Replace Nosetests with Pytest as test runner (nilearn#419)

* Replace nosetests with pytest as test runner

* Replaced yield asserts with standard asserts (pytest unsupported)

* Replaced nilearn with nistats references

* Fixed: Makefile uses tabs not spaces

* Moved pytest-cov to always install so --cov option always works

* Skip testing reporting module when no matplotlib

* Skip testing reporting module when no matplotlib - 2

* Skip testing reporting module when no matplotlib - 3

Author: kchawla-pi

Makefile

@@ -4,7 +4,7 @@
 
 PYTHON ?= python
 CYTHON ?= cython
-NOSETESTS ?= nosetests
+TESTRUNNER ?= nosetests
 CTAGS ?= ctags
 
 all: clean test doc-plot pdf
@@ -29,16 +29,13 @@ inplace:
 	$(PYTHON) setup.py build_ext -i
 
 test-code:
-	$(NOSETESTS) -s nistats
+	python -m pytest --pyargs nistats --cov=nistats
 test-doc:
-	$(NOSETESTS) -s --with-doctest --doctest-tests --doctest-extension=rst \
-	--doctest-extension=inc --doctest-fixtures=_fixture doc/ \
-	
+	pytest --doctest-glob='*.rst' `find doc/ -name '*.rst'`
 
 test-coverage:
 	rm -rf coverage .coverage
-	$(NOSETESTS) -s --with-coverage --cover-html --cover-html-dir=coverage \
-	--cover-package=nistats nistats
+ 	pytest --pyargs nistats --showlocals --cov=nistats --cov-report=html:coverage
 
 test: test-code test-doc
 

continuous_integration/install.sh

@@ -22,7 +22,7 @@ create_new_venv() {
     deactivate
     virtualenv --system-site-packages testvenv
     source testvenv/bin/activate
-    pip install nose
+    pip install nose pytest pytest-cov
 }
 
 print_conda_requirements() {
@@ -33,7 +33,7 @@ print_conda_requirements() {
     # if yes which version to install. For example:
     #   - for numpy, NUMPY_VERSION is used
     #   - for scikit-learn, SCIKIT_LEARN_VERSION is used
-    TO_INSTALL_ALWAYS="pip nose libgfortran=3.0=0 nomkl"
+    TO_INSTALL_ALWAYS="pip nose pytest pytest-cov libgfortran=3.0=0 nomkl"
     REQUIREMENTS="$TO_INSTALL_ALWAYS"
     TO_INSTALL_MAYBE="python numpy scipy matplotlib scikit-learn pandas"
     for PACKAGE in $TO_INSTALL_MAYBE; do

nistats/conftest.py

@@ -0,0 +1,32 @@
+from distutils.version import LooseVersion
+
+import numpy as np
+import pytest
+from _pytest.doctest import DoctestItem
+
+try:
+    import matplotlib
+except ImportError:
+    collect_ignore = ['reporting',
+                      'tests/test_glm_reporter.py',
+                      'tests/test_reporting.py',
+                      'tests/test_sphinx_report.py',
+                      ]
+else:
+    matplotlib  # Prevents flake8 erring due to unused entities.
+
+
+def pytest_collection_modifyitems(items):
+    # numpy changed the str/repr formatting of numpy arrays in 1.14. We want to
+    # run doctests only for numpy >= 1.14.Adapted from scikit-learn
+    if LooseVersion(np.__version__) < LooseVersion('1.14'):
+        reason = 'doctests are only run for numpy >= 1.14'
+        skip_doctests = True
+    else:
+        skip_doctests = False
+
+    if skip_doctests:
+        skip_marker = pytest.mark.skip(reason=reason)
+        for item in items:
+            if isinstance(item, DoctestItem):
+                item.add_marker(skip_marker)

nistats/reporting/__init__.py

@@ -20,7 +20,7 @@
 from ._get_clusters_table import get_clusters_table
 from ._plot_matrices import plot_contrast_matrix, plot_design_matrix
 from .glm_reporter import make_glm_report
-from.sphinx_report import _ReportScraper
+from .sphinx_report import _ReportScraper
 
 __all__ = [compare_niimgs,
            get_clusters_table,

nistats/tests/test_utils.py

@@ -122,18 +122,18 @@ def test_pos_recipr():
     X = np.array([2, 1, -1, 0], dtype=np.int8)
     eX = np.array([0.5, 1, 0, 0])
     Y = positive_reciprocal(X)
-    yield assert_array_almost_equal, Y, eX
-    yield assert_equal, Y.dtype.type, np.float64
+    assert_array_almost_equal, Y, eX
+    assert_equal, Y.dtype.type, np.float64
     X2 = X.reshape((2, 2))
     Y2 = positive_reciprocal(X2)
-    yield assert_array_almost_equal, Y2, eX.reshape((2, 2))
+    assert_array_almost_equal, Y2, eX.reshape((2, 2))
     # check that lists have arrived
     XL = [0, 1, -1]
-    yield assert_array_almost_equal, positive_reciprocal(XL), [0, 1, 0]
+    assert_array_almost_equal, positive_reciprocal(XL), [0, 1, 0]
     # scalars
-    yield assert_equal, positive_reciprocal(-1), 0
-    yield assert_equal, positive_reciprocal(0), 0
-    yield assert_equal, positive_reciprocal(2), 0.5
+    assert_equal, positive_reciprocal(-1), 0
+    assert_equal, positive_reciprocal(0), 0
+    assert_equal, positive_reciprocal(2), 0.5
 
 
 def test_img_table_checks():

requirements-dev.txt

@@ -5,3 +5,5 @@ scipy
 scikit-learn
 pandas
 matplotlib
+pytest
+pytest-cov

setup.cfg

@@ -3,13 +3,11 @@
 [bdist_rpm]
 doc-files = doc
 
-[nosetests]
-verbosity = 2
-detailed-errors = 1
-with-coverage = 1
-cover-package = nistats
-#pdb = 1
-#pdb-failures = 1
-with-doctest=1
-doctest-extension=rst
-ignore-files=plot_.*.py
+[tool:pytest]
+doctest_optionflags = NORMALIZE_WHITESPACE ELLIPSIS
+junit_family = xunit2
+addopts =
+	--doctest-modules
+	-s
+	-vv
+	--durations=0