Merge pull request #1721 from PrincetonUniversity/devel

Devel
PrincetonUniversity · Jul 20, 2020 · 16e9407 · 16e9407
2 parents 0374dca + 9124c03
commit 16e9407
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Showing 72 changed files with 32,470 additions and 1,510 deletions.
diff --git a/.github/workflows/pnl-ci.yml b/.github/workflows/pnl-ci.yml
@@ -99,7 +99,7 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
 
     - name: Test with pytest
-      run: pytest --junit-xml=tests_out.xml --verbosity=0 -n auto
+      run: pytest --junit-xml=tests_out.xml --verbosity=0 -n auto --maxprocesses=2
 
     - name: Upload test results
       uses: actions/upload-artifact@v1

diff --git a/Scripts/Debug/bryant_lca_with_termination.py b/Scripts/Debug/bryant_lca_with_termination.py
@@ -1,6 +1,4 @@
 import psyneulink as pnl
-import numpy as np
-import pytest
 
 cueInterval = pnl.TransferMechanism(default_variable=[[0.0]],
                                     size=1,
@@ -60,4 +58,4 @@
 csiController.log.print_entries()
 cueInterval.log.print_entries()
 taskLayer.log.print_entries()
-# csiController.control_signals[0].log.print_entries()
+# csiController.control_signals[0].log.print_entries()
diff --git a/Scripts/Debug/predator_prey_opt/predator_prey_dmt.py b/Scripts/Debug/predator_prey_opt/predator_prey_dmt.py
@@ -1,4 +1,3 @@
-import sys
 import os
 import timeit
 import numpy as np

diff --git a/Scripts/Examples/Rumelhart Semantic Network.py b/Scripts/Examples/Rumelhart Semantic Network.py
@@ -1,6 +1,4 @@
 from psyneulink import *
-import numpy as np
-import typecheck as tc
 
 # This script implements the following network, first described in Rumelhart and Todd
 # (Rumelhart, D. E., & Todd, P. M. (1993). Learning and connectionist representations. Attention and performance XIV:

diff --git a/docs/source/_static/css/custom.css b/docs/source/_static/css/custom.css
@@ -1,62 +1,3 @@
-/*!**/
-/*Sets bottom-margin size for list elements in the main body of the document to 12px.*/
-/*Because Sphinx includes the table of contents in the main section, we then reset just the list elements*/
-/*in that section to 0px.*/
-/* *!*/
-
-h1, h2{
-    margin-bottom:12px;
-}
-
-li{
-    margin-top:12px;
-}
-
-ul.simple{
-    margin-bottom:12px!important;
-}
-
-ol.simple{
-    margin-bottom:12px!important;
-}
-
-.section #overview {
-    margin-top: 24px;
-}
-
-#sections p,
-#sections .simple,
-#sections li{
-    margin-top:0px;
-    margin-bottom:0px!important;
-}
-
-.toctree-wrapper.compound li, div#sections li{
-    margin-top: 0px !important;
-}
-
-.toctree-wrapper.compound ul.simple{
-    display: none
-}
-
-#welcome-to-psyneulink-logo .simple li,
-#welcome-to-logo .simple li,
-#basics-and-sampler .simple li,
-#basics-and-sampler .simple p,
-#quick-reference #sections li,
-#core li,
-#contributors li,
-#table-of-contents li,
-#indices-and-tables li,
-.wy-menu-vertical li,
-.section #contents li,
-.section #contents p,
-.section #contents dd,
-.section #contents dt,
-.section #contents dl,
-.section #contents ul,
-.section #contents ol
-{
-    margin-top:0px;
-    margin-bottom:0px!important;
-}
+/*
+CSS styles defined in this file will be loaded into the docs at build time
+*/
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -173,6 +173,7 @@
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
+html_css_files = ['css/custom.css']
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied

diff --git a/psyneulink/core/components/__init__.py b/psyneulink/core/components/__init__.py
@@ -40,6 +40,9 @@
 from .shellclasses import *
 from .ports import *
 
+from psyneulink.library.components.mechanisms.processing.integrator.ddm import DDM
+from psyneulink.core.globals.preferences.basepreferenceset import BasePreferenceSet, ComponentDefaultPrefDicts, PreferenceLevel
+
 __all__ = [
     'InitError'
 ]
@@ -62,27 +65,17 @@ def __str__(self):
 
 #region ***************************************** MECHANISM SUBCLASSES *************************************************
 
-from psyneulink.core.components.mechanisms.mechanism import MechanismRegistry
-from psyneulink.core.components.mechanisms.mechanism import Mechanism_Base
-from psyneulink.core.components.mechanisms.processing.defaultprocessingmechanism \
-    import DefaultProcessingMechanism_Base
-from psyneulink.core.components.mechanisms.modulatory.control.controlmechanism \
-    import ControlMechanism
 register_category(entry=ControlMechanism,
                   base_class=Mechanism_Base,
                   registry=MechanismRegistry,
                   context=kwInitPy)
 
-from psyneulink.core.components.mechanisms.modulatory.control.defaultcontrolmechanism \
-    import DefaultControlMechanism
 register_category(entry=DefaultControlMechanism,
                   base_class=Mechanism_Base,
                   registry=MechanismRegistry,
                   context=kwInitPy)
 
 # DDM (used as DefaultMechanism)
-
-from psyneulink.library.components.mechanisms.processing.integrator.ddm import DDM
 register_category(entry=DDM,
                   base_class=Mechanism_Base,
                   registry=MechanismRegistry,
@@ -113,46 +106,38 @@ def __str__(self):
 #              while still indexing multiple uses of the same base name within an owner
 #
 # Port registry
-from psyneulink.core.components.ports.port import PortRegistry
-from psyneulink.core.components.ports.port import Port_Base
 
 # InputPort
-from psyneulink.core.components.ports.inputport import InputPort
 register_category(entry=InputPort,
                   base_class=Port_Base,
                   registry=PortRegistry,
                   context=kwInitPy)
 
 # ParameterPort
-from psyneulink.core.components.ports.parameterport import ParameterPort
 register_category(entry=ParameterPort,
                   base_class=Port_Base,
                   registry=PortRegistry,
                   context=kwInitPy)
 
 # OutputPort
-from psyneulink.core.components.ports.outputport import OutputPort
 register_category(entry=OutputPort,
                   base_class=Port_Base,
                   registry=PortRegistry,
                   context=kwInitPy)
 
 # LearningSignal
-from psyneulink.core.components.ports.modulatorysignals.learningsignal import LearningSignal
 register_category(entry=LearningSignal,
                   base_class=Port_Base,
                   registry=PortRegistry,
                   context=kwInitPy)
 
 # ControlSignal
-from psyneulink.core.components.ports.modulatorysignals.controlsignal import ControlSignal
 register_category(entry=ControlSignal,
                   base_class=Port_Base,
                   registry=PortRegistry,
                   context=kwInitPy)
 
 # GatingSignal
-from psyneulink.core.components.ports.modulatorysignals.gatingsignal import GatingSignal
 register_category(entry=GatingSignal,
                   base_class=Port_Base,
                   registry=PortRegistry,
@@ -162,32 +147,26 @@ def __str__(self):
 # Projection -----------------------------------------------------------------------------------------------------------
 
 # Projection registry
-from psyneulink.core.components.projections.projection import ProjectionRegistry
-from psyneulink.core.components.projections.projection import Projection_Base
 
 # MappingProjection
-from psyneulink.core.components.projections.pathway.mappingprojection import MappingProjection
 register_category(entry=MappingProjection,
                   base_class=Projection_Base,
                   registry=ProjectionRegistry,
                   context=kwInitPy)
 
 # LearningProjection
-from psyneulink.core.components.projections.modulatory.learningprojection import LearningProjection
 register_category(entry=LearningProjection,
                   base_class=Projection_Base,
                   registry=ProjectionRegistry,
                   context=kwInitPy)
 
 # ControlProjection
-from psyneulink.core.components.projections.modulatory.controlprojection import ControlProjection
 register_category(entry=ControlProjection,
                   base_class=Projection_Base,
                   registry=ProjectionRegistry,
                   context=kwInitPy)
 
 # GatingProjection
-from psyneulink.core.components.projections.modulatory.gatingprojection import GatingProjection
 register_category(entry=GatingProjection,
                   base_class=Projection_Base,
                   registry=ProjectionRegistry,
@@ -271,23 +250,17 @@ def __str__(self):
 #endregion
 
 #region ***************************************** CLASS _PREFERENCES ***************************************************
-from psyneulink.core.globals.preferences.basepreferenceset \
-    import BasePreferenceSet, ComponentDefaultPrefDicts, PreferenceLevel
-
-from psyneulink.core.components.shellclasses import System_Base
 System_Base.classPreferences = BasePreferenceSet(owner=System_Base,
                                                  prefs=ComponentDefaultPrefDicts[PreferenceLevel.INSTANCE],
                                                  level=PreferenceLevel.INSTANCE,
                                                  context=".__init__.py")
 
-from psyneulink.core.components.shellclasses import Process_Base
 Process_Base.classPreferences = BasePreferenceSet(owner=Process_Base,
                                                   prefs=ComponentDefaultPrefDicts[PreferenceLevel.INSTANCE],
                                                   level=PreferenceLevel.INSTANCE,
                                                   context=".__init__.py")
 
 
-from psyneulink.core.components.shellclasses import Mechanism
 Mechanism.classPreferences = BasePreferenceSet(owner=Mechanism,
                                                prefs=ComponentDefaultPrefDicts[PreferenceLevel.CATEGORY],
                                                level=PreferenceLevel.TYPE,
@@ -299,7 +272,6 @@ def __str__(self):
                                          context=".__init__.py")
 
 
-from psyneulink.core.components.shellclasses import Port
 Port.classPreferences = BasePreferenceSet(owner=Port,
                                           prefs=ComponentDefaultPrefDicts[PreferenceLevel.CATEGORY],
                                           level=PreferenceLevel.CATEGORY,
@@ -315,13 +287,11 @@ def __str__(self):
                                                        level=PreferenceLevel.TYPE,
                                                        context=".__init__.py")
 
-from psyneulink.core.components.shellclasses import Projection
 Projection.classPreferences = BasePreferenceSet(owner=Projection,
                                                 prefs=ComponentDefaultPrefDicts[PreferenceLevel.CATEGORY],
                                                 level=PreferenceLevel.CATEGORY,
                                                 context=".__init__.py")
 
-from psyneulink.core.components.functions.function import Function
 Function.classPreferences = BasePreferenceSet(owner=Function,
                                               prefs=ComponentDefaultPrefDicts[PreferenceLevel.CATEGORY],
                                               level=PreferenceLevel.CATEGORY,

diff --git a/psyneulink/core/components/component.py b/psyneulink/core/components/component.py
@@ -483,18 +483,14 @@
 import inspect
 import logging
 import numbers
-import re
 import types
 import warnings
-import weakref
 
 from abc import ABCMeta
 from collections.abc import Iterable
-from collections import OrderedDict, UserDict
 from enum import Enum, IntEnum
 
 import numpy as np
-import typecheck as tc
 
 from psyneulink.core import llvm as pnlvm
 from psyneulink.core.globals.context import \
@@ -2438,7 +2434,6 @@ def _validate_params(self, request_set, target_set=None, context=None):
 
                 elif target_set is not None:
                     # Copy any iterables so that deletions can be made to assignments belonging to the instance
-                    from collections.abc import Iterable
                     if not isinstance(param_value, Iterable) or isinstance(param_value, str):
                         target_set[param_name] = param_value
                     else:

diff --git a/psyneulink/core/components/functions/distributionfunctions.py b/psyneulink/core/components/functions/distributionfunctions.py
@@ -23,7 +23,6 @@
 Functions that return one or more samples from a distribution.
 
 """
-from enum import IntEnum
 
 import numpy as np
 import typecheck as tc

diff --git a/psyneulink/core/components/functions/function.py b/psyneulink/core/components/functions/function.py
@@ -308,10 +308,6 @@ def _output_type_setter(value, owning_component):
     # https://github.com/PrincetonUniversity/PsyNeuLink/issues/895 is solved
     # properly(meaning Mechanism values may be something other than 2D np array)
     try:
-        # import here because if this package is not installed, we can assume
-        # the user is probably not dealing with compilation so no need to warn
-        # unecessarily
-        import llvmlite
         if (
             isinstance(owning_component.owner, Mechanism)
             and (

diff --git a/psyneulink/core/components/functions/objectivefunctions.py b/psyneulink/core/components/functions/objectivefunctions.py
@@ -20,7 +20,6 @@
 """
 
 import functools
-import itertools
 
 import numpy as np
 import typecheck as tc

diff --git a/psyneulink/core/components/functions/optimizationfunctions.py b/psyneulink/core/components/functions/optimizationfunctions.py
@@ -2344,8 +2344,7 @@ def _import_elfi():
         # https://github.com/scikit-optimize/scikit-optimize/issues/637
         # Lets import and set the backend to PS to be safe. We aren't plotting anyway
         # I guess. Only do this on Mac OS X
-        from sys import platform
-        if platform == "darwin":
+        if sys.platform == "darwin":
             import matplotlib
             matplotlib.use('PS')
 

diff --git a/psyneulink/core/components/functions/statefulfunctions/integratorfunctions.py b/psyneulink/core/components/functions/statefulfunctions/integratorfunctions.py
@@ -25,8 +25,6 @@
 
 """
 
-import itertools
-import numbers
 import warnings
 
 import numpy as np

diff --git a/psyneulink/core/components/functions/statefulfunctions/memoryfunctions.py b/psyneulink/core/components/functions/statefulfunctions/memoryfunctions.py
@@ -22,7 +22,7 @@
 
 """
 
-from collections import deque, OrderedDict
+from collections import deque
 
 import numpy as np
 import typecheck as tc

diff --git a/psyneulink/core/components/functions/statefulfunctions/statefulfunction.py b/psyneulink/core/components/functions/statefulfunctions/statefulfunction.py
@@ -16,13 +16,12 @@
 
 """
 
-import numpy as np
+import abc
 import typecheck as tc
-import itertools
 import warnings
 import numbers
 
-import abc
+import numpy as np
 
 from psyneulink.core import llvm as pnlvm
 from psyneulink.core.components.component import DefaultsFlexibility