Merge pull request #119 from matthiaskoenig/develop

library updates for 0.3.3 release
matthiaskoenig · Apr 29, 2019 · e3add7e · e3add7e
2 parents 3048bc8 + 336fae9
commit e3add7e
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Showing 10 changed files with 5 additions and 113 deletions.
diff --git a/README.md b/README.md
@@ -63,7 +63,7 @@ pip install -e .
 ```
 
 ## Release notes
-### 0.3.1
+### 0.3.1 - 0.3.3
 * libSBML 5.18.0
 * initial distrib support
 

diff --git a/requirements.txt b/requirements.txt
@@ -1 +1 @@
-.
+.
diff --git a/sbmlutils/_version.py b/sbmlutils/_version.py
@@ -1,7 +1,7 @@
 """
 Definition of version string.
 """
-__version__ = "0.3.2"
+__version__ = "0.3.3"
 
 PROGRAM_VERSION = __version__
 PROGRAM_NAME = 'sbmlutils'
diff --git a/sbmlutils/distrib/distrib_all.xml → sbmlutils/distrib/distrib.xml b/sbmlutils/distrib/distrib_all.xml → sbmlutils/distrib/distrib.xml
diff --git a/sbmlutils/distrib/uncertainty.xml b/sbmlutils/distrib/uncertainty.xml
@@ -4,7 +4,6 @@
     <listOfParameters>
       <parameter id="p1" value="1" units="mole" constant="false">
         <distrib:listOfUncertainties>
-          <distrib:uncertainty/>
           <distrib:uncertainty metaid="meta_uncertainty1" distrib:name="Basic example: 5.0 +- 0.3 [2.0 - 8.0]">
             <annotation>
               <body xmlns="http://www.w3.org/1999/xhtml">

diff --git a/sbmlutils/distrib/uncertainty_uncert_parameter.xml b/sbmlutils/distrib/uncertainty_uncert_parameter.xml
diff --git a/sbmlutils/distrib/uncertainty_uncertspan.xml b/sbmlutils/distrib/uncertainty_uncertspan.xml
diff --git a/sbmlutils/distrib/uncertainty_uncertvalue.xml b/sbmlutils/distrib/uncertainty_uncertvalue.xml
diff --git a/sbmlutils/tests/modelcreator/test_modelcreator.py b/sbmlutils/tests/modelcreator/test_modelcreator.py
@@ -64,6 +64,5 @@ def test_create_distrib():
     distrib_factory.create_distrib(tmp=True)
 
 
-@pytest.mark.skip(reason="Uncertainty currently not supported in libsbml-5.18.0")
 def test_create_distrib():
     distrib_factory.create_distrib(tmp=True)
diff --git a/setup.py b/setup.py
@@ -77,14 +77,13 @@ def read(*names, **kwargs):
         "pyexcel-xlsx>=0.5.7",
 
         # standards
-        "python-libsbml>=5.18.0",
+        "python-libsbml-experimental>=5.18.0",
         "phrasedml>=1.0.9",  # not working on py37
         "antimony>=2.9.4",  # not working on py37
 
         # simulation
         "libroadrunner>=1.5.3",
-        # "cobra @ git+ssh://git@github.com/opencobra/cobrapy@sbml-bugfixes",  # libSBML 5.18.0 dependencies
-        "cobra>=0.15.2",
+        "cobra>=0.15.3",
         "optlang>=1.4.4",
 
         # misc