From 7177259966a80e1aa4b3f93a355bb8f633e16b33 Mon Sep 17 00:00:00 2001
From: Dolev Goldberger <dolevg@mail.tau.ac.il>
Date: Mon, 27 Jul 2026 12:05:28 +0300
Subject: [PATCH 1/2] update to work with python 3.13

---
 prepare.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/prepare.py b/prepare.py
index 262ec10..89365a7 100755
--- a/prepare.py
+++ b/prepare.py
@@ -7,6 +7,7 @@
 import getpass
 from datetime import timedelta
 import multiprocessing as mp
+import builtins
 from sys import argv
 from time import sleep
 import pickle
@@ -70,15 +71,15 @@ def runAll(cls):
             if auth == 'n' or auth == 'N':
                 exit(0)
             elif auth == 'y' or auth == 'Y':
-                pool = mp.Pool(processes=min(cls.maxNumProcesses,len(cls.processPool)))
+                pool = mp.Pool(processes=builtins.min(cls.maxNumProcesses,len(cls.processPool)))
                 result = pool.map(execute, cls.processPool)
             elif auth == 'qlimit':
                 qlimit = input("Maximum number of jobs to queue simultaneously?".format(n=str(len(cls.processPool)),queue=queueName))
                 cls.qlimit = int(qlimit)
-                pool = mp.Pool(processes=min(cls.maxNumProcesses,len(cls.processPool)))
+                pool = mp.Pool(processes=builtins.min(cls.maxNumProcesses,len(cls.processPool)))
                 result = pool.map(executeWithQueueLimit, cls.processPool)
             elif int(auth)>0 and int(auth)<len(cls.processPool):
-                pool = mp.Pool(processes=min(cls.maxNumProcesses,int(auth)))
+                pool = mp.Pool(processes=builtins.min(cls.maxNumProcesses,int(auth)))
                 result = pool.map(execute, cls.processPool[:int(auth)])
             else:
                 print("Unrecognized directive.")
@@ -107,12 +108,13 @@ def __init__(self, js):
 paramIterator = itertools.chain.from_iterable(paramSets)
 
 #begin the iteration:
+print(paramIterator)
 for term in paramIterator:
     pdict = dict(zip(labels, term))
     p = Struct(**pdict)#This makes it convenient to access the parameters as p.whatever...
     outdir = item_name(prefix, pdict, secondary_keys=secondary_keys,excluded_keys=excluded_keys)
     for valname,valfunc in post_data:
-        pdict[valname] = valfunc(pdict)
+        pdict[valname] = valfunc(pdict)       
     p_contents = template.format(**pdict)
     p_runfile = process_runfile(runfile, pdict, cwd+'/'+outdir)
 

From dd4ae233f06b38c733d7f0d8dadfd38c704dda58 Mon Sep 17 00:00:00 2001
From: Dolev goldberger <dolevg@mail.tau.ac.il>
Date: Tue, 28 Jul 2026 13:53:41 +0300
Subject: [PATCH 2/2] Use explicit NumPy import

---
 prepare.py | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/prepare.py b/prepare.py
index 89365a7..d219c6a 100755
--- a/prepare.py
+++ b/prepare.py
@@ -1,13 +1,12 @@
 #!/usr/bin/env python
 from __future__ import print_function
-from numpy import *
+import numpy as np
 import itertools
 from os import path, makedirs, getcwd, chdir
 from subprocess import call, check_output
 import getpass
 from datetime import timedelta
 import multiprocessing as mp
-import builtins
 from sys import argv
 from time import sleep
 import pickle
@@ -71,15 +70,15 @@ def runAll(cls):
             if auth == 'n' or auth == 'N':
                 exit(0)
             elif auth == 'y' or auth == 'Y':
-                pool = mp.Pool(processes=builtins.min(cls.maxNumProcesses,len(cls.processPool)))
+                pool = mp.Pool(processes=min(cls.maxNumProcesses,len(cls.processPool)))
                 result = pool.map(execute, cls.processPool)
             elif auth == 'qlimit':
                 qlimit = input("Maximum number of jobs to queue simultaneously?".format(n=str(len(cls.processPool)),queue=queueName))
                 cls.qlimit = int(qlimit)
-                pool = mp.Pool(processes=builtins.min(cls.maxNumProcesses,len(cls.processPool)))
+                pool = mp.Pool(processes=min(cls.maxNumProcesses,len(cls.processPool)))
                 result = pool.map(executeWithQueueLimit, cls.processPool)
             elif int(auth)>0 and int(auth)<len(cls.processPool):
-                pool = mp.Pool(processes=builtins.min(cls.maxNumProcesses,int(auth)))
+                pool = mp.Pool(processes=min(cls.maxNumProcesses,int(auth)))
                 result = pool.map(execute, cls.processPool[:int(auth)])
             else:
                 print("Unrecognized directive.")
@@ -108,13 +107,12 @@ def __init__(self, js):
 paramIterator = itertools.chain.from_iterable(paramSets)
 
 #begin the iteration:
-print(paramIterator)
 for term in paramIterator:
     pdict = dict(zip(labels, term))
     p = Struct(**pdict)#This makes it convenient to access the parameters as p.whatever...
     outdir = item_name(prefix, pdict, secondary_keys=secondary_keys,excluded_keys=excluded_keys)
     for valname,valfunc in post_data:
-        pdict[valname] = valfunc(pdict)       
+        pdict[valname] = valfunc(pdict)
     p_contents = template.format(**pdict)
     p_runfile = process_runfile(runfile, pdict, cwd+'/'+outdir)