Port lib/test_util.py to pytest by utkbansal · Pull Request #1413 · MDAnalysis/mdanalysis

utkbansal · 2017-06-20T17:09:44Z

Fixes partially #884

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Tests?
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CHANGELOG updated?
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utkbansal · 2017-06-20T17:25:49Z

Looks like the original coverage.py package was developed by Ned Batchelder and cover-package used with nose and pytest-cov used with pytest are just wrappers around it. I'm guessing they will merge just fine.

orbeckst · 2017-06-20T17:45:53Z

testsuite/MDAnalysisTests/lib/test_util.py

 #
 from __future__ import absolute_import, division

+from unittest import TestCase


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.)

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

utkbansal · 2017-06-20T18:25:12Z

Why us Travis complaining /home/travis/.travis/job_stages: line 54: pytest: command not found ??

ci-helpers clearly state that pytest is already installed.

kain88-de · 2017-06-20T18:28:54Z

.travis.yml

    - 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"
    # Install griddataformats from PIP so that scipy is only installed in the full build (#1147)
-    - PIP_DEPENDENCIES='griddataformats'
+    - PIP_DEPENDENCIES='griddataformats pytest pytest-cov'


please add them do conda. They are both available on the conda-forge channel. This might also be messing up your pytest installation. But I'm not sure about that.

I would still prefer pytest as a conda dependency.

@kain88-de Should I add them to CONDA _DEPENDENCIES or CONDA_ALL_DEPENDENCIES?

you need to add them to both. We can check in another PR why they aren't installed automatically.

kain88-de · 2017-06-20T18:32:09Z

testsuite/MDAnalysisTests/lib/test_util.py



-class TestFilename(object):
+class TestFilename(TestCase):


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.

No, I'm using it because only classes that inherit from TestCase get their setUp and tearDown methods executed.

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

utkbansal · 2017-06-20T18:41:27Z

I have flipped the MAIN_CMD command so that pytest is executed first - this will just make my life easier and shouldn't change anything.

kain88-de · 2017-06-20T18:52:39Z

@utkbansal if you could remove the yield based test that would be great. They do generate quite a lot of noise in the output.

utkbansal · 2017-06-20T18:55:03Z

We have a lot of yield based tests all over the code, I can suppress the warning for now - if that is fine. Getting rid of them and using parameterize would need significant efforts(I guess) and was planned to be done in part 2.

kain88-de · 2017-06-20T18:59:10Z

Suppressing the warnings for now is fine.

utkbansal · 2017-06-21T07:58:05Z

Wohoo! Coverage increased! 😬

jbarnoud · 2017-06-21T08:37:38Z

And the full test build is passing (likely by chance, but still!).

kain88-de · 2017-06-21T09:18:44Z

.travis.yml

-    - 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"


why the version pinning?

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.

should be able to do conda upgrade pytest?

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

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.

utkbansal · 2017-06-21T10:55:09Z

Should be ready to merge, only the full build times out. We might not need the full build to succeed for the last commit as it was only shifting requirements from pip to conda and the commit previous to this verifies that coverage works and has not dropped.

richardjgowers · 2017-06-21T11:10:22Z

@utkbansal awesome, one module down! Can you try and get the unfinished coordinates port PR up ASAP so we can see what changes are required.

utkbansal added 2 commits June 20, 2017 22:36

Inital attempt to port lib/test_util.py

b88dc82

Add pytest to travis

46e2a0c

Merge nose & pytest coverage data

6d8816d

orbeckst reviewed Jun 20, 2017

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Add pytest as a pip dependency

9798e7a

utkbansal added 2 commits June 20, 2017 23:56

Force install & upgrade pytest

1140018

Execute the pytest suite first

8ed78d0

kain88-de reviewed Jun 20, 2017

View reviewed changes

Add full path to the lib module

6437b95

utkbansal added 2 commits June 21, 2017 00:34

Suppress pytest warnings

c3cc804

Fix coverage file variable names

d8a7ba9

Convert pytest & pytest-cov to conda dependencies.

a345f00

kain88-de reviewed Jun 21, 2017

View reviewed changes

richardjgowers added the testing label Jun 21, 2017

richardjgowers approved these changes Jun 21, 2017

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richardjgowers merged commit fba80e2 into MDAnalysis:develop Jun 21, 2017

richardjgowers self-assigned this Jun 21, 2017

mnmelo mentioned this pull request Jun 21, 2017

WIP: Adds support for lazy and optional importing of dependencies #1415

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