MAINT: move coverage config to setup.cfg (#1481)

* MAINT: move coverage config to setup.cfg

* TST: improve list of excludes from coverage

* Exclude defs and such from coverage

* Remove defs, clas and triple quotes from coverage excludes

* Remove decorators, add entry points to coverage skip

* Run coverage manually to improve reported coverage

* Check if failing tests still make CI fail

* Make failing tests fail CI again, remove pytest-pep8 and pytest-cov

* Remove test failure

.travis.yml

@@ -53,7 +53,7 @@ install:
     - conda create -n testenv python=$TRAVIS_PYTHON_VERSION nomkl
     - source activate testenv
     # Install packages with pip if possible, it's way faster
-    - pip install "numpy==$NUMPY_VERSION" scipy future packaging scikit-image pywavelets pytest pytest-cov;
+    - pip install "numpy==$NUMPY_VERSION" scipy future packaging scikit-image pywavelets;
     # Building pyfftw wheels sometimes fails, using a conda-forge version instead;
     # To avoid a lower version of NumPy being installed over the pip one, we exclude all dependencies
     # (PyFFTW only depends on NumPy)
@@ -72,8 +72,9 @@ script:
     # Also invoke the alternative way of running the unit tests.
     # Fail immediately after first failure to speed up the whole thing.
     - if [[ "$SKIP_TESTS" != "true" ]]; then
-        pytest --doctest-modules --cov --cov-report term-missing $TRAVIS_BUILD_DIR/odl || exit -1;
-        python -c "import odl; odl.test()" || exit -1;
+        pytest --doctest-modules $TRAVIS_BUILD_DIR/odl || exit -1;
+        echo "import odl; odl.test(['--doctest-modules'])" > $TRAVIS_BUILD_DIR/_run_tests.py;
+        coverage run $TRAVIS_BUILD_DIR/_run_tests.py;
       fi
     # Build the Sphinx doc (only for one specific build, master branch, no PR)
     # To avoid clogging the logs, we redirect stderr to /dev/null

odl/util/testutils.py

@@ -675,7 +675,7 @@ def test(arguments=None):
     this_dir = os.path.dirname(__file__)
     odl_root = os.path.abspath(os.path.join(this_dir, os.pardir, os.pardir))
 
-    args = ['-x', '{root}/odl'.format(root=odl_root)]
+    args = ['{root}/odl'.format(root=odl_root)]
 
     ignores = ['--ignore={}'.format(file) for file in collect_ignore]
     args.extend(ignores)

setup.cfg

@@ -12,6 +12,7 @@ url = https://github.com/odlgroup/odl
 download_url = https://github.com/odlgroup/odl/archive/master.zip
 platforms = any
 keywords = research, development, mathematics, prototyping, imaging, tomography
+# See https://pypi.org/classifiers/
 classifiers =
     Development Status :: 4 - Beta
     Intended Audience :: Developers
@@ -44,8 +45,6 @@ install_requires =
 python_requires = >=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*
 tests_require =
     pytest >=3.0.3
-    pytest-pep8
-    pytest-cov
     coverage >=4.0
     coveralls
 include_package_data = True
@@ -61,14 +60,10 @@ tests = odl/test, odl/pytest.ini
 [options.extras_require]
 testing =
     pytest >=3.0.3
-    pytest-pep8
-    pytest-cov
     coverage >=4.0
     coveralls
 all =
     pytest >=3.0.3
-    pytest-pep8
-    pytest-cov
     coverage >=4.0
     coveralls
     matplotlib
@@ -111,3 +106,48 @@ max-line-length = 79
 exclude =
     .git
     __pycache__
+
+[coverage:run]
+branch = False
+include =
+    odl/*
+omit =
+    */__init__.py
+    odl/test/*
+    odl/diagnostics/*
+    odl/space/entry_points.py
+    odl/util/graphics.py
+    odl/util/npy_compat.py
+    odl/util/pytest_config.py
+    odl/util/testutils.py
+
+    # Omit until we add ASTRA to our CI pipelines
+    odl/tomo/operators/ray_trafo.py
+    odl/tomo/backends/*
+
+[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:
+    assert False
+    raise AssertionError
+    raise NotImplementedError
+    return NotImplemented
+
+    # Skip imports and __all__
+    import *
+    __all__
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if False:
+    if __name__ == '__main__':
+
+ignore_errors = True
+
+[coverage:html]
+directory = htmlcov
+