attempting to refactor and clean up imports

PySCeS · Aug 24, 2020 · d510bb4 · d510bb4
1 parent ef6c95a
commit d510bb4
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Showing 10 changed files with 320 additions and 178 deletions.
diff --git a/pysces/PyscesJWSParse.py b/pysces/PyscesJWSParse.py
@@ -28,8 +28,8 @@
     pass
 
 import os, copy
-import pysces.lib.lex
-import pysces.lib.yacc
+from .lib import lex
+from .lib import yacc
 from getpass import getuser
 from time import sleep, strftime
 from scipy import MachAr
@@ -218,9 +218,9 @@ def Show(self, name, tok):
     def p_error(self, t):
         self.ParseErrors.append(('Syntax error ', t.lineno, t.value, t.type))
         print('Syntax error, Line ' + str(t.lineno) + ' : ' + str(t.value))
-        tok = pysces.lib.yacc.token()
+        tok = yacc.token()
         while tok and tok.type != 'REACTION_ID':
-            tok = pysces.lib.yacc.token()
+            tok = yacc.token()
         return tok
 
     def p_model(self, t):
@@ -500,10 +500,8 @@ def psc2jws(self, File, indir=None, outdir=None, quiet=1, debug=0):
 
         if go == 1:
             # clean up the modules
-            reload(
-                pysces.lib.lex
-            )  # brett's bugbear code these have to be here ALWAYS!!
-            reload(pysces.lib.yacc)
+            reload(lex)  # brett's bugbear code these have to be here ALWAYS!!
+            reload(yacc)
             # clean up the instance
             self.ReactionIDs = []  # List of reaction names
             self.Names = []  # List of all reagent, parameter and function names
@@ -566,9 +564,9 @@ def psc2jws(self, File, indir=None, outdir=None, quiet=1, debug=0):
                 print(self.tabmodule)
                 print(self.debugfile)
 
-            pysces.lib.lex.lex(module=self, debug=self.Debug)
-            pysces.lib.lex.input(Model)
-            pysces.lib.yacc.yacc(
+            lex.lex(module=self, debug=self.Debug)
+            lex.input(Model)
+            yacc.yacc(
                 module=self,
                 debug=self.Debug,
                 debugfile=self.debugfile,
@@ -578,14 +576,14 @@ def psc2jws(self, File, indir=None, outdir=None, quiet=1, debug=0):
             os.chdir(outdir)
 
             while 1:
-                tok = pysces.lib.lex.token()
+                tok = lex.token()
                 if not tok:
                     break
             if self.LexErrors != []:
                 print('self.LexErrors = ', self.LexErrors, '\n')
 
             while 1:
-                p = pysces.lib.yacc.parse(Model)
+                p = yacc.parse(Model)
                 if not p:
                     break
 

diff --git a/pysces/PyscesModel.py b/pysces/PyscesModel.py
@@ -62,20 +62,24 @@
 
 from getpass import getuser
 
-from pysces import model_dir as MODEL_DIR
-from pysces import output_dir as OUTPUT_DIR
-from pysces import install_dir as INSTALL_DIR
-from pysces import nleq2
-from pysces import nleq2_switch
-from pysces import pitcon
-from pysces import plt, gplt
-from pysces import PyscesStoich
-from pysces import PyscesParse
-from pysces import PyscesRandom as random
-from pysces import __SILENT_START__
-from pysces.PyscesScan import Scanner
-from pysces.core2.InfixParser import MyInfixParser
-from pysces import SED
+from . import model_dir as MODEL_DIR
+from . import output_dir as OUTPUT_DIR
+from . import install_dir as INSTALL_DIR
+from . import PyscesRandom as random
+from .PyscesScan import Scanner
+from .core2.InfixParser import MyInfixParser
+
+from . import (
+    nleq2,
+    nleq2_switch,
+    pitcon,
+    plt,
+    gplt,
+    PyscesStoich,
+    PyscesParse,
+    __SILENT_START__,
+    SED,
+)
 
 interface = None
 

diff --git a/pysces/PyscesModelMap.py b/pysces/PyscesModelMap.py
@@ -19,7 +19,7 @@
 from __future__ import absolute_import
 from __future__ import unicode_literals
 
-from pysces.version import __version__
+from .version import __version__
 
 __doc__ = '''PySCeS ModelMap module: useful for exploring model component relations'''
 

diff --git a/pysces/PyscesParse.py b/pysces/PyscesParse.py
@@ -18,14 +18,14 @@
 from __future__ import absolute_import
 from __future__ import unicode_literals
 
-from pysces.version import __version__
+from .version import __version__
 
 __doc__ = "PySCeS parser module -- uses  PLY 1.5 or newer"
 
 
 import os, copy
-import pysces.lib.lex
-import pysces.lib.yacc
+from .lib import lex
+from .lib import yacc
 from getpass import getuser
 from time import sleep, strftime
 
@@ -667,9 +667,9 @@ def p_error(self, t):
             self.ParseErrors.append(t)
         except:
             print('p_error generated a parsing error')
-        tok = pysces.lib.yacc.token()
+        tok = yacc.token()
         while tok and tok.type != 'REACTION_ID':
-            tok = pysces.lib.yacc.token()
+            tok = yacc.token()
         self.ParseOK = False
         return tok
 
@@ -1332,8 +1332,8 @@ def ParsePSC(self, modelfile, modeldir, modeloutput):
         self.ModelUsesNumpyFuncs = False
 
         # 4 hrs of debugging and these two lines solve the problem .... I'm out of here!
-        reload(pysces.lib.lex)
-        reload(pysces.lib.yacc)
+        reload(lex)
+        reload(yacc)
         # fixes the obscure reload <--> garbage collection reference overload bug ... who said scripted lang's were
         # easy to use :-) - brett 20040122
 
@@ -1379,9 +1379,9 @@ def ParsePSC(self, modelfile, modeldir, modeloutput):
             print(self.debugfile)
             print('cwd: ', os.getcwd())
 
-        self.__lexer = pysces.lib.lex.lex(module=self, debug=self.display_debug)
+        self.__lexer = lex.lex(module=self, debug=self.display_debug)
         self.__lexer.input(self.__Model)
-        self.__parser = pysces.lib.yacc.yacc(
+        self.__parser = yacc.yacc(
             module=self,
             debug=self.display_debug,
             debugfile=self.debugfile,

diff --git a/pysces/PyscesPlot2.py b/pysces/PyscesPlot2.py
@@ -18,8 +18,8 @@
 from __future__ import absolute_import
 from __future__ import unicode_literals
 
-from pysces.version import __version__
-from pysces import __SILENT_START__
+from .version import __version__
+from . import __SILENT_START__
 import subprocess, os, shutil, time, math, itertools, copy
 from getpass import getuser
 import numpy, scipy

diff --git a/pysces/PyscesSBML.py b/pysces/PyscesSBML.py
@@ -19,7 +19,7 @@
 from __future__ import absolute_import
 from __future__ import unicode_literals
 
-from pysces.version import __version__
+from .version import __version__
 
 __doc__ = '''SBML reading/writing module - now replaced by PySCeS Core2'''
 
@@ -34,7 +34,7 @@
 
 if sys.platform == 'win32':
     try:
-        import pysces.libsbml.libsbmlinit as SBML
+        import libsbml as SBML
     except Exception as e:
         print('Windows sbml load error', e)
 else:

diff --git a/pysces/core2/InfixParser.py b/pysces/core2/InfixParser.py
@@ -23,8 +23,6 @@
 # NOTE when you do this PLY adds a module name self. to all tokens
 # not sure if this is an unexpected feature or not. It can be worked around
 # but for now direct import seems the safest
-##  import pysces.lib.lex as lex
-##  import pysces.lib.yacc as yacc
 from . import lex
 from . import yacc
 import os

diff --git a/pysces/kraken/KrakenServer.py b/pysces/kraken/KrakenServer.py
@@ -31,14 +31,6 @@
 # end header
 
 __psyco_active__ = 0
-##  try:
-##  import psyco
-##  psyco.profile()
-##  __psyco_active__ = 1
-##  print 'PySCeS Module is now PsycoActive!'
-##  except:
-##  __psyco_active__ = 0
-##  __psyco_active__ = 0
 
 from pysces import TimerBox