Merge pull request #2449 from PrincetonUniversity/devel

Devel

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

@@ -48,6 +48,17 @@ runs:
           [[ ${{ runner.os }} = Windows* ]] && pip install "pywinpty<1" "terminado<0.10"
         fi
 
+    - name: Install updated package
+      if: ${{ startsWith(github.head_ref, 'dependabot/pip') && matrix.pnl-version != 'base' }}
+      shell: bash
+      id: new_package
+      run: |
+        python -m pip install --upgrade pip wheel
+        export NEW_PACKAGE=`echo '${{ github.head_ref }}' | cut -f 4 -d/ | sed 's/-gt.*//' | sed 's/-lt.*//'`
+        echo "::set-output name=new_package::$NEW_PACKAGE"
+        pip install "`echo $NEW_PACKAGE | sed 's/[-_]/./g' | xargs grep *requirements.txt -h -e | head -n1`"
+        pip show "$NEW_PACKAGE" | grep 'Version' | tee new_version.deps
+
     - name: Python dependencies
       shell: bash
       run: |
@@ -66,3 +77,11 @@ runs:
             pip cache remove -v $P || true
           fi
         done
+
+    - name: Check updated package
+      if: ${{ startsWith(github.head_ref, 'dependabot/pip') && matrix.pnl-version != 'base' }}
+      shell: bash
+      run: |
+        pip show ${{ steps.new_package.outputs.new_package }} | grep 'Version' | tee installed_version.deps
+        cmp -s new_version.deps installed_version.deps || echo "::error::Package version restricted by dependencies: ${{ steps.new_package.outputs.new_package }}"
+        diff new_version.deps installed_version.deps

.github/workflows/compare-comment.yml

@@ -18,7 +18,7 @@ jobs:
     steps:
     - name: 'Download docs artifacts'
       id: docs-artifacts
-      uses: actions/github-script@v5
+      uses: actions/github-script@v6
       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@v5
+      uses: actions/github-script@v6
       with:
         script: |
           var fs = require('fs');

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

@@ -65,7 +65,7 @@ jobs:
         branch: master
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
         architecture: ${{ matrix.python-architecture }}
@@ -94,17 +94,21 @@ jobs:
     - name: Add git tag
       # The generated docs include PNL version,
       # set it to a fixed value to prevent polluting the diff
+      # This needs to be done after installing PNL
+      # to not interfere with dependency resolution
+      id: add_zero_tag
       if: github.event_name == 'pull_request'
-      run: git tag --force 'v999.999.999.999'
+      run: git tag --force 'v0.0.0.0'
 
     - name: Build Documentation
       run: make -C docs/ html -e SPHINXOPTS="-aE -j auto"
 
     - name: Remove git tag
       # The generated docs include PNL version,
-      # This was set to a fixed value to prevent polluting the diff
-      if: github.event_name == 'pull_request' && always()
-      run: git tag -d 'v999.999.999.999'
+      # A special tag was set to a fixed value
+      # to prevent polluting the diff
+      if: steps.add_zero_tag.outcome != 'skipped'
+      run: git tag -d 'v0.0.0.0'
 
     - name: Upload Documentation
       uses: actions/upload-artifact@v3
@@ -151,7 +155,7 @@ jobs:
         ref: gh-pages
 
     - name: Download branch docs
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v3
       with:
         name: Documentation-head-${{ matrix.os }}-${{ matrix.python-version }}-x64
         path: _built_docs/${{ github.ref }}
@@ -168,7 +172,7 @@ 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@v2
+      uses: actions/download-artifact@v3
       with:
         name: Documentation-head-${{ matrix.os }}-${{ matrix.python-version }}-x64
         # This overwrites files in current directory

.github/workflows/pnl-ci.yml

@@ -22,10 +22,6 @@ jobs:
         extra-args: ['']
         os: [ubuntu-latest, macos-latest, windows-latest]
         include:
-          # 3.7 is broken on macos-11, https://github.com/actions/virtual-environments/issues/4230
-          - python-version: 3.7
-            python-architecture: 'x64'
-            os: macos-10.15
           # add 32-bit build on windows
           - python-version: 3.8
             python-architecture: 'x86'
@@ -54,7 +50,7 @@ jobs:
       run: git fetch --tags origin master
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
         architecture: ${{ matrix.python-architecture }}

.github/workflows/test-release.yml

@@ -21,7 +21,7 @@ jobs:
       uses: actions/checkout@v3
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -78,13 +78,13 @@ jobs:
 
     steps:
     - name: Download dist files
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v3
       with:
         name: Python-dist-files
         path: dist/
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -141,7 +141,7 @@ jobs:
 
     steps:
     - name: Download dist files
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v3
       with:
         name: Python-dist-files
         path: dist/
@@ -175,13 +175,13 @@ jobs:
 
     steps:
     - name: Download dist files
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v3
       with:
         name: Python-dist-files
         path: dist/
 
     - name: Upload dist files to release
-      uses: actions/github-script@v5
+      uses: actions/github-script@v6
       with:
         script: |
           const fs = require('fs')

.gitignore

@@ -1,9 +1,9 @@
 
 # Created by https://www.gitignore.io/api/osx,python,pycharm
 
-# Ignore JSON files created in tests/json/
+# Ignore JSON files created in tests/mdf/
 # Maybe these should be generated in tmpdir instead
-tests/json/*.json
+tests/mdf/*.json
 
 # Log files created by SLURM jobs in this directory
 Scripts/Debug/predator_prey_opt/logs/

conftest.py

@@ -33,7 +33,22 @@
 def pytest_addoption(parser):
     parser.addoption('--{0}'.format(mark_stress_tests), action='store_true', default=False, help='Run {0} tests (long)'.format(mark_stress_tests))
 
+    parser.addoption('--fp-precision', action='store', default='fp64', choices=['fp32', 'fp64'],
+                     help='Set default fp precision for the runtime compiler. Default: fp64')
+
+def pytest_sessionstart(session):
+    precision = session.config.getvalue("--fp-precision")
+    if precision == 'fp64':
+        pnlvm.LLVMBuilderContext.default_float_ty = pnlvm.ir.DoubleType()
+    elif precision == 'fp32':
+        pnlvm.LLVMBuilderContext.default_float_ty = pnlvm.ir.FloatType()
+    else:
+        assert False, "Unsupported precision parameter: {}".format(precision)
+
 def pytest_runtest_setup(item):
+    # Check that all 'cuda' tests are also marked 'llvm'
+    assert 'llvm' in item.keywords or 'cuda' not in item.keywords
+
     for m in marks_default_skip:
         if m in item.keywords and not item.config.getvalue(m):
             pytest.skip('{0} tests not requested'.format(m))
@@ -97,6 +112,16 @@ def comp_mode_no_llvm():
     # dummy fixture to allow 'comp_mode' filtering
     pass
 
+@pytest.helpers.register
+def llvm_current_fp_precision():
+    float_ty = pnlvm.LLVMBuilderContext.get_current().float_ty
+    if float_ty == pnlvm.ir.DoubleType():
+        return 'fp64'
+    elif float_ty == pnlvm.ir.FloatType():
+        return 'fp32'
+    else:
+        assert False, "Unknown floating point type: {}".format(float_ty)
+
 @pytest.helpers.register
 def get_comp_execution_modes():
     return [pytest.param(pnlvm.ExecutionMode.Python),

cuda_requirements.txt

@@ -1 +1 @@
-pycuda >2018, <2022
+pycuda >2018, <2023

dev_requirements.txt

@@ -1,5 +1,5 @@
 jupyter<=1.0.0
-pytest<7.1.2
+pytest<7.1.3
 pytest-benchmark<3.4.2
 pytest-cov<3.0.1
 pytest-helpers-namespace<2021.12.30

doc_requirements.txt

@@ -1,3 +1,3 @@
-psyneulink-sphinx-theme<1.2.3.1
+psyneulink-sphinx-theme<1.2.4.1
 sphinx<4.2.1
 sphinx_autodoc_typehints<1.16.0