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Increase testing parallelism #3620

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merged 17 commits into from May 25, 2018

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jigold commented May 17, 2018

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environment PYSPARK_SUBMIT_ARGS: '--conf spark.driver.extraClassPath=' + projectDir + '/build/libs/hail-all-spark.jar --conf spark.executor.extraClassPath=' + projectDir + '/build/libs/hail-all-spark.jar pyspark-shell'
environment PYSPARK_PYTHON: 'python3'
environment NOSE_NOLOGCAPTURE: '1'
commandLine 'pytest',

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@tpoterba

tpoterba May 17, 2018

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I think I figured why pytest was faster than nose -- we aren't running pytest with coverage enabled

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@jigold

jigold May 17, 2018

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I always get error messages abt coverage not being available. I think this was on the cloud too. I can double check.

commandLine 'pytest',
'-n',
parallelism,
'--dist=loadscope',

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@danking

danking May 18, 2018

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I can't find the docs for this option, can you point me to them?

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@danking

danking May 18, 2018

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Disregard I see that this is an option on pytest-xdist rather than pytest.

@@ -909,16 +909,6 @@ def test_pca(self):
_, _, loadings = hl.pca(mt.GT.n_alt_alleles(), k=2, compute_loadings=False)
self.assertEqual(loadings, None)

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@danking

danking May 18, 2018

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It seems bad to completely remove a test?

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@tpoterba

tpoterba May 18, 2018

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we briefly discussed this yesterday. This test was created as part of our "if you fix a bug, make a test" policy, and fixed a bug caused by PCA doing its own AST/eval stuff. PCA now calls the base expr API, so this test is totally unnecessary. The expr stuff should be tested in its own modules, and PCA should be tested for its own method correctness (#3613), but we shouldn't need to test whether all expressions are valid input for PCA (doing this everywhere would be insane!)

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@tpoterba

tpoterba May 18, 2018

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also, I don't think this is even a valid test given that we don't guarantee determinism

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@danking

danking May 18, 2018

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Ok! In the future, let's try to keep these changes as separate PRs with a description as to why we are removing it. I'll approve now! 😀

@@ -909,16 +909,6 @@ def test_pca(self):
_, _, loadings = hl.pca(mt.GT.n_alt_alleles(), k=2, compute_loadings=False)
self.assertEqual(loadings, None)

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@danking

danking May 18, 2018

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Ok! In the future, let's try to keep these changes as separate PRs with a description as to why we are removing it. I'll approve now! 😀

@@ -17,3 +17,4 @@ dependencies:
- pip:
- parsimonious
- ipykernel
- pytest-xdist

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@tpoterba

tpoterba May 18, 2018

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we need pytest in the dependencies as well.

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@tpoterba

tpoterba May 18, 2018

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you can remove nose also

@jigold

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jigold commented May 22, 2018

@tpoterba I had everything working locally, but hadn't updated master. Unfortunately, there's a test failure in the new test you added for index_globals and I can't figure out how to fix it. I tried creating the environment separately and the pli field was there. Could you please take a look?

_____________ [doctest] hail.matrixtable.MatrixTable.index_globals _____________
[gw0] darwin -- Python 3.6.1 //anaconda/envs/py36/bin/python
UNEXPECTED EXCEPTION: AttributeError("StructExpression instance has no field, method, or property 'pli'\n    Hint: use 'describe()' to show the names of all data fields.",)
Traceback (most recent call last):

  File "//anaconda/envs/py36/lib/python3.6/doctest.py", line 1330, in __run
    compileflags, 1), test.globs)

  File "<doctest hail.matrixtable.MatrixTable.index_globals[0]>", line 1, in <module>

  File "/Users/jigold/hail/build/tmp/doctest/python/hail/expr/expressions/typed_expressions.py", line 1161, in __getattr__
    raise AttributeError(get_nice_attr_error(self, item))

AttributeError: StructExpression instance has no field, method, or property 'pli'
    Hint: use 'describe()' to show the names of all data fields.

/Users/jigold/hail/build/tmp/doctest/python/hail/matrixtable.py:2197: UnexpectedException
============== 1 failed, 420 passed, 13 skipped in 79.03 seconds ===============
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jigold commented May 22, 2018

To test locally, ./gradlew --daemon doctest

@jigold jigold dismissed stale reviews from tpoterba and danking May 22, 2018

done

jigold added some commits May 22, 2018

x

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jigold commented May 25, 2018

@tpoterba This is all set now.

@tpoterba tpoterba merged commit 0b7c877 into hail-is:master May 25, 2018

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konradjk added a commit to konradjk/hail that referenced this pull request Jun 12, 2018

Increase testing parallelism (hail-is#3620)
* Increase testing parallelism

* rebase & address comments

* doctest improvements

* fix tutorial

* forgot to add files

* fix test

* wip

* wip

* working

* remove errant comment

* forgot to add files

* add back extension

* fix sphinx

* test delete clean

* debug make wd

* fix?

* fix directory cp

jackgoldsmith4 added a commit to jackgoldsmith4/hail that referenced this pull request Jun 25, 2018

Increase testing parallelism (hail-is#3620)
* Increase testing parallelism

* rebase & address comments

* doctest improvements

* fix tutorial

* forgot to add files

* fix test

* wip

* wip

* working

* remove errant comment

* forgot to add files

* add back extension

* fix sphinx

* test delete clean

* debug make wd

* fix?

* fix directory cp
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