Merge pull request #2748 from PrincetonUniversity/devel

Devel

Author: kmantel

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

@@ -44,14 +44,22 @@ runs:
     - name: Drop pytorch on x86
       shell: bash
       run: |
+        echo > env_constraints.txt
         if [ $(python -c 'import struct; print(struct.calcsize("P") * 8)') == 32 ]; then
           sed -i /torch/d requirements.txt
           sed -i /modeci_mdf/d requirements.txt
           # pywinpty is a transitive dependency and v1.0+ removed support for x86 wheels
-          # terminado >= 0.10.0 pulls in pywinpty >= 1.1.0
+          echo "pywinpty<1" >> env_constraints.txt
+          # jupyter_sever 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
           # scikit-learn >= 1.1.3 doesn't provide win32 wheel
-          [[ ${{ runner.os }} = Windows* ]] && pip install "pywinpty<1" "terminado<0.10" "scipy<1.9.2" "scikit-learn<1.1.3" "statsmodels<0.13.3" "jupyter-server<2" -c requirements.txt
+          echo "scikit-learn<1.1.3" >> env_constraints.txt
+          # countourpy >=1.1.0 doesn't provide win32 wheel
+          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
         fi
 
     - name: Install updated package
@@ -66,7 +74,7 @@ runs:
           echo "new_package=$NEW_PACKAGE" >> $GITHUB_OUTPUT
           # save a list of all installed packages (including pip, wheel; it's never empty)
           pip freeze --all > orig
-          pip install "$(echo $NEW_PACKAGE | sed 's/[-_]/./g' | xargs grep *requirements.txt -h -e | head -n1)"
+          pip install "$(echo $NEW_PACKAGE | sed 's/[-_]/./g' | xargs grep *requirements.txt -h -e | head -n1)" -c env_constraints.txt -c broken_trans_deps.txt
           pip show "$NEW_PACKAGE" | grep 'Version' | tee new_version.deps
           # uninstall new packages but skip those from previous steps (pywinpty, terminado on windows x86)
           # the 'orig' list is not empty (includes at least pip, wheel)
@@ -78,7 +86,7 @@ runs:
     - name: Python dependencies
       shell: bash
       run: |
-        pip install -e .[${{ inputs.features }}]
+        pip install -e .[${{ inputs.features }}] -c env_constraints.txt -c broken_trans_deps.txt
 
     - name: "Cleanup old wheels"
       shell: bash

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

@@ -24,7 +24,7 @@ jobs:
       # The entire matrix is set up and 'base' builds are pruned based
       # on event name and final configuration (ubuntu, python3.7).
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
         python-architecture: ['x64']
         os: [ubuntu-latest, macos-latest, windows-latest]
         event:
@@ -37,9 +37,13 @@ jobs:
             pnl-version: 'base'
           - os: windows-latest
             pnl-version: 'base'
-          - python-version: 3.8
+          - python-version: '3.8'
             pnl-version: 'base'
-          - python-version: 3.9
+          - python-version: '3.9'
+            pnl-version: 'base'
+          - python-version: '3.10'
+            pnl-version: 'base'
+          - python-version: '3.11'
             pnl-version: 'base'
 
     outputs:
@@ -74,7 +78,9 @@ jobs:
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
-        python-version: ${{ matrix.python-version }}
+        # 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 }}
         architecture: ${{ matrix.python-architecture }}
 
     - name: Get pip cache location

.github/workflows/pnl-ci.yml

@@ -48,22 +48,51 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ['3.7', '3.11']
         python-architecture: ['x64']
         extra-args: ['']
         os: [ubuntu, macos, windows]
         include:
+          # code-coverage build on macos python 3.9
+          - python-version: '3.9'
+            os: macos
+            extra-args: '--cov=psyneulink'
+
+          # --forked run of python only tests
+          # Python tests are enough to test potential naming issues
+          - python-version: '3.9'
+            os: ubuntu
+            extra-args: '--forked -m "not llvm"'
+
           # add 32-bit build on windows
-          - python-version: 3.8
+          - python-version: '3.8'
             python-architecture: 'x86'
             os: windows
-          # code-coverage build on macos python 3.9
-          - python-version: 3.9
+
+          # fp32 run on linux python 3.10
+          - python-version: '3.10'
+            os: ubuntu
+            extra-args: '--fp-precision=fp32'
+
+          # --benchmark-enable run on macos python 3.10
+          - python-version: '3.10'
             os: macos
-            extra-args: '--cov=psyneulink'
+            # pytest needs both '--benchmark-only' and '-m benchmark'
+            # The former fails the test if benchamrks cannot be enabled
+            # 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 3.8 build on macos since 3.7 is broken
+          # https://github.com/actions/virtual-environments/issues/4230
+          - python-version: '3.8'
+            python-architecture: 'x64'
+            os: macos
+
         exclude:
-          # 3.7 is broken on macos-11, https://github.com/actions/virtual-environments/issues/4230
-          - python-version: 3.7
+          # 3.7 is broken on macos-11,
+          # https://github.com/actions/virtual-environments/issues/4230
+          - python-version: '3.7'
             os: macos
 
     steps:
@@ -115,17 +144,25 @@ 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
+      shell: bash
+      run: |
+        python -c "import numpy; numpy.show_config()"
+        case "$RUNNER_OS" in
+          Linux*) lscpu;;
+        esac
+
     - name: Test with pytest
       timeout-minutes: 180
       run: pytest --junit-xml=tests_out.xml --verbosity=0 -n auto ${{ matrix.extra-args }}
 
     - name: Upload test results
       uses: actions/upload-artifact@v3
       with:
-        name: test-results-${{ matrix.os }}-${{ matrix.python-version }}-${{ matrix.python-architecture }}-${{ matrix.extra-args }}
+        name: test-results-${{ matrix.os }}-${{ matrix.python-version }}-${{ matrix.python-architecture }}
         path: tests_out.xml
         retention-days: 5
-      if: success() || failure()
+      if: (success() || failure()) && ! contains(matrix.extra-args, 'forked')
 
     - name: Upload coveralls code coverage
       if: contains(matrix.extra-args, '--cov=psyneulink')

CONVENTIONS.md

@@ -74,7 +74,11 @@ Extensions of Core objects
 - arguments_of_constructors, instance_attributes and instance_methods:
       lowercase and underscore separator(s) [constructor_arg, method_arg, object_attribute]
 - keywords:
-    all capitals and underscore separator(s) [KEY_WORD]
+  - all capitals and underscore separator(s) [KEY_WORD]
+  - assigned values:
+     - argument of a method or function: lower case [KEY_WORD = 'argument_value']
+     - names of a Components: upper case [KEY_WORD = 'NAME'] 
+
 DEPRECATED:
     - internal keywords:
         prepend kw followed by camelCase [kwKeyword]

Scripts/Debug/Yotam LCA Model LLVM.py

@@ -22,6 +22,16 @@
 LCA_BIN_EXECUTE=os.getenv("LCA", "LLVMRun")
 RUN_TOTAL=True
 
+def _get_execution_mode(bin_execute):
+    if bin_execute.lower() == 'llvmrun':
+        return pnl.ExecutionMode.LLVMRun
+    elif bin_execute.lower() == 'pytorch':
+        return pnl.ExecutionMode.PyTorch
+    elif bin_execute.lower() == 'python':
+        return pnl.ExecutionMode.Python
+
+    assert False, "Unknown execution mode: {}".format(bin_execute)
+
 # read in bipartite graph, return graph object, number of possible tasks, number of
 # input dimensions and number of output dimensions.
 # file format Ni No (input dimension number, output dimension number)
@@ -171,12 +181,12 @@ def get_trained_network(bipartite_graph, num_features=3, num_hidden=200, epochs=
     mnet.learn(
         inputs=input_set,
         minibatch_size=1,
-        bin_execute=MNET_BIN_EXECUTE,
+        execution_mode=_get_execution_mode(MNET_BIN_EXECUTE),
         patience=patience,
         min_delta=min_delt,
     )
     t2 = time.time()
-    print("training 1:", MNET_BIN_EXECUTE, t2-t1)
+    print("training 1 time:", MNET_BIN_EXECUTE, t2 - t1)
 
     # Apply LCA transform (values from Sebastian's code -- supposedly taken from the original LCA paper from Marius & Jay)
     if attach_LCA:
@@ -293,12 +303,12 @@ def get_trained_network_multLCA(bipartite_graph, num_features=3, num_hidden=200,
     mnet.learn(
         inputs=input_set,
         minibatch_size=input_set['epochs'],
-        bin_execute=MNET_BIN_EXECUTE,
+        execution_mode=_get_execution_mode(MNET_BIN_EXECUTE),
         patience=patience,
         min_delta=min_delt,
     )
     t2 = time.time()
-    print("training 2:", MNET_BIN_EXECUTE, t2-t1)
+    print("training 2 time:", MNET_BIN_EXECUTE, t2 - t1)
 
     for projection in mnet.projections:
         if hasattr(projection.parameters, 'matrix'):
@@ -487,9 +497,10 @@ def evaluate_net_perf_lca(mnet_lca, test_tasks, all_tasks, num_features, num_inp
         }
         print('running LCA total')
         t1 = time.time()
-        mnet_lca.run( { mnet_lca.nodes['mnet'] : inputs_total }, bin_execute=LCA_BIN_EXECUTE)
+        mnet_lca.run({mnet_lca.nodes['mnet']: inputs_total},
+                     execution_mode=_get_execution_mode(LCA_BIN_EXECUTE))
         t2 = time.time()
-        print("LCA total:", LCA_BIN_EXECUTE, t2 - t1)
+        print("LCA run total time:", LCA_BIN_EXECUTE, t2 - t1)
     # Run the outer composition, one point at a time (for debugging purposes)
     for i in range(num_test_points):
         if RUN_TOTAL:
@@ -504,9 +515,10 @@ def evaluate_net_perf_lca(mnet_lca, test_tasks, all_tasks, num_features, num_inp
 
         print('running LCA', i)
         t1 = time.time()
-        mnet_lca.run( { mnet_lca.nodes['mnet'] : input_set['inputs'] }, bin_execute=LCA_BIN_EXECUTE )
+        mnet_lca.run({mnet_lca.nodes['mnet']: input_set['inputs']},
+                     execution_mode=_get_execution_mode(LCA_BIN_EXECUTE))
         t2 = time.time()
-        print("LCA:", LCA_BIN_EXECUTE, t2 - t1)
+        print("LCA time:", LCA_BIN_EXECUTE, t2 - t1)
         iterations = mnet_lca.nodes['lca'].num_executions_before_finished if LCA_BIN_EXECUTE == "Python" else ugly_get_compile_param_value(mnet_lca, 'lca', 'num_executions_before_finished')
         print("ITERATIONS:", iterations)
         print('input: ', input_test_pts[i, :])
@@ -617,9 +629,9 @@ def evaluate_net_perf_mse(mnet, test_tasks, all_tasks, num_features, num_input_d
 
     print("running mnet2:", MNET2_BIN_EXECUTE)
     t1 = time.time()
-    mnet.run(input_set, bin_execute=MNET2_BIN_EXECUTE)
+    mnet.run(input_set, execution_mode=_get_execution_mode(MNET2_BIN_EXECUTE))
     t2 = time.time()
-    print("mnet2:", MNET2_BIN_EXECUTE, t2-t1)
+    print("mnet2 time:", MNET2_BIN_EXECUTE, t2 - t1)
 
     # Retrieve results
     output_test_pts = np.array(mnet.parameters.results.get(mnet)[-num_test_points:]).reshape(num_test_points, output_layer_size)