Merge branch 'master' into test_arbor_eden

.gitignore

@@ -122,3 +122,4 @@ report*.txt
 /utilities/tests/*.gen.c
 /utilities/tests/*_eden.py
 arm64
+/*ken.sh

omv/__init__.py

@@ -1 +1,8 @@
-__version__ = '0.2.7'
+try:
+    import importlib.metadata
+
+    __version__ = importlib.metadata.version("OSBModelValidation")
+except ImportError:
+    import importlib_metadata
+
+    __version__ = importlib_metadata.version("OSBModelValidation")

omv/analyzers/__init__.py

@@ -9,30 +9,13 @@
 from omv.analyzers.timeseries import TimeSeriesAnalyzer
 
 OMVAnalyzers = {
-    'spike times' : SpikeAnalyzer,
-    'spike rate' : RateAnalyzer,
-    'dry': DryRunAnalyzer,
-    'resting': RestingAnalyzer,
-    'morphology': MorphologyAnalyzer,
-    'temperature': TemperatureAnalyzer,
-    'activation variables': ActivationVariableAnalyzer,
-    'input resistance': InputResAnalyzer,
-    'timeseries': TimeSeriesAnalyzer
+    "spike times": SpikeAnalyzer,
+    "spike rate": RateAnalyzer,
+    "dry": DryRunAnalyzer,
+    "resting": RestingAnalyzer,
+    "morphology": MorphologyAnalyzer,
+    "temperature": TemperatureAnalyzer,
+    "activation variables": ActivationVariableAnalyzer,
+    "input resistance": InputResAnalyzer,
+    "timeseries": TimeSeriesAnalyzer,
 }
-
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-

omv/analyzers/activation.py

@@ -5,38 +5,20 @@
 
 
 class ActivationVariableAnalyzer(OMVAnalyzer):
-
     def parse_observable(self):
-        if 'file' in self.observable:
-            f = fn.FileNodeHelper(self.observable['file'], self.omt_root)
-            inform('Activation variable from file',
-                   self.observable['file'], indent=1, verbosity=1)
+        if "file" in self.observable:
+            f = fn.FileNodeHelper(self.observable["file"], self.omt_root)
+            inform(
+                "Activation variable from file",
+                self.observable["file"],
+                indent=1,
+                verbosity=1,
+            )
             return f.get_timeseries()
-    
+
     def __call__(self):
         obs = self.parse_observable()
         allin = ts.all_within_bounds(obs, (0, 1))
         if not allin:
-            inform('Activation variable outside of (0,1) interval: ',
-                   obs, indent=1)
+            inform("Activation variable outside of (0,1) interval: ", obs, indent=1)
         return allin
-
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omv/analyzers/analyzer.py

@@ -21,51 +21,60 @@ def parse_observable(self):
         pass
 
     def __call__(self):
-
         try:
             obs = self.parse_observable()
             if obs is None:
-                    inform("Could not determine observed values")
-                    return False
+                inform("Could not determine observed values")
+                return False
             if isinstance(obs, list):
                 for o in obs:
                     if not o:
                         inform("Could not determine observed values")
                         return False
-                    
+
             exp = self.parse_expected()
-            
+
             if exp is None:
-                    inform("Could not determine expected values, value None")
-                    return False
+                inform("Could not determine expected values, value None")
+                return False
             if isinstance(exp, list):
                 for e in exp:
                     if not e:
                         inform("Could not determine expected values")
                         return False
         except IOError as e:
-            inform("Input/output error when\
-                   checking for observable data: %s" % e)
+            inform(
+                "Input/output error when\
+                   checking for observable data: %s"
+                % e
+            )
             return False
-        
+
         try:
-            tolerance = float(self.observable['tolerance'])
+            tolerance = float(self.observable["tolerance"])
         except (TypeError, KeyError):  # observable can be None
             tolerance = 1e-1
 
         are_close, best_tol = compare_arrays((obs, exp), tolerance)
 
         if not are_close:
-            pretty_obs, pretty_exp = pretty_print_copypaste(obs,exp)
-            inform("Comparison of \n\
+            pretty_obs, pretty_exp = pretty_print_copypaste(obs, exp)
+            inform(
+                "Comparison of \n\
                     (observed data): %s\n\
                     and\n\
                     (expected data): %s\n\
-                    failed against tolerance %g" %
-                   (pretty_obs, pretty_exp, tolerance))
+                    failed against tolerance %g"
+                % (pretty_obs, pretty_exp, tolerance)
+            )
             if best_tol:
                 inform("A better tolerance to try is: ", best_tol, indent=1)
         else:
             if best_tol and best_tol < tolerance:
-                inform("Passed, but an even better tolerance might be: %s, as opposed to: %s (diff: %s)" % (best_tol, tolerance,(tolerance-best_tol)), indent=3, verbosity=1)
+                inform(
+                    "Passed, but an even better tolerance might be: %s, as opposed to: %s (diff: %s)"
+                    % (best_tol, tolerance, (tolerance - best_tol)),
+                    indent=3,
+                    verbosity=1,
+                )
         return are_close

omv/analyzers/dryrun.py

@@ -3,24 +3,11 @@
 
 
 class DryRunAnalyzer(OMVAnalyzer):
-
     def __init__(self, ost, expected, engine, omt_root, mep_root):
-        inform('No mep file specified. Will only run simulation using: ',
-               engine, indent=1)
+        inform(
+            "No mep file specified. Will only run simulation using: ", engine, indent=1
+        )
         self.engine = engine
 
     def __call__(self):
         return not self.engine.returncode
-
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omv/analyzers/input_resistance.py

@@ -9,46 +9,39 @@ class InputResAnalyzer(OMVAnalyzer):
     Input resistance
     """
 
-
     def parseOMT(self, to_parse):
-        f = fn.FileNodeHelper(to_parse['file_Vm'], self.omt_root)
-        f_i = fn.FileNodeHelper(to_parse['file_VC_i'], self.omt_root)
-        inform('Calculating input resistance from files:',
-               (f.filename,f_i.filename), indent=1, verbosity=1)
-        h_voltage = to_parse.get('holding voltage', -70.)
-        cmd_voltage = to_parse.get('command voltage', -80.)
-        h_window = to_parse.get('holding window', [0., 0.])
-        cmd_window = to_parse.get('command window', [0., 0.])
+        f = fn.FileNodeHelper(to_parse["file_Vm"], self.omt_root)
+        f_i = fn.FileNodeHelper(to_parse["file_VC_i"], self.omt_root)
+        inform(
+            "Calculating input resistance from files:",
+            (f.filename, f_i.filename),
+            indent=1,
+            verbosity=1,
+        )
+        h_voltage = to_parse.get("holding voltage", -70.0)
+        cmd_voltage = to_parse.get("command voltage", -80.0)
+        h_window = to_parse.get("holding window", [0.0, 0.0])
+        cmd_window = to_parse.get("command window", [0.0, 0.0])
 
         # h_window = [float(t) for t in to_parse.get('holding window', [0., 0.])[0].split()]
         # cmd_window = [float(t) for t in to_parse.get('command window', [0., 0.])[0].split()]
-        inform('Time wondow used for detection of current injections:',
-               (h_window,cmd_window), indent=2, verbosity=1)
-        input_resistance = ts.input_resistance(f.get_timeseries(), f_i.get_timeseries(), h_window, cmd_window, (h_voltage,cmd_voltage))
+        inform(
+            "Time wondow used for detection of current injections:",
+            (h_window, cmd_window),
+            indent=2,
+            verbosity=1,
+        )
+        input_resistance = ts.input_resistance(
+            f.get_timeseries(),
+            f_i.get_timeseries(),
+            h_window,
+            cmd_window,
+            (h_voltage, cmd_voltage),
+        )
         return input_resistance
-    
+
     def parse_expected(self):
         return self.expected
 
     def parse_observable(self):
         return self.parseOMT(self.observable)
-
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omv/analyzers/morphology.py

@@ -1,34 +1,16 @@
 from omv.analyzers.analyzer import OMVAnalyzer
 
+
 class MorphologyAnalyzer(OMVAnalyzer):
-
     def before_running(self):
-        if 'total area' in self.expected:
-            base = self.observable.get('base section', 'cell[0]')
+        if "total area" in self.expected:
+            base = self.observable.get("base section", "cell[0]")
             self.query = self.engine.query_area(base)
 
     def parse_expected(self):
-        return self.expected['total area']
+        return self.expected["total area"]
 
     def parse_observable(self):
         area = float(self.engine.fetch_query(self.query))
-        scale = float(self.observable.get('scaling', 1))
+        scale = float(self.observable.get("scaling", 1))
         return scale * area
-
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