Merge pull request #50 from SystemsBioinformatics/dev

0.8.4 py3.9+ compatibility release

Author: bgoli

CONTRIBUTORS.md

@@ -1,7 +1,9 @@
 # Contributors
 
-## Release 0.8.2
+## Release 0.8.4
+Many thanks go to @willigot for their suggestions and code contributions.
 
+## Release 0.8.2
 
 ## Release 0.8.1
 

README.md

@@ -1,6 +1,6 @@
 # CBMPy
 PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
-Copyright (C) 2010-2022 Brett G. Olivier, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
+Copyright (C) 2010-2023 Brett G. Olivier, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -75,4 +75,4 @@ Once you have installed CBMPy it can be easily upgraded.
 ### Anaconda update
 `conda update cbmpy`
 
-(c) Brett G. Olivier, Amsterdam, 2014-2022
+(c) Brett G. Olivier, Amsterdam, 2014-2023

RELEASES.md

@@ -1,8 +1,10 @@
 # Release history
 
-## Release 0.8.2 (2021)
+## Release 0.8.4 (2023)
+Primarily a Python 9.x compatability release
 
 
+## Release 0.8.2 (2021)
 ## Release 0.8.1 (2021-07-23)
 
 Primarily a bugfix release to fix the SymPy compatability issues as well as improved requirements handling.

cbmpy/CBCPLEX.py

@@ -1996,6 +1996,7 @@ def cplx_FluxVariabilityAnalysis(
             max_oval = numpy.NaN
         else:  # other fail
             max_oval = numpy.NaN
+
         if debug:
             cplx_writeLPtoLPTfile(
                 cpx, '%smax' % R, title='max%s=%s' % (R, max_oval), Dir=debug_dir
@@ -2016,33 +2017,38 @@ def cplx_FluxVariabilityAnalysis(
         OUTPUT_ARRAY[Ridx, 4] = round(abs(max_oval - min_oval), roundoff_span)
         OUTPUT_ARRAY[Ridx, 5] = MIN_STAT
         OUTPUT_ARRAY[Ridx, 6] = MAX_STAT
+
         if markupmodel:
             REAC = fba.getReaction(R)
             REAC.setValue(pre_sol[R])
             REAC.fva_min = min_oval
             REAC.fva_max = max_oval
             REAC.fva_status = (MIN_STAT, MAX_STAT)
-            # if MAX_STAT == 1:
-            # REAC.fva_max = max_oval
-            # else:
-            # REAC.fva_max = None
-            # if MIN_STAT == 1:
-            # REAC.fva_min = min_oval
-            # else:
-            # REAC.fva_min = None
+            #if MAX_STAT == 1:
+                #REAC.fva_max = max_oval
+            #else:
+                #REAC.fva_max = None
+            #if MIN_STAT == 1:
+                #REAC.fva_min = min_oval
+            #else:
+                #REAC.fva_min = None
             if R in REDUCED_COSTS:
                 REAC.reduced_costs = REDUCED_COSTS[R]
+
+        # TODO backport from CBGLPK line 839
         if not quiet and MAX_STAT > 1 or MIN_STAT > 1:
             print(
                 'Solver fail for reaction \"{}\" (MIN_STAT: {} MAX_STAT: {})'.format(
                     R, MIN_STAT, MAX_STAT
                 )
             )
+        # TODO backport from CBGLPK line 857
         cntr += 1
         if cntr == 200:
             tcnt += cntr
             print('FVA has processed {} of {} reactions'.format(tcnt, NUM_FLX))
             cntr = 0
+
     if quiet:
         cplx_setOutputStreams(cpx, mode='default')
     del cpx

cbmpy/CBCommon.py

@@ -71,18 +71,23 @@
 
 chemElementDefs = None
 HAVE_PYPARSING = False
-try:
-    from . import pyparsing
 
+try:
+    import pyparsing
     HAVE_PYPARSING = True
+    print('pyparsing import')
 except ImportError:
-    try:
-        print('Attempting global PyParsing import')
-        import pyparsing
+    print('INFO: please install pyparsing to enable chemical balance checking!')
+
+
+#if not HAVE_PYPARSING:
+    #if os.sys.version_info[0] == 3 and os.sys.version_info[1] < 9:
+        #try:
+            #from . import pyparsing
 
-        HAVE_PYPARSING = True
-    except ImportError:
-        print('INFO please install pyparsing to enable chemical balance checking!')
+            #HAVE_PYPARSING = True
+        #except ImportError:
+            #print('INFO please install pyparsing to enable chemical balance checking!')
 
 if HAVE_PYPARSING:
     pp_caps = "ABCDEFGHIJKLMNOPQRSTUVWXYZ"

cbmpy/CBGLPK.py

@@ -67,8 +67,12 @@
     sw.glp_set_prob_name(lp, "sample")
     sw.glp_delete_prob(lp)
     HAVE_SWIGLPK = True
-    print('\n\nCBGLPK based on swiglpk: not all methods implimented yet!')
     __solver_version__ = '{}.{}'.format(sw.GLP_MAJOR_VERSION, sw.GLP_MINOR_VERSION)
+    print(
+        'CBGLPK based on swiglpk: not all methods implimented yet!',
+        __solver_version__,
+    )
+
 except:
     raise ImportError
 
@@ -696,6 +700,7 @@ def glpk_FluxVariabilityAnalysis(
     except AttributeError:
         OUTPUT_ARRAY = numpy.zeros((NUM_FLX, 7))
     OUTPUT_NAMES = []
+    fva_ridx_fails = []
     cntr = 0
     tcnt = 0
     # this is a memory hack --> prevents solver going berserk
@@ -714,8 +719,9 @@ def glpk_FluxVariabilityAnalysis(
             # MIN
             # TODO: bgoli: see whether this also works with 'minimize'
             glpk_setObjective(cpx, 'min%s' % R, [(1, R)], 'min', reset=True)
-            ##  cplx_setBounds(c, id, min=None, max=None) # think about this
+
             MIN_STAT = glpk_Solve(cpx, method=method)
+
             if MIN_STAT == 'LPS_OPT':
                 MIN_STAT = 1
             elif MIN_STAT == 'LPS_UNBND':
@@ -724,6 +730,7 @@ def glpk_FluxVariabilityAnalysis(
                 MIN_STAT = 3
             else:
                 MIN_STAT = 4
+
             if MIN_STAT == 1:  # solved
                 min_oval = cpx.obj.value
             elif MIN_STAT == 2:  # unbound
@@ -735,17 +742,21 @@ def glpk_FluxVariabilityAnalysis(
                 min_oval = numpy.NaN
             if debug:
                 cpx.write(cpxlp=os.path.join(debug_dir, '%smin.lp' % R))
-            if MIN_STAT >= 3:
-                if gomin_cntr == 0:
-                    cpx.erase()
-                    del cpx
-                    time.sleep(0.1)
-                    cpx = glpk.LPX(mps=mps_filename)
-                    gomin_cntr += 1
-                else:
-                    GOMIN = False
+
+            if MIN_STAT > 3:
+                print('Mysterious GLPK MIN_STAT > 3: if you see this please contact a developer (not an error).')
+                #if gomin_cntr == 0:
+                    #cpx.erase()
+                    #del cpx
+                    #time.sleep(0.1)
+                    #cpx = glpk.LPX(mps=mps_filename)
+                    #gomin_cntr += 1
+                #else:
+                    #GOMIN = False
+                GOMIN = False
             else:
                 GOMIN = False
+
             if gomin_cntr >= max_error_iter:
                 GOMIN = False
 
@@ -765,6 +776,7 @@ def glpk_FluxVariabilityAnalysis(
                 MAX_STAT = 3
             else:
                 MAX_STAT = 4
+
             if MAX_STAT == 1:  # solved
                 max_oval = cpx.obj.value
             elif MAX_STAT == 2:  # unbound
@@ -775,24 +787,30 @@ def glpk_FluxVariabilityAnalysis(
             else:  # other fail
                 max_oval = numpy.NaN
 
-            if MAX_STAT >= 3:
-                if gomax_cntr == 0:
-                    cpx.erase()
-                    del cpx
-                    time.sleep(0.1)
-                    cpx = glpk.LPX(mps=mps_filename)
-                    gomax_cntr += 1
-                else:
-                    GOMAX = False
+            if MAX_STAT > 3:
+                print('Mysterious GLPK MAX_STAT > 3: if you see this please contact a developer (not an error).')
+                #if gomax_cntr == 0:
+                    #cpx.erase()
+                    #del cpx
+                    #time.sleep(0.1)
+                    #cpx = glpk.LPX(mps=mps_filename)
+                    #gomax_cntr += 1
+                #else:
+                    #GOMAX = False
+                GOMAX = False
             else:
                 GOMAX = False
+
             if gomax_cntr >= max_error_iter:
                 GOMAX = False
 
         # check for solver going berserk
-        if MIN_STAT > 1 and MAX_STAT > 1:
-            print(Ridx)
-            time.sleep(1)
+        #if MIN_STAT > 1 and MAX_STAT > 1:
+            #print(Ridx)
+            #time.sleep(1)
+
+        if debug:
+            cpx.write(cpxlp=os.path.join(debug_dir, '%smax.lp' % R))
 
         # enables using the default value as a solution if the solver fails
         if pre_opt and default_on_fail:
@@ -801,9 +819,6 @@ def glpk_FluxVariabilityAnalysis(
             if MIN_STAT > 1 and not MAX_STAT > 1:
                 min_oval = pre_sol[R]
 
-        if debug:
-            cpx.write(cpxlp=os.path.join(debug_dir, '%smax.lp' % R))
-
         OUTPUT_ARRAY[Ridx, 0] = pre_sol[R]
         if R in REDUCED_COSTS:
             OUTPUT_ARRAY[Ridx, 1] = REDUCED_COSTS[R]
@@ -820,18 +835,28 @@ def glpk_FluxVariabilityAnalysis(
             REAC.fva_status = (MIN_STAT, MAX_STAT)
             if R in REDUCED_COSTS:
                 REAC.reduced_costs = REDUCED_COSTS[R]
-        if not quiet and MAX_STAT > 1 or MIN_STAT > 1:
-            print(
-                'Solver fail for reaction \"{}\" (MIN_STAT: {} MAX_STAT: {})'.format(
-                    R, MIN_STAT, MAX_STAT
-                )
-            )
+
+        if not quiet:
+            if MAX_STAT > 1:
+                fva_ridx_fails.append((R, MAX_STAT))
+                #print(
+                    #'Solver fail for reaction \"{}\" (MIN_STAT: {} MAX_STAT: {})'.format(
+                        #R, MIN_STAT, MAX_STAT
+                    #)
+            if MIN_STAT > 1:
+                fva_ridx_fails.append((R, MIN_STAT))
+
         cntr += 1
         if cntr == 200:
             tcnt += cntr
             print('FVA has processed {} of {} reactions'.format(tcnt, NUM_FLX))
             cntr = 0
 
+    if len(fva_ridx_fails) > 0:
+        print('Optimization failed for the following FVA operations. If this is a large list consider adjusting the FVA tolerances.')
+        print(fva_ridx_fails)
+
+
     os.remove(mps_filename)
 
     # cpx.write(cpxlp='thefinaldebug.lp')

cbmpy/CBNetDB.py

@@ -141,9 +141,9 @@ def createDBTable(self, table, sqlcols):
 
         Effectively writes CREATE TABLE "table" (<id> <type>, gene TEXT PRIMARY KEY, aa_seq TEXT, nuc_seq TEXT, aa_len INT, nuc_len INT) % table
         """
-        SQL = 'CREATE TABLE %s (' % table
+        SQL = 'CREATE TABLE "{}" ('.format(table)
         for c in sqlcols:
-            SQL += ' %s,' % c
+            SQL += ' "{}",'.format(c)
         SQL = SQL[:-1]
         SQL += ' )'
         print(SQL)

cbmpy/CBSolver.py

@@ -31,6 +31,15 @@
 
 from .CBConfig import __CBCONFIG__ as __CBCONFIG__
 
+# Force the use of the CPLX solver by defining this envar
+import os
+
+if 'CBMPY_USE_CPLX' in os.environ:
+    __CBCONFIG__['SOLVER_PREF'] = 'CPLX'
+if 'CBMPY_USE_GLPK' in os.environ:
+    __CBCONFIG__['SOLVER_PREF'] = 'GLPK'
+del os
+
 __DEBUG__ = __CBCONFIG__['DEBUG']
 __version__ = __CBCONFIG__['VERSION']
 SOLVER_PREF = __CBCONFIG__['SOLVER_PREF']

cbmpy/CBWrite.py

@@ -159,7 +159,7 @@ def writeSBML3FBCV2(
     add_cbmpy_annot=True,
     add_cobra_annot=False,
     validate=False,
-    compress_bounds=True,
+    compress_bounds=False,
     zip_model=False,
     return_model_string=False,
 ):