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Dropping nose as a dependency #1480

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merged 3 commits into from Jul 18, 2017

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utkbansal commented Jul 13, 2017 •
edited by richardjgowers

Fixes #884

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PR Checklist

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

@utkbansal utkbansal referenced this pull request Jul 13, 2017

Merged

Port analysis module to pytest #1450

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kain88-de requested changes Jul 13, 2017
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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.

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utkbansal commented Jul 13, 2017

@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?
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kain88-de commented Jul 13, 2017

you can remove attr in this PR. It doesn't do anything special
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jbarnoud commented Jul 14, 2017

Since you're at it, you can update testsuite/CHANGELOG.
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richardjgowers commented Jul 14, 2017

This would officially fix #884!
.travis.yml Outdated
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'

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can't you just update the PYTEST_FLAGS variable here instead of rewriting MAIN_CMD?
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the setup.py changes are still missing

testsuite/MDAnalysisTests/__init__.py Outdated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

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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

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

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utkbansal Jul 14, 2017 •
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@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?

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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.

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

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yes
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utkbansal commented Jul 14, 2017

@kain88-de @richardjgowers @jbarnoud Is the maintainer/run_tests.sh file obsolete? Should I drop the file?
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kain88-de commented Jul 14, 2017

sure remove that as well. No one of us uses it anymore.
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jbarnoud commented Jul 14, 2017

Have a look at how to run pytest from within python.
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testsuite/INSTALL and package/MDAnalysis/tests/init.py also contain comments about nose. Please update and replace them with appropriate pytest information if applicable.

testsuite/MDAnalysisTests/__init__.py
@@ -114,6 +114,9 @@
"""
from __future__ import absolute_import
import logging
import pytest

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there are still a lot of nose comments in this file

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

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Yes please. There is no sense in having them. Only a few might be useful.
testsuite/MDAnalysisTests/__init__.py Outdated
def run(*args, **kwargs):
pytest.main()

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did you test this?

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It's still running. Everything fine till now.

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

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@kain88-de Confirmed, it works.

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update wiki with new test instructions #1489

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orbeckst commented Jul 14, 2017

We also need new instructions for the wiki #1489.
package/MDAnalysis/tests/__init__.py Outdated
@@ -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

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

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@kain88-de :mod:pytest_ ??

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with out the mod sphinx likely wouldn't link to the right page
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kain88-de requested changes Jul 16, 2017
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test_streamio and test_trpparser still contain comments about nose.

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kain88-de commented Jul 16, 2017

@utkbansal I'd appreciate if you prioritize this PR
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utkbansal commented Jul 16, 2017

@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.
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utkbansal commented Jul 16, 2017

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

utkbansal added some commits Jul 14, 2017

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Get rid of @attr
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Remove mda_nosetests and nose plugins 
Remove nose from dependencies & implement run method
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kain88-de requested changes Jul 17, 2017
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minor clean up still do to. But good progress.

testsuite/INSTALL Outdated
@@ -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

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

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and use the new pytest.xdist variable numprocesses
testsuite/MDAnalysisTests/__init__.py Outdated
@@ -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

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here we should also have a link

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`pytest <https://docs.pytest.org/en/latest/>`_
This?
testsuite/MDAnalysisTests/core/test_topologyattrs.py Outdated
@@ -36,9 +36,7 @@
assert_array_almost_equal,
assert_raises,

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can you remove this import as well. Seems like you already changed all occurrences of this
testsuite/setup.py Outdated
@@ -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',

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

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@kain88-de Remove numpy?

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yes it's already installed with MDAnalysis anyway.
@utkbansal
Drop comments for running tests with nose 
Fix Install docs

Update CHANGELOG

Cleanup docs
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@kain88-de kain88-de merged commit 3dd9d3c into MDAnalysis:develop Jul 18, 2017
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