Merge pull request #694 from ICB-DCM/develop

Release 0.10.7

Author: yannikschaelte

python/amici/sbml_import.py

@@ -86,9 +86,10 @@ def __init__(
 
         Arguments:
 
-            sbml_source:  Either a path to SBML file where the model is specified.
-            Or a model string as created by  sbml.sbmlWriter().writeSBMLToString().
-            @type string
+            sbml_source: Either a path to SBML file where the model is
+                specified, or a model string as created by
+                sbml.sbmlWriter().writeSBMLToString() or an instance of
+                libsbml.Model. @type str
 
             show_sbml_warnings: Indicates whether libSBML warnings should be
             displayed (default = True). @type bool
@@ -103,13 +104,15 @@ def __init__(
         Raises:
 
         """
-        self.sbml_reader = sbml.SBMLReader()
-
-        if from_file:
-            sbml_doc = self.sbml_reader.readSBMLFromFile(sbml_source)
+        if isinstance(sbml_source, sbml.Model):
+            self.sbml_doc = sbml_source.getSBMLDocument()
         else:
-            sbml_doc = self.sbml_reader.readSBMLFromString(sbml_source)
-        self.sbml_doc = sbml_doc
+            self.sbml_reader = sbml.SBMLReader()
+            if from_file:
+                sbml_doc = self.sbml_reader.readSBMLFromFile(sbml_source)
+            else:
+                sbml_doc = self.sbml_reader.readSBMLFromString(sbml_source)
+            self.sbml_doc = sbml_doc
 
         self.show_sbml_warnings = show_sbml_warnings
 
@@ -878,13 +881,17 @@ def processObservables(self, observables, sigmas, noise_distributions):
 
         # set cost functions
         llhYStrings = []
-        for y_name in observables:
+        for y_name in observableNames:
             llhYStrings.append(noise_distribution_to_cost_function(
                 noise_distributions.get(y_name, 'normal')))
 
         llhYValues = []
-        for llhYString, o_sym, m_sym, s_sym in zip(llhYStrings, observableSyms, measurementYSyms, sigmaYSyms):
-            f = sp.sympify(llhYString(o_sym), locals={str(o_sym): o_sym, str(m_sym): m_sym, str(s_sym): s_sym})
+        for llhYString, o_sym, m_sym, s_sym \
+                in zip(llhYStrings, observableSyms,
+                       measurementYSyms, sigmaYSyms):
+            f = sp.sympify(llhYString(o_sym), locals={str(o_sym): o_sym,
+                                                      str(m_sym): m_sym,
+                                                      str(s_sym): s_sym})
             llhYValues.append(f)
         llhYValues = sp.Matrix(llhYValues)
 

tests/testMisc.py

@@ -8,6 +8,9 @@
 import os
 import unittest
 import sympy as sp
+import libsbml
+from tempfile import TemporaryDirectory
+
 
 class TestAmiciMisc(unittest.TestCase):
     """TestCase class various AMICI Python interface functions"""
@@ -47,6 +50,18 @@ def test_csc_matrix(self):
         assert symbolList == ['a0', 'a1', 'a2']
         assert str(sparseMatrix) == 'Matrix([[a0, 0], [a1, a2]])'
 
+    def test_csc_matrix_empty(self):
+        """Test sparse CSC matrix creation for empty matrix"""
+        matrix = sp.Matrix()
+        symbolColPtrs, symbolRowVals, sparseList, symbolList, sparseMatrix = \
+            amici.ode_export.csc_matrix(matrix, 'a')
+        print(symbolColPtrs, symbolRowVals, sparseList, symbolList, sparseMatrix)
+        assert symbolColPtrs == [0]
+        assert symbolRowVals == []
+        assert sparseList == sp.Matrix(0, 0, [])
+        assert symbolList == []
+        assert str(sparseMatrix) == 'Matrix(0, 0, [])'
+
     def test_csc_matrix_vector(self):
         """Test sparse CSC matrix creation from matrix slice"""
         matrix = sp.Matrix([[1, 0], [2, 3]])
@@ -70,6 +85,29 @@ def test_csc_matrix_vector(self):
         assert symbolList == ['a2']
         assert str(sparseMatrix) == 'Matrix([[0], [a2]])'
 
+    def test_sbml2amici_no_observables(self):
+        """Test model generation works for model without observables"""
+
+        document = libsbml.SBMLDocument(3, 1)
+        model = document.createModel()
+        model.setTimeUnits("second")
+        model.setExtentUnits("mole")
+        model.setSubstanceUnits('mole')
+        c1 = model.createCompartment()
+        c1.setId('C1')
+        model.addCompartment(c1)
+        s1 = model.createSpecies()
+        s1.setId('S1')
+        s1.setCompartment('C1')
+        model.addSpecies(s1)
+
+        sbml_importer = amici.sbml_import.SbmlImporter(sbml_source=model,
+                                                       from_file=False)
+        tmpdir = TemporaryDirectory()
+        sbml_importer.sbml2amici(modelName="test",
+                                 output_dir=tmpdir.name,
+                                 observables=None)
+
 
 if __name__ == '__main__':
     suite = unittest.TestSuite()

version.txt

@@ -1 +1 @@
-0.10.6
+0.10.7