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tests for MDAnalysis.visualization #1617

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orbeckst opened this Issue Aug 14, 2017 · 5 comments

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orbeckst commented Aug 14, 2017

Modules in MDAnalysis.visualization are not tested at the moment.

Expected behaviour

All documented modules (except the legacy modules in MDAnalysis.analysis.legacy, which are documented as untested) should be tested at least at the 70% code coverage level.

At a minimum we should have tests that

  • read data
  • produce plots

It might be sufficient to check that the matplotlib objects are produced.

Actual behaviour

We are currently excluding MDAnalysis.visualization from our testing and coverage report.

Currently version of MDAnalysis:

(run python -c "import MDAnalysis as mda; print(mda.__version__)")
Current develop 0.17.0

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orbeckst Aug 14, 2017

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@tylerjereddy I assigned you as the sole author in the module but please feel free to delegate/help/convince others to contribute tests.

If you propose a minimal testing standard for visualization then we will probably adapt it for any other Something.plot() function (e.g., in PSA #1006 )

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orbeckst commented Aug 14, 2017

@tylerjereddy I assigned you as the sole author in the module but please feel free to delegate/help/convince others to contribute tests.

If you propose a minimal testing standard for visualization then we will probably adapt it for any other Something.plot() function (e.g., in PSA #1006 )

@orbeckst orbeckst added this to the 1.0 milestone Aug 14, 2017

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tylerjereddy Apr 5, 2018

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Apparently the module is 'broken' now (my fault) -- I'll coordinate with Matthieu to use the test files at http://sbcb.bioch.ox.ac.uk/flows/MDAnalysis.html to at least try to get a regression test of some sort in here -- he reminded me that this is needed this morning.

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tylerjereddy commented Apr 5, 2018

Apparently the module is 'broken' now (my fault) -- I'll coordinate with Matthieu to use the test files at http://sbcb.bioch.ox.ac.uk/flows/MDAnalysis.html to at least try to get a regression test of some sort in here -- he reminded me that this is needed this morning.

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orbeckst Apr 7, 2018

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Yes, it is broken. We would like to use it but just got zeros.

Well, untested code is broken code.

Will you be able to fix it?

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orbeckst commented Apr 7, 2018

Yes, it is broken. We would like to use it but just got zeros.

Well, untested code is broken code.

Will you be able to fix it?

@orbeckst orbeckst added the defect label Apr 7, 2018

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Will you be able to fix it?

Probably, I'm trying a few things in spare time; we'll see if I can get a PR with a regression test open today.

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tylerjereddy commented Apr 8, 2018

Will you be able to fix it?

Probably, I'm trying a few things in spare time; we'll see if I can get a PR with a regression test open today.

tylerjereddy added a commit that referenced this issue Apr 9, 2018

BUG: Fix untested MDAnalysis.visualization code
* Fixes Issue #1617 by adding regression tests
for the 2D and 3D streamplot codes

* Fixes a bug in the 2D streamplot code where
coordinates() were used instead of positions
to access the coordinates of an atomgroup

* visualization code is no longer excluded
from the test coverage report

tylerjereddy added a commit that referenced this issue Apr 9, 2018

BUG: Fix untested MDAnalysis.visualization code
* Fixes Issue #1617 by adding regression tests
for the 2D and 3D streamplot codes

* Fixes a bug in the 2D streamplot code where
coordinates() were used instead of positions
to access the coordinates of an atomgroup

* visualization code is no longer excluded
from the test coverage report

tylerjereddy added a commit that referenced this issue Apr 9, 2018

BUG: Fix untested MDAnalysis.visualization code
* Fixes Issue #1617 by adding regression tests
for the 2D and 3D streamplot codes

* Fixes a bug in the 2D streamplot code where
coordinates() were used instead of positions
to access the coordinates of an atomgroup

* visualization code is no longer excluded
from the test coverage report

* appropriate CHANGELOG and README adjustments

richardjgowers added a commit that referenced this issue Apr 10, 2018

BUG: Fix untested MDAnalysis.visualization code
* Fixes Issue #1617 by adding regression tests
for the 2D and 3D streamplot codes

* Fixes a bug in the 2D streamplot code where
coordinates() were used instead of positions
to access the coordinates of an atomgroup

* visualization code is no longer excluded
from the test coverage report

* appropriate CHANGELOG and README adjustments
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orbeckst May 1, 2018

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Fixed in PR #1859

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orbeckst commented May 1, 2018

Fixed in PR #1859

@orbeckst orbeckst closed this May 1, 2018

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