Merge pull request #439 from sandialabs/bugfix-densitymx-slow

Fix densitymx slow bug.

.github/workflows/extras.yml

@@ -50,19 +50,7 @@ jobs:
         # but still compile Cython extensions
         python -m pip install -e .[testing]
         python setup.py build_ext --inplace
-    - name: Run test_packages Ubuntu
-      if: ${{matrix.os == 'ubuntu-latest'}}
-      run: |
-        python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
-        python -m pytest -v -n auto --dist loadscope --ignore=test/test_packages/mpi --ignore=test/test_packages/notebooks test/test_packages
-    - name: Run test_packages Windows
-      if: ${{matrix.os == 'windows-latest'}}
-      run: |
-        python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
-        python -m pytest -v -n auto --dist loadscope --ignore=test/test_packages/mpi --ignore=test/test_packages/notebooks test/test_packages
-    - name: Run test_packages MacOS
-      if: ${{matrix.os == 'macos-latest'}}
-
+    - name: Run test_packages
       run: |
         python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
         python -m pytest -v -n auto --dist loadscope --ignore=test/test_packages/mpi --ignore=test/test_packages/notebooks test/test_packages

.github/workflows/main-mac.yml

@@ -43,15 +43,13 @@ jobs:
         python -m pip install flake8
         python -m pip install -e .[testing]
         python setup.py build_ext --inplace
-        # python -m pip freeze  # this isn't relevant anymore since pip install builds a wheel separately
     - name: Lint with flake8
       run: |
         # Critical errors, exit on failure
         flake8 . --count --show-source --statistics --config=.flake8-critical
         # Standard PEP8, allowed to fail since exit-zero treats all errors as warnings
         flake8 . --exit-zero --statistics
-    - name: Run unit tests MacOS  
-      if: ${{matrix.os == 'macos-latest'}}
+    - name: Run unit tests
       run: |
        python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
        python -m pytest -n auto --dist loadscope --cov=pygsti test/unit

.github/workflows/main-minimal.yml

@@ -48,21 +48,14 @@ jobs:
         python -m pip install flake8
         python -m pip install -e .[testing]
         python setup.py build_ext --inplace
-        # python -m pip freeze  # this isn't relevant anymore since pip install builds a wheel separately
     - name: Lint with flake8
       if: ${{matrix.os != 'windows-latest'}}
       run: |
         # Critical errors, exit on failure
         flake8 . --count --show-source --statistics --config=.flake8-critical
         # Standard PEP8, allowed to fail since exit-zero treats all errors as warnings
         flake8 . --exit-zero --statistics
-    - name: Run unit tests ubuntu
-      if: ${{matrix.os == 'ubuntu-latest'}}
-      run: |
-       python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
-       python -m pytest -n auto --dist loadscope --cov=pygsti test/unit
-    - name: Run unit tests windows  
-      if: ${{matrix.os == 'windows-latest'}}
+    - name: Run unit tests
       run: |
        python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
        python -m pytest -n auto --dist loadscope --cov=pygsti test/unit

.github/workflows/main-no-cython.yml

@@ -0,0 +1,54 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Build and run tests (No Cython)
+
+on:
+  push:
+    branches: [ "beta", "master" ]
+  pull_request:
+    branches: [ "**:**" ]
+  # Allow running manually from Actions tab
+  workflow_dispatch:
+
+env:
+  SKIP_DEAP: 1
+
+jobs:
+  build: # Main build + unit test check
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: [3.8, 3.9, '3.10', '3.11']
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up installation environment (Ubuntu or Windows)
+      if: ${{matrix.os == 'ubuntu-latest' || matrix.os == 'windows-latest'}}
+      run: |
+        ./.github/ci-scripts/before_install.sh
+    - name: Set up installation environment (MacOS)
+      if: ${{matrix.os == 'macos-latest'}}
+      run: |
+        ./.github/ci-scripts/before_install_macos.sh
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache pip packages
+      uses: actions/cache@v4
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('setup.py') }}-${{ hashFiles('**/*requirements.txt') }}
+    - name: Install package
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install wheel
+        python -m pip install flake8
+        python -m pip install -e .[testing_no_cython]
+    - name: Run unit tests
+      run: |
+       python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
+       python -m pytest -n auto --dist loadscope --cov=pygsti test/unit

.github/workflows/main.yml

@@ -45,7 +45,6 @@ jobs:
         python -m pip install flake8
         python -m pip install -e .[testing]
         python setup.py build_ext --inplace
-        # python -m pip freeze  # this isn't relevant anymore since pip install builds a wheel separately
     - name: Lint with flake8
       if: ${{matrix.os != 'windows-latest'}}
       run: |
@@ -54,12 +53,6 @@ jobs:
         # Standard PEP8, allowed to fail since exit-zero treats all errors as warnings
         flake8 . --exit-zero --statistics
     - name: Run unit tests ubuntu
-      if: ${{matrix.os == 'ubuntu-latest'}}
-      run: |
-       python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
-       python -m pytest -n auto --dist loadscope --cov=pygsti test/unit
-    - name: Run unit tests windows  
-      if: ${{matrix.os == 'windows-latest'}}
       run: |
        python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
        python -m pytest -n auto --dist loadscope --cov=pygsti test/unit

.github/workflows/notebook.yml

@@ -56,18 +56,7 @@ jobs:
         # but still compile Cython extensions
         python -m pip install -e .[testing]
         python setup.py build_ext --inplace
-    - name: Run notebook regression ubuntu
-      if: ${{matrix.os == 'ubuntu-latest'}}
-      run: |
-       python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
-       python -m pytest -n auto --nbval-lax --dist loadscope --nbval-current-env jupyter_notebooks
-    - name: Run notebook regression windows 
-      if: ${{matrix.os == 'windows-latest'}}
-      run: |
-       python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
-       python -m pytest -n auto --nbval-lax --dist loadscope --nbval-current-env jupyter_notebooks
-    - name: Run notebook regression MacOS  
-      if: ${{matrix.os == 'macos-latest'}}
+    - name: Run notebook regression
       run: |
        python -Ic "import pygsti; print(pygsti.__version__); print(pygsti.__path__)"
        python -m pytest -n auto --nbval-lax --dist loadscope --nbval-current-env jupyter_notebooks

pygsti/evotypes/densitymx_slow/opreps.py

@@ -174,7 +174,7 @@ def __init__(self, name, basis, state_space):
         state_space = _StateSpace.cast(state_space)
         assert(superop.shape[0] == state_space.dim)
 
-        super(OpRepStandard, self).__init__(superop, state_space)
+        super(OpRepStandard, self).__init__(superop, basis, state_space)
 
 
 class OpRepKraus(OpRep):

setup.py

@@ -92,6 +92,9 @@
 # which is unavailable in some common environments.
 extras['no_mpi'] = [e for e in extras['complete'] if e != 'mpi4py']
 
+# Add testing_no_cython target, identical to `testing` but no cython
+extras['testing_no_cython'] = [e for e in extras['testing'] if e != 'cython']
+
 
 # Configure setuptools_scm to build the post-release version number
 def custom_version():
@@ -131,7 +134,8 @@ def setup_with_extensions(extensions=None):
         cmdclass={'build_ext': build_ext_compiler_check},
         description='A python implementation of Gate Set Tomography',
         long_description=descriptionTxt,
-        author='Erik Nielsen, Kenneth Rudinger, Timothy Proctor, John Gamble, Robin Blume-Kohout',
+        author='Erik Nielsen, Stefan Seritan, Corey Ostrove, Riley Murray, Jordan Hines, ' +\
+            'Kenneth Rudinger, Timothy Proctor, John Gamble, Robin Blume-Kohout',
         author_email='pygsti@sandia.gov',
         packages=[
             'pygsti',