From e9b693a0d2376a0a1bd3e6770448143e5273c77f Mon Sep 17 00:00:00 2001
From: Pedro Mendes <mendes@copasi.org>
Date: Fri, 18 Oct 2024 10:27:25 -0400
Subject: [PATCH] removing globals

---
 src/sbmodelr.py | 41 +++++++++++++++++++----------------------
 1 file changed, 19 insertions(+), 22 deletions(-)

diff --git a/src/sbmodelr.py b/src/sbmodelr.py
index 1e3a281..86a1f1b 100755
--- a/src/sbmodelr.py
+++ b/src/sbmodelr.py
@@ -15,7 +15,7 @@
 #TODO: modification between units? (would need to select species and reaction)
 #TODO: hexagonal arrays? (please no!)
 
-__version__ = "1.0a8"
+__version__ = "1.0b1"
 
 import os
 import re
@@ -32,14 +32,9 @@
 #######################
 # GLOBAL VARIABLES #
 
-parser = None
-args = None
-seedmodelfile = None
 r = None
 c = None
 l = None
-ignc = None
-trate = None
 coupleconst = None
 tVmax = None
 tKm = None
@@ -374,7 +369,7 @@ def read_network(network_file):
 ############
 
 def main():
-    global parser, args, seedmodelfile, r, c, l, ignc, trate, coupleconst, tVmax, tKm, th, taurinit, taudinit, v0init, vsyninit, gcinit, linkg, grnV, grna, grnh, mediumVol, transported, sp, odelink, base, ext, sbmll, sbmlv, nmodels, dim, fsuff, desc, apdx1, gridr, gridc, gridl, links, digraph, link, seedmodel, mparams, seednparams, pfixed, passg, pode, mcomps, seedncomps, cfixed, cassg, code, mspecs, seednspecs, sreact, sfixed, sassg, sode, mreacts, seednreacts, mevents, seednevents, base_model_summary, scanitems, noisy_species, noisy_param, noisy_comp, seedname, cmd, nnotes, index, munits, newfilename, newname, newmodel, it, miriam, modf, p, i, apdx, nname, iv, nt, an, cp, scheme, tok, tok2, rs, t, mapp, key, nmk, k2, ex, timeonlyevents, etd, entd, netype, ttype, rateconst, suffa, rname, rscheme, thisrateconst, rmap, suffb, tc, ss, mca, le, tsa, cs, lna, sen, seff, scau, ssec, ps, srw, sit, newit, nopt, exps, tcs 
+    global r, c, l, coupleconst, tVmax, tKm, th, taurinit, taudinit, v0init, vsyninit, gcinit, linkg, grnV, grna, grnh, mediumVol, transported, sp, odelink, base, ext, sbmll, sbmlv, nmodels, dim, fsuff, desc, apdx1, gridr, gridc, gridl, links, digraph, link, seedmodel, mparams, seednparams, pfixed, passg, pode, mcomps, seedncomps, cfixed, cassg, code, mspecs, seednspecs, sreact, sfixed, sassg, sode, mreacts, seednreacts, mevents, seednevents, base_model_summary, scanitems, noisy_species, noisy_param, noisy_comp, seedname, cmd, nnotes, index, munits, newfilename, newname, newmodel, it, miriam, modf, p, i, apdx, nname, iv, nt, an, cp, scheme, tok, tok2, rs, t, mapp, key, nmk, k2, ex, timeonlyevents, etd, entd, netype, ttype, rateconst, suffa, rname, rscheme, thisrateconst, rmap, suffb, tc, ss, mca, le, tsa, cs, lna, sen, seff, scau, ssec, ps, srw, sit, newit, nopt, exps, tcs
     
     #####
     #  1. parsing the command line
@@ -2390,22 +2385,24 @@ def main():
             nopt['expression'] = fix_expression(nopt['expression'], apdx1, ignc)
             set_opt_settings(nopt,newmodel)
             ops = get_opt_parameters(model=seedmodel)
-            for p in ops.index:
-                # rename the CN
-                ops.loc[p, 'cn'] = fix_expression(ops.loc[p].at['cn'] ,apdx1, ignc)
-                # rename the index
-                newp = fix_expression(p,apdx1, ignc)
-                ops.rename(index={p: newp}, inplace=True)
-            set_opt_parameters(ops, model=newmodel)
+            if ops is not None:
+                for p in ops.index:
+                    # rename the CN
+                    ops.loc[p, 'cn'] = fix_expression(ops.loc[p].at['cn'] ,apdx1, ignc)
+                    # rename the index
+                    newp = fix_expression(p,apdx1, ignc)
+                    ops.rename(index={p: newp}, inplace=True)
+                set_opt_parameters(ops, model=newmodel)
             cst = get_opt_constraints(model=seedmodel)
-            # deal with constraints
-            for p in cst.index:
-                # rename the CN
-                cst.loc[p, 'cn'] = fix_expression(cst.loc[p].at['cn'] ,apdx1, ignc)
-                # rename the index
-                newp = fix_expression(p,apdx1, ignc)
-                cst.rename(index={p: newp}, inplace=True)
-            set_opt_constraints(cst, model=newmodel)
+            if cst is not None:
+                # deal with constraints
+                for p in cst.index:
+                    # rename the CN
+                    cst.loc[p, 'cn'] = fix_expression(cst.loc[p].at['cn'] ,apdx1, ignc)
+                    # rename the index
+                    newp = fix_expression(p,apdx1, ignc)
+                    cst.rename(index={p: newp}, inplace=True)
+                set_opt_constraints(cst, model=newmodel)
             print(' Warning: in Optimization task the objective function and the search parameters were converted to those of the first unit only.')
 
         # We won't do Parameter estimation but need to issue a warning if it was set