Feature/package tests #451

mr-c · 2014-06-03T19:43:45Z

Work in progress

Includes the beginnings of a unification of the various custom C++ exception classes

mr-c · 2014-06-03T20:27:50Z

This will eventually address #220

mr-c · 2014-06-09T21:15:50Z

Works for me. After install run: nosetests khmer --attr '!known_failing'

mr-c · 2014-06-10T19:15:37Z

Is it mergable
Did it pass the tests?
N/A If it introduces new functionality in scripts/ is it tested?
Check for code coverage.
Is it well formatted? Look at pep8/pylint, cppcheck, and
make doc output. Use autopep8 and astyle -A10 --max-code-length=80
if needed.
Is it documented in the Changelog?
N/A Was spellcheck run on the source code and documentation after changes
were made?

mr-c · 2014-06-10T19:18:01Z

test this please

mr-c · 2014-06-10T19:30:19Z

Ready for review and merging @ctb @luizirber @camillescott

ctb · 2014-06-10T19:34:32Z

jenkins-build.sh

@@ -45,7 +45,8 @@ fi
 if type hg >/dev/null 2>&1
 then
 	rm -Rf sphinx-contrib
-	hg clone http://bitbucket.org/mcrusoe/sphinx-contrib
+	#hg clone http://bitbucket.org/mcrusoe/sphinx-contrib
+	hg clone http://athyra.ged.msu.edu/~mcrusoe/sphinx-contrib


Is this intentional?

Yes, many jobs have been dying due to bitbucket's lack of uptime.

On Tue, Jun 10, 2014 at 3:34 PM, C. Titus Brown notifications@github.com
wrote:

In jenkins-build.sh:

@@ -45,7 +45,8 @@ fi
if type hg >/dev/null 2>&1
then
rm -Rf sphinx-contrib

hg clone http://bitbucket.org/mcrusoe/sphinx-contrib

#hg clone http://bitbucket.org/mcrusoe/sphinx-contrib

hg clone http://athyra.ged.msu.edu/~mcrusoe/sphinx-contrib

Is this intentional?

—
Reply to this email directly or view it on GitHub
https://github.com/ged-lab/khmer/pull/451/files#r13614226.

On Tue, Jun 10, 2014 at 12:40:26PM -0700, Michael R. Crusoe wrote:

@@ -45,7 +45,8 @@ fi
if type hg >/dev/null 2>&1
then
rm -Rf sphinx-contrib

hg clone http://bitbucket.org/mcrusoe/sphinx-contrib

#hg clone http://bitbucket.org/mcrusoe/sphinx-contrib

hg clone http://athyra.ged.msu.edu/~mcrusoe/sphinx-contrib

Yes, many jobs have been dying due to bitbucket's lack of uptime.

Hmm, OK, I suppose it's ok to rely on athyra then...

The real solution is to clean up my additions to autoprogram:
https://bitbucket.org/birkenfeld/sphinx-contrib/pull-request/59/enhance-autoprogram-include-usage-summary/diff#comment-1610430

On Tue, Jun 10, 2014 at 3:41 PM, C. Titus Brown notifications@github.com
wrote:

In jenkins-build.sh:

@@ -45,7 +45,8 @@ fi
if type hg >/dev/null 2>&1
then
rm -Rf sphinx-contrib

hg clone http://bitbucket.org/mcrusoe/sphinx-contrib

#hg clone http://bitbucket.org/mcrusoe/sphinx-contrib

hg clone http://athyra.ged.msu.edu/~mcrusoe/sphinx-contrib

On Tue, Jun 10, 2014 at 12:40:26PM -0700, Michael R. Crusoe wrote: > @@
-45,7 +45,8 @@ fi > if type hg >/dev/null 2>&1 > then > rm -Rf
sphinx-contrib > - hg clone http://bitbucket.org/mcrusoe/sphinx-contrib >

#hg clone http://bitbucket.org/mcrusoe/sphinx-contrib > + hg clone
http://athyra.ged.msu.edu/~mcrusoe/sphinx-contrib Yes, many jobs have
been dying due to bitbucket's lack of uptime.
Hmm, OK, I suppose it's ok to rely on athyra then...

—
Reply to this email directly or view it on GitHub
https://github.com/ged-lab/khmer/pull/451/files#r13614549.

ctb · 2014-06-10T19:36:39Z

I dislike the demotion of tests/ to khmer/tests/ in the directory hierarchy. Is there no way to avoid this?

mr-c · 2014-06-10T19:41:50Z

It needs to be inside the khmer namespace as it gets installed into
site-packages

On Tue, Jun 10, 2014 at 3:36 PM, C. Titus Brown notifications@github.com
wrote:

I dislike the demotion of tests/ to khmer/tests/ in the directory
hierarchy. Is there no way to avoid this?

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Reply to this email directly or view it on GitHub
#451 (comment).

ctb · 2014-06-10T20:06:21Z

See 'package_dir', https://docs.python.org/2/distutils/setupscript.html, and #467.

mr-c · 2014-06-11T00:59:33Z

test this please

mr-c · 2014-06-11T01:03:29Z

Failing because I added additional error checking without unit tests!

mr-c · 2014-06-13T01:35:23Z

This is ready for review and merging @ctb @luizirber @camillescott

mr-c · 2014-06-13T05:09:15Z

Fixing the memory leaks saves 9.9 MB of memory while running the tests. I wonder how much it will help with regular datasets.

ctb · 2014-06-13T11:12:49Z

Remaining issue -- 'make test' recompiles zlib (but not bzip2) - could you fix, please?

Also, when I install in a virtualenv on athyra and run the tests:

 nosetests fiz/lib/python2.7/site-packages/khmer-1.0.1_118_gd46d5de-py2.7-linux-x86_64.egg/ -a \!known_failing

I get a number of failures with "No module named screed", even though screed is installed. Any ideas?

Also, I can't seem to run just 'nosetests khmer', as in http://scikit-learn.org/stable/install.html#testing. Thoughts?

Finally, could you enable 'import khmer; khmer.test()'? Thanks!

mr-c · 2014-06-13T20:53:21Z

My testing regime

mcrusoe@athyra:~$ virtualenv -p python2 khmer-package-tests-env
mcrusoe@athyra:~/khmer$ cd khmer-package-tests-env/
mcrusoe@athyra:~/khmer-package-tests-env$ source bin/activate
(khmer-package-tests-env)mcrusoe@athyra:~/khmer-package-tests-env$ easy_install -U setuptools
(khmer-package-tests-env)mcrusoe@athyra:~/khmer-package-tests-env$ pip install git+https://github.com/ged-lab/khmer.git@feature/package-tests#egg=khmer           
(khmer-package-tests-env)mcrusoe@athyra:~/khmer-package-tests-env$ pip install nose
(khmer-package-tests-env)mcrusoe@athyra:~/khmer-package-tests-env$ nosetests khmer --attr '!known_failing'
...................................................................................................................................................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 355 tests in 9.650s
OK

mr-c · 2014-06-13T21:11:20Z

On Fri, Jun 13, 2014 at 7:12 AM, C. Titus Brown notifications@github.com
wrote:

Remaining issue -- 'make test' recompiles zlib (but not bzip2) - could you
fix, please?

Fixed

Also, when I install in a virtualenv on athyra and run the tests:

nosetests fiz/lib/python2.7/site-packages/khmer-1.0.1_118_gd46d5de-py2.7-linux-x86_64.egg/ -a !known_failing

I get a number of failures with "No module named screed", even though
screed is installed. Any ideas?

Also, I can't seem to run just 'nosetests khmer', as in
http://scikit-learn.org/stable/install.html#testing. Thoughts?

As documented in my previous comment, nosetests khmer --attr
'!known_failing" works in any subdirectory of the virtualenv while it is
active.

Finally, could you enable 'import khmer; khmer.test()'? Thanks!

Why? Scikit removed their equivalent.

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Reply to this email directly or view it on GitHub
#451 (comment).

mr-c · 2014-06-13T21:14:06Z

test this please

mr-c · 2014-06-13T23:25:37Z

test this please

add target for python test coverage text report; clarified where the HTML report is Added additional tests remove unused code as per #441 (comment) remove scripts that used CountingHash::max_hamming1_count Document code & sandbox script removal

Including a couple notable memory leaks!

… target

ctb · 2014-06-14T11:10:55Z

OK, it all works for me. Merging!

Feature/package tests

ctb reviewed Jun 10, 2014
View reviewed changes

mr-c added this to the v1.0.2 milestone Jun 10, 2014

ctb mentioned this pull request Jun 11, 2014

consider not shipping tests/ data/ doc/ examples/ in the PyPI tarball #419

Closed

mr-c mentioned this pull request Jun 11, 2014

Remove unused functions from khmer/_khmermodule.cc and lib/ #441

Closed

mr-c mentioned this pull request Jun 13, 2014

khmer/_khmermodule.cc needs more tests #438

Closed

mr-c added 8 commits June 13, 2014 19:29

tests runnable after installation

6bf9985

refinements for jenkins

9f7b129

astyle

b814554

Changelog reordering

cacbc31

valgrind inspired cleanups

3f689f0

memleaks begone

2fc721a

more gifts from valgrind

6480a7e

Including a couple notable memory leaks!

mr-c added 4 commits June 13, 2014 19:32

split coverity target in two: -build and -upload. Added configuration…

51e3d32

… target

match types

ab5b5ed

undo change to lib building

9a535b2

PEP8

1e34b4f

ctb added a commit that referenced this pull request Jun 14, 2014

Merge pull request #451 from ged-lab/feature/package-tests

4700707

Feature/package tests

ctb merged commit 4700707 into master Jun 14, 2014

ctb deleted the feature/package-tests branch June 14, 2014 11:11

ctb mentioned this pull request Jun 14, 2014

be able to run tests after pip install khmer #220

Closed

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Feature/package tests #451

Feature/package tests #451

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Feature/package tests #451

Feature/package tests #451

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