "voltage_base", "val": [-73.9134, 1.6714, -4.817202527918724, 0.027690237877764368, 1.9500000000000002, 0], "n": 2, "fid": 288, "strict_stim": true, "__comment": {"source": "cADpyr/L4PC", "meta": {"version": "aca7043"}}},
-      {"feature": "Spikecount", "val": [0.0, 0.001, 0.0, 0.001, -3.0, 0], "n": 2, "fid": 308, "strict_stim": true, "__comment": {"source": "cADpyr/L4PC", "meta": {"version": "aca7043"}}}
+      {"feature": "spike_count", "val": [0.0, 0.001, 0.0, 0.001, -3.0, 0], "n": 2, "fid": 308, "strict_stim": true, "__comment": {"source": "cADpyr/L4PC", "meta": {"version": "aca7043"}}}
     ]
   }, 
   "IV_-100": {

diff --git a/examples/sscx_sample_dir/config/params/final.json b/examples/sscx_sample_dir/config/params/final.json
@@ -65,7 +65,7 @@
             "_.Step_140.soma.v.inv_second_ISI": 0.12459028529028007,
             "_.bAP.dend1.v.maximum_voltage_from_voltagebase": 0.6002072733124426,
             "_.bAP.ca_prox_basal.cai.maximum_voltage_from_voltagebase": 4.200408804664744,
-            "_.bAP.soma.v.Spikecount": 0,
+            "_.bAP.soma.v.spike_count": 0,
             "_.Step_140.soma.v.voltage_after_stim": 1.9994617502528271,
             "_.SpikeRec_all.soma.v.decay_time_constant_after_stim": 0.10085645832784906,
             "_.Step_280.soma.v.inv_fourth_ISI": 1.0352480907823978,
@@ -79,7 +79,7 @@
             "_.APWaveform_360.soma.v.AP2_amp": 1.2849194517061855,
             "_.Step_140.soma.v.voltage_base": 4.375568090259795,
             "_.Step_280.soma.v.inv_time_to_first_spike": 0.31328662092696996,
-            "_.RMP.soma.v.Spikecount": 0,
+            "_.RMP.soma.v.spike_count": 0,
             "_.bAP.dend2.v.maximum_voltage_from_voltagebase": 1.8354820176163507,
             "_.Step_200.soma.v.AHP_depth": 1.7706451237580105,
             "_.Step_200.soma.v.time_to_last_spike": 0.3030673891317257,

diff --git a/examples/synplas_sample_dir/config/params/final.json b/examples/synplas_sample_dir/config/params/final.json
@@ -65,7 +65,7 @@
             "_.Step_140.soma.v.inv_second_ISI": 0.12459028529028007,
             "_.bAP.dend1.v.maximum_voltage_from_voltagebase": 0.6002072733124426,
             "_.bAP.ca_prox_basal.cai.maximum_voltage_from_voltagebase": 4.200408804664744,
-            "_.bAP.soma.v.Spikecount": 0,
+            "_.bAP.soma.v.spike_count": 0,
             "_.Step_140.soma.v.voltage_after_stim": 1.9994617502528271,
             "_.SpikeRec_all.soma.v.decay_time_constant_after_stim": 0.10085645832784906,
             "_.Step_280.soma.v.inv_fourth_ISI": 1.0352480907823978,
@@ -79,7 +79,7 @@
             "_.APWaveform_360.soma.v.AP2_amp": 1.2849194517061855,
             "_.Step_140.soma.v.voltage_base": 4.375568090259795,
             "_.Step_280.soma.v.inv_time_to_first_spike": 0.31328662092696996,
-            "_.RMP.soma.v.Spikecount": 0,
+            "_.RMP.soma.v.spike_count": 0,
             "_.bAP.dend2.v.maximum_voltage_from_voltagebase": 1.8354820176163507,
             "_.Step_200.soma.v.AHP_depth": 1.7706451237580105,
             "_.Step_200.soma.v.time_to_last_spike": 0.3030673891317257,
@@ -173,7 +173,7 @@
             "_.Step_140.soma.v.inv_second_ISI": 0.11491646526546874,
             "_.bAP.dend1.v.maximum_voltage_from_voltagebase": 0.3933547355204061,
             "_.bAP.ca_prox_basal.cai.maximum_voltage_from_voltagebase": 0.5317743149017081,
-            "_.bAP.soma.v.Spikecount": 0,
+            "_.bAP.soma.v.spike_count": 0,
             "_.Step_140.soma.v.voltage_after_stim": 2.068875307329713,
             "_.SpikeRec_all.soma.v.decay_time_constant_after_stim": 0.12010551765357895,
             "_.Step_280.soma.v.inv_fourth_ISI": 0.7202659800227095,
@@ -187,7 +187,7 @@
             "_.APWaveform_360.soma.v.AP2_amp": 0.4910291906341208,
             "_.Step_140.soma.v.voltage_base": 4.344090204362258,
             "_.Step_280.soma.v.inv_time_to_first_spike": 0.4962190069156973,
-            "_.RMP.soma.v.Spikecount": 0,
+            "_.RMP.soma.v.spike_count": 0,
             "_.bAP.dend2.v.maximum_voltage_from_voltagebase": 1.186952930680964,
             "_.Step_200.soma.v.AHP_depth": 1.5876494345794483,
             "_.Step_200.soma.v.time_to_last_spike": 0.8317664467168655,