Merge pull request #1399 from PrincetonUniversity/devel

Devel

.appveyor.yml

@@ -8,7 +8,7 @@ branches:
     - appveyor
     - /devel.*/
     - /.*-avy/
-    - /.*-ci/
+    - /ci-.*/
 
 environment:
   PYTHONWARNINGS: ignore::DeprecationWarning
@@ -20,10 +20,6 @@ environment:
     EXTRA_ARGS: -m llvm
   - PYTHON: Python37
     EXTRA_ARGS: -m llvm
-  - PYTHON: Python36
-    ARCH: -x64
-  - PYTHON: Python37
-    ARCH: -x64
 
 install:
   - if not exist %GRAPHVIZ_INSTALLER% appveyor-retry curl https://graphviz.gitlab.io/_pages/Download/windows/%GRAPHVIZ_INSTALLER% -o %GRAPHVIZ_INSTALLER%
@@ -32,7 +28,9 @@ install:
   - pip install --user -U pip
   - pip --version
   # certifi upgrade is needed by pytest-profiling (it does not set the dependencies right)
-  - pip install --user -U certifi
+  # Restrict pywin32 to <226 to work around appveyor issue:
+  # https://help.appveyor.com/discussions/problems/25404-pywin32226-the-specified-module-could-not-be-found
+  - pip install --user -U certifi "pywin32<226"
   - pip install --user git+https://github.com/benureau/leabra.git@master
 
   # pytorch does not distribute windows packages over pypi. Install it directly.

.github/workflows/pnl-ci.yml

@@ -0,0 +1,61 @@
+name: PsyNeuLink CI
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      max-parallel: 7
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        exclude:
+          - os: windows-latest
+            python-version: 3.8
+          - os: macos-latest
+            python-version: 3.8
+
+    steps:
+    - uses: actions/checkout@v1
+      with:
+        fetch-depth: 10
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: MacOS dependencies
+      run: HOMEBREW_NO_AUTO_UPDATE=1 brew install graphviz
+      if: matrix.os == 'macos-latest'
+    - name: Linux dependencies
+      run: sudo apt-get install -y graphviz
+      if: matrix.os == 'ubuntu-latest'
+    - name: Windows dependencies
+      run: |
+        choco install --no-progress -y graphviz
+        python -m pip install --upgrade pip
+        pip install torch -f https://download.pytorch.org/whl/cpu/torch_stable.html
+      if: matrix.os == 'windows-latest'
+    - name: Python3.8 dependencies setup
+      run: |
+        sed -i.tmp "/torch/d" requirements.txt
+        pip install cython llvmlite==0.26
+      if: matrix.python-version == '3.8'
+      env:
+        LLVM_CONFIG: llvm-config-6.0
+    - name: Shared dependencies
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .[dev]
+        pip install --user git+https://github.com/benureau/leabra.git@master
+    - name: Lint with flake8
+      shell: bash
+      run: |
+        pip install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --exit-zero --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: pytest

.travis.yml

@@ -4,6 +4,7 @@ branches:
     - devel
     - /devel-.*/
     - /travis.*/
+    - /ci-.*/
 
 language: shell
 
@@ -13,14 +14,20 @@ os:
 dist: bionic
 
 env:
-  matrix:
+  jobs:
+    - PYTHON=3.8.0
     - PYTHON=3.7.5
     - PYTHON=3.6.8
   global:
     - PYTHONWARNINGS="ignore::DeprecationWarning"
     - PIP_PROGRESS_BAR="off"
     - COVERALLS_PARALLEL=true
 
+jobs:
+  exclude:
+    - env: PYTHON=3.8.0
+      os: osx
+
 # Cache downloaded(built) python packages
 # and homebrew downloads
 cache:
@@ -59,7 +66,20 @@ before_install:
   - |
     # Install venv on Linux using Ubuntu distributed python
     if [ "$TRAVIS_OS_NAME" == "linux" ]; then
-      sudo apt-get install -y python${PYTHON%.*}-dev python${PYTHON%.*}-venv
+      if [ ${PYTHON%.*} == "3.8" ]; then
+        # There are a lot fewer wheels distributed for python3.8.
+        # We end up building a lot of them locally. Install the dev packages
+        EXTRA_PKGS="gfortran llvm-8-dev liblapack-dev python3.8-distutils"
+        sudo apt-add-repository -y ppa:deadsnakes/ppa
+        sudo apt-get update
+        export LLVM_CONFIG=llvm-config-8
+        export CXXFLAGS=-fPIC
+        # Drop torch for now
+        sed -i '/torch/d' requirements.txt
+        # Cython is needed to build scikit-learn
+        EXTRA_PIP="cython"
+      fi
+      sudo apt-get install -y python${PYTHON%.*}-dev python${PYTHON%.*}-venv $EXTRA_PKGS
       python${PYTHON%.*} -m venv $HOME/venv
       # Provide fake xdg-open
       echo "#!/bin/sh" > $HOME/venv/bin/xdg-open
@@ -70,6 +90,11 @@ before_install:
   - python --version
   - pip install -U pip
   - pip --version
+  - |
+    # Install undeclared dependencies
+    if [ "x$EXTRA_PIP" != "x" ]; then
+      pip install $EXTRA_PIP
+    fi
 
 install:
   - pip install coveralls

Scripts/Examples/Composition/StabilityFlexibility.py

@@ -169,10 +169,6 @@ def computeAccuracy(variable):
                            intensity_cost_function=pnl.Linear(slope=0.),
                            allocation_samples=search_range)
 
-
-
-
-
 objective_mech = pnl.ObjectiveMechanism(monitor=[inputLayer, stimulusInfo,
                                                  (pnl.PROBABILITY_UPPER_THRESHOLD, decisionMaker),
                                                  (pnl.PROBABILITY_LOWER_THRESHOLD, decisionMaker)],
@@ -187,15 +183,15 @@ def computeAccuracy(variable):
                                                    control_signals=[signal])
 
 inputs = {inputLayer: INPUT, stimulusInfo: stimulusInput}
-stabilityFlexibility.add_model_based_optimizer(meta_controller)
+stabilityFlexibility.add_controller(meta_controller)
 stabilityFlexibility.enable_model_based_optimizer = True
 
 print("Beginning of Run")
 
-for i in range(1, len(stabilityFlexibility.model_based_optimizer.input_ports)):
-    stabilityFlexibility.model_based_optimizer.input_ports[i].function.reinitialize()
+for i in range(1, len(stabilityFlexibility.controller.input_ports)):
+    stabilityFlexibility.controller.input_ports[i].function.reinitialize()
 
-stabilityFlexibility.show_graph(show_model_based_optimizer=True)
+# stabilityFlexibility.show_graph(show_controller=True)
 
 # stabilityFlexibility.run(inputs)
 # print(stabilityFlexibility.results)

Scripts/Examples/System/Leabra-Demo.py

@@ -46,7 +46,7 @@
 # The leabra network and LeabraMechanism experience this bug equally.
 
 # NOTE: The reason TransferMechanisms are used below is because there is currently a bug where LeabraMechanism
-# (and other `Mechanism`s with multiple input ports) cannot be used as origin Mechanisms for a System. If you desire
+# (and other `Mechanism` with multiple input ports) cannot be used as origin Mechanisms for a System. If you desire
 # to use a LeabraMechanism as an origin Mechanism, you can work around this bug by creating two `TransferMechanism`s
 # as origin Mechanisms instead, and have these two TransferMechanisms pass their output to the InputPorts of
 # the LeabraMechanism.

Scripts/Models (Under Development)/Bustamante_Stroop_XOR_LVOC_Model.py

@@ -68,8 +68,8 @@ def objective_function(v):
     name='Task Decision',
     # function=pnl.NavarroAndFuss,
     output_ports=[
-        pnl.DDM_OUTPUT.PROBABILITY_UPPER_THRESHOLD,
-        pnl.DDM_OUTPUT.PROBABILITY_LOWER_THRESHOLD
+        pnl.PROBABILITY_UPPER_THRESHOLD,
+        pnl.PROBABILITY_LOWER_THRESHOLD
     ]
 )
 

Scripts/Models (Under Development)/Bustamante_Stroop_XOR_LVOC_Model_VZ.py

@@ -96,9 +96,9 @@ def adj_cost_fct(v):
                 t0=.4
         ),
         output_ports=[
-            pnl.DDM_OUTPUT.PROBABILITY_UPPER_THRESHOLD,
-            pnl.DDM_OUTPUT.PROBABILITY_LOWER_THRESHOLD,
-            pnl.DDM_OUTPUT.RESPONSE_TIME
+            pnl.PROBABILITY_UPPER_THRESHOLD,
+            pnl.PROBABILITY_LOWER_THRESHOLD,
+            pnl.RESPONSE_TIME
         ]
 )
 

Scripts/Models (Under Development)/ColorMotionTask_FULL.py

@@ -126,7 +126,7 @@ def incongruent(colorResponse, motionResponse):
                        noise=0.5,
                        t0=0.2,
                        threshold=0.45),
-               output_ports=[DDM_OUTPUT.PROBABILITY_UPPER_THRESHOLD, DDM_OUTPUT.RESPONSE_TIME],
+               output_ports=[PROBABILITY_UPPER_THRESHOLD, RESPONSE_TIME],
                )
 
 c = Composition(name='ColorMotion Task')

Scripts/Models (Under Development)/ColorMotionTask_SIMPLE.py

@@ -13,7 +13,7 @@
                        noise=0.5,
                        t0=0.2,
                        threshold=0.45),
-               output_ports=[DDM_OUTPUT.PROBABILITY_UPPER_THRESHOLD, DDM_OUTPUT.RESPONSE_TIME],
+               output_ports=[PROBABILITY_UPPER_THRESHOLD, RESPONSE_TIME],
                )
 
 c = Composition(name='ColorMotion Task')

Scripts/Models (Under Development)/Predator-Prey Model DEMO.py

@@ -186,13 +186,13 @@ def objective_function(variable):
 agent_comp.enable_controller = True
 agent_comp.controller_mode = BEFORE
 
-if SHOW_GRAPH is 'SIMPLE':
+if SHOW_GRAPH == 'SIMPLE':
     agent_comp.show_graph(show_cim=True)
-if SHOW_GRAPH is 'CONTROL':
+if SHOW_GRAPH == 'CONTROL':
     agent_comp.show_graph(show_model_based_optimizer=True, show_cim=True)
-if SHOW_GRAPH is 'NODE STRUCTURE':
+if SHOW_GRAPH == 'NODE STRUCTURE':
     agent_comp.show_graph(show_model_based_optimizer=True, show_node_structure=True, show_cim=True)
-if SHOW_GRAPH is 'FULL':
+if SHOW_GRAPH == 'FULL':
     agent_comp.show_graph(show_model_based_optimizer=True,
                           show_cim=True,
                           show_node_structure=ALL,

dev_requirements.txt

@@ -8,6 +8,6 @@ pytest-helpers-namespace
 pytest-xdist
 jupyter
 sphinx
-sphinx_rtd_theme
+psyneulink-sphinx-theme
 ipykernel
 ipython

docs/source/conf.py

@@ -131,10 +131,10 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-import sphinx_rtd_theme
-html_theme = "sphinx_rtd_theme"
+import psyneulink_sphinx_theme
+html_theme = "psyneulink_sphinx_theme"
 # Add any paths that contain custom themes here, relative to this directory.
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+html_theme_path = [psyneulink_sphinx_theme.get_html_theme_path()]
 html_theme_options = {
     'navigation_depth': 5
 }
@@ -168,7 +168,7 @@
 # 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
 # directly to the root of the documentation.

psyneulink/core/components/component.py

@@ -1123,7 +1123,7 @@ def __init__(self,
             self.componentName = self.componentType
 
         # ENFORCE REGISRY
-        if self.__class__.__bases__[0].__bases__[0].__bases__[0].__name__ is 'ShellClass':
+        if self.__class__.__bases__[0].__bases__[0].__bases__[0].__name__ == 'ShellClass':
             try:
                 self.__class__.__bases__[0].registry
             except AttributeError:
@@ -2846,7 +2846,7 @@ def _get_param_value_from_tuple(self, param_spec):
         ALLOWABLE_TUPLE_SPEC_CLASSES = (ModulatoryProjection_Base, ModulatorySignal, ModulatoryMechanism_Base)
 
         # If the 2nd item is a CONTROL or LEARNING SPEC, return the first item as the value
-        if (isinstance(param_spec, tuple) and len(param_spec) is 2 and
+        if (isinstance(param_spec, tuple) and len(param_spec) == 2 and
                 not isinstance(param_spec[1], (dict, list, np.ndarray)) and
                 (param_spec[1] in ALLOWABLE_TUPLE_SPEC_KEYWORDS or
                  isinstance(param_spec[1], ALLOWABLE_TUPLE_SPEC_CLASSES) or

psyneulink/core/components/functions/function.py

@@ -154,7 +154,7 @@
 from psyneulink.core.globals.preferences.basepreferenceset import is_pref_set, REPORT_OUTPUT_PREF
 from psyneulink.core.globals.preferences.preferenceset import PreferenceEntry, PreferenceLevel
 from psyneulink.core.globals.registry import register_category
-from psyneulink.core.globals.utilities import object_has_single_value, parameter_spec, safe_len
+from psyneulink.core.globals.utilities import object_has_single_value, parameter_spec, safe_len, get_global_seed
 
 __all__ = [
     'ArgumentTherapy', 'EPSILON', 'Function_Base', 'function_keywords', 'FunctionError', 'FunctionOutputType',
@@ -521,6 +521,11 @@ def __deepcopy__(self, memo):
         new = super().__deepcopy__(memo)
         # ensure copy does not have identical name
         register_category(new, Function_Base, new.name, FunctionRegistry)
+        try:
+            # HACK: Make sure any copies are re-seeded to avoid dependent RNG.
+            new.random_state.seed([get_global_seed()])
+        except:
+            pass
         return new
 
     @handle_external_context()