Merge pull request #3271 from PrincetonUniversity/devel

Devel

Author: kmantel

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

@@ -73,6 +73,8 @@ runs:
           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
+          # fastkde >= 2.1.3 doesn't provide win32 wheel
+          echo "fastkde < 2.1.3" >> env_constraints.txt
         fi
 
     - name: Install updated package
@@ -109,6 +111,18 @@ runs:
       shell: bash
       run: |
         pip install ${{ steps.dist.outputs.wheel }}[${{ inputs.features }}] -c env_constraints.txt -c broken_trans_deps.txt
+      env:
+        # Setting CXXFLAGS works around a missing include that breaks the build
+        # of onnx-1/17.0 on recent gcc/clang compilers.
+        # This should be removed once onnx wheels for Python 3.13 are available.
+        # Note that the MS Visual C equivalent option needs to start with an extra
+        # space otherwise the argument gets interpreted as a file location.
+        CXXFLAGS: ${{ startsWith(runner.os, 'windows') && ' /FI cstdint' || '-include cstdint' }}
+        # Setting TEMP works around broken onnx-1.17.0 build on windows where
+        # too long paths in default TEMP directory don't work with msbuild.
+        # This should be removed once onnx wheels for Python 3.13 are available.
+        # Note that $TEMP is only used to set pip's build location on Windows.
+        TEMP: ${{ runner.temp }}
 
     - name: Cleanup old wheels
       shell: bash

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

@@ -6,6 +6,8 @@ on:
       - 'dependabot/**'
     tags:
       - 'v*'
+    paths-ignore:
+      - '.github/workflows/pnl-ci.yml'
   pull_request:
 
 # run only the latest instance of this workflow job for the current branch/PR
@@ -21,7 +23,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
         os: [ubuntu-latest, macos-latest, windows-latest]
         pnl-version: ${{ (github.event_name == 'push') && fromJSON('["head"]') || fromJSON('["head", "base"]') }}
         exclude:
@@ -37,6 +39,8 @@ jobs:
             pnl-version: 'base'
           - python-version: '3.12'
             pnl-version: 'base'
+          - python-version: '3.13'
+            pnl-version: 'base'
 
     outputs:
       on_master: ${{ steps.on_master.outputs.on-branch }}

.github/workflows/pnl-ci.yml

@@ -33,7 +33,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.11', '3.12']
+        python-version: ['3.8', '3.11', '3.12', '3.13']
         python-architecture: ['x64']
         extra-args: ['']
         os: [ubuntu, macos, windows]
@@ -138,11 +138,12 @@ jobs:
     - name: Lint with flake8
       shell: bash
       run: |
-        pip install flake8
+        pip install flake8 flake8-unused-arguments
         # 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
+        flake8 --select=U100 --unused-arguments-ignore-stub-functions --unused-arguments-ignore-lambdas --unused-arguments-ignore-nested-functions --unused-arguments-ignore-variadic-names --extend-exclude tests/functions/test_user_defined_func.py tests/
 
     - name: Print numpy info
       shell: bash
@@ -158,6 +159,24 @@ jobs:
           Windows*) wmic cpu get description,currentclockspeed,NumberOfCores,NumberOfEnabledCore,NumberOfLogicalProcessors; wmic memorychip get capacity,speed,status,manufacturer ;;
         esac
 
+    # Windows runners use MS Edge as the default pdf viewer.
+    # This causes issues if any of the tests calls show_graph()
+    # or any other routine that by default produces a .pdf file
+    # and opens is in the default application.
+    # The problem with MS Edge is that it intermittently fails
+    # to exit and hangs the entire CI job in the last step.
+    # see: https://github.com/actions/runner/issues/3383
+    # Removing the default .pdf file association on windows is
+    # quite difficult because it needs to check multiple places
+    # and elevated privileges.
+    # Installing an alternative pdf viewer works around the issue
+    # as it prevents MS Edge from running when .pdf is displayed.
+    - name: Install windows pdf viewer
+      shell: bash
+      if: ${{ matrix.os == 'windows' }}
+      run: |
+          choco install --no-progress -y sumatrapdf.install
+
     - name: Test with pytest
       timeout-minutes: 180
       run: pytest --junit-xml=tests_out.xml --verbosity=0 -n logical --capture=sys -o console_output_style=count ${{ matrix.extra-args }}
@@ -188,5 +207,14 @@ jobs:
       if: matrix.version-restrict == ''
       with:
         name: dist-${{ matrix.os }}-${{ matrix.python-version }}-${{ matrix.python-architecture }}
-        path: ${{ steps.install.outputs.wheel }} ${{ steps.install.outputs.sdist }}
+        path: |
+          ${{ steps.install.outputs.wheel }}
+          ${{ steps.install.outputs.sdist }}
         retention-days: 2
+
+    # this step is kept for debugging hangs at the end of runner execution.
+    - name: List running processes
+      shell: pwsh
+      if: ${{ matrix.os == 'windows' }}
+      run: |
+        Get-Process;

.github/workflows/test-release.yml

@@ -25,31 +25,34 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
+    - name: Install setup dependencies
+      shell: bash
+      run: pip install build twine
+
     - name: Create Python Dist files
       id: create_dist
       shell: bash
       run: |
         # We don't care about the python version used.
-        pip install setuptools wheel
-        python setup.py sdist
-        python setup.py bdist_wheel
+        python -m build -v
         cd dist
         echo "sdist=$(ls *.tar.gz)" >> $GITHUB_OUTPUT
         echo "wheel=$(ls *.whl)" >> $GITHUB_OUTPUT
 
     - name: Upload Python dist files
       uses: actions/upload-artifact@v4
       with:
-        name: Python-dist-files
+        name: psyneulink-${{ github.ref_name }}-dist
         path: dist/
-        retention-days: 1
+        retention-days: 30
+
+    - name: Validate dist files
+      shell: bash
+      run: twine check --strict dist/*
 
     - name: Upload dist files to test PyPI
       shell: bash
       run: |
-        # Include implicit dependency on setuptools{,-rust} and preinstall wheel
-        pip install setuptools setuptools-rust wheel
-        pip install twine
         # This expects TWINE_USERNAME, TWINE_PASSWORD, and TWINE_REPOSITORY_URL
         # environment variables
         # It's not possible to condition steps on env or secrets,
@@ -69,7 +72,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
         os: [ubuntu-latest, macos-latest, windows-latest]
         dist: [wheel, sdist]
 
@@ -80,7 +83,7 @@ jobs:
     - name: Download dist files
       uses: actions/download-artifact@v4
       with:
-        name: Python-dist-files
+        name: psyneulink-${{ github.ref_name }}-dist
         path: dist/
 
     - name: Set up Python ${{ matrix.python-version }}
@@ -118,7 +121,7 @@ jobs:
     - name: Run tests
       shell: bash
       # run only tests/. We don't care about codestyle/docstyle at this point
-      timeout-minutes: 80
+      timeout-minutes: 180
       run: |
         # remove sources to prevent conflict with the isntalled package
         rm -r -f psyneulink/ docs/ bin/ Matlab/
@@ -143,15 +146,20 @@ jobs:
     - name: Download dist files
       uses: actions/download-artifact@v4
       with:
-        name: Python-dist-files
+        name: psyneulink-${{ github.ref_name }}-dist
         path: dist/
 
+    - name: Install setup dependencies
+      shell: bash
+      run: pip install twine
+
+    - name: Validate dist files
+      shell: bash
+      run: twine check --strict dist/*
+
     - name: Upload dist files to PyPI
       shell: bash
       run: |
-        # Include implicit dependency on setuptools{,-rust} and preinstall wheel
-        pip3 install --user setuptools setuptools-rust wheel
-        pip3 install --user twine
         # This expects TWINE_USERNAME, TWINE_PASSWORD, and TWINE_REPOSITORY_URL
         # environment variables
         # It's not possible to condition steps on env or secrets,
@@ -177,13 +185,17 @@ jobs:
     - name: Download dist files
       uses: actions/download-artifact@v4
       with:
-        name: Python-dist-files
+        name: psyneulink-${{ github.ref_name }}-dist
         path: dist/
 
     - name: Upload dist files to release
       shell: bash
       env:
         GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       run: |
-        previous_release=$(gh --repo ${{ github.repository }} release list | head -n 1 | awk '{print $1}')
-        gh --repo ${{ github.repository }} release create --generate-notes --notes-start-tag "$previous_release" ${{ github.ref }} dist/*
+        previous_release=$(gh --repo ${{ github.repository }} release list -L 1 | cut -f1)
+        if [[ -z "$previous_release" ]]; then
+          echo "No previous release found"
+          exit 1
+        fi
+        gh --repo ${{ github.repository }} release create --generate-notes --notes-start-tag "$previous_release" ${{ github.ref_name }} dist/*

MANIFEST.in

@@ -8,3 +8,5 @@ recursive-include tests *.py
 recursive-include tutorial *.ipynb
 include versioneer.py
 include psyneulink/_version.py
+
+include psyneulink/library/models/results/*.json

README.rst

@@ -1,10 +1,14 @@
-.. image:: https://badge.fury.io/py/psyneulink.svg
+.. |pypi-badge| image:: https://badge.fury.io/py/psyneulink.svg
     :target: https://badge.fury.io/py/psyneulink
-.. image:: https://github.com/PrincetonUniversity/PsyNeuLink/workflows/PsyNeuLink%20CI/badge.svg?branch=master
+
+.. |build-badge| image:: https://github.com/PrincetonUniversity/PsyNeuLink/workflows/PsyNeuLink%20CI/badge.svg?branch=master
     :target: https://github.com/PrincetonUniversity/PsyNeuLink/actions
-.. image:: https://mybinder.org/badge.svg
+
+.. |binder-badge| image:: https://mybinder.org/badge.svg
     :target: https://mybinder.org/v2/gh/PrincetonUniversity/PsyNeuLink/master
 
+|pypi-badge| |build-badge| |binder-badge|
+
 .. *****************************************************************************************
 .. ****** NOTE:  UPDATES TO THIS PAGE SHOULD ALSO BE MADE TO docs/source.index.rst *********
 .. *****************************************************************************************
@@ -46,7 +50,7 @@ It is:
 
  ..
 
- - *computationally general* -- it can be used to implement, seamlessly integrate, and simulate interactions among
+ - *computationally general* -- it can be used to implement, seamlessly integrate, and simulate interactions among
    disparate components that vary in their granularity of representation and function (from individual neurons or
    neural populations to functional subsystems and abstract cognitive functions) and at any time scale of execution.
 
@@ -85,7 +89,7 @@ it is presently less well suited to efforts involving massively large computatio
 
 Other packages currently better suited to such applications are:
 `Emergent <https://grey.colorado.edu/emergent/index.php/Main_Page>`_ for biologically-inspired neural network models
-`Pytorch <https://pytorch.org>`_ and `TensorFlow <https://www.tensorflow.org>`_ (for deep learning models);
+`Pytorch <pytorch_>`_ and `TensorFlow <https://www.tensorflow.org>`_ (for deep learning models);
 `HDDM <http://ski.clps.brown.edu/hddm_docs/>`_ (for Drift Diffusion Models);
 `ACT-R <http://act-r.psy.cmu.edu>`_ (for production system models);
 `Genesis <http://www.genesis-sim.org>`_,
@@ -102,7 +106,7 @@ That said, priorities for ongoing development of PsyNeuLink are:
     i) acceleration, using just-in-time compilation methods and parallelization
        (see `Compilation`, and `Vesely et al., 2022 <http://www.cs.yale.edu/homes/abhishek/jvesely-cgo22.pdf>`_);
     ii) enhancement of the API to facilitate wrapping modules from other packages for integration into the PsyNeuLink
-        environment (examples currently exist for `Pytorch <https://pytorch.org>`_ ) and translating into a standard
+        environment (examples currently exist for `Pytorch <pytorch_>`_) and translating into a standard
         `Model Description Format (MDF) <https://github.com/ModECI/MDF>`_;
     iii) integration of tools for parameter estimation, model comparison and data fitting
          (see `ParameterEstimationComposition`); and
@@ -254,3 +258,5 @@ License
     Unless required by applicable law or agreed to in writing, software distributed under the License is distributed
     on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
     See the License for the specific language governing permissions and limitations under the License.
+
+.. _pytorch: https://pytorch.org

Scripts/Examples/Rumelhart Semantic Network.py

@@ -19,14 +19,14 @@
 #   Representation_Input (REP_IN)
 
 # Construct Mechanisms
-rep_in = TransferMechanism(input_shapes=10, name='REP_IN')
-rel_in = TransferMechanism(input_shapes=11, name='REL_IN')
-rep_hidden = TransferMechanism(input_shapes=4, function=Logistic, name='REP_HIDDEN')
-rel_hidden = TransferMechanism(input_shapes=5, function=Logistic, name='REL_HIDDEN')
-rep_out = TransferMechanism(input_shapes=10, function=Logistic, name='REP_OUT')
-prop_out = TransferMechanism(input_shapes=12, function=Logistic, name='PROP_OUT')
-qual_out = TransferMechanism(input_shapes=13, function=Logistic, name='QUAL_OUT')
-act_out = TransferMechanism(input_shapes=14, function=Logistic, name='ACT_OUT')
+rep_in = ProcessingMechanism(input_shapes=10, name='REP_IN')
+rel_in = ProcessingMechanism(input_shapes=11, name='REL_IN')
+rep_hidden = ProcessingMechanism(input_shapes=4, function=Logistic, name='REP_HIDDEN')
+rel_hidden = ProcessingMechanism(input_shapes=5, function=Logistic, name='REL_HIDDEN')
+rep_out = ProcessingMechanism(input_shapes=10, function=Logistic, name='REP_OUT')
+prop_out = ProcessingMechanism(input_shapes=12, function=Logistic, name='PROP_OUT')
+qual_out = ProcessingMechanism(input_shapes=13, function=Logistic, name='QUAL_OUT')
+act_out = ProcessingMechanism(input_shapes=14, function=Logistic, name='ACT_OUT')
 
 # Construct Composition
 comp = Composition(name='Rumelhart Semantic Network')