Dropping nose as a dependency #1480

utkbansal · 2017-07-13T15:38:21Z

Fixes #884

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

kain88-de

nose also has to be removed from setup.py our nose wrapper script should be removed. Also grep and look through the repository if we mention nose anywhere else and should replace it with pytest.

utkbansal · 2017-07-13T20:36:19Z

@kain88-de We've got from nose.plugins.attrib import attr all over the tests. Can't go ahead with this until I get rid of all attr. Should that be done in this PR or a separate one?

kain88-de · 2017-07-13T20:39:36Z

you can remove attr in this PR. It doesn't do anything special

jbarnoud · 2017-07-14T09:40:04Z

Since you're at it, you can update testsuite/CHANGELOG.

richardjgowers · 2017-07-14T10:08:06Z

This would officially fix #884!

kain88-de · 2017-07-14T11:29:49Z

.travis.yml

-           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}'
+           MAIN_CMD='pytest testsuite/MDAnalysisTests/ ${PYTEST_FLAGS} --cov=MDAnalysis'


can't you just update the PYTEST_FLAGS variable here instead of rewriting MAIN_CMD?

kain88-de

the setup.py changes are still missing

kain88-de · 2017-07-14T14:22:11Z

testsuite/MDAnalysisTests/__init__.py

@@ -150,28 +147,4 @@
    in_dir,
    assert_nowarns,
 )
-from MDAnalysisTests.core.util import make_Universe
-
-def run(*args, **kwargs):


it would be nice if you could keep this method. This is shown in our docs how to run the tests yourself from an installation of MDAnalysisTests

So this will then be deleted when we do the next release?

@kain88-de This function has calls to loaded_plugins which comes from from MDAnalysisTests.plugins which in turn depend upon nose. What should I do?

modify this function so that I can still to MDAnalysisTests.run() in an interpreter. This should start the pytest tests. I don't really care how the function is doing that. But it has to be rewritten.

So basically, I'm writing a wrapper to run pytest via this run method?

utkbansal · 2017-07-14T14:23:54Z

@kain88-de @richardjgowers @jbarnoud Is the maintainer/run_tests.sh file obsolete? Should I drop the file?

kain88-de · 2017-07-14T14:25:06Z

sure remove that as well. No one of us uses it anymore.

jbarnoud · 2017-07-14T14:44:26Z

Have a look at how to run pytest from within python.

kain88-de

testsuite/INSTALL and package/MDAnalysis/tests/init.py also contain comments about nose. Please update and replace them with appropriate pytest information if applicable.

kain88-de · 2017-07-14T14:55:30Z

testsuite/MDAnalysisTests/__init__.py

@@ -114,6 +114,9 @@
 """
 from __future__ import absolute_import
 import logging
+
+import pytest
+


there are still a lot of nose comments in this file

@kain88-de Do I have to update all the comments involving nose in all the files?

Yes please. There is no sense in having them. Only a few might be useful.

kain88-de · 2017-07-14T14:56:03Z

testsuite/MDAnalysisTests/__init__.py

+
+def run(*args, **kwargs):
+    pytest.main()


did you test this?

It's still running. Everything fine till now.

Do I have to update all comments related to nose in all files?

@kain88-de Confirmed, it works.

orbeckst · 2017-07-14T15:51:10Z

We also need new instructions for the wiki #1489.

kain88-de · 2017-07-15T10:40:21Z

package/MDAnalysis/tests/__init__.py

@@ -92,16 +92,14 @@
 Writing test cases
 ==================

-The unittests use the :mod:`unittest` module together with nose_. See the
+The unittests use the :mod:`pytest` module. See the


This should be pytest_ so that it links in the docs.

@kain88-de :mod:pytest_ ??

with out the mod sphinx likely wouldn't link to the right page

kain88-de

test_streamio and test_trpparser still contain comments about nose.

kain88-de · 2017-07-16T17:06:33Z

@utkbansal I'd appreciate if you prioritize this PR

utkbansal · 2017-07-16T17:49:53Z

@kain88-de The test in test_streamio that has a comment on nose is a yield based test. I'd rather leave it there till I fix it properly.

utkbansal · 2017-07-16T17:51:34Z

@kain88-de Will this PR be squashed and merged or can I clean up the history?

Remove nose from dependencies & implement run method

kain88-de

minor clean up still do to. But good progress.

kain88-de · 2017-07-17T12:23:53Z

testsuite/INSTALL

@@ -84,9 +84,9 @@ From sources

 From the top directory of the checked out sources:

-  ./testsuite/MDAnalysisTests/mda_nosetests --exe -v --processes=4 --process-timeout=120 
+  pytest /testsuite/MDAnalysisTests/ -n=3


please add a note that the pytest-xdist package should be installed to run tests in parallel.

and use the new pytest.xdist variable numprocesses

kain88-de · 2017-07-17T12:23:53Z

testsuite/MDAnalysisTests/__init__.py

@@ -90,22 +67,13 @@
 Writing test cases
 ==================

-The unittests use the :mod:`unittest` module together with nose_. See the
+The unittests use the :mod:`pytest` module. See the


here we should also have a link

`pytest <https://docs.pytest.org/en/latest/>`_
This?

kain88-de · 2017-07-17T12:23:53Z

testsuite/MDAnalysisTests/core/test_topologyattrs.py

@@ -36,9 +36,7 @@
    assert_array_almost_equal,
    assert_raises,


can you remove this import as well. Seems like you already changed all occurrences of this

kain88-de · 2017-07-17T12:23:53Z

testsuite/setup.py

@@ -213,7 +213,7 @@ def dynamic_author_list():
          long_description=LONG_DESCRIPTION,
          install_requires=[
              'MDAnalysis=={0!s}'.format(RELEASE),  # same as this release!
-              'nose>=1.3.7',
+              'numpy>=1.10.4',


Please remove this line when you do the rebase. It's not there in develop right now.

@kain88-de Remove numpy?

yes it's already installed with MDAnalysis anyway.

Fix Install docs Update CHANGELOG Cleanup docs

utkbansal mentioned this pull request Jul 13, 2017

Port analysis module to pytest #1450

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utkbansal force-pushed the utkbansal:f-u-nose branch from c911ae2 to 0dd3309 Jul 14, 2017

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orbeckst mentioned this pull request Jul 14, 2017

update wiki with new test instructions #1489

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Get rid of @attr

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utkbansal force-pushed the utkbansal:f-u-nose branch from 94d1e5c to 97c5f98 Jul 16, 2017

Remove mda_nosetests and nose plugins

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Remove nose from dependencies & implement run method

utkbansal force-pushed the utkbansal:f-u-nose branch from 97c5f98 to a89b59d Jul 16, 2017

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Drop comments for running tests with nose

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Fix Install docs Update CHANGELOG Cleanup docs

utkbansal force-pushed the utkbansal:f-u-nose branch from a89b59d to 299a939 Jul 18, 2017

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MDAnalysis / mdanalysis

Dropping nose as a dependency #1480

Dropping nose as a dependency #1480

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utkbansal commented Jul 13, 2017 • edited by richardjgowers

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edited by richardjgowers

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