Merge pull request #584 from sys-bio/develop

Update for python 3.12

docs/_notebooks/core/tellurium_examples.rst

@@ -169,12 +169,12 @@ conditions resulting in different steady states reached.
     print(r.selections)
     
     initValue = 0.05
-    m = r.simulate (0, 4, 100, selections=["time", "S1"])
+    m = r.simulate (0, 4, 100, selections=["time", "[S1]"])
     
     for i in range (0,12):
         r.reset()
         r['[S1]'] = initValue
-        res = r.simulate (0, 4, 100, selections=["S1"])
+        res = r.simulate (0, 4, 100, selections=["[S1]"])
         m = np.concatenate([m, res], axis=1)
         initValue += 1
     

tellurium/VERSION.txt

@@ -1 +1 @@
-2.2.9
+2.2.10

tellurium/__init__.py

@@ -136,13 +136,6 @@
     executeInlineOmexFromFile,
 )
 
-# Package utilities
-from tellurium.utils.package import (
-    searchPackage,
-    installPackage,
-    upgradePackage,
-    uninstallPackage,
-)
 from tellurium.utils.misc import(
     saveToFile,
     readFromFile,

tellurium/teconverters/convert_omex.py

@@ -9,7 +9,6 @@
 import getpass
 
 
-import imp  # reloads because numl is overwriting symbols
 try:
     import libcombine
 except ImportError:

tellurium/tests/test_examples.py

@@ -6,8 +6,8 @@
 import unittest
 
 import os
-import imp
 from tellurium.tests.helpers import filesInDirectory
+from importlib.machinery import SourceFileLoader
 
 # ----------------------------------------------------------------
 # List of python files to test
@@ -44,7 +44,7 @@ def test(self=None):
         """ Test failes if Exception in execution of f. """
         if self is not None:
             print(filePath)
-            imp.load_source(os.path.basename(filePath)[:-3], filePath)
+            SourceFileLoader(os.path.basename(filePath)[:-3], filePath).load_module()
     return test
 
 

tellurium/utils/misc.py

@@ -85,7 +85,7 @@ def runTool (toolFileName):
         root, waste = os.path.split(p)
         toolFileName[0] = root + '\\telluriumTools\\' + toolFileName[0] + '\\' + toolFileName[0] + '.exe'
         return subprocess.check_output(toolFileName)
-    except subprocess.CalledProcessError as e:
+    except subprocess.CalledProcessError:
         raise Exception('Tool failed to run correctly or could not be found')
 
 # ---------------------------------------------------------------------
@@ -98,7 +98,7 @@ def getODEsFromSBMLFile (fileName):
     
     >>> te.getODEsFromSBMLFile ('mymodel.xml')
     """
-    sbmlStr = te.readFromFile (fileName)
+    sbmlStr = readFromFile (fileName)
     extractor = ODEExtractor (sbmlStr)
     return extractor.toString()
 
@@ -197,7 +197,6 @@ def __init__(self, sbmlStr):
         self.use_species_names = False
         self.use_ids = True
 
-        from collections import defaultdict
         self.accumulators = {}
         self.accumulator_list = []
 

tellurium/utils/omex.py

@@ -57,9 +57,9 @@ def __init__(self, location, format=None, formatKey=None, master=False, descript
 
     def __str__(self):
         if self.master:
-            return '<*master* Entry {} | {}>'.format(self.master, self.location, self.format)
+            return '<*master* Entry {} | {}>'.format(self.location, self.format)
         else:
-            return '<Entry {} | {}>'.format(self.master, self.location, self.format)
+            return '<Entry {} | {}>'.format(self.location, self.format)
 
 
 class Creator(object):
@@ -90,7 +90,7 @@ def combineArchiveFromDirectory(directory, omexPath, creators=None, creators_for
 
     print(manifest_path)
     if os.path.exists(manifest_path):
-        warnings.warn("Manifest file exists in directory, but not used in COMBINE archive creation: %s".format(manifest_path))
+        warnings.warn("Manifest file exists in directory {}, but not used in COMBINE archive creation: %s".format(manifest_path))
 
     # add the base entry
     entries = [

tellurium/utils/uncertainty.py

@@ -8,7 +8,6 @@
 te.setDefaultPlottingEngine("matplotlib")
 import numpy as np 
 import random
-import roadrunner
 import matplotlib
 import matplotlib.pyplot as plt
 import matplotlib.gridspec as gs