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Increase testing parallelism #3620
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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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I think I figured why pytest was faster than nose -- we aren't running pytest with coverage enabled
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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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I can't find the docs for this option, can you point me to them?
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Disregard I see that this is an option on pytest-xdist rather than pytest.
python/hail/tests/test_methods.py
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@@ -909,16 +909,6 @@ def test_pca(self): | |||
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_, _, loadings = hl.pca(mt.GT.n_alt_alleles(), k=2, compute_loadings=False) | |||
self.assertEqual(loadings, None) | |||
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It seems bad to completely remove a test?
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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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also, I don't think this is even a valid test given that we don't guarantee determinism
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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! 😀
python/hail/tests/test_methods.py
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@@ -909,16 +909,6 @@ def test_pca(self): | |||
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_, _, loadings = hl.pca(mt.GT.n_alt_alleles(), k=2, compute_loadings=False) | |||
self.assertEqual(loadings, None) | |||
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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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we need pytest in the dependencies as well.
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you can remove nose also
@tpoterba I had everything working locally, but hadn't updated master. Unfortunately, there's a test failure in the new test you added for
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To test locally, |
@tpoterba This is all set now. |
* 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
* 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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