Merge pull request #3176 from PrincetonUniversity/devel

Devel

.github/actions/install-pnl/action.yml

@@ -57,7 +57,7 @@ runs:
           sed -i /modeci_mdf/d requirements.txt
           # pywinpty is a transitive dependency and v1.0+ removed support for x86 wheels
           echo "pywinpty<1" >> env_constraints.txt
-          # jupyter_sever pulls jupyter_server_terminals which depends on in pywinpty >= 2.0.3
+          # jupyter_server >= 2 pulls jupyter_server_terminals which depends on in pywinpty >= 2.0.3
           echo "jupyter_server<2" >> env_constraints.txt
           # scipy >=1.9.2 doesn't provide win32 wheel and GA doesn't have working fortran on windows
           echo "scipy<1.9.2" >> env_constraints.txt
@@ -67,6 +67,12 @@ runs:
           echo "contourpy<1.1.0" >> env_constraints.txt
           # pillow >= 10.0.0 doesn't provide win32 wheel
           echo "pillow < 10.0.0" >> env_constraints.txt
+          # pandas >= 2.1.0 doesn't provide win32 wheel
+          echo "pandas < 2.1.0" >> env_constraints.txt
+          # llvmlite >= 0.42.0 doesn't provide win32 wheel
+          echo "llvmlite < 0.42.0" >> env_constraints.txt
+          # matplotlib >=3.8.0 doesn't provide win32 wheel
+          echo "matplotlib < 3.8.0" >> env_constraints.txt
         fi
 
     - name: Install updated package

.github/workflows/pnl-ci-docs.yml

@@ -21,16 +21,14 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
         os: [ubuntu-latest, macos-latest, windows-latest]
         pnl-version: ${{ (github.event_name == 'push') && fromJSON('["head"]') || fromJSON('["head", "base"]') }}
         exclude:
           - os: macos-latest
             pnl-version: 'base'
           - os: windows-latest
             pnl-version: 'base'
-          - python-version: '3.7'
-            pnl-version: 'base'
           - python-version: '3.8'
             pnl-version: 'base'
           - python-version: '3.9'
@@ -40,14 +38,6 @@ jobs:
           - python-version: '3.12'
             pnl-version: 'base'
 
-            # Python 3.7 x64 on macos-14 (arm64) images is broken [0]
-            # and arm64 version is not available [1].
-            # Restrict python 3.7 macos runs to macos-13
-            # [0] https://github.com/actions/setup-python/issues/855
-            # [1] https://github.com/actions/setup-python/issues/856
-          - python-version: '3.7'
-            os: macos-latest
-
     outputs:
       on_master: ${{ steps.on_master.outputs.on-branch }}
 
@@ -80,9 +70,7 @@ jobs:
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
-        # Block python3.7.17 on macos. see:
-        # https://github.com/actions/setup-python/issues/682
-        python-version: ${{ (matrix.os == 'macos-latest' && matrix.python-version == '3.7') && '3.7.16' || matrix.python-version }}
+        python-version: ${{ matrix.python-version }}
 
     - name: Get pip cache location
       shell: bash

.github/workflows/pnl-ci.yml

@@ -33,7 +33,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7', '3.11', '3.12']
+        python-version: ['3.8', '3.11', '3.12']
         python-architecture: ['x64']
         extra-args: ['']
         os: [ubuntu, macos, windows]
@@ -51,7 +51,7 @@ jobs:
             extra-args: '--forked -m "not llvm"'
 
           # add 32-bit build on windows
-          - python-version: '3.8'
+          - python-version: '3.9'
             python-architecture: 'x86'
             os: windows
 
@@ -70,22 +70,18 @@ jobs:
             # https://github.com/ionelmc/pytest-benchmark/issues/243
             extra-args: '-m benchmark --benchmark-enable --benchmark-only --benchmark-min-rounds=2 --benchmark-max-time=0.001 --benchmark-warmup=off -n0 --dist=no'
 
-          # add python 3.7 with deps restricted to min supported version
-          - python-version: '3.7'
-            python-architecture: 'x64'
-            os: ubuntu
-            version-restrict: 'min'
-
-          # add python 3.8 build on macos since 3.7 is broken
-          # https://github.com/actions/virtual-environments/issues/4230
-          # use default python-architecture
+          # add python 3.8 with deps restricted to min supported version
+          # use default python architecture
+          # https://github.com/actions/setup-python/issues/960
           - python-version: '3.8'
             os: macos
+            version-restrict: 'min'
 
         exclude:
-          # 3.7 is broken on macos-11,
-          # https://github.com/actions/virtual-environments/issues/4230
-          - python-version: '3.7'
+          # 3.8/x64 python is broken on aarch64 macos runners
+          # https://github.com/actions/setup-python/issues/960
+          - python-version: '3.8'
+            python-architecture: 'x64'
             os: macos
 
     steps:
@@ -112,7 +108,8 @@ jobs:
       if: ${{ matrix.version-restrict == 'min' }}
       shell: bash
       run: |
-        sed -i '/^[^#]/s/>=/==/' *requirements.txt
+        # macos/bsd sed requires backup suffix argument to -i
+        sed -i=.bak -e '/^[^#]/s/>=/==/' *requirements.txt
         git config user.name "github actions"
         git config user.email "none"
         git commit -a -m "Restrict version of direct dependencies to min"

.github/workflows/test-release.yml

@@ -69,14 +69,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9, '3.10', 3.11, 3.12]
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
         os: [ubuntu-latest, macos-latest, windows-latest]
         dist: [wheel, sdist]
-        exclude:
-          # 3.7 is broken on macos-11,
-          # https://github.com/actions/virtual-environments/issues/4230
-          - python-version: '3.7'
-            os: macos-latest
 
     runs-on: ${{ matrix.os }}
     needs: [create-python-dist]

Scripts/Models (Under Development)/EGO/Using EMComposition/Coffee Shop World/DeclanParams.py

@@ -72,6 +72,7 @@ def calc_prob(em_preds, test_ys):
     normalize_field_weights = True, # whether to normalize the field weights during memory retrieval
     normalize_memories = False, # whether to normalize the memory during memory retrieval
     # normalize_memories = True, # whether to normalize the memory during memory retrieval
+    normalize_memories = False, # whether to normalize the memory vectors
     # softmax_temperature = None, # temperature of the softmax used during memory retrieval (smaller means more argmax-like
     softmax_temperature = .1, # temperature of the softmax used during memory retrieval (smaller means more argmax-like
     # softmax_temperature = ADAPTIVE, # temperature of the softmax used during memory retrieval (smaller means more argmax-like

doc_requirements.txt

@@ -1,3 +1,3 @@
-psyneulink-sphinx-theme<1.2.4.1
+psyneulink-sphinx-theme<1.2.6.0
 sphinx<4.2.1
 sphinx_autodoc_typehints<1.16.0

docs/source/AutodiffComposition.rst

@@ -6,6 +6,7 @@ AutodiffComposition
     *Related*
 
     * `Composition_Learning`
+    * `Composition_Bias_Nodes`
 
 .. automodule:: psyneulink.library.compositions.autodiffcomposition
    :members:

docs/source/Core.rst

@@ -69,6 +69,8 @@ Core
 
             - `TransferFunctions`
 
+            - `TimerFunctions`
+
             - `TransformFunctions`
 
       - `StatefulFunctions`

docs/source/IntegratorMechanisms.rst

@@ -12,3 +12,4 @@ IntegratorMechanisms
 
    DDM
    EpisodicMemoryMechanism
+   TimerMechanism

docs/source/NonStatefulFunctions.rst

@@ -15,4 +15,5 @@ Functions that do *not* depend on a previous value.
    OptimizationFunctions
    SelectionFunctions
    TransferFunctions
+   TimerFunctions
    TransformFunctions

docs/source/TimerFunctions.rst

@@ -0,0 +1,10 @@
+TimerFunctions
+==============
+
+.. toctree::
+   :maxdepth: 3
+
+.. automodule:: psyneulink.core.components.functions.nonstateful.timerfunctions
+   :members: TimerFunction, LinearTimer, AcceleratingTimer, DeceleratingTimer, AsymptoticTimer
+   :private-members:
+   :exclude-members: Parameters

docs/source/TimerMechanism.rst

@@ -0,0 +1,7 @@
+TimerMechanism
+==============
+
+.. automodule:: psyneulink.library.components.mechanisms.processing.integrator.timermechanism
+   :members:
+   :private-members:
+   :exclude-members: random, Parameters

docs/source/TransferFunctions.rst

@@ -4,7 +4,8 @@ TransferFunctions
 .. toctree::
    :maxdepth: 3
 
-.. automodule:: psyneulink.core.components.functions.transferfunctions
-   :members: TransferFunction, Identity, Linear, Exponential, Logistic, Tanh, ReLU, Angle, Gaussian, GaussianDistort, BinomialDistort, Dropout, SoftMax, LinearMatrix, TransferWithCosts, CostFunctions
+.. automodule:: psyneulink.core.components.functions.nonstateful.transferfunctions
+   :members: TransferFunction, Identity, Linear, Exponential, Logistic, Tanh,ReLU, Angle, Gaussian, GaussianDistort, BinomialDistort, Dropout, SoftMax, LinearMatrix, TransferWithCosts,
+CostFunctions
    :private-members:
    :exclude-members: Parameters

psyneulink/core/components/component.py

@@ -1413,19 +1413,15 @@ def _is_compilation_state(p):
     def _get_state_ids(self):
         return [sp.name for sp in self._get_compilation_state()]
 
-    @property
+    @functools.cached_property
     def llvm_state_ids(self):
-        ids = getattr(self, "_state_ids", None)
-        if ids is None:
-            ids = self._get_state_ids()
-            setattr(self, "_state_ids", ids)
-        return ids
+        return self._get_state_ids()
 
     def _get_state_initializer(self, context):
         def _convert(p):
             x = p.get(context)
             if p.name == 'matrix': # Flatten matrix
-                val = tuple(np.asfarray(x).flatten())
+                val = tuple(np.asarray(x, dtype=float).ravel())
             elif isinstance(x, np.random.RandomState):
                 state = x.get_state(legacy=False)
 
@@ -1569,13 +1565,9 @@ def _is_compilation_param(p):
     def _get_param_ids(self):
         return [p.name for p in self._get_compilation_params()]
 
-    @property
+    @functools.cached_property
     def llvm_param_ids(self):
-        ids = getattr(self, "_param_ids", None)
-        if ids is None:
-            ids = self._get_param_ids()
-            setattr(self, "_param_ids", ids)
-        return ids
+        return self._get_param_ids()
 
     def _is_param_modulated(self, p):
         try:
@@ -1626,7 +1618,7 @@ def _get_values(p):
             elif p.name == 'num_trials_per_estimate': # Should always be int
                 return 0 if param is None else int(param)
             elif p.name == 'matrix': # Flatten matrix
-                return tuple(np.asfarray(param).flatten())
+                return tuple(np.asarray(param, dtype=float).ravel())
             return _convert(param)
 
         return tuple(map(_get_values, self._get_compilation_params()))

psyneulink/core/components/functions/__init__.py

@@ -1,13 +1,14 @@
 from . import function
 from .nonstateful import selectionfunctions, objectivefunctions, optimizationfunctions, transformfunctions, \
-    learningfunctions, transferfunctions, distributionfunctions, fitfunctions
+    learningfunctions, timerfunctions, transferfunctions, distributionfunctions, fitfunctions
 from . import stateful
 from .stateful import integratorfunctions, memoryfunctions
 from . import userdefinedfunction
 
 from .function import *
-from psyneulink.core.components.functions.nonstateful.transformfunctions import *
 from psyneulink.core.components.functions.nonstateful.transferfunctions import *
+from psyneulink.core.components.functions.nonstateful.timerfunctions import *
+from psyneulink.core.components.functions.nonstateful.transformfunctions import *
 from psyneulink.core.components.functions.nonstateful.selectionfunctions import *
 from psyneulink.core.components.functions.nonstateful.distributionfunctions import *
 from psyneulink.core.components.functions.nonstateful.objectivefunctions import *
@@ -21,8 +22,9 @@
 
 __all__ = list(function.__all__)
 __all__.extend(userdefinedfunction.__all__)
-__all__.extend(transformfunctions.__all__)
 __all__.extend(transferfunctions.__all__)
+__all__.extend(timerfunctions.__all__)
+__all__.extend(transformfunctions.__all__)
 __all__.extend(selectionfunctions.__all__)
 __all__.extend(stateful.__all__)
 __all__.extend(distributionfunctions.__all__)

psyneulink/core/components/functions/function.py

@@ -534,13 +534,16 @@ class Function_Base(Function):
     Attributes
     ----------
 
-    variable: value
+    variable: number
         format and default value can be specified by the :keyword:`variable` argument of the constructor;  otherwise,
         they are specified by the Function's :keyword:`class_defaults.variable`.
 
     function : function
         called by the Function's `owner <Function_Base.owner>` when it is executed.
 
+    value : number
+        the result returned by calling the Function.
+
     COMMENT:
     enable_output_type_conversion : Bool : False
         specifies whether `function output type conversion <Function_Output_Type_Conversion>` is enabled.
@@ -554,7 +557,7 @@ class Function_Base(Function):
         specifies whether the return value of the function is different than the shape of either is outermost dimension
         (axis 0) of its  its `variable <Function_Base.variable>`, or any of the items in the next dimension (axis 1).
         Used to determine whether the shape of the inputs to the `Component` to which the function is assigned
-        should be based on the `variable <Function_Base.variable>` of the function or its `value <Function.value>`.
+        should be based on the `variable <Function_Base.variable>` of the function or its `value <Function_Base.value>`.
     COMMENT
 
     owner : Component
@@ -832,7 +835,7 @@ def convert_output_type(self, value, output_type=None):
         # Note: if 2D or 1D array has more than two items, generate exception
         elif output_type is FunctionOutputType.NP_0D_ARRAY:
             if object_has_single_value(value):
-                value = np.asfarray(value)
+                value = np.asarray(value, dtype=float)
             else:
                 raise FunctionError(f"Can't convert value ({value}) with more than a single number to a raw number.")
 

psyneulink/core/components/functions/nonstateful/objectivefunctions.py

@@ -993,7 +993,7 @@ def _gen_llvm_function_body(self, ctx, builder, params, _, arg_in, arg_out, *, t
         v2 = builder.gep(arg_in, [ctx.int32_ty(0), ctx.int32_ty(1), ctx.int32_ty(0)])
 
         acc_ptr = builder.alloca(ctx.float_ty)
-        builder.store(ctx.float_ty(-0.0), acc_ptr)
+        builder.store(acc_ptr.type.pointee(-0.0), acc_ptr)
 
         kwargs = {"ctx": ctx, "v1": v1, "v2": v2, "acc": acc_ptr}
         if self.metric == DIFFERENCE or self.metric == NORMED_L0_SIMILARITY:
@@ -1010,15 +1010,16 @@ def _gen_llvm_function_body(self, ctx, builder, params, _, arg_in, arg_out, *, t
             denom1_acc = builder.alloca(ctx.float_ty)
             denom2_acc = builder.alloca(ctx.float_ty)
             for loc in numer_acc, denom1_acc, denom2_acc:
-                builder.store(ctx.float_ty(-0.0), loc)
+                builder.store(loc.type.pointee(-0.0), loc)
+
             kwargs['numer_acc'] = numer_acc
             kwargs['denom1_acc'] = denom1_acc
             kwargs['denom2_acc'] = denom2_acc
             inner = functools.partial(self.__gen_llvm_cosine, **kwargs)
         elif self.metric == MAX_ABS_DIFF:
             del kwargs['acc']
             max_diff_ptr = builder.alloca(ctx.float_ty)
-            builder.store(ctx.float_ty(float("NaN")), max_diff_ptr)
+            builder.store(max_diff_ptr.type.pointee(float("NaN")), max_diff_ptr)
             kwargs['max_diff_ptr'] = max_diff_ptr
             inner = functools.partial(self.__gen_llvm_max_diff, **kwargs)
         elif self.metric == CORRELATION:
@@ -1028,7 +1029,7 @@ def _gen_llvm_function_body(self, ctx, builder, params, _, arg_in, arg_out, *, t
             acc_x2_ptr = builder.alloca(ctx.float_ty)
             acc_y2_ptr = builder.alloca(ctx.float_ty)
             for loc in [acc_x_ptr, acc_y_ptr, acc_xy_ptr, acc_x2_ptr, acc_y2_ptr]:
-                builder.store(ctx.float_ty(-0.0), loc)
+                builder.store(loc.type.pointee(-0.0), loc)
             del kwargs['acc']
             kwargs['acc_x'] = acc_x_ptr
             kwargs['acc_y'] = acc_y_ptr
@@ -1078,7 +1079,7 @@ def _gen_llvm_function_body(self, ctx, builder, params, _, arg_in, arg_out, *, t
             acc_x2 = builder.load(acc_x2_ptr)
             acc_y2 = builder.load(acc_y2_ptr)
 
-            # We'll need meanx,y below
+            # We'll need mean_x,y below
             mean_x = builder.fdiv(acc_x, n)
             mean_y = builder.fdiv(acc_y, n)
 
@@ -1122,7 +1123,7 @@ def _gen_llvm_function_body(self, ctx, builder, params, _, arg_in, arg_out, *, t
 
             # ret =  1 - abs(corr)
             ret = builder.call(fabs, [corr])
-            ret = builder.fsub(ctx.float_ty(1), ret)
+            ret = builder.fsub(ret.type(1), ret)
 
         if arg_out.type.pointee != ret.type:
             # Some instances use 2d output values
@@ -1139,7 +1140,7 @@ def _gen_llvm_function_body(self, ctx, builder, params, _, arg_in, arg_out, *, t
         with builder.if_else(normalize_b) as (then, otherwise):
             with then:
                 norm_factor = input_length ** 2 if self.metric == ENERGY else input_length
-                normalized = builder.fdiv(ret, ctx.float_ty(norm_factor), name="normalized")
+                normalized = builder.fdiv(ret, ret.type(norm_factor), name="normalized")
                 builder.store(normalized, arg_out)
             with otherwise:
                 builder.store(ret, arg_out)