Changes in the documentation and removal of PyPet includes

bin/l2l-fun-ce-gaussmix.py

@@ -4,8 +4,7 @@
 
 import numpy as np
 
-from pypet import Environment
-from pypet import pypetconstants
+from l2l.utils.environment import Environment
 
 from l2l.optimizees.functions.optimizee import FunctionGeneratorOptimizee
 from l2l.optimizees.functions.benchmarked_functions import BenchmarkedFunctions
@@ -39,14 +38,12 @@ def main():
     traj_file = os.path.join(paths.output_dir_path, 'data.h5')
 
     # Create an environment that handles running our simulation
-    # This initializes a PyPet environment
+    # This initializes an environment
     env = Environment(trajectory=name, filename=traj_file, file_title='{} data'.format(name),
                       comment='{} data'.format(name),
                       add_time=True,
                       freeze_input=True,
                       multiproc=True,
-                      use_scoop=True,
-                      wrap_mode=pypetconstants.WRAP_MODE_LOCAL,
                       automatic_storing=True,
                       log_stdout=False,  # Sends stdout to logs
                       )

bin/l2l-fun-ce.py

@@ -35,7 +35,7 @@ def main():
     traj_file = os.path.join(paths.output_dir_path, 'data.h5')
 
     # Create an environment that handles running our simulation
-    # This initializes a PyPet environment
+    # This initializes an environment
     env = Environment(trajectory=name, filename=traj_file, file_title='{} data'.format(name),
                       comment='{} data'.format(name),
                       add_time=True,

bin/l2l-fun-es.py

@@ -31,7 +31,7 @@ def run_experiment():
     print("All output logs can be found in directory ", paths.logs_path)
 
     # Create an environment that handles running our simulation
-    # This initializes a PyPet environment
+    # This initializes an environment
     env = Environment(
         trajectory=trajectory_name,
         filename=paths.output_dir_path,

bin/l2l-fun-face.py

@@ -3,8 +3,7 @@
 
 import numpy as np
 
-from pypet import Environment
-from pypet import pypetconstants
+from l2l.utils.environment import Environment
 
 from l2l.optimizees.functions import tools as function_tools
 from l2l.optimizees.functions.benchmarked_functions import BenchmarkedFunctions
@@ -36,14 +35,13 @@ def main():
     traj_file = os.path.join(paths.output_dir_path, 'data.h5')
 
     # Create an environment that handles running our simulation
-    # This initializes a PyPet environment
+    # This initializes an environment
     env = Environment(trajectory=name, filename=traj_file, file_title='{} data'.format(name),
                       comment='{} data'.format(name),
                       add_time=True,
                       freeze_input=True,
                       multiproc=True,
                       use_scoop=True,
-                      wrap_mode=pypetconstants.WRAP_MODE_LOCAL,
                       automatic_storing=True,
                       log_stdout=False,  # Sends stdout to logs
                       )

bin/l2l-fun-ga.py

@@ -42,7 +42,7 @@ def main():
     traj_file = os.path.join(paths.output_dir_path, 'data.h5')
 
     # Create an environment that handles running our simulation
-    # This initializes a PyPet environment
+    # This initializes an environment
     env = Environment(trajectory=name, filename=traj_file, file_title='{} data'.format(name),
                       comment='{} data'.format(name),
                       add_time=True,

bin/l2l-fun-gd.py

@@ -38,7 +38,7 @@ def main():
     traj_file = os.path.join(paths.output_dir_path, 'data.h5')
 
     # Create an environment that handles running our simulation
-    # This initializes a PyPet environment
+    # This initializes an environment
     env = Environment(trajectory=name, filename=traj_file, file_title='{} data'.format(name),
                       comment='{} data'.format(name),
                       add_time=True,

bin/l2l-fun-gs.py

@@ -35,7 +35,7 @@ def main():
     traj_file = os.path.join(paths.output_dir_path, 'data.h5')
 
     # Create an environment that handles running our simulation
-    # This initializes a PyPet environment
+    # This initializes an environment
     env = Environment(trajectory=name, filename=traj_file, file_title='{} data'.format(name),
                       comment='{} data'.format(name),
                       add_time=True,

bin/l2l-fun-pt.py

@@ -2,7 +2,7 @@
 import os
 
 import numpy as np
-from pypet import Environment
+from l2l.utils.environment import Environment
 
 from l2l.optimizees.functions import tools as function_tools
 from l2l.optimizees.functions.benchmarked_functions import BenchmarkedFunctions
@@ -33,7 +33,7 @@ def main():
     traj_file = os.path.join(paths.output_dir_path, 'data.h5')
 
     # Create an environment that handles running our simulation
-    # This initializes a PyPet environment
+    # This initializes an environment
     env = Environment(trajectory=name, filename=traj_file, file_title='{} data'.format(name),
                       comment='{} data'.format(name),
                       add_time=True,

bin/l2l-fun-sa.py

@@ -35,7 +35,7 @@ def main():
     traj_file = os.path.join(paths.output_dir_path, 'data.h5')
 
     # Create an environment that handles running our simulation
-    # This initializes a PyPet environment
+    # This initializes an environment
     env = Environment(trajectory=name, filename=traj_file, file_title='{} data'.format(name),
                       comment='{} data'.format(name),
                       add_time=True,

bin/l2l-funall.py

@@ -3,7 +3,7 @@
 import itertools
 
 import numpy as np
-from pypet import Environment
+from l2l.utils.environment import Environment
 
 from l2l.optimizees.functions.benchmarked_functions import BenchmarkedFunctions
 from l2l.optimizees.functions.optimizee import FunctionGeneratorOptimizee
@@ -73,7 +73,7 @@ def main():
         optimizer_parameters = optimizer_parameters_fn()
 
         # Create an environment that handles running our simulation
-        # This initializes a PyPet environment
+        # This initializes an environment
         env = Environment(trajectory=name, filename=traj_file, file_title='{} data'.format(name),
                           comment='{} data'.format(name),
                           # freeze_input=True,

bin/l2l-mnist-ce.py

@@ -31,7 +31,7 @@ def run_experiment():
     print("All output logs can be found in directory ", paths.logs_path)
 
     # Create an environment that handles running our simulation
-    # This initializes a PyPet environment
+    # This initializes an environment
     env = Environment(
         trajectory=trajectory_name,
         filename=paths.output_dir_path,

bin/l2l-mnist-es.py

@@ -2,7 +2,7 @@
 from datetime import datetime
 
 import numpy as np
-from pypet import Environment
+from l2l.utils.environment import Environment
 
 from l2l import dict_to_list
 from l2l.logging_tools import create_shared_logger_data, configure_loggers
@@ -30,7 +30,7 @@ def run_experiment():
     print("All output logs can be found in directory ", paths.logs_path)
 
     # Create an environment that handles running our simulation
-    # This initializes a PyPet environment
+    # This initializes an environment
     env = Environment(
         trajectory=trajectory_name,
         filename=paths.output_dir_path,

bin/l2l-template.py

@@ -5,8 +5,7 @@
 
 import logging.config
 
-from pypet import Environment
-from pypet import pypetconstants
+from l2l.utils.environment import Environment
 
 from l2l.logging_tools import create_shared_logger_data, configure_loggers
 from l2l.optimizees.optimizee import Optimizee
@@ -41,16 +40,14 @@ def main():
     print("All output logs can be found in directory ", paths.logs_path)
 
     # Create an environment that handles running our simulation
-    # This initializes a PyPet environment. See Pypet documentation for more details on environment and trajectory.
+    # This initializes an environment. This environment is based on the Pypet implementation.
     # Uncomment 'freeze_input', 'multipproc', 'use_scoop' and 'wrap_mode' lines to disable running the experiment
     # across cores and nodes.
     env = Environment(trajectory=name, filename=paths.output_dir_path, file_title='{} data'.format(name),
                       comment='{} data'.format(name),
                       add_time=True,
                       freeze_input=False,
                       multiproc=True,
-                      use_scoop=True,
-                      wrap_mode=pypetconstants.WRAP_MODE_LOCAL,
                       automatic_storing=True,
                       log_stdout=False,  # Sends stdout to logs
                       )

l2l/optimizers/gridsearch/optimizer.py

@@ -2,7 +2,7 @@
 from collections import namedtuple
 
 import numpy as np
-from pypet.utils.explore import cartesian_product
+from l2l.utils.tools import cartesian_product
 
 from l2l import DictEntryType
 from l2l import dict_to_list

l2l/optimizers/optimizer.py

@@ -1,6 +1,6 @@
 from collections import namedtuple
 
-from pypet import cartesian_product
+from l2l.utils.tools import cartesian_product
 
 from l2l import get_grouped_dict