Merge pull request #5 from jeremymchacon/master

2 small commits to fix path issues and make more specific setup.py for pypi
segrelab · Sep 15, 2020 · 0d49126 · 0d49126
2 parents f42ce67 + c9c0230
commit 0d49126
Show file tree

Hide file tree

Showing 2 changed files with 13 additions and 13 deletions.
diff --git a/cometspy/comets.py b/cometspy/comets.py
@@ -49,13 +49,16 @@ def __init__(self, layout, parameters, working_dir=''):
             try:
                 self.GUROBI_HOME = os.environ['GUROBI_HOME']
             except:
-                self.GUROBI_HOME = ''
-                print("could not find environmental variable GUROBI_COMETS_HOME or GUROBI_HOME")
-                print("COMETS will not work with GUROBI until this is solved. ")
-                print("Here is a solution:")
-                print("    1. import os and set os.environ['GUROBI_HOME'] then try to make a comets object again")
-                print("       e.g.   import os")
-                print("              os.environ['GUROBI_HOME'] = 'C:\\\\gurobi902\\\\win64'")          
+                try:
+                    self.GUROBI_HOME = os.environ['COMETS_GUROBI_HOME']
+                except:                      
+                    self.GUROBI_HOME = ''
+                    print("could not find environmental variable GUROBI_COMETS_HOME or GUROBI_HOME or COMETS_GUROBI_HOME")
+                    print("COMETS will not work with GUROBI until this is solved. ")
+                    print("Here is a solution:")
+                    print("    1. import os and set os.environ['GUROBI_HOME'] then try to make a comets object again")
+                    print("       e.g.   import os")
+                    print("              os.environ['GUROBI_HOME'] = 'C:\\\\gurobi902\\\\win64'")          
         self.COMETS_HOME = os.environ['COMETS_HOME']
         self.VERSION = os.path.splitext(os.listdir(os.environ['COMETS_HOME'] +
                                                    '/bin')[0])[0]
@@ -248,7 +251,7 @@ def run(self, delete_files=True):
                     # ' -Djava.library.path=' + self.D_JAVA_LIB_PATH +
                     ' edu.bu.segrelab.comets.Comets -loader' +
                     ' edu.bu.segrelab.comets.fba.FBACometsLoader' +
-                    ' -script ' + c_script)
+                    ' -script "' + c_script + '"')
         p = sp.Popen(self.cmd, shell=True, stdout=sp.PIPE, stderr=sp.STDOUT)
 
         self.run_output, self.run_errors = p.communicate()

diff --git a/setup.py b/setup.py
@@ -16,14 +16,11 @@
         # I get to this in a second
         'numpy',
         'cobra',
-        'pandas'],
+        'pandas>=1.0.0'],
     classifiers=[
         'Development Status :: 4 - Beta',  # "3 - Alpha", "4 - Beta", "5 - Production/Stable"
         'Intended Audience :: Science/Research',      # Define that your audience are developers
-        'License :: OSI Approved :: MIT License',   # Again, pick a license
-        'Programming Language :: Python :: 3',      # Supported pyhton versions
-        'Programming Language :: Python :: 3.4',
-        'Programming Language :: Python :: 3.5',
+        'License :: OSI Approved :: MIT License',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',