Merge pull request #3176 from PrincetonUniversity/devel

Devel

Author: kmantel

.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