Merge pull request #670 from bashtage/cython-cov-attempt

CI: Attempt to manually get cython coverage

Author: bashtage

.coveragerc

@@ -0,0 +1,62 @@
+[run]
+source = linearmodels
+branch = True
+omit =
+    */results/*
+    */_version.py
+    */compat/*
+    */conftest.py
+plugins = Cython.Coverage
+
+[report]
+# Regexes for lines to exclude from consideration
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise NotImplementedError
+    except NotImplementedError
+    raise AssertionError
+
+    # Ignore pass
+    pass
+
+    # Do not complain about missing debug-only code:
+    def __repr__
+    if self\\.debug
+
+    # Ignore failure messages
+    pytest.xfail
+
+    # Ignore ImportError protection
+    raise ImportError
+    except ImportError
+
+    # Ignore type checking code
+    if TYPE_CHECKING
+    elif TYPE_CHECKING
+
+    # Cython function declarations
+    cdef
+
+    # Cython functions with void
+    cdef void
+
+    # Numba jit decorators
+    @jit
+
+    # Do not complain if non-runnable code is not run:
+    if 0:
+    if __name__ == .__main__.:
+
+include = */linearmodels/*
+omit =
+  */_version.py
+  */compat/*
+  *recursions.py
+  *samplers.py
+ignore_errors = True
+
+[html]
+directory = coverage_html_report

azure-pipelines.yml

@@ -13,6 +13,7 @@ variables:
   PYTHONHASHSEED: 12345678 # Ensure tests are correctly gathered by xdist
   TEST_INSTALL: false
   MPLBACKEND: agg
+  PYTEST_PATTERN: "(not slow)"
   coverage: true
   test.install: false
   pip.pre: false

ci/azure_template_posix.yml

@@ -16,15 +16,15 @@ jobs:
     vmImage: ${{ parameters.vmImage }}
   strategy:
     matrix:
-      python310_minimums_wheel:
+      python310_minimums:
         python.version: '3.10'
         NUMPY: 1.22.3
         SCIPY: 1.8.0
         PANDAS: 1.3.0
         STATSMODELS: 0.13.1
         XARRAY: 0.21.0
         FORMULAIC: 1.2.1
-        test.wheel: true
+        PYTEST_PATTERN: "(slow or not slow)"
       python310_mid_sdist:
         python.version: '3.10'
         NUMPY: 1.23.0
@@ -62,11 +62,15 @@ jobs:
         XXHASH: true
         PYARROW: true
         BUILD_FLAGS: '-Csetup-args=-Dno-binary=true'
+      python312_cython_coverage:
+        python.version: '3.12'
+        BUILD_FLAGS: '-Csetup-args=-Dcython-coverage=true'
+        cython.coverage: true
       python313_latest:
         python.version: '3.13'
         XXHASH: true
         PYARROW: true
-        BUILD_FLAGS: '-Csetup-args=-Dcython-coverage=true'
+        PYTEST_PATTERN: "(slow or not slow)"
       python313_copy_on_write:
         python.version: '3.12'
         XXHASH: true
@@ -92,8 +96,7 @@ jobs:
       jupyter kernelspec list
     displayName: 'Install dependencies'
 
-  - script: |
-      python -m pip list
+  - script: python -m pip list
     displayName: 'List Configuration'
 
   - script: |
@@ -126,6 +129,13 @@ jobs:
     displayName: 'Install linearmodels (editable)'
     condition: and(ne(variables['test.wheel'], 'true'), ne(variables['test.sdist'], 'true'))
 
+  - script: |
+      pushd linearmodels/panel
+      cython --verbose -M --fast-fail -3  -X cpow=True -X boundscheck=False -X wraparound=False -X cdivision=True -X binding=True -X linetrace=True _utility.pyx
+      popd
+    displayName: 'Transpile Cython to C for coverage support'
+    condition: eq(variables['cython.coverage'], 'true')
+
   - script: |
       echo "Testing site packages"
       mkdir test_run_dir
@@ -137,16 +147,16 @@ jobs:
 
   - script: |
       echo "Testing editable install"
-      export COVERAGE_OPTS="--cov=linearmodels --cov-report xml:coverage.xml --cov-report term"
-      echo pytest -m "${PYTEST_PATTERN}" --junitxml=junit/test-results.xml -n auto --durations=25 ${COVERAGE_OPTS} ${BUILD_FLAGS} linearmodels/tests 
+      export COVERAGE_OPTS="--cov-config=.coveragerc --cov=linearmodels --cov-branch --cov-report xml:coverage.xml --cov-report term"
+      echo pytest -m "${PYTEST_PATTERN}" --junitxml=junit/test-results.xml -n auto --durations=25 ${COVERAGE_OPTS} linearmodels/tests 
       pytest -m "${PYTEST_PATTERN}" --junitxml=junit/test-results.xml -n auto --durations=25 ${COVERAGE_OPTS} linearmodels/tests
     displayName: 'Run tests (editable)'
     condition: and(and(ne(variables['test.wheel'], 'true'), ne(variables['test.sdist'], 'true')), ne(variables['pip.pre'], 'true'))
 
   - script: |
       echo "Testing pip-pre"
-      export COVERAGE_OPTS="--cov=linearmodels --cov-report xml:coverage.xml --cov-report term"
-      echo pytest -m "${PYTEST_PATTERN}" --junitxml=junit/test-results.xml -n auto --durations=25 ${COVERAGE_OPTS} ${BUILD_FLAGS} linearmodels/tests
+      export COVERAGE_OPTS="--cov-config=.coveragerc --cov=linearmodels --cov-branch --cov-report=xml:coverage.xml --cov-report=term"
+      echo pytest -m "${PYTEST_PATTERN}" --junitxml=junit/test-results.xml -n auto --durations=25 ${COVERAGE_OPTS} linearmodels/tests
       pytest -m "${PYTEST_PATTERN}" --junitxml=junit/test-results.xml -n auto --durations=25 ${COVERAGE_OPTS}  linearmodels/tests
     displayName: 'Run tests (pip pre)'
     condition: eq(variables['pip.pre'], 'true')

linearmodels/meson.build

@@ -29,17 +29,18 @@ inc_np = include_directories(incdir_numpy, is_system: true)
 # Copy the main __init__.py to the build dir.
 # Some submodules (linalg, special, optimize) add pxd files to this.
 # Needed to trick Cython, it won't do a relative import outside a package
+_cython_tree = [fs.copyfile('__init__.py')]
 cython_args = [
-    '-Xcpow=True',
-    '-Xboundscheck=False',
-    '-Xwraparound=False',
-    '-Xcdivision=True',
-    '-Xbinding=True'
+    '-X cpow=True',
+    '-X boundscheck=False',
+    '-X wraparound=False',
+    '-X cdivision=True',
+    '-X binding=True'
 ]
 cython_c_args =  ['-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION']
 if get_option('cython-coverage')
   message('Building with Cython coverage support')
-  cython_args += ['-Xlinetrace=True']
+  cython_args += ['-X linetrace=True']
   cython_c_args += ['-DCYTHON_TRACE=1']
 endif
 

linearmodels/panel/meson.build

@@ -5,7 +5,7 @@ if not get_option('no-binary')
         install: true,
         include_directories: [inc_np],
         subdir: 'linearmodels/panel',
-        cython_args: cython_args,
         c_args: cython_c_args,
+        cython_args: cython_args,
     )
 endif

pyproject.toml

@@ -311,9 +311,9 @@ include_trailing_comma=true
 use_parentheses=true
 
 [tool.coverage.run]
-source = ["linearmodels"]
+source = [ "linearmodels" ]
 branch = true
-plugins = ["Cython.Coverage"]
+plugins = [ "Cython.Coverage" ]
 omit = [
   # Version file
   "*/_version.py",

requirements-test.txt

@@ -1,4 +1,4 @@
-black[jupyter]==24.4.0
+black[jupyter]~=25.9.0
 coverage
 flake8
 isort