Correcting coverage calculations (#310)

* remove unnecessary files

* remove builddist

* remove py37 from test.yml

* simplify setup.py

* remove unused passenv in tox

* move tests out of package

* update Makefile

* update Makefile remove old nosetest commands

* delete .codeclimate.yml

* stay with the old versioneer

* update .gitignore

* update make clean paths after moving tests out

* Correctly calculating the coverage

* add back bdist_wheel to setup.cfg

* Revert "add back bdist_wheel to setup.cfg"

This reverts commit 37da209.

* add back docs to test.yml

* tox fix envdir

* tox pytest add -sx flags

* use coverage instead of pytest-cov

* revert envdir

* revert deps

* revert pytest

* add usedevelop=True

* use pytest-cov back again

* upload coverage only once

* remove py37 from gh actions

* report cpp coverage as well as python

* performance: separate coverage tox environment

* performance pytest-xdist for test tox env

* separate coverage ci action

removed unnecessary if check in coverage yaml

switch  to codecov-action@v3

add .codecov.yml with branch coverage gcov

add --branches flag to gcovr

branch detection: no codecov.yml

gcovr treat pratials as hits

gcov to give txt output

delete .codecov.yml

mention txt format gcovr

try json format for gcovr

gcovr output -> xml

* rename Python coverage-> coverage since we add c++ as well

* update test.yml comment for clarity

.github/workflows/build.yml

@@ -55,7 +55,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-20.04, macos-latest, windows-latest]
-        python: [cp37, cp38, cp39, cp310, cp311]
+        python: [cp38, cp39, cp310, cp311]
         arch: [x86_64, amd64]
         exclude:
           - os: macos-latest

.github/workflows/test.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v2
@@ -26,10 +26,32 @@ jobs:
         pip install tox tox-gh-actions
 
     - name: Run tox
-      run: tox
+      run: tox  # this does not call docs
+
+  coverage:
+    runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        pip install tox tox-gh-actions
+
+    - name: Run tox coverage
+      run: tox -e coverage  # specify the coverage environment
 
     - name: "Upload coverage to Codecov"
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v3
       with:
         fail_ci_if_error: false
   docs:

.gitignore

@@ -12,10 +12,12 @@
 .vscode
 *.so
 coverage.xml
+cpp_coverage.xml
 docs/bin
 docs/lib
 docs/source/lib
 bin
 *.tox-info.json
 *.ipynb_checkpoints
 lib
+fllog.txt

Makefile

@@ -1,5 +1,3 @@
-TEST_REQUIREMENTS=nose coverage virtualenv
-
 all: install
 install: clean
 	python setup.py sdist
@@ -25,27 +23,20 @@ doc_upload: doc
 	git commit -m "Updating docs" && \
 	git push "git@github.com:BlueBrain/eFEL.git" master:gh-pages --force && \
 	rm -rf .git
-install_test_requirements:
-	pip install -q $(TEST_REQUIREMENTS) --upgrade
 update_version:
 	cd efel && \
 	python -c 'import version; version._get_version_number()' && \
 	git add GITHASH.txt && \
 	git add VERSION.txt && \
 	git commit -m 'Updated version number'
-test: virtualenv install install_test_requirements
-	cd efel/tests; nosetests -s -v -x --with-coverage --cover-xml \
-	   --cover-package efel 
-debugtest: virtualenv install install_test_requirements
-	cd efel/tests; nosetests -a debugtest -s -v -x --with-coverage --cover-xml \
-	   --cover-package efel 
 pypi: test
 	pip install twine --upgrade
 	rm -rf dist
 	python setup.py sdist bdist
 	twine upload dist/*
 clean:
-	rm -rf efel/tests/log/fllog.txt
+	rm -f tests/log/fllog.txt
+	rm -f fllog.txt
 	rm -rf build_cmake
 	rm -rf build
 	rm -rf docs/build

efel/__init__.py

@@ -23,6 +23,5 @@
 from efel.api import *
 import efel.io
 
-from ._version import get_versions
-__version__ = get_versions()['version']
-del get_versions
+from . import _version
+__version__ = _version.get_versions()['version']

pyproject.toml

@@ -0,0 +1,10 @@
+[tool.coverage.run]
+omit = [
+    "efel/_version.py"
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "raise NotImplementedError"
+]

setup.cfg

@@ -10,7 +10,3 @@ versionfile_source = efel/_version.py
 versionfile_build = efel/_version.py
 tag_prefix = 
 parentdir_prefix =
-
-# Package support both python 2.6 and 2.7
-[bdist_wheel]
-universal = 1

setup.py

@@ -1,7 +1,5 @@
 """ eFEL setup """
 
-# pylint: disable=C0325
-
 """
 Copyright (c) 2015, EPFL/Blue Brain Project
 
@@ -21,10 +19,8 @@
  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 """
 
-try:
-    from setuptools import setup, Extension
-except ImportError:
-    from distutils.core import setup, Extension  # pylint: disable=E0611,F0401
+
+from setuptools import setup, Extension
 
 import os
 import versioneer
@@ -67,14 +63,22 @@
         'cppcore',
         filename) for filename in cppcore_headers]
 
+
+coverage_flags = []
+if os.environ.get('EFEL_COVERAGE_BUILD'):
+    coverage_flags = ['-fprofile-arcs', '-ftest-coverage']
+
 cppcore = Extension('efel.cppcore',
                     sources=cppcore_sources,
-                    include_dirs=['efel/cppcore/'])
+                    include_dirs=['efel/cppcore/'],
+                    extra_compile_args=coverage_flags,
+                    extra_link_args=coverage_flags)
+
 setup(
     name="efel",
     version=versioneer.get_version(),
     cmdclass=versioneer.get_cmdclass(),
-    install_requires=['numpy>=1.6', 'six'],
+    install_requires=['numpy>=1.6'],
     extras_require={'neo': ['neo[neomatlabio]>=0.5.1']},
     packages=['efel', 'efel.pyfeatures', 'efel.units'],
     author="BlueBrain Project, EPFL",
@@ -90,11 +94,11 @@
     "features to be calculated. The library will then extract the requested "
     "features and return the values to the user.",
     license="LGPLv3",
-    keywords=(
+    keywords=[
         'feature',
         'extraction',
         'electrophysiology',
-        'BlueBrainProject'),
+        'BlueBrainProject'],
     url='https://github.com/BlueBrain/eFEL',
     classifiers=[
         'Development Status :: 4 - Beta',
@@ -108,8 +112,6 @@
         'Topic :: Utilities'],
     package_data={
         '': ['DependencyV5.txt',
-             'VERSION.txt',
              'README.md',
-             'GITHASH.txt',
              'units/units.json'] + cppcore_headers},
     ext_modules=[cppcore])

tox.ini

@@ -1,34 +1,52 @@
 [tox]
-envlist = docs,py3-{style,test}
+envlist = docs,py3-{test}
 minversion = 4
 [gh-actions]
 python =
-    3.7: py3
     3.8: py3
     3.9: py3
     3.10: py3
     3.11: py3
+
+
 [testenv]
-envdir =
-    py3{7,8,9,10,11,}{,-style,-test}: {toxworkdir}/py3
+envdir = {toxworkdir}/py3-test
 deps =
-    pytest
-    pytest-cov
-    coverage
-    scipy
-    style: pycodestyle
+    pytest>=7.3.1
+    scipy>=1.10.1
+    pycodestyle>=2.11.0
+    pytest-xdist>=3.3.1
+extras =
+    neo
+usedevelop=True
+commands =
+    pycodestyle --ignore=E402,W503,W504 efel tests
+    pytest -sx -n auto tests
+
+
+[testenv:coverage]
+envdir = {toxworkdir}/py3-coverage
+setenv =
+    EFEL_COVERAGE_BUILD = 1
+deps =
+    pytest>=7.3.1
+    scipy>=1.10.1
+    pytest-cov>=4.1.0
+    coverage>=7.3.0
+    gcovr
 allowlist_externals =
     make
-    find
+    rm
 extras =
     neo
-passenv = https_proxy
+usedevelop=True
 commands =
     make clean
-
-    style: pycodestyle --ignore=E402,W503,W504 efel
-
-    test: pytest -sx --cov=efel --cov-report=xml efel/tests
+    python setup.py build_ext --inplace
+    pytest -sx --cov=efel --cov=tests --cov-report=xml tests
+    gcovr --print-summary -r . --xml -o cpp_coverage.xml
+    rm -f ./*.gcov
+    coverage report -m
 
 
 [testenv:docs]