Merge pull request #429 from sys-bio/develop

Pull to HEAD
sys-bio · Jan 24, 2019 · 1be924c · 1be924c
2 parents 08705f3 + 796c632
commit 1be924c
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Showing 6 changed files with 13 additions and 12 deletions.
diff --git a/requirements.txt b/requirements.txt
@@ -5,7 +5,7 @@ matplotlib>=2.0.2
 pandas>=0.20.2
 
 # SBW-derived
-libroadrunner>=1.4.24
+libroadrunner>=1.5.3
 phrasedml>=1.0.9
 antimony>=2.9.4
 rrplugins>=1.1.10

diff --git a/tellurium/VERSION.txt b/tellurium/VERSION.txt
@@ -1 +1 @@
-2.1.4
+2.1.5
diff --git a/tellurium/sedml/tesedml.py b/tellurium/sedml/tesedml.py
@@ -1544,7 +1544,7 @@ def outputPlotSettings():
 
         # all lines of same cuve have same color
         settings = PlotSettings(
-            colors=[u'C0', u'C1', u'C2', u'C3', u'C4', u'C5', u'C6', u'C7', u'C8', u'C9'],
+            colors=[u'#1f77b4', u'#ff7f0e', u'#2ca02c', u'#d62728', u'#9467bd', u'#8c564b', u'#e377c2', u'#7f7f7f', u'#bcbd22', u'#17becf'],
             figsize=(9, 5),
             dpi=80,
             facecolor='w',

diff --git a/tellurium/teconverters/inline_omex.py b/tellurium/teconverters/inline_omex.py
@@ -52,7 +52,7 @@ def __init__(self, sources):
             description=DumpJSONInfo(),
             creator=readCreator()
         )
-
+        
         # Convert antimony to sbml
         for t, loc, master in (
         (x['source'], x['location'] if 'location' in x else None, x['master'] if 'master' in x else None)
@@ -88,7 +88,7 @@ def __init__(self, sources):
 
 
     @classmethod
-    def fromString(cls, omex_str):
+    def fromString(cls, omex_str, comp=False):
         """Given mixed Antimony/PhraSEDML, separates out the constituent parts.
         Assumes that Antimony and PhraSEDML are not mixed on the same line.
 
@@ -183,10 +183,11 @@ def add_source(src, type, args):
                     sources.remove(src)
                 elif src['type'] == 'antimony':
                     antimony_combined += src['source']
-            sources = [{
-                'source': antimony_combined,
-                'type': 'antimony',
-            }]
+            if comp:
+                sources = [{
+                    'source': antimony_combined,
+                    'type': 'antimony',
+                }]
             if phrasedml_combined:
                 sources.append({
                     'source': phrasedml_combined,

diff --git a/tellurium/tellurium.py b/tellurium/tellurium.py
@@ -695,12 +695,12 @@ def exportInlineOmex(inline_omex, export_location):
     saveInlineOMEX(inline_omex, export_location)
 
 
-def executeInlineOmex(inline_omex):
+def executeInlineOmex(inline_omex, comp=False):
     """ Execute inline phrasedml and antimony.
 
     :param inline_omex: String containing inline phrasedml and antimony.
     """
-    in_omex = teconverters.inlineOmex.fromString(inline_omex)
+    in_omex = teconverters.inlineOmex.fromString(inline_omex, comp=comp)
     in_omex.executeOmex()
 
 

diff --git a/tellurium/tests/test_tellurium.py b/tellurium/tests/test_tellurium.py
@@ -283,7 +283,7 @@ def test_jarnac_vs(self):
     def test_jarnac_dv(self):
         r = te.loada(self.ant_str)
         m1 = r.dv()
-        m2 = r.model.getStateVectorRate()
+        m2 = r.getRatesOfChange()
         self.assertTrue(np.allclose(m1, m2))
 
     def test_jarnac_rv(self):