Merge pull request statsmodels#5188 from bashtage/cycov-rebase

BLD/TST: Add coverage for Cython files

Author: josef-pkt

.coveragerc

@@ -1,10 +1,37 @@
 # .coveragerc to control coverage.py
 [run]
-branch = False
+source = statsmodels
+branch = True
+
+omit =
+    # print_version is untestable
+    */print_version.py
+    # skip compatibility code
+    */compat/*
+    # Unused file
+    */results/gee_generate_tests.py
+    # Results for tests
+    */tests/results/*
+    # Simulation checks
+    */tests/*_simulation_check.py
+    # Misc non-test files in test directories
+    */tests/_*
+    */tests/e*
+    */tests/c*
+    */tests/d*
+    */tests/g*
+    */tests/m*
+    */tests/p*
+    */tests/r*
+    */tests/s*
+    # Versioneer
+    */_version.py
 
 [report]
 show_missing = True
 
+ignore_errors = False
+
 # Regexes for lines to exclude from consideration
 exclude_lines =
     # Have to re-enable the standard pragma
@@ -17,12 +44,13 @@ exclude_lines =
     # Don't complain if tests don't hit defensive assertion code:
     raise AssertionError
     raise NotImplementedError
+    except NotImplementedError
+    # Ignore pass
+    pass
 
     # Don't complain if non-runnable code isn't run:
     if 0:
     if __name__ == .__main__.:
 
-ignore_errors = False
-
 [html]
 directory = coverage_html_report

.travis.yml

@@ -23,6 +23,7 @@ env:
     - BLAS="mkl blas=*=mkl" # Use Intel MKL by default
     - BUILD_INIT=tools/ci/travis_conda.sh
     - DEPEND_ALWAYS="pyyaml joblib pip colorama"
+    - SM_CYTHON_COVERAGE=false # Run takes > 1 hour and so not feasible
 
 matrix:
   fast_finish: true
@@ -100,6 +101,8 @@ notifications:
     on_success: always
 
 before_install:
+  # Ensure latest tags are available
+  - git fetch --tags
   # Show information about CPU running job to understand BLAS issues
   - sudo lshw -class processor
   # Fix for headless TravisCI
@@ -114,7 +117,12 @@ before_install:
   - |
     if [ ${COVERAGE} = true ]; then
         pip install codecov coverage coveralls pytest-cov
-        export COVERAGE_OPTS="--cov-config=.travis_coveragerc --cov=statsmodels"
+        if [ -z ${SM_CYTHON_COVERAGE} ] || [ ${SM_CYTHON_COVERAGE} = false ]; then
+          export COVERAGE_OPTS="--cov-config=tools/coveragerc/.coveragerc_travis --cov=statsmodels"
+        else
+          export COVERAGE_OPTS="--cov-config=tools/coveragerc/.coveragerc_cython --cov=statsmodels"
+        fi
+        echo "Cython coverage:" ${SM_CYTHON_COVERAGE}
     else
         export COVERAGE_OPTS=""
     fi
@@ -124,7 +132,6 @@ before_install:
 
 # Install packages
 install:
-  - python setup.py build_ext --inplace
   - python setup.py develop
 
 script:
@@ -138,5 +145,5 @@ script:
   - ./lint.sh
 
 after_success:
-  - if [ ${COVERAGE} = true ]; then coveralls --rcfile=${SRCDIR}/.travis_coveragerc; fi
+  - if [ ${COVERAGE} = true ]; then coveralls --rcfile=${SRCDIR}/tools/coveragerc/.coveragerc_travis; fi
   - if [ ${COVERAGE} = true ]; then codecov; fi

MANIFEST.in

@@ -1,4 +1,4 @@
-global-include *.csv *.py *.txt *.pyx *.pxd *.pxi *.c *.h
+global-include *.csv *.py *.txt *.pyx *.pyx.in *.pxd *.pxi *.c *.h
 include MANIFEST.in
 include README.rst
 

requirements.txt

@@ -0,0 +1,4 @@
+numpy>=1.11
+scipy>=0.18
+pandas>=0.18
+patsy>=0.5

setup.py

@@ -1,3 +1,10 @@
+"""
+To build with coverage of Cython files
+export SM_CYTHON_COVERAGE=1
+python setup.py develop
+pytest --cov-config=tools/coveragerc/.coveragerc_cython --cov=statsmodels \
+       statsmodels
+"""
 import fnmatch
 import os
 import sys
@@ -86,6 +93,7 @@
                'Environment :: Console',
                'Programming Language :: Cython',
                'Programming Language :: Python :: 2.7',
+               'Programming Language :: Python :: 3.4',
                'Programming Language :: Python :: 3.5',
                'Programming Language :: Python :: 3.6',
                'Programming Language :: Python :: 3.7',
@@ -112,8 +120,13 @@
 ##############################################################################
 # Extension Building
 ##############################################################################
-COMPILER_DIRECTIVES = {}
-DEFINE_MACROS = []
+CYTHON_COVERAGE = os.environ.get('SM_CYTHON_COVERAGE', False)
+CYTHON_COVERAGE = CYTHON_COVERAGE in ('1', 'true', '"true"')
+CYTHON_TRACE_NOGIL = str(int(CYTHON_COVERAGE))
+if CYTHON_COVERAGE:
+    print('Building with coverage for Cython code')
+COMPILER_DIRECTIVES = {'linetrace': CYTHON_COVERAGE}
+DEFINE_MACROS = [('CYTHON_TRACE_NOGIL', CYTHON_TRACE_NOGIL)]
 
 
 exts = dict(
@@ -268,14 +281,14 @@ def process_tempita(source_name):
 ##############################################################################
 package_data = defaultdict(list)
 filetypes = ['*.csv', '*.txt', '*.dta']
-for root, dirnames, filenames in os.walk(pjoin(os.getcwd(), 'statsmodels', 'datasets')):  # noqa: E501
+for root, _, filenames in os.walk(pjoin(os.getcwd(), 'statsmodels', 'datasets')):  # noqa: E501
     matches = []
     for filetype in filetypes:
         for filename in fnmatch.filter(filenames, filetype):
             matches.append(filename)
     if matches:
         package_data['.'.join(relpath(root).split(os.path.sep))] = filetypes
-for root, dirnames, filenames in os.walk(pjoin(os.getcwd(), 'statsmodels')):
+for root, _, _ in os.walk(pjoin(os.getcwd(), 'statsmodels')):
     if root.endswith('results'):
         package_data['.'.join(relpath(root).split(os.path.sep))] = filetypes
 

tools/ci/travis_conda.sh

@@ -12,7 +12,7 @@ PKGS="${PKGS} patsy"; if [ ${PATSY} ]; then PKGS="${PKGS}=${PATSY}"; fi
 PKGS="${PKGS} pandas"; if [ ${PANDAS} ]; then PKGS="${PKGS}=${PANDAS}"; fi
 PKGS="${PKGS} Cython"; if [ ${CYTHON} ]; then PKGS="${PKGS}=${CYTHON}"; fi
 if [ ${USEMPL} = true ]; then PKGS="${PKGS} matplotlib"; if [ ${MATPLOTLIB} ]; then PKGS="${PKGS}=${MATPLOTLIB}"; fi; fi
-if [ ${COVERAGE} = true ]; then export COVERAGE_OPTS=" --cov-config=.travis_coveragerc --cov=statsmodels "; else export COVERAGE_OPTS=""; fi
+if [ ${COVERAGE} = true ]; then export COVERAGE_OPTS=" --cov-config=.coveragerc_travis --cov=statsmodels "; else export COVERAGE_OPTS=""; fi
 echo conda create --yes --quiet -n statsmodels-test python=${PYTHON} ${BLAS} ${PKGS} ${OPTIONAL} ${DEPEND_ALWAYS}
 conda create --yes --quiet -n statsmodels-test python=${PYTHON} ${BLAS} ${PKGS} ${OPTIONAL} ${DEPEND_ALWAYS}
 source activate statsmodels-test

tools/coveragerc/.coveragerc_cython

@@ -0,0 +1,56 @@
+[run]
+source = statsmodels
+branch = True
+plugins = Cython.Coverage
+
+omit =
+    # print_version is untestable
+    */print_version.py
+    # skip compatibility code
+    */compat/*
+    # Unused file
+    */results/gee_generate_tests.py
+    # Results for tests
+    */tests/results/*
+    # Simulation checks
+    */tests/*_simulation_check.py
+    # Misc non-test files in test directories
+    */tests/_*
+    */tests/e*
+    */tests/c*
+    */tests/d*
+    */tests/g*
+    */tests/m*
+    */tests/p*
+    */tests/r*
+    */tests/s*
+    # Versioneer
+    */_version.py
+
+[report]
+show_missing = True
+
+ignore_errors = True
+
+# Regexes for lines to exclude from consideration
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code:
+    def __repr__
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+    except NotImplementedError
+    # Ignore pass
+    pass
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:
+
+[html]
+directory = cython_coverage_report

.travis_coveragerc renamed to tools/coveragerc/.coveragerc_travis

@@ -1,12 +1,11 @@
 [run]
+source = statsmodels
 branch = True
-include =
-    */statsmodels/*
 
 omit =
     # print_version is untestable
     */print_version.py
-    # skip compatability code
+    # skip compatibility code
     */compat/*
     # Unused file
     */results/gee_generate_tests.py
@@ -27,8 +26,11 @@ omit =
     # Versioneer
     */_version.py
 
-
 [report]
+show_missing = True
+
+ignore_errors = True
+
 # Regexes for lines to exclude from consideration
 exclude_lines =
     # Have to re-enable the standard pragma
@@ -41,8 +43,11 @@ exclude_lines =
     # Don't complain if tests don't hit defensive assertion code:
     raise AssertionError
     raise NotImplementedError
+    except NotImplementedError
+
+    # Ignore pass
+    pass
 
     # Don't complain if non-runnable code isn't run:
     if 0:
     if __name__ == .__main__.:
-    if name == .__main__.:

tox.ini

@@ -0,0 +1,68 @@
+##############################################################################
+# Intended to simplify local generation of coverage of Cython files
+#
+# tox -e cython-coverage
+#
+# will produce a HTML report showing line-by-line coverage
+#
+# can be used to run standard tests on Python 2.7, 3.5, 3.6, and 3.7 or a
+# run with coverage but without coverage of Cython files using
+#
+# tox -e ENV
+#
+# where env is one of the values in envlist or all environments (slow)
+#
+# tox
+#
+##############################################################################
+[tox]
+envlist = 
+    py27
+    py35
+    py36
+    py37
+    coverage
+    cython-coverage
+
+[testenv]
+deps =
+    -rrequirements.txt
+    cython
+    matplotlib
+    joblib
+    pytest>=3
+    pytest-xdist
+setenv =
+    MKL_NUM_THREADS=1
+    NUMEXPR_NUM_THREADS=1
+    OMP_NUM_THREADS=1
+    OPENBLAS_NUM_THREADS=1
+changedir = {homedir}
+commands =
+    python -c "import statsmodels;statsmodels.test(['-n 2'], exit=True)"
+
+[testenv:coverage]
+usedevelop = True
+deps =
+    {[testenv]deps}
+    pytest-cov
+setenv =
+    {[testenv]setenv}
+    SM_CYTHON_COVERAGE=false
+changedir = {toxinidir}
+commands =
+    coverage erase
+    pytest -n 2 --cov-config .coveragerc --cov-report html --cov=statsmodels statsmodels
+
+[testenv:cython-coverage]
+usedevelop = True
+deps =
+    {[testenv]deps}
+    pytest-cov
+setenv =
+    {[testenv]setenv}
+    SM_CYTHON_COVERAGE=true
+changedir = {toxinidir}
+commands =
+    coverage erase
+    pytest -n 2 --cov-config tools/coveragerc/.coveragerc_cython --cov-report html --cov=statsmodels statsmodels