Add InterRDF_s #70
Add InterRDF_s #70
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@VOD555 if Travis fails, please check. This time the reason was missing cython for MDA devel installations. I merged master and this might fix it but in general, say something if CI fails due to issues outside the PR so that this can be fixed and your PR be moved along. In general, no-one bothers reviewing if there's still a red CI fail mark because experienced PR authors are expected to fix all their failures on their own. Exceptions are "cries for help" along the lines "Please have a look, I need more eyes to find this issue or solve this problem." |
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For the linter error: use the same trick as in Line 90 in a718250 |
Codecov Report
@@ Coverage Diff @@
## master #70 +/- ##
==========================================
+ Coverage 96.75% 97.14% +0.39%
==========================================
Files 8 8
Lines 431 491 +60
Branches 60 70 +10
==========================================
+ Hits 417 477 +60
Misses 8 8
Partials 6 6
Continue to review full report at Codecov.
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| @pytest.fixture(scope='module') | ||
| def rdf_s(u, sels): | ||
| return InterRDF_s(u, sels).run() |
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Can you test with different n_blocks?
I don't know if this is actually testing multiple blocks or not. We need to know that the "accumulator" is working with multiple blocks.
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Should work with @pytest.mark.parametrize.
pmda/test/test_rdf_s.py
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| # should see same results from analysis.rdf.InterRDF_s | ||
| # and pmda.rdf.InterRDF_s | ||
| nrdf = rdf.InterRDF_s(u, sels).run() | ||
| prdf = InterRDF_s(u, sels).run(n_jobs=3) |
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@orbeckst Here is one that is testing multiple blocks. Maybe I should add one test for "n_blocks=1" case
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@orbeckst An error is raised on the use of the get= keyword in the new version of dask(http://docs.dask.org/en/latest/changelog.html) |
| # and pmda.rdf.InterRDF_s | ||
| nrdf = rdf.InterRDF_s(u, sels).run() | ||
| prdf = InterRDF_s(u, sels).run(n_blocks=n_blocks) | ||
| assert_almost_equal(nrdf.count[0][0][0], prdf.count[0][0][0]) |
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Why compare just one element? Shouldn't
assert_almost_equal(nrdf.count, prdf.count)work?
pmda/test/test_rdf_s.py
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| @pytest.fixture(scope='module') | ||
| def rdf_s(u, sels): |
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Test with different schedulers:
def rdf_s(u, sels, scheduler)There was a problem hiding this comment.
(The scheduler fixture is defined in conftest.py and should run this calculation with all dask schedulers.)
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Gets error with =========================================================================================== test session starts ============================================================================================
platform linux -- Python 3.6.5, pytest-3.6.2, py-1.5.3, pluggy-0.6.0 -- /home/shujie/anaconda3/envs/py36/bin/python
cachedir: ../../.pytest_cache
rootdir: /home/shujie/pmda, inifile: setup.cfg
plugins: pep8-1.0.6, cov-2.5.1, hypothesis-3.66.1
collected 38 items
test_rdf_s.py::test_nbins PASSED [ 2%]
test_rdf_s.py::test_range PASSED [ 5%]
test_rdf_s.py::test_count_size[distributed-1] ERROR [ 7%]
test_rdf_s.py::test_count[distributed-1] ERROR [ 10%]
test_rdf_s.py::test_double_run[distributed-1] ERROR [ 13%]
test_rdf_s.py::test_cdf[distributed-1] ERROR [ 15%]
test_rdf_s.py::test_reduce[distributed-1] ERROR [ 18%]
test_rdf_s.py::test_count_size[multiprocessing-1] PASSED [ 21%]
test_rdf_s.py::test_count[multiprocessing-1] PASSED [ 23%]
test_rdf_s.py::test_double_run[multiprocessing-1] PASSED [ 26%]
test_rdf_s.py::test_cdf[multiprocessing-1] PASSED [ 28%]
test_rdf_s.py::test_reduce[multiprocessing-1] PASSED [ 31%]
test_rdf_s.py::test_count_size[multiprocessing-2] PASSED [ 34%]
test_rdf_s.py::test_count[multiprocessing-2] PASSED [ 36%]
test_rdf_s.py::test_double_run[multiprocessing-2] PASSED [ 39%]
test_rdf_s.py::test_cdf[multiprocessing-2] PASSED [ 42%]
test_rdf_s.py::test_reduce[multiprocessing-2] PASSED [ 44%]
test_rdf_s.py::test_count_size[distributed-2] ERROR [ 47%]
test_rdf_s.py::test_count[distributed-2] ERROR [ 50%]
test_rdf_s.py::test_double_run[distributed-2] ERROR [ 52%]
test_rdf_s.py::test_cdf[distributed-2] ERROR [ 55%]
test_rdf_s.py::test_reduce[distributed-2] ERROR [ 57%]
test_rdf_s.py::test_count_size[single-threaded-2] PASSED [ 60%]
test_rdf_s.py::test_count[single-threaded-2] PASSED [ 63%]
test_rdf_s.py::test_double_run[single-threaded-2] PASSED [ 65%]
test_rdf_s.py::test_cdf[single-threaded-2] PASSED [ 68%]
test_rdf_s.py::test_reduce[single-threaded-2] PASSED [ 71%]
test_rdf_s.py::test_count_size[single-threaded-1] PASSED [ 73%]
test_rdf_s.py::test_count[single-threaded-1] PASSED [ 76%]
test_rdf_s.py::test_double_run[single-threaded-1] PASSED [ 78%]
test_rdf_s.py::test_cdf[single-threaded-1] PASSED [ 81%]
test_rdf_s.py::test_reduce[single-threaded-1] PASSED [ 84%]
test_rdf_s.py::test_same_result[1] PASSED [ 86%]
test_rdf_s.py::test_same_result[2] PASSED [ 89%]
test_rdf_s.py::test_same_result[3] PASSED [ 92%]
test_rdf_s.py::test_same_result[4] PASSED [ 94%]
test_rdf_s.py::test_density[True-13275.775528444701] PASSED [ 97%]
test_rdf_s.py::test_density[False-0.021915460340071267] PASSED [100%]
================================================================================================== ERRORS ================================================================================================== |
pmda/rdf.py
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| super(InterRDF_s, self).__init__(u, atomgroups) | ||
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| # List of pairs of AtomGroups | ||
| self.ags = ags |
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Ok, the failure is due to this line. distributed cannot pass atomgroups to blocks.
Fixes #60
Changes made in this Pull Request:
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