Merge pull request #1873 from PrincetonUniversity/devel

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PrincetonUniversity · Jan 11, 2021 · 9f942f6 · 9f942f6
2 parents f136d8b + 20eef5b
commit 9f942f6
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Showing 13 changed files with 598 additions and 149 deletions.
diff --git a/.github/workflows/pnl-ci.yml b/.github/workflows/pnl-ci.yml
@@ -27,24 +27,24 @@ jobs:
       if: startsWith(runner.os, 'Linux')
       with:
         path: ~/.cache/pip/wheels
-        key: ${{ runner.os }}-python-${{ matrix.python-version }}-${{ matrix.python-architecture }}-pip-wheels-${{ github.sha }}
-        restore-keys: ${{ runner.os }}-python-${{ matrix.python-version }}-${{ matrix.python-architecture }}-pip-wheels
+        key: ${{ runner.os }}-python-${{ matrix.python-version }}-${{ matrix.python-architecture }}-pip-wheels-v2-${{ github.sha }}
+        restore-keys: ${{ runner.os }}-python-${{ matrix.python-version }}-${{ matrix.python-architecture }}-pip-wheels-v2
 
     - name: MacOS wheels cache
       uses: actions/[email protected]
       if: startsWith(runner.os, 'macOS')
       with:
         path: ~/Library/Caches/pip/wheels
-        key: ${{ runner.os }}-python-${{ matrix.python-version }}-${{ matrix.python-architecture }}-pip-wheels-${{ github.sha }}
-        restore-keys: ${{ runner.os }}-python-${{ matrix.python-version }}-${{ matrix.python-architecture }}-pip-wheels
+        key: ${{ runner.os }}-python-${{ matrix.python-version }}-${{ matrix.python-architecture }}-pip-wheels-v2-${{ github.sha }}
+        restore-keys: ${{ runner.os }}-python-${{ matrix.python-version }}-${{ matrix.python-architecture }}-pip-wheels-v2
 
     - name: Windows wheels cache
       uses: actions/[email protected]
       if: startsWith(runner.os, 'Windows')
       with:
         path: ~\AppData\Local\pip\Cache\wheels
-        key: ${{ runner.os }}-python-${{ matrix.python-version }}-${{ matrix.python-architecture }}-pip-wheels-${{ github.sha }}
-        restore-keys: ${{ runner.os }}-python-${{ matrix.python-version }}-${{ matrix.python-architecture }}-pip-wheels
+        key: ${{ runner.os }}-python-${{ matrix.python-version }}-${{ matrix.python-architecture }}-pip-wheels-v2-${{ github.sha }}
+        restore-keys: ${{ runner.os }}-python-${{ matrix.python-version }}-${{ matrix.python-architecture }}-pip-wheels-v2
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/[email protected]
@@ -64,17 +64,19 @@ jobs:
       run: choco install --no-progress -y graphviz --version=2.38.0.20190211
       if: startsWith(runner.os, 'Windows')
 
-    - name: Windows pytorch
-      run: |
-        python -m pip install --upgrade pip wheel
-        pip install torch -f https://download.pytorch.org/whl/cpu/torch_stable.html
-      if: startsWith(runner.os, 'Windows') && matrix.python-architecture != 'x86'
     - name: Shared dependencies
       shell: bash
       run: |
-        python -m pip install --upgrade pip wheel
+        # explicitly install numpy (https://github.com/pypa/pip/issues/9239)
+        python -m pip install --upgrade pip wheel $(grep numpy requirements.txt)
         pip install -e .[dev]
 
+    - name: Windows pytorch
+      shell: bash
+      run: |
+        pip install $(grep -o 'torch[0-9<=\.]*' requirements.txt) -f https://download.pytorch.org/whl/cpu/torch_stable.html
+      if: startsWith(runner.os, 'Windows') && matrix.python-architecture != 'x86'
+
     - name: Cleanup old wheels
       shell: bash
       run: |
@@ -101,7 +103,7 @@ jobs:
       run: pytest --junit-xml=tests_out.xml --verbosity=0 -n auto --maxprocesses=2
 
     - name: Upload test results
-      uses: actions/[email protected].1
+      uses: actions/[email protected].2
       with:
         name: test-results-${{ matrix.os }}-${{ matrix.python-version }}-${{ matrix.python-architecture }}
         path: tests_out.xml
@@ -115,7 +117,7 @@ jobs:
       if: contains(github.ref, 'tags')
 
     - name: Upload dist packages
-      uses: actions/[email protected].1
+      uses: actions/[email protected].2
       with:
         name: dist-${{ matrix.os }}-${{ matrix.python-version }}-${{ matrix.python-architecture }}
         path: dist/

diff --git a/.travis.yml b/.travis.yml
@@ -13,7 +13,8 @@ dist: bionic
 arch:
   - amd64
   - arm64
-  - ppc64le
+# Disabled due to intermittent failures and long running times
+#  - ppc64le
 # Disabled until grpcio works with s390x
 # https://github.com/grpc/grpc/issues/23797
 #  - s390x

diff --git a/psyneulink/core/components/functions/statefulfunctions/statefulfunction.py b/psyneulink/core/components/functions/statefulfunctions/statefulfunction.py
@@ -17,19 +17,20 @@
 """
 
 import abc
+import collections
 import typecheck as tc
 import warnings
 import numbers
 
 import numpy as np
 
 from psyneulink.core import llvm as pnlvm
-from psyneulink.core.components.component import DefaultsFlexibility, _has_initializers_setter
+from psyneulink.core.components.component import DefaultsFlexibility, _has_initializers_setter, ComponentsMeta
 from psyneulink.core.components.functions.function import Function_Base, FunctionError
 from psyneulink.core.components.functions.distributionfunctions import DistributionFunction
 from psyneulink.core.globals.keywords import STATEFUL_FUNCTION_TYPE, STATEFUL_FUNCTION, NOISE, RATE
 from psyneulink.core.globals.parameters import Parameter
-from psyneulink.core.globals.utilities import parameter_spec, iscompatible, object_has_single_value, convert_to_np_array
+from psyneulink.core.globals.utilities import parameter_spec, iscompatible, object_has_single_value, convert_to_np_array, contains_type
 from psyneulink.core.globals.preferences.basepreferenceset import is_pref_set
 from psyneulink.core.globals.context import ContextFlags, handle_external_context
 
@@ -196,6 +197,15 @@ class Parameters(Function_Base.Parameters):
         initializer = Parameter(np.array([0]), pnl_internal=True)
         has_initializers = Parameter(True, setter=_has_initializers_setter, pnl_internal=True)
 
+        def _validate_noise(self, noise):
+            if (
+                isinstance(noise, collections.Iterable)
+                # assume ComponentsMeta are functions
+                and contains_type(noise, ComponentsMeta)
+            ):
+                # TODO: make this validation unnecessary by handling automatically?
+                return 'functions in a list must be instantiated and have the desired noise variable shape'
+
     @handle_external_context()
     @tc.typecheck
     def __init__(self,

diff --git a/psyneulink/core/compositions/composition.py b/psyneulink/core/compositions/composition.py
@@ -8029,16 +8029,21 @@ def run(
             a cycle is not specified, it is assigned its `default values <Parameter_Defaults>` when initialized
             (see `Composition_Cycles_and_Feedback` additional details).
 
-            reset_stateful_functions_to : Dict { Node : Object | iterable [Object] } : default None
-                object or iterable of objects to be passed as arguments to nodes' reset methods when their
-                respective reset_stateful_function_when conditions are met. These are used to seed the stateful attributes
-                of Mechanisms that have stateful functions. If a node's reset_stateful_function_when condition is set to
-                Never, but they are listed in the reset_stateful_functions_to dict, then they will be reset once at the
-                beginning of the run, using the provided values.
-
-        reset_stateful_functions_when :  Condition : default Never()
-            sets the reset_stateful_function_when condition for all nodes in the Composition that currently have their
-            reset_stateful_function_when condition set to `Never <Never>` for the duration of the run.
+        reset_stateful_functions_to : Dict { Node : Object | iterable [Object] } : default None
+            object or iterable of objects to be passed as arguments to nodes' reset methods when their
+            respective reset_stateful_function_when conditions are met. These are used to seed the stateful attributes
+            of Mechanisms that have stateful functions. If a node's reset_stateful_function_when condition is set to
+            Never, but they are listed in the reset_stateful_functions_to dict, then they will be reset once at the
+            beginning of the run, using the provided values. For a more in depth explanation of this argument, see
+            `Resetting Parameters of StatefulFunctions <Composition_Reset>`.
+
+        reset_stateful_functions_when :  Dict { Node: Condition } | Condition : default Never()
+            if type is dict, sets the reset_stateful_function_when attribute for each key Node to its corresponding value
+            Condition. if type is Condition, sets the reset_stateful_function_when attribute for all nodes in the
+            Composition that currently have their reset_stateful_function_when conditions set to `Never <Never>`.
+            in either case, the specified Conditions persist only for the duration of the run, after which the nodes'
+            reset_stateful_functions_when attributes are returned to their previous Conditions. For a more in depth
+            explanation of this argument, see `Resetting Parameters of StatefulFunctions <Composition_Reset>`.
 
         skip_initialization : bool : default False
 

diff --git a/psyneulink/core/globals/log.py b/psyneulink/core/globals/log.py
@@ -1401,7 +1401,10 @@ def nparray(self,
             # If any time values are empty, revert to indexing the entries;
             #    this requires that all entries have the same length
             else:
-                max_len = max([len(self.logged_entries[e][eid]) for e in entries])
+                try:
+                    max_len = max([len(self.logged_entries[e][eid]) for e in entries])
+                except KeyError:
+                    max_len = 0
 
                 # If there are no time values, only support entries of the same length
                 # Must dealias both e and zeroth entry because either/both of these could be 'value'
@@ -1751,7 +1754,11 @@ def _assemble_entry_data(self, entry, time_values, execution_id=None):
         # entry = self._dealias_owner_name(entry)
         row = []
         time_col = iter(time_values)
-        data = self.logged_entries[entry][execution_id]
+        try:
+            data = self.logged_entries[entry][execution_id]
+        except KeyError:
+            return [None]
+
         time = next(time_col, None)
         for i in range(len(self.logged_entries[entry][execution_id])):
             # iterate through log entry tuples:

diff --git a/psyneulink/core/globals/utilities.py b/psyneulink/core/globals/utilities.py
@@ -132,6 +132,7 @@
     'scalar_distance', 'sinusoid',
     'tensor_power', 'TEST_CONDTION', 'type_match',
     'underscore_to_camelCase', 'UtilitiesError', 'unproxy_weakproxy', 'create_union_set', 'merge_dictionaries',
+    'contains_type'
 ]
 
 logger = logging.getLogger(__name__)
@@ -1789,3 +1790,25 @@ def gen_friendly_comma_str(items):
             divider = f',{divider}'
 
         return f"{', '.join(items[:-1])}{divider}{items[-1]}"
+
+
+def contains_type(
+    arr: collections.Iterable,
+    typ: typing.Union[type, typing.Tuple[type, ...]]
+) -> bool:
+    """
+        Returns:
+            True if **arr** is a possibly nested Iterable that contains
+            an instance of **typ** (or one type in **typ** if tuple)
+
+        Note: `isinstance(**arr**, **typ**)` should be used to check
+        **arr** itself if needed
+    """
+    try:
+        for a in arr:
+            if isinstance(a, typ) or (a is not arr and contains_type(a, typ)):
+                return True
+    except TypeError:
+        pass
+
+    return False
diff --git a/psyneulink/core/llvm/builder_context.py b/psyneulink/core/llvm/builder_context.py
@@ -86,6 +86,7 @@ class LLVMBuilderContext:
     _llvm_generation = 0
     int32_ty = ir.IntType(32)
     float_ty = ir.DoubleType()
+    bool_ty = ir.IntType(1)
 
     def __init__(self):
         self._modules = []
@@ -318,7 +319,9 @@ def convert_python_struct_to_llvm_ir(self, t):
                 return ir.ArrayType(elems_t[0], len(elems_t))
             return ir.LiteralStructType(elems_t)
         elif type(t) is tuple:
-            elems_t = (self.convert_python_struct_to_llvm_ir(x) for x in t)
+            elems_t = [self.convert_python_struct_to_llvm_ir(x) for x in t]
+            if len(elems_t) > 0 and all(x == elems_t[0] for x in elems_t):
+                return ir.ArrayType(elems_t[0], len(elems_t))
             return ir.LiteralStructType(elems_t)
         elif isinstance(t, enum.Enum):
             # FIXME: Consider enums of non-int type