Merge pull request #2852 from PrincetonUniversity/devel

Devel
PrincetonUniversity · Dec 15, 2023 · f062be4 · f062be4
2 parents 424971b + 5a21b89
commit f062be4
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Showing 169 changed files with 84,750 additions and 6,396 deletions.
diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -2,7 +2,7 @@ name: "CodeQL"
 
 on:
   push:
-    branches: [ "master", "devel" ]
+    branches: [ "master", "devel", "codeql" ]
     paths-ignore:
       - 'docs/**'
   pull_request:
@@ -33,18 +33,26 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 100
 
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v2
+        uses: github/codeql-action/init@v3
         with:
           languages: ${{ matrix.language }}
           queries: +security-and-quality
 
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v2
+        uses: github/codeql-action/autobuild@v3
+
+      - name: Cache cleanup
+        shell: bash
+        run: |
+          $CODEQL_PYTHON -m pip cache info
+          $CODEQL_PYTHON -m pip cache purge
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v2
+        uses: github/codeql-action/analyze@v3
         with:
           category: "/language:${{ matrix.language }}"
diff --git a/.github/workflows/compare-comment.yml b/.github/workflows/compare-comment.yml
@@ -18,7 +18,7 @@ jobs:
     steps:
     - name: 'Download docs artifacts'
       id: docs-artifacts
-      uses: actions/github-script@v6
+      uses: actions/github-script@v7
       with:
         script: |
           var artifacts = await github.rest.actions.listWorkflowRunArtifacts({
@@ -70,7 +70,7 @@ jobs:
         (diff -r docs-base docs-head && echo 'No differences!' || true) | tee ./result.diff
 
     - name: Post comment with docs diff
-      uses: actions/github-script@v6
+      uses: actions/github-script@v7
       with:
         script: |
           var fs = require('fs');

diff --git a/.github/workflows/pnl-ci-docs.yml b/.github/workflows/pnl-ci-docs.yml
@@ -22,7 +22,7 @@ jobs:
       fail-fast: false
       # Matrix setup is a hacky way to include 'base' build in pull requests
       # The entire matrix is set up and 'base' builds are pruned based
-      # on event name and final configuration (ubuntu, python3.7).
+      # on event name and final configuration (ubuntu, python3.11).
       matrix:
         python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
         python-architecture: ['x64']
@@ -37,29 +37,29 @@ jobs:
             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'
             pnl-version: 'base'
           - python-version: '3.10'
             pnl-version: 'base'
-          - python-version: '3.11'
-            pnl-version: 'base'
 
     outputs:
       on_master: ${{ steps.on_master.outputs.on-branch }}
 
     steps:
-    # increased fetch-depth and tag checkout needed as in pnl-ci.yml
+    # Increased fetch-depth and tag checkout needed compared to pnl-ci.yml
     - name: Checkout sources
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       if: ${{ matrix.pnl-version == 'head' }}
       with:
         fetch-depth: 200
         ref: ${{ github.ref }}
 
     - name: Checkout pull base
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       if: ${{ matrix.pnl-version == 'base' }}
       with:
         fetch-depth: 200
@@ -76,7 +76,7 @@ jobs:
         branch: master
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         # Block python3.7.17 on macos. see:
         # https://github.com/actions/setup-python/issues/682
@@ -146,7 +146,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7]
+        python-version: [3.11]
         os: [ubuntu-latest]
 
     runs-on: ${{ matrix.os }}
@@ -163,7 +163,7 @@ jobs:
 
     steps:
     - name: Checkout docs
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         ref: gh-pages
 

diff --git a/.github/workflows/pnl-ci.yml b/.github/workflows/pnl-ci.yml
@@ -1,6 +1,8 @@
 name: PsyNeuLink CI
 
 on:
+  schedule:
+    - cron: "22 2 * * *"
   push:
     branches-ignore:
       - 'dependabot/**'
@@ -52,6 +54,7 @@ jobs:
         python-architecture: ['x64']
         extra-args: ['']
         os: [ubuntu, macos, windows]
+        version-restrict: ['']
         include:
           # code-coverage build on macos python 3.9
           - python-version: '3.9'
@@ -78,11 +81,18 @@ jobs:
           - python-version: '3.10'
             os: macos
             # pytest needs both '--benchmark-only' and '-m benchmark'
-            # The former fails the test if benchamrks cannot be enabled
+            # The former fails the test if benchmarks cannot be enabled
+            # (e.g. due to --dist setting)
             # The latter works around a crash in pytest when collecting tests:
             # 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
           - python-version: '3.8'
@@ -100,7 +110,7 @@ jobs:
     # version string from versioneer (must have history to a prior tag);
     # otherwise install fails due to circular dependency with modeci_mdf
     - name: Checkout sources
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 200
 
@@ -110,11 +120,20 @@ jobs:
       run: git fetch --tags origin master
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
         architecture: ${{ matrix.python-architecture }}
 
+    - name: Restrict version of direct dependencies
+      if: ${{ matrix.version-restrict == 'min' }}
+      shell: bash
+      run: |
+        sed -i '/^[^#]/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"
+
     - name: Get pip cache location
       shell: bash
       id: pip_cache

diff --git a/.github/workflows/test-release.yml b/.github/workflows/test-release.yml
@@ -18,10 +18,10 @@ jobs:
       wheel: ${{ steps.create_dist.outputs.wheel }}
     steps:
     - name: Checkout sources
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -84,7 +84,7 @@ jobs:
         path: dist/
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -113,7 +113,7 @@ jobs:
       run: pip install dist/${{ needs.create-python-dist.outputs.sdist }}[dev]
 
     - name: Get tests from the repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Run tests
       shell: bash
@@ -181,7 +181,7 @@ jobs:
         path: dist/
 
     - name: Upload dist files to release
-      uses: actions/github-script@v6
+      uses: actions/github-script@v7
       with:
         script: |
           const fs = require('fs')

diff --git a/.gitignore b/.gitignore
@@ -198,3 +198,4 @@ tests/*.pdf
 
 /tests/mdf/*.json
 /tests/mdf/*.yml
+/Scripts/ScratchPad FIGURES/
diff --git a/Scripts/Examples/Rumelhart Semantic Network.py b/Scripts/Examples/Rumelhart Semantic Network.py
@@ -36,4 +36,4 @@
 comp.add_backpropagation_learning_pathway(pathway=[rel_hidden, qual_out])
 comp.add_backpropagation_learning_pathway(pathway=[rel_hidden, act_out])
 comp.add_backpropagation_learning_pathway(pathway=[rep_in, rep_hidden, rel_hidden])
-comp.show_graph(show_learning=True)
+comp.show_graph()