Merge pull request #558 from sys-bio/develop

Merge for new maintenance release.

README.md

@@ -108,8 +108,8 @@ following the instructions on [this page](https://github.com/sys-bio/tellurium/w
 We strongly suggest you to completely remove the older version of Tellurium Spyder IDE prior to installing one of the 2.1.0+ versions.
 
 1. Download Tellurium Spyder for Windows:
-    * [Python 3.7](https://sourceforge.net/projects/pytellurium/files/Tellurium-2.3/2.3.3/Tellurium-2.3.3-Python-3.7-win64-setup.exe/download)
-    * [Python 3.8](https://sourceforge.net/projects/pytellurium/files/Tellurium-2.3/2.3.3/Tellurium-2.3.3-Python-3.8-win64-setup.exe/download)
+    * [Python 3.7](https://sourceforge.net/projects/pytellurium/files/Tellurium-2.3/2.3.5/Tellurium-2.3.5-Python-3.7-win64-setup.exe/download)
+    * [Python 3.8](https://sourceforge.net/projects/pytellurium/files/Tellurium-2.3/2.3.5/Tellurium-2.3.5-Python-3.8-win64-setup.exe/download)
 2. Double-click the installer to start the installation
 3. Follow the instructions
 

requirements.txt

@@ -3,10 +3,10 @@ scipy>=1.5.1
 matplotlib>=2.0.2
 pandas>=0.20.2
 libroadrunner>=2.0.3
-rrplugins>=2.0.3
-phrasedml>=1.0.9
+rrplugins>=2.0.3; platform_machine != "arm64"
+phrasedml>=1.0.9; (python_version < '3.10' and platform_machine != "arm64")
 antimony>=2.12.0
-sbml2matlab>=0.9.1
+sbml2matlab>=0.9.1; (python_version < '3.10' and platform_machine != "arm64")
 python-libsbml>=5.18.0
 python-libnuml>=1.0.0
 python-libsedml>=2.0.17

setup.py

@@ -48,10 +48,7 @@
           'pandas>=0.20.2',
           # SBW-derived
           'libroadrunner>=2.0.3',
-          'rrplugins>=2.0.3',
-          'phrasedml>=1.0.9',
           'antimony>=2.12.0',
-          'sbml2matlab>=0.9.1',
           # standards
           'python-libsbml>=5.18.0',
           'python-libnuml>=1.0.0',
@@ -69,5 +66,14 @@
           'ipykernel>=4.6.1',
           # testing
           'pytest',
-          ]
+          ],
+      extras_require={
+        ':(python_version < "3.10" and platform_machine != "arm64")': [
+          'phrasedml>=1.0.9',
+          'sbml2matlab>=0.9.1',
+          ],
+        ': platform_machine != "arm64"': [
+          'rrplugins>=2.0.3',
+          ],
+          },
       )

spyder_mod/Spyder 5.1.5/site-packages/spyder/config/main.py

@@ -147,7 +147,7 @@
               'pylab/inline/width': 6,
               'pylab/inline/height': 4,
               'pylab/inline/bbox_inches': True,
-              'startup/run_lines': 'import antimony; import sbml2matlab; import rrplugins; import numpy; import scipy; import matplotlib; import roadrunner; import tellurium as te',
+              'startup/run_lines': 'import antimony; import rrplugins; import numpy; import scipy; import matplotlib; import roadrunner; import tellurium as te',
               'startup/use_run_file': False,
               'startup/run_file': '',
               'greedy_completer': False,

tellurium/VERSION.txt

@@ -1 +1 @@
-2.2.2.1
+2.2.3

tellurium/__init__.py

@@ -22,9 +22,16 @@
 # Converters
 from .teconverters import (
     antimonyConverter,
-    inlineOmex,
 )
 
+try:
+    #Might not exist if we don't have phrasedml.
+    from .teconverters import (
+        inlineOmex,
+    )
+except:
+    pass
+
 # Model import
 from .tellurium import (
     loadAntimonyModel,

tellurium/analysis/parameterscan.py

@@ -679,7 +679,7 @@ def plot2DParameterScan(self):
 
                 if (i == len(self.p1Range) - 1):
                     axarr[i, j].set_xlabel('%s = %.2f' % (self.p2, k2))
-                if (j is 0):
+                if (j == 0):
                     axarr[i, j].set_ylabel('%s = %.2f' % (self.p1, k1))
 
         f.show()

tellurium/roadrunner/extended_roadrunner.py

@@ -46,8 +46,6 @@ def __init__(self, *args, **kwargs):
 
         'getConservedMoietyValues',
         'getNumConservedMoieties',
-        'getNumDepFloatingSpecies',
-        'getNumIndFloatingSpecies',
 
         'getReactionIds',
         'getReactionRates',

tellurium/teconverters/__init__.py

@@ -6,8 +6,11 @@
 
 from .convert_omex import inlineOmexImporter, OmexFormatDetector
 
-from .convert_phrasedml import phrasedmlImporter
+try:
+    from .convert_phrasedml import phrasedmlImporter
+    from .inline_omex import inlineOmex, saveInlineOMEX
+except:
+    pass
 
 from .antimony_sbo import SBOError
 
-from .inline_omex import inlineOmex, saveInlineOMEX

tellurium/teconverters/convert_omex.py

@@ -4,7 +4,6 @@
 from __future__ import print_function, division, absolute_import
 import os
 import re
-import shutil
 import tempfile
 import json
 import getpass
@@ -16,8 +15,10 @@
 except ImportError:
     import tecombine as libcombine
 
-
-from .convert_phrasedml import phrasedmlImporter
+try:
+    from .convert_phrasedml import phrasedmlImporter
+except:
+    pass
 from .convert_antimony import antimonyConverter
 
 class OmexFormatDetector:
@@ -146,8 +147,11 @@ def executeOmex(self):
 
         :return:
         """
-        import phrasedml
-        phrasedml.clearReferencedSBML()
+        try:
+            import phrasedml
+            phrasedml.clearReferencedSBML()
+        except:
+            pass
 
         workingDir = tempfile.mkdtemp(suffix="_sedml")
         self.writeFiles(workingDir)
@@ -163,8 +167,11 @@ def exportToCombine(self, outfile):
         """ Export Omex instance as combine archive.
 
         :param outfile: A path to the output file"""
-        import phrasedml
-        phrasedml.clearReferencedSBML()
+        try:
+            import phrasedml
+            phrasedml.clearReferencedSBML()
+        except:
+            pass
 
         archive = libcombine.CombineArchive()
         description = libcombine.OmexDescription()
@@ -232,18 +239,14 @@ def fromFile(cls, path):
         if not os.path.isfile(path):
             raise IOError('No such file: {}'.format(path))
 
-        d = None
         if not os.access(os.getcwd(), os.W_OK):
-            d = os.getcwd()
             os.chdir(tempfile.gettempdir())
 
         omex = libcombine.CombineArchive()
         if not omex.initializeFromArchive(path):
             raise IOError('Could not read COMBINE archive.')
         importer = inlineOmexImporter(omex)
 
-        # if d is not None:
-            # os.chdir(d)
         return importer
 
     def __init__(self, omex):
@@ -445,13 +448,14 @@ def toInlineOmex(self, detailedErrors=True):
         for entry in self.sedml_entries:
             sedml_str = self.omex.extractEntryToString(entry.getLocation()).replace('BIOMD0000000012,xml',
                                                                                     'BIOMD0000000012.xml')
+            phrasedml_output = ""
             try:
                 phrasedml_output = phrasedmlImporter.fromContent(
                     sedml_str,
                     self.makeSBMLResourceMap(self.fixSep(os.path.dirname(entry.getLocation())))
                 ).toPhrasedml().rstrip().replace('compartment', 'compartment_')
             except Exception as e:
-                errmsg = 'Could not read embedded SED-ML file {}.'.format(entry.getLocation())
+                errmsg = 'Could not read embedded SED-ML file or could not convert to phraSED-ML: {}.\n{}'.format(entry.getLocation(), e.what())
                 try:
                     try:
                         import libsedml