Port topology module #1420

utkbansal · 2017-06-21T19:10:25Z

Fixes #

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Tests?
Docs?
CHANGELOG updated?
Issue raised/referenced?

utkbansal · 2017-06-22T19:30:14Z

This should hopefully get coverage back to normal.

utkbansal · 2017-06-22T21:55:57Z

@richardjgowers @kain88-de Minor increase in coverage! A review would be helpful.

kain88-de · 2017-06-23T07:19:07Z

@jbarnoud & @mnmelo can you have a look I don't have time currently.

jbarnoud

Style is much better than in the PR on utils. Just one file where the imports are reordered.

I did not notice any tests that are missing, but I figured out why I had test that appeared discovered in pytest but not in nose: while we generally avoided docstring in tests to have a readable log in nose, we still have some. Nose does display the docstring instead of the test name in the verbose view; pytest doesn't. It means that it is difficult to accurately compare the two logs, but also that we will be able to have docstrings in tests. Yeah!

jbarnoud · 2017-06-23T08:56:08Z

testsuite/MDAnalysisTests/topology/test_mmtf.py

@@ -1,19 +1,22 @@
 from __future__ import absolute_import
-from numpy.testing import (


Please, fix the import order.

jbarnoud · 2017-06-23T08:58:24Z

testsuite/MDAnalysisTests/topology/test_tprparser.py

@@ -63,42 +66,81 @@ class TPRBase(TPRAttrs):
 # All these classes should be generated in a loop. Yet, nose test generation
 # seems to work only with functions, and not with classes.
 class TestTPR400(TPRBase):
+
+    __test__ = True


This all file will be much better with fixtures. Not for this PR, but this test suite will really profits from the move to pytest.

utkbansal · 2017-06-23T13:06:29Z

@jbarnoud @richardjgowers This should be ready to merge now.

utkbansal · 2017-06-23T14:08:58Z

Apparently, the hostname "dropbox.com" cannot be resolved during the full build.

kain88-de · 2017-06-23T14:48:33Z

Apparently, the hostname "dropbox.com" cannot be resolved during the full build.

We need more information. This message alone doesn't give me much when the build is restarted. When did it try to access dropbox would be valuable information for example.

jbarnoud · 2017-06-23T14:51:15Z

On 06/23/2017 04:48 PM, Max Linke wrote: Apparently, the hostname "dropbox.com" cannot be resolved during the full build. We need more information. This message alone doesn't give me much when the build is restarted. When did it try to access dropbox would be valuable information for example. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1420 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABUWuiSOGsbEOOPvKDxoUFXyDX9YTqemks5sG9BCgaJpZM4OBZLH>.

I did restart the job. Hole is downloaded from dropbox apparently. This time, dropbox.com could not be resolved. It seams to be just a transient error, the install phase is done now which means that dropox was found.

utkbansal · 2017-06-23T14:51:23Z

if [[ $NAME == 'full' ]]; then \
      bash ./maintainer/install_hole.sh $TRAVIS_OS_NAME "${HOME}/${MDA_OPTPACKAGES}"; \
      HOLE_BINDIR="${HOME}/${MDA_OPTPACKAGES}/hole2/exe"; \
      export PATH=${PATH}:${HOLE_BINDIR}; \
  fi
  
Downloading hole2-NotForProfit-2.2.004-Linux-x86_64.tar.gz from https://www.dropbox.com/s/jukpwlohhi20r17/hole2-NotForProfit-2.2.004-Linux-x86_64.tar.gz?dl=1...
curl: (6) Couldn't resolve host 'www.dropbox.com'
[install_hole.sh] ERROR: Failed to download hole2-NotForProfit-2.2.004-Linux-x86_64.tar.gz from https://www.dropbox.com/s/jukpwlohhi20r17/hole2-NotForProfit-2.2.004-Linux-x86_64.tar.gz?dl=1 [1]

It tries to download some hole dependency from dropbox and that is a part of the ci-helpers we are using.

jbarnoud · 2017-06-23T15:29:27Z

@kain88-de @richardjgowers Can I merge, or should I wait for 0.16.2 to be released?

richardjgowers · 2017-06-23T15:43:57Z

@jbarnoud yeah tests aren't user facing, so we can merge this

richardjgowers · 2017-06-23T15:45:30Z

@jbarnoud I take that back, maybe we're not doing pytest in 16.2... #1401

orbeckst · 2017-06-24T01:08:06Z

#1420 (comment)

It tries to download some hole dependency from dropbox and that is a part of the ci-helpers we are using.

Just some background: hole is not part of the ci-helpers. It is an external software that we use for the MDAnalysis.analysis.hole module. In order to test the module, we need to install the software. The license of hole is very unfriendly so the only legal approach (as far as we could figure out) is to always download it from the official site, which happens to be a dropbox location...

Or at least that was the story until 2 minutes ago when I figured out that hole is now open source: https://github.com/osmart/hole2 ... so I think we will soon have conda packages. ;-) #1429

richardjgowers · 2017-06-25T11:04:13Z

@utkbansal So this PR didn't actually add topology to the pytest list in travis.yml 😆

utkbansal · 2017-06-25T11:08:49Z

Oh man! Rebasing and stuff can be very confusing if you have 4 PRs in parallel. 😆

richardjgowers · 2017-06-25T11:09:22Z

Put it in the xdist pr

jbarnoud · 2017-06-25T11:13:24Z

On 06/25/2017 01:09 PM, Richard Gowers wrote: Put it in the xdist pr — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1420 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABUWukmyOaDP_1CI1hqmEbk3_rapJM3Hks5sHj_jgaJpZM4OBZLH>.

Just to reiterate a previous suggestion: having a file that list the modules for nose and an other file that lists the modules for pytest would reduce the need for rebasing. One problem we currently have is that every PR from Utkarsh change the same two lines in .travis.yml. Having the lists in separate files would hopefully reduce the conflicts.

utkbansal · 2017-06-25T11:14:52Z

@jbarnoud Makes more sense now!

utkbansal added 2 commits June 22, 2017 00:35

Port topology to pytest

ba05619

Add __test__ attributes and get rid of static methods

1f64af4

orbeckst added testing Continuous Integration and removed Continuous Integration labels Jun 22, 2017

jbarnoud requested changes Jun 23, 2017

View reviewed changes

Fix imports

92cfc72

Import TestCase

e400486

richardjgowers assigned jbarnoud Jun 23, 2017

jbarnoud approved these changes Jun 23, 2017

View reviewed changes

richardjgowers merged commit c27ace3 into MDAnalysis:develop Jun 24, 2017

Port topology module #1420

Port topology module #1420

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utkbansal commented Jun 25, 2017

		@@ -1,19 +1,22 @@
		from __future__ import absolute_import
		from numpy.testing import (

Port topology module #1420

Port topology module #1420

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utkbansal commented Jun 21, 2017

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