Merge branch 'master' into master

BlueBrain · Aug 23, 2024 · e05291c · e05291c
2 parents a38ff24 + d46979b
commit e05291c
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
         include:
           - os: macos-12
             python-version: "3.10"
@@ -34,7 +34,7 @@ jobs:
       run: tox
 
     - name: "Upload coverage to Codecov"
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         fail_ci_if_error: false
diff --git a/README.rst b/README.rst
@@ -85,7 +85,7 @@ News
 Requirements
 ============
 
-* `Python 3.8+ <https://www.python.org/downloads/release/python-380/>`_
+* `Python 3.9+ <https://www.python.org/downloads/release/python-390/>`_
 * `Pip <https://pip.pypa.io>`_ (installed by default in newer versions of Python)
 * `Neuron 7.4+ <http://neuron.yale.edu/>`_ (compiled with Python support)
 * `eFEL eFeature Extraction Library <https://github.com/BlueBrain/eFEL>`_ (automatically installed by pip)

diff --git a/bluepyopt/ephys/morphologies.py b/bluepyopt/ephys/morphologies.py
@@ -318,6 +318,8 @@ def load(morpho_filename, replace_axon):
             morpho = arbor.load_component(morpho_filename).component
         elif morpho_suffix == '.swc':
             morpho = arbor.load_swc_arbor(morpho_filename)
+            # turn loaded_morphology into morphology type
+            morpho = morpho.morphology
         elif morpho_suffix == '.asc':
             morpho = arbor.load_asc(morpho_filename).morphology
         else:

diff --git a/bluepyopt/ephys/protocols.py b/bluepyopt/ephys/protocols.py
@@ -602,7 +602,12 @@ def instantiate_iclamp_stimuli(self, decor, use_labels=False):
         for i, stim in enumerate(self.stimuli):
             if not isinstance(stim, stimuli.SynapticStimulus):
                 if hasattr(stim, 'envelope'):
-                    arb_iclamp = arbor.iclamp(stim.envelope())
+                    envelope = stim.envelope()
+                    envelope = [
+                        (t * arbor.units.ms, curr * arbor.units.nA)
+                        for (t, curr) in envelope
+                    ]
+                    arb_iclamp = arbor.iclamp(envelope)
                 else:
                     raise ValueError('Stimulus must provide envelope method '
                                      ' or be of type NrnNetStimStimulus to be'
@@ -648,7 +653,9 @@ def instantiate_recordings(self, cell_model, use_labels=False):
 
             cell_model.probe('voltage',
                              arb_loc.ref if use_labels else arb_loc.loc,
-                             frequency=10)  # could be a parameter
+                             f"probe-{i}",
+                             # frequency could be a parameter
+                             frequency=10 * arbor.units.kHz)
 
         return cell_model
 

diff --git a/bluepyopt/ephys/simulators.py b/bluepyopt/ephys/simulators.py
@@ -372,9 +372,11 @@ def run(self, arb_cell_model, tstop=None, dt=None):
         dt = dt if dt is not None else self.dt
 
         if dt is not None:
-            return arb_cell_model.run(tfinal=tstop, dt=dt)
+            return arb_cell_model.run(
+                tfinal=tstop * arbor.units.ms, dt=dt * arbor.units.ms
+            )
         else:
-            return arb_cell_model.run(tfinal=tstop)
+            return arb_cell_model.run(tfinal=tstop * arbor.units.ms)
 
 
 class ArbSimulatorException(Exception):

diff --git a/bluepyopt/ephys/templates/acc/decor_acc_template.jinja2 b/bluepyopt/ephys/templates/acc/decor_acc_template.jinja2
@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (decor
     {%- for mech, params in global_mechs.items() %}
     {%- if mech is not none %}
@@ -10,7 +10,7 @@
     {%- endif %}
     {%- else %}
     {%- for param in params %}
-    (default ({{ param.name }} {{ param.value }}))
+    (default ({{ param.name }} {{ param.value }} (scalar 1.0)))
     {%- endfor %}
     {%- endif %}
     {%- endfor %}
@@ -27,13 +27,13 @@
     {%- endif %}
     {%- else %}
     {%- for param in params %}
-    (paint {{loc.ref}} ({{ param.name }} {{ param.value }}))
+    (paint {{loc.ref}} ({{ param.name }} {{ param.value }} (scalar 1.0)))
     {%- endfor %}
     {%- endif %}
     {%- endfor %}
 
     {%- for synapse_name, mech_params in pprocess_mechs[loc].items() %}
-    (place {{loc.ref}} (synapse (mechanism "{{ mech_params.mech }}" {%- for param in mech_params.params %} ("{{ param.name }}" {{ param.value }}){%- endfor %})) "{{ synapse_name }}")
+    (place {{loc.ref}} (synapse (mechanism "{{ mech_params.mech }}" {%- for param in mech_params.params %} ("{{ param.name }}" {{ param.value }} (scalar 1.0)){%- endfor %})) "{{ synapse_name }}")
     {%- endfor %}
 
     {%- endfor %}))
diff --git a/bluepyopt/ephys/templates/acc/label_dict_acc_template.jinja2 b/bluepyopt/ephys/templates/acc/label_dict_acc_template.jinja2
@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (label-dict
   {%- for loc, label in label_dict.items() %}
     {{ label.defn }}

diff --git a/bluepyopt/tests/test_ephys/test_create_acc.py b/bluepyopt/tests/test_ephys/test_create_acc.py
@@ -537,7 +537,7 @@ def run_short_sim(cable_cell):
     arb_cell_model.properties.catalogue.extend(arbor.bbp_catalogue(), "BBP::")
 
     # Run a very short simulation to test mechanism instantiation
-    arb_cell_model.run(tfinal=0.1)
+    arb_cell_model.run(tfinal=0.1 * arbor.units.ms)
 
 
 @pytest.mark.unit
@@ -665,6 +665,10 @@ def check_acc_dir(test_dir, ref_dir):
             with open(ref_dir_file / file) as f:
                 ref_file = f.read()
             assert ref_file == test_file
+            # check that load_component is not raising any error here
+            fpath = pathlib.Path(test_dir) / file
+            if fpath.suffix == "acc":
+                arbor.load_component(fpath).component
 
 
 @pytest.mark.unit

diff --git a/bluepyopt/tests/test_ephys/test_parameterscalers.py b/bluepyopt/tests/test_ephys/test_parameterscalers.py
@@ -1,7 +1,9 @@
 """Test ephys.parameterscalers"""
 
 import json
-
+import pathlib
+import tempfile
+import arbor
 
 import pytest
 
@@ -143,3 +145,33 @@ def test_parameterscalers_iexpr_generator_unsupported_attr():
                              'unsupported attribute tau.'):
         iexpr = value_scaler.acc_scale_iexpr(
             value=value, constant_formatter=lambda v: '%.9g' % v)
+
+
+@pytest.mark.unit
+def test_parameterscalers_iexpr():
+    """ephys.parameterscalers: Test iexpr"""
+    # iexpr from bluepyopt/tests/test_ephys/test_parameterscalers.py
+    iexpr = '(sub (scalar 0.62109375) ' \
+            '(mul (log (pi) ) ' \
+            '(exp (div (distance (region "soma")) ' \
+            '(scalar 0.421875) ) ) ) )'
+
+    # modified decor as in
+    # bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_cell_decor.acc
+    simple_cell_decor_with_iexpr = \
+        '(arbor-component\n' \
+        '  (meta-data (version "0.9-dev"))\n' \
+        '  (decor\n' \
+        '    (paint (region "soma") ' \
+        '(membrane-capacitance 0.01 (scalar 1.0)))\n' \
+        '    (paint (region "soma") ' \
+        '(scaled-mechanism (density (mechanism "default::hh" ' \
+        '("gnabar" 0.10299326453483033) ("gkbar" 0.027124836082684685))) ' \
+        f'("gkbar" {iexpr})))))'
+
+    with tempfile.TemporaryDirectory() as test_dir:
+        decor_filename = pathlib.Path(test_dir).joinpath("decor.acc")
+        with open(decor_filename, "w") as f:
+            f.write(simple_cell_decor_with_iexpr)
+        # check that load_component is not raising any error here
+        arbor.load_component(decor_filename).component
diff --git a/bluepyopt/tests/test_ephys/testdata/acc/CCell/CCell_decor.acc b/bluepyopt/tests/test_ephys/testdata/acc/CCell/CCell_decor.acc
@@ -1,10 +1,10 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (decor
-    (default (gSKv3_1bar_SKv3_1 65))
-    (paint (region "soma") (gSKv3_1bar_SKv3_1 65))
-    (paint (region "soma") (gSKv3_1bar_SKv3_1 65))
+    (default (gSKv3_1bar_SKv3_1 65 (scalar 1.0)))
+    (paint (region "soma") (gSKv3_1bar_SKv3_1 65 (scalar 1.0)))
+    (paint (region "soma") (gSKv3_1bar_SKv3_1 65 (scalar 1.0)))
     (paint (region "dend") (density (mechanism "BBP::Ih")))
-    (paint (region "apic") (gSKv3_1bar_SKv3_1 65))
-    (paint (region "apic") (gSKv3_1bar_SKv3_1 65))
+    (paint (region "apic") (gSKv3_1bar_SKv3_1 65 (scalar 1.0)))
+    (paint (region "apic") (gSKv3_1bar_SKv3_1 65 (scalar 1.0)))
     (paint (region "apic") (density (mechanism "BBP::Ih")))))
diff --git a/bluepyopt/tests/test_ephys/testdata/acc/CCell/CCell_label_dict.acc b/bluepyopt/tests/test_ephys/testdata/acc/CCell/CCell_label_dict.acc
@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (label-dict 
     (region-def "all" (all)) 
     (region-def "apic" (tag 4)) 

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/CCell/simple_axon_replacement.acc b/bluepyopt/tests/test_ephys/testdata/acc/CCell/simple_axon_replacement.acc
@@ -1,6 +1,6 @@
 (arbor-component 
   (meta-data 
-    (version "0.1-dev"))
+    (version "0.9-dev"))
   (morphology 
     (branch 0 -1 
       (segment 0 

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/expsyn/simple_cell_decor.acc b/bluepyopt/tests/test_ephys/testdata/acc/expsyn/simple_cell_decor.acc
@@ -1,6 +1,6 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (decor
-    (paint (region "soma") (membrane-capacitance 0.01))
+    (paint (region "soma") (membrane-capacitance 0.01 (scalar 1.0)))
     (paint (region "soma") (density (mechanism "default::pas")))
-    (place (locset "somacenter") (synapse (mechanism "default::expsyn" ("tau" 10))) "expsyn")))
+    (place (locset "somacenter") (synapse (mechanism "default::expsyn" ("tau" 10 (scalar 1.0)))) "expsyn")))
diff --git a/bluepyopt/tests/test_ephys/testdata/acc/expsyn/simple_cell_label_dict.acc b/bluepyopt/tests/test_ephys/testdata/acc/expsyn/simple_cell_label_dict.acc
@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (label-dict
     (region-def "all" (all))
     (region-def "soma" (tag 1))

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/l5pc/C060114A7_axon_replacement.acc b/bluepyopt/tests/test_ephys/testdata/acc/l5pc/C060114A7_axon_replacement.acc
@@ -1,6 +1,6 @@
 (arbor-component 
   (meta-data 
-    (version "0.1-dev"))
+    (version "0.9-dev"))
   (morphology 
     (branch 0 -1 
       (segment 0 

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/l5pc/C060114A7_modified.acc b/bluepyopt/tests/test_ephys/testdata/acc/l5pc/C060114A7_modified.acc
@@ -1,6 +1,6 @@
 (arbor-component 
   (meta-data 
-    (version "0.1-dev"))
+    (version "0.9-dev"))
   (morphology 
     (branch 0 -1 
       (segment 0 

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/l5pc/l5pc_decor.acc b/bluepyopt/tests/test_ephys/testdata/acc/l5pc/l5pc_decor.acc
@@ -1,22 +1,22 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (decor
-    (default (membrane-potential -65))
-    (default (temperature-kelvin 307.14999999999998))
-    (default (membrane-capacitance 0.01))
-    (default (axial-resistivity 100))
+    (default (membrane-potential -65 (scalar 1.0)))
+    (default (temperature-kelvin 307.14999999999998 (scalar 1.0)))
+    (default (membrane-capacitance 0.01 (scalar 1.0)))
+    (default (axial-resistivity 100 (scalar 1.0)))
     (paint (region "all") (density (mechanism "default::pas/e=-75" ("g" 3.0000000000000001e-05))))
-    (paint (region "soma") (ion-reversal-potential "na" 50))
-    (paint (region "soma") (ion-reversal-potential "k" -85))
+    (paint (region "soma") (ion-reversal-potential "na" 50 (scalar 1.0)))
+    (paint (region "soma") (ion-reversal-potential "k" -85 (scalar 1.0)))
     (paint (region "soma") (density (mechanism "BBP::NaTs2_t" ("gNaTs2_tbar" 0.98395500000000002))))
     (paint (region "soma") (density (mechanism "BBP::SKv3_1" ("gSKv3_1bar" 0.30347200000000002))))
     (paint (region "soma") (density (mechanism "BBP::SK_E2" ("gSK_E2bar" 0.0084069999999999995))))
     (paint (region "soma") (density (mechanism "BBP::Ca_HVA" ("gCa_HVAbar" 0.00099400000000000009))))
     (paint (region "soma") (density (mechanism "BBP::Ca_LVAst" ("gCa_LVAstbar" 0.00033300000000000002))))
     (paint (region "soma") (density (mechanism "BBP::CaDynamics_E2" ("gamma" 0.00060899999999999995) ("decay" 210.48528400000001))))
     (paint (region "soma") (density (mechanism "BBP::Ih" ("gIhbar" 8.0000000000000007e-05))))
-    (paint (region "axon") (ion-reversal-potential "na" 50))
-    (paint (region "axon") (ion-reversal-potential "k" -85))
+    (paint (region "axon") (ion-reversal-potential "na" 50 (scalar 1.0)))
+    (paint (region "axon") (ion-reversal-potential "k" -85 (scalar 1.0)))
     (paint (region "axon") (density (mechanism "BBP::NaTa_t" ("gNaTa_tbar" 3.1379679999999999))))
     (paint (region "axon") (density (mechanism "BBP::Nap_Et2" ("gNap_Et2bar" 0.0068269999999999997))))
     (paint (region "axon") (density (mechanism "BBP::K_Pst" ("gK_Pstbar" 0.97353800000000001))))
@@ -26,11 +26,11 @@
     (paint (region "axon") (density (mechanism "BBP::Ca_HVA" ("gCa_HVAbar" 0.00098999999999999999))))
     (paint (region "axon") (density (mechanism "BBP::Ca_LVAst" ("gCa_LVAstbar" 0.0087519999999999994))))
     (paint (region "axon") (density (mechanism "BBP::CaDynamics_E2" ("gamma" 0.0029099999999999998) ("decay" 287.19873100000001))))
-    (paint (region "dend") (membrane-capacitance 0.02))
+    (paint (region "dend") (membrane-capacitance 0.02 (scalar 1.0)))
     (paint (region "dend") (density (mechanism "BBP::Ih" ("gIhbar" 8.0000000000000007e-05))))
-    (paint (region "apic") (ion-reversal-potential "na" 50))
-    (paint (region "apic") (ion-reversal-potential "k" -85))
-    (paint (region "apic") (membrane-capacitance 0.02))
+    (paint (region "apic") (ion-reversal-potential "na" 50 (scalar 1.0)))
+    (paint (region "apic") (ion-reversal-potential "k" -85 (scalar 1.0)))
+    (paint (region "apic") (membrane-capacitance 0.02 (scalar 1.0)))
     (paint (region "apic") (density (mechanism "BBP::NaTs2_t" ("gNaTs2_tbar" 0.026145000000000002))))
     (paint (region "apic") (density (mechanism "BBP::SKv3_1" ("gSKv3_1bar" 0.0042259999999999997))))
     (paint (region "apic") (density (mechanism "BBP::Im" ("gImbar" 0.00014300000000000001))))

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/l5pc/l5pc_label_dict.acc b/bluepyopt/tests/test_ephys/testdata/acc/l5pc/l5pc_label_dict.acc
@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (label-dict
     (region-def "all" (all))
     (region-def "soma" (tag 1))

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/l5pc_py37/l5pc_decor.acc b/bluepyopt/tests/test_ephys/testdata/acc/l5pc_py37/l5pc_decor.acc
@@ -1,22 +1,22 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (decor
-    (default (membrane-potential -65))
-    (default (temperature-kelvin 307.14999999999998))
-    (default (membrane-capacitance 0.01))
-    (default (axial-resistivity 100))
+    (default (membrane-potential -65 (scalar 1.0)))
+    (default (temperature-kelvin 307.14999999999998 (scalar 1.0)))
+    (default (membrane-capacitance 0.01 (scalar 1.0)))
+    (default (axial-resistivity 100 (scalar 1.0)))
     (paint (region "all") (density (mechanism "default::pas/e=-75" ("g" 3.0000000000000001e-05))))
-    (paint (region "soma") (ion-reversal-potential "na" 50))
-    (paint (region "soma") (ion-reversal-potential "k" -85))
+    (paint (region "soma") (ion-reversal-potential "na" 50 (scalar 1.0)))
+    (paint (region "soma") (ion-reversal-potential "k" -85 (scalar 1.0)))
     (paint (region "soma") (density (mechanism "BBP::NaTs2_t" ("gNaTs2_tbar" 0.98395500000000002))))
     (paint (region "soma") (density (mechanism "BBP::SKv3_1" ("gSKv3_1bar" 0.30347200000000002))))
     (paint (region "soma") (density (mechanism "BBP::SK_E2" ("gSK_E2bar" 0.0084069999999999995))))
     (paint (region "soma") (density (mechanism "BBP::Ca_HVA" ("gCa_HVAbar" 0.00099400000000000009))))
     (paint (region "soma") (density (mechanism "BBP::Ca_LVAst" ("gCa_LVAstbar" 0.00033300000000000002))))
     (paint (region "soma") (density (mechanism "BBP::CaDynamics_E2" ("gamma" 0.00060899999999999995) ("decay" 210.48528400000001))))
     (paint (region "soma") (density (mechanism "BBP::Ih" ("gIhbar" 8.0000000000000007e-05))))
-    (paint (region "axon") (ion-reversal-potential "na" 50))
-    (paint (region "axon") (ion-reversal-potential "k" -85))
+    (paint (region "axon") (ion-reversal-potential "na" 50 (scalar 1.0)))
+    (paint (region "axon") (ion-reversal-potential "k" -85 (scalar 1.0)))
     (paint (region "axon") (density (mechanism "BBP::NaTa_t" ("gNaTa_tbar" 3.1379679999999999))))
     (paint (region "axon") (density (mechanism "BBP::Nap_Et2" ("gNap_Et2bar" 0.0068269999999999997))))
     (paint (region "axon") (density (mechanism "BBP::K_Pst" ("gK_Pstbar" 0.97353800000000001))))
@@ -26,11 +26,11 @@
     (paint (region "axon") (density (mechanism "BBP::Ca_HVA" ("gCa_HVAbar" 0.00098999999999999999))))
     (paint (region "axon") (density (mechanism "BBP::Ca_LVAst" ("gCa_LVAstbar" 0.0087519999999999994))))
     (paint (region "axon") (density (mechanism "BBP::CaDynamics_E2" ("gamma" 0.0029099999999999998) ("decay" 287.19873100000001))))
-    (paint (region "dend") (membrane-capacitance 0.02))
+    (paint (region "dend") (membrane-capacitance 0.02 (scalar 1.0)))
     (paint (region "dend") (density (mechanism "BBP::Ih" ("gIhbar" 8.0000000000000007e-05))))
-    (paint (region "apic") (ion-reversal-potential "na" 50))
-    (paint (region "apic") (ion-reversal-potential "k" -85))
-    (paint (region "apic") (membrane-capacitance 0.02))
+    (paint (region "apic") (ion-reversal-potential "na" 50 (scalar 1.0)))
+    (paint (region "apic") (ion-reversal-potential "k" -85 (scalar 1.0)))
+    (paint (region "apic") (membrane-capacitance 0.02 (scalar 1.0)))
     (paint (region "apic") (density (mechanism "BBP::NaTs2_t" ("gNaTs2_tbar" 0.026145000000000002))))
     (paint (region "apic") (density (mechanism "BBP::SKv3_1" ("gSKv3_1bar" 0.0042259999999999997))))
     (paint (region "apic") (density (mechanism "BBP::Im" ("gImbar" 0.00014300000000000001))))

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_axon_replacement.acc b/bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_axon_replacement.acc
@@ -1,6 +1,6 @@
 (arbor-component 
   (meta-data 
-    (version "0.1-dev"))
+    (version "0.9-dev"))
   (morphology 
     (branch 0 -1 
       (segment 0 

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_cell_decor.acc b/bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_cell_decor.acc
@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (decor
-    (paint (region "soma") (membrane-capacitance 0.01))
+    (paint (region "soma") (membrane-capacitance 0.01 (scalar 1.0)))
     (paint (region "soma") (density (mechanism "default::hh" ("gnabar" 0.10299326453483033) ("gkbar" 0.027124836082684685))))))
diff --git a/bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_cell_label_dict.acc b/bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_cell_label_dict.acc
@@ -1,5 +1,5 @@
 (arbor-component
-  (meta-data (version "0.1-dev"))
+  (meta-data (version "0.9-dev"))
   (label-dict
     (region-def "all" (all))
     (region-def "soma" (tag 1))

diff --git a/bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_modified.acc b/bluepyopt/tests/test_ephys/testdata/acc/simplecell/simple_modified.acc
@@ -1,6 +1,6 @@
 (arbor-component 
   (meta-data 
-    (version "0.1-dev"))
+    (version "0.9-dev"))
   (morphology 
     (branch 0 -1 
       (segment 0