diff --git a/CADETMatch.pyproj b/CADETMatch.pyproj
index 9516585..3bcf5ff 100644
--- a/CADETMatch.pyproj
+++ b/CADETMatch.pyproj
@@ -60,7 +60,6 @@
-
diff --git a/CADETMatch/cache.py b/CADETMatch/cache.py
index e7e068b..fe55ebf 100644
--- a/CADETMatch/cache.py
+++ b/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
diff --git a/CADETMatch/evo.py b/CADETMatch/evo.py
index 47c720c..5fd3f90 100644
--- a/CADETMatch/evo.py
+++ b/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)
diff --git a/CADETMatch/fitness.py b/CADETMatch/fitness.py
index 143fd15..425786b 100644
--- a/CADETMatch/fitness.py
+++ b/CADETMatch/fitness.py
@@ -1,5 +1,4 @@
import numpy
-from deap import base
class Fitness2(base.Fitness):
diff --git a/CADETMatch/match.py b/CADETMatch/match.py
index fc08e65..c72babf 100644
--- a/CADETMatch/match.py
+++ b/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:
diff --git a/CADETMatch/pareto.py b/CADETMatch/pareto.py
index 9da8356..1ea7351 100644
--- a/CADETMatch/pareto.py
+++ b/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"
diff --git a/CADETMatch/search/altScore.py b/CADETMatch/search/altScore.py
index 82ad712..0792501 100644
--- a/CADETMatch/search/altScore.py
+++ b/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:
diff --git a/CADETMatch/search/gradient.py b/CADETMatch/search/gradient.py
index 9510cad..28034af 100644
--- a/CADETMatch/search/gradient.py
+++ b/CADETMatch/search/gradient.py
@@ -14,7 +14,7 @@
name = "Gradient"
-def run(cache, tools, creator):
+def run(cache):
"run the parameter estimation"
random.seed()
diff --git a/CADETMatch/search/graphSpace.py b/CADETMatch/search/graphSpace.py
index 4fd03e6..3720a38 100644
--- a/CADETMatch/search/graphSpace.py
+++ b/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()
diff --git a/CADETMatch/search/mcmc.py b/CADETMatch/search/mcmc.py
index 11c91a1..7455922 100644
--- a/CADETMatch/search/mcmc.py
+++ b/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(
diff --git a/CADETMatch/search/multistart.py b/CADETMatch/search/multistart.py
index d76876a..601e957 100644
--- a/CADETMatch/search/multistart.py
+++ b/CADETMatch/search/multistart.py
@@ -15,7 +15,7 @@
name = "Multistart"
-def run(cache, tools, creator):
+def run(cache):
"run the parameter estimation"
random.seed()
diff --git a/CADETMatch/search/nsga3.py b/CADETMatch/search/nsga3.py
index 85628f0..e98e234 100644
--- a/CADETMatch/search/nsga3.py
+++ b/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')
diff --git a/CADETMatch/search/scoretest.py b/CADETMatch/search/scoretest.py
index 24e71d8..c05220f 100644
--- a/CADETMatch/search/scoretest.py
+++ b/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:
diff --git a/CADETMatch/search/unsga3.py b/CADETMatch/search/unsga3.py
index f2252d4..898ccc0 100644
--- a/CADETMatch/search/unsga3.py
+++ b/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')
diff --git a/CADETMatch/util.py b/CADETMatch/util.py
index 37f5da6..c951cbb 100644
--- a/CADETMatch/util.py
+++ b/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
diff --git a/setup.py b/setup.py
index 283b5c2..1ae03af 100644
--- a/setup.py
+++ b/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',