removed deap as a dependency

CADETMatch.pyproj

@@ -60,7 +60,6 @@
     <Compile Include="CADETMatch\abstract\__init__.py" />
     <Compile Include="CADETMatch\cache.py" />
     <Compile Include="CADETMatch\calc_coeff.py" />
-    <Compile Include="CADETMatch\code_test.py" />
     <Compile Include="CADETMatch\de.py" />
     <Compile Include="CADETMatch\de_snooker.py" />
     <Compile Include="CADETMatch\evo.py" />

CADETMatch/cache.py

@@ -8,7 +8,6 @@
 import jstyleson
 import numpy
 from cadet import Cadet
-from deap import tools
 from sklearn import preprocessing
 
 import CADETMatch.plugins as plugins

CADETMatch/evo.py

@@ -3,7 +3,6 @@
 
 import numpy
 from cadet import Cadet
-from deap import creator, tools
 
 import CADETMatch.cache as cache
 import CADETMatch.progress as progress
@@ -151,4 +150,4 @@ def runExperimentBase(
 def run(cache):
     "run the parameter estimation"
     searchMethod = cache.settings.get("searchMethod", "UNSGA3")
-    return cache.search[searchMethod].run(cache, tools, creator)
+    return cache.search[searchMethod].run(cache)

CADETMatch/fitness.py

@@ -1,5 +1,4 @@
 import numpy
-from deap import base
 
 
 class Fitness2(base.Fitness):

CADETMatch/match.py

@@ -12,7 +12,6 @@
 import numpy
 import functools
 from cadet import H5, Cadet
-from deap import base, creator, tools
 
 import CADETMatch.evo as evo
 import CADETMatch.gradFD as gradFD
@@ -26,7 +25,6 @@ def main(map_function):
     path = sys.argv[1]
     setup(cache, path, map_function)
     gradFD.setupTemplates(cache)
-    # grad.setupTemplates(cache)
     hof = evo.run(cache)
 
     multiprocessing.get_logger().info("altScoress %s", cache.altScores)
@@ -133,7 +131,6 @@ def print_version():
         ("corner", "2.2.1"),
         ("emcee", "3.0.2"),
         ("SALib", "1.3.11"),
-        ("deap", "1.3.1"),
         ("psutil", "5.8.0"),
         ("numpy", "1.21.1"),
         ("openpyxl", "3.0.7"),
@@ -145,7 +142,8 @@ def print_version():
         ("seaborn", "0.11.1"),
         ("scikit-learn", "0.24.2"),
         ("jstyleson", "0.2.0"),
-        ('filelock', "3.0.12")
+        ('filelock', "3.0.12"),
+        ('pymoo', '0.4.2.2')
     ]
 
     for module, version_tested in modules:

CADETMatch/pareto.py

@@ -6,7 +6,7 @@
 
 import numpy
 class ParetoFront:
-    "Modification of the pareto front in DEAP that takes cache as an argument to update to use for similar comparison"
+    "Pareto front designed to be compatible with DEAP"
 
     def __init__(self, dimensions, similar=None, similar_fit=None, slice_object=slice(None)):
         if similar is None:
@@ -135,7 +135,7 @@ def getBestScores(self):
         return numpy.min(data, 0)
 
 class DummyFront(ParetoFront):
-    "Modification of the pareto front in DEAP that takes cache as an argument to update to use for similar comparison"
+    "Pareto front designed to be compatible with DEAP"
 
     def __init__(self, dimensions=None, similar=None):
         "This is here for API compatibility, don't do anything"

CADETMatch/search/altScore.py

@@ -17,7 +17,7 @@
 name = "AltScore"
 
 
-def run(cache, tools, creator):
+def run(cache):
     "run the parameter estimation"
     path = Path(cache.settings["resultsDirBase"], cache.settings["csv"])
     with path.open("a", newline="") as csvfile:

CADETMatch/search/gradient.py

@@ -14,7 +14,7 @@
 name = "Gradient"
 
 
-def run(cache, tools, creator):
+def run(cache):
     "run the parameter estimation"
     random.seed()
 

CADETMatch/search/graphSpace.py

@@ -17,7 +17,7 @@
 "This is not actually an optimization method. It is used to sample a space and generate graphs to see what the space looks like."
 
 
-def run(cache, tools, creator):
+def run(cache):
     "run the parameter estimation"
     random.seed()
 

CADETMatch/search/mcmc.py

@@ -896,7 +896,7 @@ def write_interval(
         write_interval.last_time = time.time()
 
 
-def run(cache, tools, creator):
+def run(cache):
     "run the parameter estimation"
     random.seed()
     checkpointFile = Path(

CADETMatch/search/multistart.py

@@ -15,7 +15,7 @@
 name = "Multistart"
 
 
-def run(cache, tools, creator):
+def run(cache):
     "run the parameter estimation"
     random.seed()
 

CADETMatch/search/nsga3.py

@@ -4,6 +4,6 @@
 name = "NSGA3"
 
 
-def run(cache, tools, creator):
+def run(cache):
     "run the parameter estimation"
     return CADETMatch.pymoo_config.run(cache, 'nsga3')

CADETMatch/search/scoretest.py

@@ -14,7 +14,7 @@
 name = "ScoreTest"
 
 
-def run(cache, tools, creator):
+def run(cache):
     "run the parameter estimation"
     path = Path(cache.settings["resultsDirBase"], cache.settings["csv"])
     with path.open("a", newline="") as csvfile:

CADETMatch/search/unsga3.py

@@ -4,7 +4,7 @@
 name = "UNSGA3"
 
 
-def run(cache, tools, creator):
+def run(cache):
     "run the parameter estimation"
     return CADETMatch.pymoo_config.run(cache, 'unsga3')
 

CADETMatch/util.py

@@ -19,7 +19,6 @@
 import scipy.signal
 from addict import Dict
 from cadet import H5, Cadet
-from deap import tools
 
 import CADETMatch.calc_coeff as calc_coeff
 import CADETMatch.sub as sub

setup.py

@@ -21,7 +21,7 @@
           'emcee>=3.0.2',
           'SAlib',
           'corner>=2.1.0',
-          'deap>=1.3.1',
+          'pymoo>=0.4.2.2',
           'psutil>=5.7.0',
           'openpyxl>=3.0.3',
           'numpy>=1.18.5',