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Port lib/test_util.py to pytest #1413

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Merged
richardjgowers merged 10 commits into from
Jun 21, 2017
Merged

Port lib/test_util.py to pytest #1413

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b88dc82
Inital attempt to port lib/test_util.py
utkbansal Jun 20, 2017
46e2a0c
Add pytest to travis
utkbansal Jun 20, 2017
6d8816d
Merge nose & pytest coverage data
utkbansal Jun 20, 2017
9798e7a
Add pytest as a pip dependency
utkbansal Jun 20, 2017
1140018
Force install & upgrade pytest
utkbansal Jun 20, 2017
8ed78d0
Execute the pytest suite first
utkbansal Jun 20, 2017
6437b95
Add full path to the lib module
utkbansal Jun 20, 2017
c3cc804
Suppress pytest warnings
utkbansal Jun 20, 2017
d8a7ba9
Fix coverage file variable names
utkbansal Jun 21, 2017
a345f00
Convert pytest & pytest-cov to conda dependencies.
utkbansal Jun 21, 2017
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24 changes: 13 additions & 11 deletions .travis.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -23,15 +23,16 @@ env:
- PYTHON_VERSION=2.7
- COVERALLS=false
- NOSE_FLAGS="--processes=2 --process-timeout=400 --no-open-files --with-timer --timer-top-n 50"
- NOSE_TEST_LIST1="analysis auxiliary coordinates core formats topology utils"
- NOSE_TEST_LIST2="lib"
- NOSE_COVERAGE1="coverage1"
- NOSE_COVERAGE2="coverage2"
- MAIN_CMD="python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST1} ${NOSE_FLAGS}; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST2} ${NOSE_FLAGS}"
- NOSE_TEST_LIST="analysis auxiliary coordinates core formats topology utils"
- PYTEST_FLAGS="--disable-pytest-warnings"
- PYTEST_LIST="testsuite/MDAnalysisTests/lib"
- NOSE_COVERAGE_FILE="nose_coverage"
- PYTEST_COVERAGE_FILE="pytest_coverage"
- MAIN_CMD="pytest ${PYTEST_LIST} ${PYTEST_FLAGS}; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST} ${NOSE_FLAGS}"
- SETUP_CMD=""
- BUILD_CMD="pip install -v package/ && pip install testsuite/"
- CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer"
- CONDA_ALL_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib netcdf4 scikit-learn scipy seaborn coveralls clustalw=2.1"
- CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer pytest=3.1.2 pytest-cov=2.5.1"
- CONDA_ALL_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib netcdf4 scikit-learn scipy seaborn coveralls clustalw=2.1 pytest=3.1.2 pytest-cov=2.5.1"
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@kain88-de kain88-de Jun 21, 2017

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why the version pinning?

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@utkbansal utkbansal Jun 21, 2017 •
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Conda already says that it has pytest installed and still it did not work. Also, the version it has is 2.7, so there has been a major release after that.

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@richardjgowers richardjgowers Jun 21, 2017

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should be able to do conda upgrade pytest?

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@utkbansal utkbansal Jun 21, 2017

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@richardjgowers after the source ci-helpers/travis/setup_conda.sh step?

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@kain88-de kain88-de Jun 21, 2017

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the older version comes from astropy. They specifically install an older version of pytest for themselves. Leave the pinning for now. I'm asking what they use as a preferred way to use a newer pytest version.

# Install griddataformats from PIP so that scipy is only installed in the full build (#1147)
- PIP_DEPENDENCIES='griddataformats'
- CONDA_CHANNELS='biobuilds conda-forge'
Expand All @@ -47,7 +48,7 @@ matrix:
env: NAME='minimal'
PYTHON_VERSION=2.7
MEMLEAK='--with-memleak'
MAIN_CMD='python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST1} ${NOSE_FLAGS} ${MEMLEAK}; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST2} ${NOSE_FLAGS} ${MEMLEAK}'
MAIN_CMD='pytest ${PYTEST_LIST} ${PYTEST_FLAGS}; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST} ${NOSE_FLAGS} ${MEMLEAK}'

- os: linux
env: NAME="Doc"
Expand All @@ -66,8 +67,9 @@ matrix:

- os: linux
env: NAME='full'
COVERAGE='--with-coverage --cover-package MDAnalysis'
MAIN_CMD='export COVERAGE_FILE=$NOSE_COVERAGE1; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST1} ${NOSE_FLAGS} ${COVERAGE}; export COVERAGE_FILE=$NOSE_COVERAGE2; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST2} ${NOSE_FLAGS} ${COVERAGE}'
NOSE_COVERAGE='--with-coverage --cover-package MDAnalysis'
PYTEST_COVERAGE='--cov=MDAnalysis'
MAIN_CMD='export COVERAGE_FILE=$PYTEST_COVERAGE_FILE; pytest ${PYTEST_LIST} ${PYTEST_FLAGS} ${PYTEST_COVERAGE}; export COVERAGE_FILE=$NOSE_COVERAGE_FILE; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST} ${NOSE_FLAGS} ${NOSE_COVERAGE}'
CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES}
COVERALLS='true'

Expand Down Expand Up @@ -108,7 +110,7 @@ script:
after_success:
- |
if [[ $COVERALLS == 'true' ]]; then \
coverage combine $NOSE_COVERAGE1 $NOSE_COVERAGE2; \
coverage combine $NOSE_COVERAGE_FILE $PYTEST_COVERAGE_FILE; \
coveralls; \
fi
# can't use test here since this leads to travis fails even though the build passes
Expand Down
12 changes: 7 additions & 5 deletions testsuite/MDAnalysisTests/lib/test_util.py
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Expand Up @@ -21,6 +21,8 @@
#
from __future__ import absolute_import, division

from unittest import TestCase
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@orbeckst orbeckst Jun 20, 2017

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Is using unittest really necessary? I thought we can get rid of it. pytest supports setup_method()/teardown_method() (instead of setUp()) https://docs.pytest.org/en/2.7.3/xunit_setup.html

(I know that it also supports running UnitTest classes.)

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@utkbansal utkbansal Jun 20, 2017

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I missed that somehow! I'll read more about this and try to get rid of unittest. Thanks!


from six.moves import range, StringIO
import six

Expand Down Expand Up @@ -124,7 +126,7 @@ def test_strings(self):
assert_equal(util.iterable(u"unicode string"), False)


class TestFilename(object):
class TestFilename(TestCase):
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@kain88-de kain88-de Jun 20, 2017

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You are using TestCase here to make the test classes discoverable to pytest. This means this class isn't normally picked up by pytest. Please make sure the class has no init method. You can also run pytest with --collect-only to make sure all tests are picked up quickly.

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@utkbansal utkbansal Jun 20, 2017 •
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No, I'm using it because only classes that inherit from TestCase get their setUp and tearDown methods executed.

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@kain88-de kain88-de Jun 20, 2017

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So we need this for a swift conversion and then remove it one by one again later. check

def setUp(self):
self.root = "foo"
self.filename = "foo.psf"
Expand Down Expand Up @@ -161,7 +163,7 @@ def testNamedStream(self):
assert_equal(ns.name, self.filename2)


class TestGeometryFunctions(object):
class TestGeometryFunctions(TestCase):
def setUp(self):
self.e1 = np.array([1., 0, 0])
self.e2 = np.array([0, 1., 0])
Expand Down Expand Up @@ -230,7 +232,7 @@ def testDihedral(self):
cd = bc + self.e3
assert_almost_equal(mdamath.dihedral(ab, bc, cd), -np.pi / 2)

class TestMakeWhole(object):
class TestMakeWhole(TestCase):
"""Set up a simple system:

+-----------+
Expand Down Expand Up @@ -442,7 +444,7 @@ def _fill_cache(self, name, value):
self._cache[name] = value


class TestCachedDecorator(object):
class TestCachedDecorator(TestCase):
def setUp(self):
self.obj = Class_with_Caches()

Expand Down Expand Up @@ -895,7 +897,7 @@ def test_blocks_of_VE(self):
assert_raises(ValueError, util.blocks_of, arr, 2, 1)


class TestNamespace(object):
class TestNamespace(TestCase):
def setUp(self):
self.ns = util.Namespace()

Expand Down