Integrating more feedback from Anil, fixed L5PC ACC test

lukasgd · lukasgd · commit 04ce61439f89 · 2023-01-04T21:44:39.000+01:00
diff --git a/bluepyopt/ephys/create_acc.py b/bluepyopt/ephys/create_acc.py
@@ -5,7 +5,7 @@
 import io
 import logging
 import pathlib
-from collections import namedtuple, OrderedDict
+from collections import ChainMap, namedtuple, OrderedDict
 import re
 
 import jinja2
@@ -24,12 +24,23 @@
 RangeIExpr = namedtuple('RangeIExpr', 'name, value, scale')
 
 
-# Define Neuron to Arbor parameter conversions (conv defaults to identity)
 class ArbVar:
+    """Definition of a Neuron to Arbor parameter conversion"""
+
     def __init__(self, name, conv=None):
+        """Constructor
+
+        Args:
+            name (str): Arbor parameter name
+            conv (): Conversion of parameter value from Neuron units
+            to Arbor (defaults to identity)
+        """
         self.name = name
         self.conv = conv
 
+    def __repr__(self):
+        return 'ArbVar(%s, %s)' % (self.name, self.conv)
+
 
 class Nrn2ArbParamAdapter:
     """Converts a Neuron parameter to Arbor format (name and value)"""
@@ -220,9 +231,9 @@ def process_global(cls, params):
             params (): List of global parameters in Neuron format
 
         Returns:
-            A mapping of mechanism to parameters. The mechanism parameters are
-            in Arbor format (mechanism name is None for non-mechanism
-            parameters).
+            A mapping of mechanism to parameters representing Arbor global
+            properties. The mechanism parameters are in Arbor format
+            (mechanism name is None for non-mechanism parameters).
         """
         return cls._format_params_and_group_by_mech(
             [Location(name=name, value=value)
@@ -240,10 +251,11 @@ def process_local(cls, params, channels):
             channels (): Mapping of Arbor label to co-located NMODL mechanisms
 
         Returns:
-            In the first component, a two-level mapping of Arbor label to
-            mechanism to parameters. The mechanism parameters are in Arbor
-            format (mechanism name is None for non-mechanism parameters).
-            In the second component, the global properties found are returned.
+            The return value is a tuple. In the first component, a two-level
+            mapping of Arbor label to mechanism to parameters. The mechanism
+            parameters are in Arbor format (mechanism name is None for
+            non-mechanism parameters). In the second component, the
+            Arbor global properties found are returned.
         """
         local_mechs = dict()
         global_properties = dict()
@@ -253,9 +265,12 @@ def process_local(cls, params, channels):
 
             # move Arbor global properties to global_params
             mechs, global_props = cls._separate_global_properties(loc, mechs)
-            for mech, props in global_props.items():
-                global_properties[mech] = \
-                    global_properties.get(mech, []) + props
+            if global_props.keys() != {None}:
+                raise CreateAccException(
+                    'Support for Arbor default mechanisms not implemented.')
+            # iterate over global_props items if above exception triggers
+            global_properties[None] = \
+                global_properties.get(None, []) + global_props[None]
             local_mechs[loc] = mechs
         return local_mechs, global_properties
 
@@ -509,19 +524,18 @@ def _arb_populate_label_dict(local_mechs, local_scaled_mechs, pprocess_mechs):
 
     label_dict = dict()
 
-    for acc_labels in [local_mechs.keys(),
-                       local_scaled_mechs.keys(),
-                       pprocess_mechs.keys()]:
-        for acc_label in acc_labels:
-            if acc_label.name in label_dict and \
-                    acc_label != label_dict[acc_label.name]:
-                raise CreateAccException(
-                    'Label %s already exists in' % acc_label.name +
-                    ' label_dict with different s-expression: '
-                    ' %s != %s.' % (label_dict[acc_label.name].loc,
-                                    acc_label.loc))
-            elif acc_label.name not in label_dict:
-                label_dict[acc_label.name] = acc_label
+    acc_labels = ChainMap(local_mechs, local_scaled_mechs, pprocess_mechs)
+
+    for acc_label in acc_labels:
+        if acc_label.name in label_dict and \
+                acc_label != label_dict[acc_label.name]:
+            raise CreateAccException(
+                'Label %s already exists in' % acc_label.name +
+                ' label_dict with different s-expression: '
+                ' %s != %s.' % (label_dict[acc_label.name].loc,
+                                acc_label.loc))
+        elif acc_label.name not in label_dict:
+            label_dict[acc_label.name] = acc_label
 
     return label_dict
 
@@ -592,6 +606,9 @@ def create_acc(mechs,
         of a custom template
     '''
 
+    if custom_jinja_params is None:
+        custom_jinja_params = {}
+
     if pathlib.Path(morphology).suffix.lower() not in ['.swc', '.asc']:
         raise CreateAccException("Morphology file %s not supported in Arbor "
                                  " (only supported types are .swc and .asc)."
@@ -642,9 +659,6 @@ def create_acc(mechs,
                                            default_location_order,
                                            _arb_loc_desc)
 
-    if custom_jinja_params is None:
-        custom_jinja_params = {}
-
     filenames = {
         name: template_name + (name if name.startswith('.') else "_" + name)
         for name in templates.keys()}
@@ -825,7 +839,7 @@ def read_acc(cell_json_filename):
 
 class CreateAccException(Exception):
 
-    """All exceptions generated by create_acc module"""
+    """Exceptions generated by create_acc module"""
 
     def __init__(self, message):
         """Constructor"""
diff --git a/bluepyopt/tests/test_ephys/test_create_acc.py b/bluepyopt/tests/test_ephys/test_create_acc.py
@@ -583,19 +583,28 @@ def test_cell_model_create_acc_replace_axon_without_instantiate():
 def check_acc_dir(test_dir, ref_dir):
     assert os.listdir(ref_dir) == os.listdir(test_dir)
 
+    ref_dir_ver_suffix = '_py' + ''.join(sys.version.split('.')[:2])
+    ref_dir_ver = ref_dir.parent / (ref_dir.name + ref_dir_ver_suffix)
+
     for file in os.listdir(ref_dir):
+
+        if (ref_dir_ver / file).exists():
+            ref_dir_file = ref_dir_ver
+        else:
+            ref_dir_file = ref_dir
+
         if file.endswith('.json'):
             with open(os.path.join(test_dir, file)) as f:
                 cell_json_dict = json.load(f)
-            with open(ref_dir / file) as f:
+            with open(ref_dir_file / file) as f:
                 ref_cell_json = json.load(f)
             for k in ref_cell_json:
                 if k != 'produced_by':
                     assert ref_cell_json[k] == cell_json_dict[k]
         else:
             with open(os.path.join(test_dir, file)) as f:
                 test_file = f.read()
-            with open(ref_dir / file) as f:
+            with open(ref_dir_file / file) as f:
                 ref_file = f.read()
             assert ref_file == test_file
 
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
@@ -9,13 +9,13 @@
         2)
       (segment 1 
         (point 262.996735 -9.641676 -3.380000 0.690000)
-        (point 262.745453 -24.639570 -3.380000 0.690000)
+        (point 262.745453 -24.639572 -3.380000 0.690000)
         2)
       (segment 2 
-        (point 262.745453 -24.639570 -3.380000 0.460000)
+        (point 262.745453 -24.639572 -3.380000 0.460000)
         (point 262.494171 -39.637466 -3.380000 0.460000)
         2)
       (segment 3 
         (point 262.494171 -39.637466 -3.380000 0.460000)
-        (point 262.242889 -54.635361 -3.380000 0.460000)
+        (point 262.242889 -54.635365 -3.380000 0.460000)
         2))))
diff --git a/bluepyopt/tests/test_ephys/testdata/acc/l5pc/C060114A7_modified.acc b/bluepyopt/tests/test_ephys/testdata/acc/l5pc/C060114A7_modified.acc
@@ -21690,13 +21690,13 @@
         2)
       (segment 5372 
         (point 262.996735 -9.641676 -3.380000 0.690000)
-        (point 262.745453 -24.639570 -3.380000 0.690000)
+        (point 262.745453 -24.639572 -3.380000 0.690000)
         2)
       (segment 5373 
-        (point 262.745453 -24.639570 -3.380000 0.460000)
+        (point 262.745453 -24.639572 -3.380000 0.460000)
         (point 262.494171 -39.637466 -3.380000 0.460000)
         2)
       (segment 5374 
         (point 262.494171 -39.637466 -3.380000 0.460000)
-        (point 262.242889 -54.635361 -3.380000 0.460000)
+        (point 262.242889 -54.635365 -3.380000 0.460000)
         2))))
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
@@ -0,0 +1,37 @@
+(arbor-component
+  (meta-data (version "0.1-dev"))
+  (decor
+    (default (membrane-potential -65))
+    (default (temperature-kelvin 307.14999999999998))
+    (default (membrane-capacitance 0.01))
+    (default (axial-resistivity 100))
+    (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") (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") (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))))
+    (paint (region "axon") (density (mechanism "BBP::K_Tst" ("gK_Tstbar" 0.089259000000000005))))
+    (paint (region "axon") (density (mechanism "BBP::SK_E2" ("gSK_E2bar" 0.0071040000000000001))))
+    (paint (region "axon") (density (mechanism "BBP::SKv3_1" ("gSKv3_1bar" 1.0219450000000001))))
+    (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") (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") (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))))
+    (paint (region "apic") (scaled-mechanism (density (mechanism "BBP::Ih" ("gIhbar" 8.0000000000000007e-05))) ("gIhbar" (add (mul (scalar -1) (scalar 0.86960000000000004) ) (mul (scalar 2.0870000000000002) (exp (mul (distance (region "soma")) (scalar 0.0030999999999999999) ) ) ) ))))))
