Started tests for gnm. #803
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| 'DCD parser not available. Are you using python 3?') | ||
| def setUp(self): | ||
| self.tmpdir = tempdir.TempDir() | ||
| self.universe = MDAnalysis.Universe(PSF, DCD) |
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Would the test make sense on MDAnalysisTests.datafiles.XTC rather than DCD? It would allow to run the test on python 3.
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Thanks. |
| del self.tmpdir | ||
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| def test_gnm(self): | ||
| self.gnm = MDAnalysis.analysis.gnm.GNMAnalysis(self.universe) |
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Does not need to be in the instance namespace: self.gnm could be just gnm. Then it is not needed to delete it latter as it will just not live out of the function scope.
Thank you for mentioning it. |
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Your test covers about 60% of the gnm module. Do you want to tackle what is left? Or at least increase the coverage? As it is now, it is a good start but the module cannot be considered supported yet. Otherwise, it looks good to me. |
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Thanks. Will you merge this PR, or wait for me to write a (mostly) completed test for gnm, and to send a new PR? |
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On 28/03/16 13:20, Zhenbo Li wrote:
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I added some tests, and coverage reached 80%, leaving I added tests for closeContactGNMAnalysis, but such test is very slow. It costed 294.926s on my computer(before adding it, it costs me only 15.524s). So I added Can this PR be merged now? |
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Great! This seems mergeable. There is a few cases you miss and that do not seem difficult to test:
Are you willing to give them a try? |
Signed-off-by: Zhenbo Li <[email protected]>
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Tests for these situations added. |
Update of AUTHORS and CHANGELOG with inferred author contributions.
* Removed duplicate mattwthompson in 0.20.0 changelog entry.: mattwthompson was placed twice by accident, this removes this duplication.
* Addition of missing authors.
An retrospective analysis of the authors found via `git shortlog -s -n --email --branches="develop"` found several commits by authors which were not present in the `AUTHORS.md` file.
- Zhenbo Li: commited via PR: Started tests for gnm. #803 and Make Travis run tests on OSX. #771,
- Jenna M. Swarthout via PR Update CoC according to suggestions from current CoC committee #4289 and Point to new reporting form link (owned by [email protected]) #4298,
- Bradley Dice via PR Fix GSD Windows compatibility #2384 ,
- David Minh via PR #2668
There seemed to be no indications in the above mentioned PRs that the author did not want to be in the authors file, it looks like it was just forgotten.
* Addition of missing entries from the changelog
Continued cross referencing of the git shortlog output but also accounting for the changelog identified several individuals that had not been included in the changelog entries for the release they contributed under. They were added to the relevant entry of the changelog based on the merge commit date.
Please note that for Tone Bengsten, we a) had no github handle (so they were assigned @tbengtsen), and b) no specific commit. Given we know that this individual was including alongside the encore merge, they were assigned to the 0.16.0 release.
* Update CHANGELOG
* PR #1218
* PR #1284 and #1408
* PR #4109
* based on git history
* PRs #803 and #771 (author addition, changelog addition)
* PR #2255 and #2221
* PR #1225
* PR #4289 and #4298
* PR #4031
* PR #4085
* PR #3635
* PR #2356
* PR #2559
* No GH handle - Encore author addition @tbengtsen
* PR #4184
* PR #2614
* PR #2219
* PR #2384
* PR #2668
* Add missing entry for Jenna
Thanks to @fiona-naughton for helping out with digging into this data :)
Co-authored-by: Fiona Naughton <[email protected]>
Co-authored-by: Oliver Beckstein <[email protected]>
Related to #743
I followed commit 33e15b6 , and added a test for gnm.
PR Checklist
Signed-off-by: Zhenbo Li [email protected]