Fix reproducibility test

fc/cli.py

@@ -30,13 +30,17 @@ def run_protocol():
 def extract_outputs():
     """Extract CSV files of outputs from a single HDF5 file."""
     parser = argparse.ArgumentParser(description='Extract CSV files from a protocol output HDF5 file')
+    parser.add_argument('-o', '--output', help='a specific output name to extract')
     parser.add_argument('h5path', help='path to the HDF5 file containing all outputs')
     args = parser.parse_args()
 
     with tables.open_file(args.h5path, 'r') as h5file:
         output_folder = os.path.dirname(args.h5path)
-        for output in h5file.root.output._v_leaves.keys():
-            extract_output(h5file, output, output_folder)
+        if args.output:
+            extract_output(h5file, args.output, output_folder)
+        else:
+            for output in h5file.root.output._v_leaves.keys():
+                extract_output(h5file, output, output_folder)
 
 
 def check_syntax():

fc/code_generation.py

@@ -12,9 +12,14 @@
 from cellmlmanip.parser import SYMPY_SYMBOL_DELIMITER, Transpiler
 from cellmlmanip.printer import Printer
 
-# Tell cellmlmanip to create _exp objects instead of exp objects. This prevents Sympy doing simplification (or
+# Tell cellmlmanip to create _exp objects instead of exp objects, etc. This prevents Sympy doing simplification (or
 # canonicalisation) resulting in weird errors with exps in some cardiac models.
 Transpiler.set_mathml_handler('exp', sympy.Function('_exp'))
+Transpiler.set_mathml_handler('abs', sympy.Function('_abs'))
+Transpiler.set_mathml_handler('sqrt', sympy.Function('_sqrt'))
+Transpiler.set_mathml_handler('sin', sympy.Function('_sin'))
+Transpiler.set_mathml_handler('cos', sympy.Function('_cos'))
+Transpiler.set_mathml_handler('acos', sympy.Function('_acos'))
 
 
 # Shared Jinja environment
@@ -129,8 +134,13 @@ class WebLabPrinter(Printer):
     def __init__(self, symbol_function=None, derivative_function=None):
         super().__init__(symbol_function, derivative_function)
 
-        # Deal with _exp function introduced to avoid simplification
+        # Deal with functions introduced to avoid simplification
         self._function_names['_exp'] = 'math.exp'
+        self._function_names['_abs'] = 'math.fabs'
+        self._function_names['_sqrt'] = 'math.sqrt'
+        self._function_names['_sin'] = 'math.sin'
+        self._function_names['_cos'] = 'math.cos'
+        self._function_names['_acos'] = 'math.acos'
 
 
 def get_unique_names(model):

fc/data_loading.py

@@ -36,8 +36,16 @@ def load(file_path):
         f = gzip.GzipFile(real_path, 'rb')
     else:
         f = open(real_path, 'r')
-    f.readline()  # strip comment line
-    dims = list(map(int, f.readline().split(',')))[1:]
-    array = np.loadtxt(f, dtype=float)
+    # Check for presence of comment line indicating special n-d format
+    comment = f.readline()
+    if comment.startswith('#'):
+        dims = list(map(int, f.readline().strip().split(',')))[1:]
+        array = np.loadtxt(f, dtype=float)
+        result = V.Array(array.reshape(tuple(dims)))
+    else:
+        # Simple 1d column-oriented data
+        f.seek(0)
+        array = np.loadtxt(f, dtype=float)
+        result = V.Array(array)
     f.close()
-    return V.Array(array.reshape(tuple(dims)))
+    return result

fc/simulations/model.py

@@ -186,7 +186,7 @@ def simulate(self, end_point):
         for name, expr in self.input_exprs.items():
             self.proto.set_input(name, expr.evaluate(self.sim_env))
 #         self.proto.SetOutputfolder(self.output_path) #TODO
-        self.proto.run()
+        self.proto.run(write_out=False)
 
 
 class TestOdeModel(AbstractOdeModel):

test/output/real/aslanidi_Purkinje_model_2009/NCX_block/outputs_scaled_APD90.csv

@@ -1,13 +1,13 @@
 # APD90
 1,11
-113.7025702663205
-112.2887184503283
-110.8843715004111
-109.489444734739
-108.1039583517426
-106.7280027680522
-105.3634125858407
-104.0082867478811
-102.6624630270142
-101.3265499071116
-100
+1.137024883097638082e+02
+1.122889659381754655e+02
+1.108847784389487572e+02
+1.094895502345863036e+02
+1.081041933317954857e+02
+1.067280965952242440e+02
+1.053635702981335669e+02
+1.040084862165954291e+02
+1.026628406790865569e+02
+1.013265493794613405e+02
+1.000000000000000000e+02

test/output/real/aslanidi_Purkinje_model_2009/NCX_block/outputs_scaled_resting_potential.csv

@@ -1,13 +1,13 @@
 # Resting potential
 1,11
--99.71737459216668
--99.74588090866968
--99.77434325432121
--99.80273737709383
--99.83108615772576
--99.85937196116815
--99.88760584136625
--99.91579160696091
--99.94392018712578
--99.97198403007278
--100
+-9.971737498371513198e+01
+-9.974588083467261868e+01
+-9.977434409535084114e+01
+-9.980273908271838934e+01
+-9.983108771753339283e+01
+-9.985937258207981415e+01
+-9.988760600541388612e+01
+-9.991579180449498665e+01
+-9.994392106046188928e+01
+-9.997198485451123418e+01
+-1.000000000000000000e+02