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MDAnalysis / pmda

Parallel algorithms for MDAnalysis
https://www.mdanalysis.org/pmda/
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Add InterRDF_s #70

Closed VOD555 closed 6 years ago

VOD555 commented 6 years ago

Fixes #60

Changes made in this Pull Request:

PR Checklist

orbeckst commented 6 years ago

@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."

orbeckst commented 6 years ago

For the linter error: use the same trick as in https://github.com/MDAnalysis/pmda/blob/a7182506d68f34eecb0f23bda884f009cd00d86d/pmda/rdf.py#L90

codecov[bot] commented 6 years ago

Codecov Report

Merging #70 into master will increase coverage by 0.39%. The diff coverage is 100%.

Impacted file tree graph

@@            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
Impacted Files Coverage Δ
pmda/rdf.py 100% <100%> (ø) :arrow_up:

Continue to review full report at Codecov.

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VOD555 commented 6 years ago

@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)

orbeckst commented 6 years ago

That happened quickly!

So we now HAVE to finish PR #66!

EDIT: "quickly" because PR #66 talked about updated to Dask 0.18 and now we have 0.20 and it's an error.

EDIT 2: Fix referenced PR: not #60 but #66

VOD555 commented 6 years ago

Gets error with distributed

=========================================================================================== 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 ==================================================================================================