Merge pull request #2897 from PrincetonUniversity/devel

Devel

Author: kmantel

.github/workflows/codeql.yml

@@ -46,8 +46,11 @@ jobs:
       - name: Autobuild
         uses: github/codeql-action/autobuild@v3
 
-      - name: Cache cleanup
+      - name: Pip cache cleanup
         shell: bash
+        # CODEQL_PYTHON is only defined if dependencies were installed [0]
+        # [0] https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning?learn=code_security_actions&learnProduct=code-security#analyzing-python-dependencies
+        if: ${{ env.CODEQL_PYTHON != '' }}
         run: |
           $CODEQL_PYTHON -m pip cache info
           $CODEQL_PYTHON -m pip cache purge

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

@@ -92,7 +92,7 @@ jobs:
         echo "pip_cache_dir=$(python -m pip cache dir)" | tee -a $GITHUB_OUTPUT
 
     - name: Wheels cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ${{ steps.pip_cache.outputs.pip_cache_dir }}/wheels
         key: ${{ runner.os }}-python-${{ matrix.python-version }}-${{ matrix.python-architecture }}-pip-wheels-${{ hashFiles('requirements.txt', 'doc_requirements.txt') }}-${{ github.sha }}
@@ -124,19 +124,21 @@ jobs:
       run: git tag -d 'v0.0.0.0'
 
     - name: Upload Documentation
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: Documentation-${{matrix.pnl-version}}-${{ matrix.os }}-${{ matrix.python-version }}-${{ matrix.python-architecture }}
         retention-days: 1
         path: docs/build/html
 
     - name: Store PR number
-      if: ${{ github.event_name == 'pull_request' }}
+      # The 'base' variant runs only on pull requests and has only one job
+      if: ${{ matrix.pnl-version == 'base' }}
       run: echo ${{ github.event.pull_request.number }} > ./pr_number.txt
 
     - name: Upload PR number for other workflows
-      if: ${{ github.event_name == 'pull_request' }}
-      uses: actions/upload-artifact@v3
+      # The 'base' variant runs only on pull requests and has only one job
+      if: ${{ matrix.pnl-version == 'base' }}
+      uses: actions/upload-artifact@v4
       with:
           name: pr_number
           path: ./pr_number.txt
@@ -168,7 +170,7 @@ jobs:
         ref: gh-pages
 
     - name: Download branch docs
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: Documentation-head-${{ matrix.os }}-${{ matrix.python-version }}-x64
         path: _built_docs/${{ github.ref }}
@@ -185,7 +187,7 @@ jobs:
       if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/devel' || github.ref == 'refs/heads/docs'
 
     - name: Download main docs
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: Documentation-head-${{ matrix.os }}-${{ matrix.python-version }}-x64
         # This overwrites files in current directory

.github/workflows/pnl-ci.yml

@@ -143,7 +143,7 @@ jobs:
         echo "pip_cache_dir=$(python -m pip cache dir)" | tee -a $GITHUB_OUTPUT
 
     - name: Wheels cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ${{ steps.pip_cache.outputs.pip_cache_dir }}/wheels
         key: ${{ runner.os }}-python-${{ matrix.python-version }}-${{ matrix.python-architecture }}-pip-wheels-${{ hashFiles('requirements.txt', 'dev_requirements.txt') }}-${{ github.sha }}
@@ -163,22 +163,28 @@ jobs:
         # 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: Print test machine/env info
+    - name: Print numpy info
       shell: bash
       run: |
         python -c "import numpy; numpy.show_config()"
+
+    - name: Print machine info
+      shell: bash
+      run: |
         case "$RUNNER_OS" in
-          Linux*) lscpu;;
+          Linux*) lscpu; lsmem;;
+          macOS*) sysctl -a | grep '^hw' ;;
+          Windows*) wmic cpu get description,currentclockspeed,NumberOfCores,NumberOfEnabledCore,NumberOfLogicalProcessors; wmic memorychip get capacity,speed,status,manufacturer ;;
         esac
 
     - name: Test with pytest
       timeout-minutes: 180
-      run: pytest --junit-xml=tests_out.xml --verbosity=0 -n auto ${{ matrix.extra-args }}
+      run: pytest --junit-xml=tests_out.xml --verbosity=0 -n logical ${{ matrix.extra-args }}
 
     - name: Upload test results
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
-        name: test-results-${{ matrix.os }}-${{ matrix.python-version }}-${{ matrix.python-architecture }}
+        name: test-results-${{ matrix.os }}-${{ matrix.python-version }}-${{ matrix.python-architecture }}-${{ matrix.version-restrict }}
         path: tests_out.xml
         retention-days: 5
       if: (success() || failure()) && ! contains(matrix.extra-args, 'forked')
@@ -202,7 +208,8 @@ jobs:
         python setup.py sdist bdist_wheel
 
     - name: Upload dist packages
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
+      if: matrix.version-restrict == ''
       with:
         name: dist-${{ matrix.os }}-${{ matrix.python-version }}-${{ matrix.python-architecture }}
         path: dist/

.github/workflows/test-release.yml

@@ -38,7 +38,7 @@ jobs:
         echo "wheel=$(ls *.whl)" >> $GITHUB_OUTPUT
 
     - name: Upload Python dist files
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: Python-dist-files
         path: dist/
@@ -78,7 +78,7 @@ jobs:
 
     steps:
     - name: Download dist files
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: Python-dist-files
         path: dist/
@@ -126,7 +126,7 @@ jobs:
         pytest  --junit-xml=tests_out.xml --verbosity=0 -n auto tests
 
     - name: Upload test results
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: test-results-${{ matrix.os }}-${{ matrix.python-version }}
         path: tests_out.xml
@@ -141,7 +141,7 @@ jobs:
 
     steps:
     - name: Download dist files
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: Python-dist-files
         path: dist/
@@ -175,7 +175,7 @@ jobs:
 
     steps:
     - name: Download dist files
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: Python-dist-files
         path: dist/

broken_trans_deps.txt

@@ -29,3 +29,15 @@ cattrs != 23.1.1; python_version < '3.8'
 # cattrs==23.2.{1,2} breaks json serialization
 # https://github.com/python-attrs/cattrs/issues/453
 cattrs != 23.2.1, != 23.2.2
+
+# The following need at least sphinx-5 without indicating it in dependencies:
+# * sphinxcontrib-applehelp >=1.0.8,
+# * sphinxcontrib-devhelp >=1.0.6,
+# * sphinxcontrib-htmlhelp >=2.0.5,
+# * sphinxcontrib-serializinghtml >=1.1.10,
+# * sphinxcontrib-qthelp >=1.0.7
+sphinxcontrib-applehelp <1.0.8
+sphinxcontrib-devhelp <1.0.6
+sphinxcontrib-htmlhelp <2.0.5
+sphinxcontrib-serializinghtml <1.1.10
+sphinxcontrib-qthelp <1.0.7

cuda_requirements.txt

@@ -1 +1 @@
-pycuda >2018, <2023
+pycuda >2018, <2024

dev_requirements.txt

@@ -1,6 +1,6 @@
 jupyter<1.0.1
 packaging<24.0
-pytest<7.4.4
+pytest<8.0.1
 pytest-benchmark<4.0.1
 pytest-cov<4.1.1
 pytest-forked<1.7.0

psyneulink/core/components/component.py

@@ -1301,7 +1301,7 @@ def _get_compilation_state(self):
                      "intensity"}
         # Prune subcomponents (which are enabled by type rather than a list)
         # that should be omitted
-        blacklist = { "objective_mechanism", "agent_rep", "projections"}
+        blacklist = { "objective_mechanism", "agent_rep", "projections", "shadow_inputs"}
 
         # Only mechanisms use "value" state, can execute 'until finished',
         # and need to track executions
@@ -1426,7 +1426,8 @@ def _get_compilation_params(self):
                      "randomization_dimension", "save_values", "save_samples",
                      "max_iterations", "duplicate_keys",
                      "search_termination_function", "state_feature_function",
-                     "search_function",
+                     "search_function", "weight", "exponent", "gating_signal_params",
+                     "retain_old_simulation_data",
                      # not used in compiled learning
                      "learning_results", "learning_signal", "learning_signals",
                      "error_matrix", "error_signal", "activation_input",

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

@@ -1442,7 +1442,8 @@ def _function(self,
         elif operation == CROSS_ENTROPY:
             v1 = variable[0]
             v2 = variable[1]
-            combination = np.where(np.logical_and(v1 == 0, v2 == 0), 0.0, v1 * np.log(v2))
+            both_zero = np.logical_and(v1 == 0, v2 == 0)
+            combination = v1 * np.where(both_zero, 0.0, np.log(v2, where=np.logical_not(both_zero)))
         else:
             raise FunctionError("Unrecognized operator ({0}) for LinearCombination function".
                                 format(operation.self.Operation.SUM))

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

@@ -26,6 +26,7 @@
 
 import numpy as np
 from beartype import beartype
+from scipy.special import erfinv
 
 from psyneulink._typing import Optional
 
@@ -371,11 +372,6 @@ def _function(self,
                  params=None,
                  ):
 
-        try:
-            from scipy.special import erfinv
-        except:
-            raise FunctionError("The UniformToNormalDist function requires the SciPy package.")
-
         mean = self._get_current_parameter_value(DIST_MEAN, context)
         standard_deviation = self._get_current_parameter_value(STANDARD_DEVIATION, context)
         random_state = self.parameters.random_state._get(context)