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Merge commit '13f1092a7afdf3ddddaf5366ddf6b8d1080c0e99' into feat/com…
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* commit '13f1092a7afdf3ddddaf5366ddf6b8d1080c0e99':
  rename packages and modules to lowercase, and handle relevant import changes
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kmantel committed Apr 5, 2018
2 parents 88b5de5 + 13f1092 commit 0fce07c
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Showing 181 changed files with 1,235 additions and 1,239 deletions.
12 changes: 6 additions & 6 deletions Scripts/DEBUGGING SCRIPTS/AGT Test Script.py
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from PsyNeuLink.Components.Functions.Function import FHNIntegrator
from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.TransferMechanism import TransferMechanism
from PsyNeuLink.Components.Process import process
from PsyNeuLink.Components.System import system
from PsyNeuLink.Library.Subsystems.AGT.AGTControlMechanism import AGTControlMechanism
from PsyNeuLink.Library.Subsystems.AGT.LCControlMechanism import LCControlMechanism
from psyneulink.components.functions.function import FHNIntegrator
from psyneulink.components.mechanisms.processing.transfermechanism import TransferMechanism
from psyneulink.components.process import process
from psyneulink.components.system import system
from psyneulink.library.subsystems.agt.agtcontrolmechanism import AGTControlMechanism
from psyneulink.library.subsystems.agt.lccontrolmechanism import LCControlMechanism

decision_mech = TransferMechanism(name='Decision_Mech')

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12 changes: 6 additions & 6 deletions Scripts/DEBUGGING SCRIPTS/EVC Gratton Script - SEBASTIAN.py
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# from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.Deprecated.LinearMechanism import *

from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.TransferMechanism import *
from PsyNeuLink.Components.Process import process
from PsyNeuLink.Components.Projections.ModulatoryProjections.ControlProjection import ControlProjection
from PsyNeuLink.Components.System import system
from PsyNeuLink.Globals.Keywords import *
from PsyNeuLink.Library.Mechanisms.AdaptiveMechanisms import EVCControlMechanism
from psyneulink.components.mechanisms.processing.transfermechanism import *
from psyneulink.components.process import process
from psyneulink.components.projections.modulatory.controlprojection import ControlProjection
from psyneulink.components.system import system
from psyneulink.globals.keywords import *
from psyneulink.library.mechanisms.adaptive import EVCControlMechanism


def test_search_function(controller=None, **kwargs):
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# from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.Deprecated.LinearMechanism import *

from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.TransferMechanism import *
from PsyNeuLink.Components.Process import process
from PsyNeuLink.Components.States.ModulatorySignals.ControlSignal import ControlSignal
from PsyNeuLink.Components.System import system
from PsyNeuLink.Globals.Keywords import *
from PsyNeuLink.Library.Mechanisms.AdaptiveMechanisms import EVCControlMechanism
from psyneulink.components.mechanisms.processing.transfermechanism import *
from psyneulink.components.process import process
from psyneulink.components.states.modulatorysignals.controlsignal import ControlSignal
from psyneulink.components.system import system
from psyneulink.globals.keywords import *
from psyneulink.library.mechanisms.adaptive import EVCControlMechanism

random.seed(0)
np.random.seed(0)
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10 changes: 5 additions & 5 deletions Scripts/DEBUGGING SCRIPTS/LCMechanism Test Script.py
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@@ -1,8 +1,8 @@
from PsyNeuLink.Components.Functions.Function import Linear, Logistic
from PsyNeuLink.Components.Functions.Function import ModulationParam
from PsyNeuLink.Components.Mechanisms.AdaptiveMechanisms.GatingMechanism.GatingMechanism import GatingMechanism
from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.TransferMechanism import TransferMechanism
from PsyNeuLink.Library.Subsystems.AGT.LCControlMechanism import LCControlMechanism
from psyneulink.components.functions.function import Linear, Logistic
from psyneulink.components.functions.function import ModulationParam
from psyneulink.components.mechanisms.adaptive.gating.gatingmechanism import GatingMechanism
from psyneulink.components.mechanisms.processing.transfermechanism import TransferMechanism
from psyneulink.library.subsystems.agt.lccontrolmechanism import LCControlMechanism


my_mech_1 = TransferMechanism(function=Linear, name='my_linear_mechanism')
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@@ -1,11 +1,11 @@
from PsyNeuLink.Components.Functions.Function import Logistic
from PsyNeuLink.Components.Mechanisms.AdaptiveMechanisms.GatingMechanism.GatingMechanism import GatingMechanism
from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.TransferMechanism import TransferMechanism
from PsyNeuLink.Components.Process import process
from PsyNeuLink.Components.States.ModulatorySignals.GatingSignal import GatingSignal
from PsyNeuLink.Components.States.OutputState import *
from PsyNeuLink.Components.System import system
from PsyNeuLink.Scheduling.Condition import AfterNCalls
from psyneulink.components.functions.function import Logistic
from psyneulink.components.mechanisms.adaptive.gating.gatingmechanism import GatingMechanism
from psyneulink.components.mechanisms.processing.transfermechanism import TransferMechanism
from psyneulink.components.process import process
from psyneulink.components.states.modulatorysignals.gatingsignal import GatingSignal
from psyneulink.components.states.outputstate import *
from psyneulink.components.system import system
from psyneulink.scheduling.condition import AfterNCalls

# from PsyNeuLink.Globals.Run import run, construct_inputs

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function=Logistic,
default_variable = [0,0,0])

from PsyNeuLink.Components.States.InputState import InputState
from psyneulink.components.states.inputstate import InputState

my_input_state = InputState(
# owner=Output_Layer,
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12 changes: 6 additions & 6 deletions Scripts/DEBUGGING SCRIPTS/OLD/EVC Gratton Script_Bug1.py
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@@ -1,11 +1,11 @@
# from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.Deprecated.LinearMechanism import *

from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.TransferMechanism import *
from PsyNeuLink.Components.Process import process
from PsyNeuLink.Components.Projections.ModulatoryProjections.ControlProjection import ControlProjection
from PsyNeuLink.Components.System import system
from PsyNeuLink.Globals.Keywords import *
from PsyNeuLink.Library.Subsystems.EVC.EVCControlMechanism import EVCControlMechanism
from psyneulink.components.mechanisms.processing.transfermechanism import *
from psyneulink.components.process import process
from psyneulink.components.projections.modulatory.controlprojection import ControlProjection
from psyneulink.components.system import system
from psyneulink.globals.keywords import *
from psyneulink.library.subsystems.evc.evccontrolmechanism import EVCControlMechanism


def test_search_function(controller=None, **kwargs):
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12 changes: 6 additions & 6 deletions Scripts/DEBUGGING SCRIPTS/OLD/EVC Gratton Script_Bug2.py
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@@ -1,11 +1,11 @@
# from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.Deprecated.LinearMechanism import *

from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.TransferMechanism import *
from PsyNeuLink.Components.Process import process
from PsyNeuLink.Components.Projections.ModulatoryProjections.ControlProjection import ControlProjection
from PsyNeuLink.Components.System import system
from PsyNeuLink.Globals.Keywords import *
from PsyNeuLink.Library.Subsystems.EVC.EVCControlMechanism import EVCControlMechanism
from psyneulink.components.mechanisms.processing.transfermechanism import *
from psyneulink.components.process import process
from psyneulink.components.projections.modulatory.controlprojection import ControlProjection
from psyneulink.components.system import system
from psyneulink.globals.keywords import *
from psyneulink.library.subsystems.evc.evccontrolmechanism import EVCControlMechanism


def test_search_function(controller=None, **kwargs):
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12 changes: 6 additions & 6 deletions Scripts/DEBUGGING SCRIPTS/OLD/EVC Gratton Script_Bug3.py
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@@ -1,11 +1,11 @@
# from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.Deprecated.LinearMechanism import *

from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.TransferMechanism import *
from PsyNeuLink.Components.Process import process
from PsyNeuLink.Components.Projections.ModulatoryProjections.ControlProjection import ControlProjection
from PsyNeuLink.Components.System import system
from PsyNeuLink.Globals.Keywords import *
from PsyNeuLink.Library.Mechanisms.AdaptiveMechanisms import EVCControlMechanism
from psyneulink.components.mechanisms.processing.transfermechanism import *
from psyneulink.components.process import process
from psyneulink.components.projections.modulatory.controlprojection import ControlProjection
from psyneulink.components.system import system
from psyneulink.globals.keywords import *
from psyneulink.library.mechanisms.adaptive import EVCControlMechanism


def test_search_function(controller=None, **kwargs):
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12 changes: 6 additions & 6 deletions Scripts/DEBUGGING SCRIPTS/OLD/EVC Gratton Script_Bug4.py
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@@ -1,11 +1,11 @@
# from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.Deprecated.LinearMechanism import *

from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.TransferMechanism import *
from PsyNeuLink.Components.Process import process
from PsyNeuLink.Components.Projections.ModulatoryProjections.ControlProjection import ControlProjection
from PsyNeuLink.Components.System import system
from PsyNeuLink.Globals.Keywords import *
from PsyNeuLink.Library.Mechanisms.AdaptiveMechanisms import EVCControlMechanism
from psyneulink.components.mechanisms.processing.transfermechanism import *
from psyneulink.components.process import process
from psyneulink.components.projections.modulatory.controlprojection import ControlProjection
from psyneulink.components.system import system
from psyneulink.globals.keywords import *
from psyneulink.library.mechanisms.adaptive import EVCControlMechanism


def test_search_function(controller=None, **kwargs):
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12 changes: 6 additions & 6 deletions Scripts/DEBUGGING SCRIPTS/OLD/EVC Gratton Script_Bug5.py
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@@ -1,11 +1,11 @@
# from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.Deprecated.LinearMechanism import *

from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.TransferMechanism import *
from PsyNeuLink.Components.Process import process
from PsyNeuLink.Components.Projections.ModulatoryProjections.ControlProjection import ControlProjection
from PsyNeuLink.Components.System import system
from PsyNeuLink.Globals.Keywords import *
from PsyNeuLink.Library.Mechanisms.AdaptiveMechanisms import EVCControlMechanism
from psyneulink.components.mechanisms.processing.transfermechanism import *
from psyneulink.components.process import process
from psyneulink.components.projections.modulatory.controlprojection import ControlProjection
from psyneulink.components.system import system
from psyneulink.globals.keywords import *
from psyneulink.library.mechanisms.adaptive import EVCControlMechanism


def test_search_function(controller=None, **kwargs):
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@@ -1,11 +1,11 @@
# from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.Deprecated.LinearMechanism import *

from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.TransferMechanism import *
from PsyNeuLink.Components.Process import process
from PsyNeuLink.Components.Projections.ModulatoryProjections.ControlProjection import ControlProjection
from PsyNeuLink.Components.System import system
from PsyNeuLink.Globals.Keywords import *
from PsyNeuLink.Library.Mechanisms.AdaptiveMechanisms import EVCControlMechanism
from psyneulink.components.mechanisms.processing.transfermechanism import *
from psyneulink.components.process import process
from psyneulink.components.projections.modulatory.controlprojection import ControlProjection
from psyneulink.components.system import system
from psyneulink.globals.keywords import *
from psyneulink.library.mechanisms.adaptive import EVCControlMechanism

random.seed(0)
np.random.seed(0)
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@@ -1,11 +1,11 @@
# from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.Deprecated.LinearMechanism import *
from PsyNeuLink.Components.Mechanisms.AdaptiveMechanisms.ControlMechanism.EVCControlMechanism import EVCControlMechanism
from psyneulink.components.mechanisms.adaptive.control.EVCControlMechanism import EVCControlMechanism

from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.TransferMechanism import *
from PsyNeuLink.Components.Process import process
from PsyNeuLink.Components.Projections.ModulatoryProjections.ControlProjection import ControlProjection
from PsyNeuLink.Components.System import system
from PsyNeuLink.Globals.Keywords import *
from psyneulink.components.mechanisms.processing.transfermechanism import *
from psyneulink.components.process import process
from psyneulink.components.projections.modulatory.controlprojection import ControlProjection
from psyneulink.components.system import system
from psyneulink.globals.keywords import *

# import random
# random.seed(0)
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12 changes: 6 additions & 6 deletions Scripts/DEBUGGING SCRIPTS/OLD/EVC_Gratton_Script_Validation.py
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@@ -1,11 +1,11 @@
# from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.Deprecated.LinearMechanism import *
from PsyNeuLink.Components.Projections.ControlProjection import ControlProjection
from psyneulink.components.projections.ControlProjection import ControlProjection

from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.TransferMechanism import *
from PsyNeuLink.Components.Process import process
from PsyNeuLink.Components.System import system
from PsyNeuLink.Globals.Keywords import *
from PsyNeuLink.Library.Mechanisms.AdaptiveMechanisms import EVCControlMechanism
from psyneulink.components.mechanisms.processing.transfermechanism import *
from psyneulink.components.process import process
from psyneulink.components.system import system
from psyneulink.globals.keywords import *
from psyneulink.library.mechanisms.adaptive import EVCControlMechanism


def test_search_function(controller=None, **kwargs):
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@@ -1,10 +1,10 @@
# from PsyNeuLink.Components.Functions.Function import Logistic, random_matrix
from PsyNeuLink.Components.Functions.Function import Logistic
from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.TransferMechanism import TransferMechanism
from PsyNeuLink.Components.Process import process
from PsyNeuLink.Components.Projections.PathwayProjections.MappingProjection import MappingProjection
from PsyNeuLink.Components.System import system
from PsyNeuLink.Scheduling.TimeScale import TimeScale
from psyneulink.components.functions.function import Logistic
from psyneulink.components.mechanisms.processing.transfermechanism import TransferMechanism
from psyneulink.components.process import process
from psyneulink.components.projections.pathway.mappingprojection import MappingProjection
from psyneulink.components.system import system
from psyneulink.scheduling.timescale import TimeScale

Input_Layer = TransferMechanism(name='Input Layer',
function=Logistic,
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@@ -1,11 +1,11 @@
# from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.Deprecated.LinearMechanism import *

from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.TransferMechanism import *
from PsyNeuLink.Components.Process import process
from PsyNeuLink.Components.Projections.ModulatoryProjections.ControlProjection import ControlProjection
from PsyNeuLink.Components.System import system
from PsyNeuLink.Globals.Keywords import *
from PsyNeuLink.Library.Subsystems.EVC.EVCControlMechanism import EVCControlMechanism
from psyneulink.components.mechanisms.processing.transfermechanism import *
from psyneulink.components.process import process
from psyneulink.components.projections.modulatory.controlprojection import ControlProjection
from psyneulink.components.system import system
from psyneulink.globals.keywords import *
from psyneulink.library.subsystems.evc.evccontrolmechanism import EVCControlMechanism


def test_search_function(controller=None, **kwargs):
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@@ -1,8 +1,8 @@
# from PsyNeuLink.Components.Functions.Function import Logistic, random_matrix
from PsyNeuLink.Components.Functions.Function import Logistic
from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.TransferMechanism import TransferMechanism
from PsyNeuLink.Components.Projections.PathwayProjections.MappingProjection import MappingProjection
from PsyNeuLink.Components.System import *
from psyneulink.components.functions.function import Logistic
from psyneulink.components.mechanisms.processing.transfermechanism import TransferMechanism
from psyneulink.components.projections.pathway.mappingprojection import MappingProjection
from psyneulink.components.system import *

# specification of task environment
NFeatures = 2
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@@ -1,8 +1,8 @@
from PsyNeuLink.Components.Functions.Function import Linear, Logistic
from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.TransferMechanism import TransferMechanism
from PsyNeuLink.Components.Projections.PathwayProjections.MappingProjection import MappingProjection
from PsyNeuLink.Components.System import *
from PsyNeuLink.Globals.Keywords import *
from psyneulink.components.functions.function import Linear, Logistic
from psyneulink.components.mechanisms.processing.transfermechanism import TransferMechanism
from psyneulink.components.projections.pathway.mappingprojection import MappingProjection
from psyneulink.components.system import *
from psyneulink.globals.keywords import *

process_prefs = {REPORT_OUTPUT_PREF: True,
VERBOSE_PREF: False}
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@@ -1,9 +1,9 @@
from PsyNeuLink.Components.Functions.Function import Linear, Logistic
from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.TransferMechanism import TransferMechanism
from PsyNeuLink.Components.Projections.PathwayProjections.MappingProjection import MappingProjection
from PsyNeuLink.Components.System import *
from PsyNeuLink.Globals.Keywords import *
from PsyNeuLink.Library.Subsystems.EVC.EVCControlMechanism import EVCControlMechanism
from psyneulink.components.functions.function import Linear, Logistic
from psyneulink.components.mechanisms.processing.transfermechanism import TransferMechanism
from psyneulink.components.projections.pathway.mappingprojection import MappingProjection
from psyneulink.components.system import *
from psyneulink.globals.keywords import *
from psyneulink.library.subsystems.evc.evccontrolmechanism import EVCControlMechanism

process_prefs = {REPORT_OUTPUT_PREF: True,
VERBOSE_PREF: False}
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@@ -1,7 +1,7 @@
from PsyNeuLink.Components.Functions.Function import Linear, Logistic
from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.TransferMechanism import TransferMechanism
from PsyNeuLink.Components.System import *
from PsyNeuLink.Globals.Keywords import *
from psyneulink.components.functions.function import Linear, Logistic
from psyneulink.components.mechanisms.processing.transfermechanism import TransferMechanism
from psyneulink.components.system import *
from psyneulink.globals.keywords import *

process_prefs = {REPORT_OUTPUT_PREF: True,
VERBOSE_PREF: False}
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8 changes: 4 additions & 4 deletions Scripts/DEBUGGING SCRIPTS/OLD/StroopEVCforDST.py
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Expand Up @@ -5,10 +5,10 @@
@author: lauraab
"""

from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.TransferMechanism import TransferMechanism
from PsyNeuLink.Components.Projections.ModulatoryProjections.ControlProjection import ControlProjection
from PsyNeuLink.Components.System import *
from PsyNeuLink.Library.Subsystems.EVC.EVCControlMechanism import EVCControlMechanism
from psyneulink.components.mechanisms.processing.transfermechanism import TransferMechanism
from psyneulink.components.projections.modulatory.controlprojection import ControlProjection
from psyneulink.components.system import *
from psyneulink.library.subsystems.evc.evccontrolmechanism import EVCControlMechanism

#helpful commands! .show() .excute()
color_word_combine = TransferMechanism(name='color_word_combine', function = Linear()) #default_variable = [1], #JON HOW TO MAKE THIS A SUBTRACTION?
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8 changes: 4 additions & 4 deletions Scripts/DEBUGGING SCRIPTS/OLD/Stroop_model_markus.py
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@@ -1,8 +1,8 @@
# from PsyNeuLink.Components.Functions.Function import Logistic, random_matrix
from PsyNeuLink.Components.Functions.Function import Logistic
from PsyNeuLink.Components.Mechanisms.ProcessingMechanisms.TransferMechanism import TransferMechanism
from PsyNeuLink.Components.Projections.PathwayProjections.MappingProjection import MappingProjection
from PsyNeuLink.Components.System import *
from psyneulink.components.functions.function import Logistic
from psyneulink.components.mechanisms.processing.transfermechanism import TransferMechanism
from psyneulink.components.projections.pathway.mappingprojection import MappingProjection
from psyneulink.components.system import *

# specification of task environment
NFeatures = 1
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