Replaces outdated method in encore.covariance_matrix #3621

mtiberti · 2022-04-11T13:10:09Z

Fixes #3539

Changes made in this Pull Request:

Replaced the non-existing method from an older version with current API
added a couple of tests to test the codepath

PR Checklist

Tests?
Docs?
CHANGELOG updated?
Issue raised/referenced?

pep8speaks · 2022-04-11T13:10:13Z

Hello @mtiberti! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file testsuite/MDAnalysisTests/analysis/test_encore.py:

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Comment last updated at 2022-04-12 01:14:37 UTC

codecov · 2022-04-11T13:32:07Z

Codecov Report

Merging #3621 (dc9a9e9) into develop (459c04e) will increase coverage by 0.01%.
The diff coverage is 100.00%.

@@             Coverage Diff             @@
##           develop    #3621      +/-   ##
===========================================
+ Coverage    94.23%   94.25%   +0.01%     
===========================================
  Files          190      190              
  Lines        24790    24790              
  Branches      3340     3340              
===========================================
+ Hits         23362    23366       +4     
+ Misses        1380     1376       -4     
  Partials        48       48

Impacted Files	Coverage Δ
package/MDAnalysis/analysis/encore/covariance.py	`93.84% <100.00%> (+6.15%)`	⬆️

Continue to review full report at Codecov.

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orbeckst

lgtm, thanks!

orbeckst · 2022-04-12T01:15:47Z

@jbarnoud could you please have a quick look, too, and I'd leave you in charge getting it merged, if you don't mind.

jbarnoud

Thank you!

mtiberti added 6 commits April 9, 2022 11:43

fixed code path for when using reference structure

478d995

added explicit tests to test code paths in covariance_matrix

ca4dc62

updated CHANGELOG

c1c5a17

removed leftover whitespace

c867484

removed superseded test draft

de8d74f

Merge branch 'develop' into fix3539_encore_covariance_reference

bf28a63

github-actions bot added the Component-Analysis label Apr 11, 2022

added PR number to CHANGELOG

57af2d5

orbeckst approved these changes Apr 12, 2022

View reviewed changes

Merge branch 'develop' into fix3539_encore_covariance_reference

dc9a9e9

orbeckst assigned jbarnoud Apr 12, 2022

jbarnoud approved these changes Apr 12, 2022

View reviewed changes

jbarnoud merged commit 5166163 into develop Apr 12, 2022

orbeckst deleted the fix3539_encore_covariance_reference branch April 14, 2022 17:27

orbeckst mentioned this pull request Apr 14, 2022

replace atoms.coordinates() with atoms.positions #3467

Closed

2 tasks

wouterboomsma mentioned this pull request Sep 11, 2023

Test coverage for ENCORE needs to be increased MDAnalysis/mdaencore#29

Open

IAlibay added the maintainability label Sep 25, 2023

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Replaces outdated method in encore.covariance_matrix #3621

Replaces outdated method in encore.covariance_matrix #3621

mtiberti commented Apr 11, 2022 •

edited by orbeckst

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pep8speaks commented Apr 11, 2022 •

edited

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codecov bot commented Apr 11, 2022 •

edited

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orbeckst commented Apr 12, 2022

jbarnoud left a comment

Replaces outdated method in encore.covariance_matrix #3621

Replaces outdated method in encore.covariance_matrix #3621

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mtiberti commented Apr 11, 2022 • edited by orbeckst Loading

PR Checklist

pep8speaks commented Apr 11, 2022 • edited Loading

Comment last updated at 2022-04-12 01:14:37 UTC

codecov bot commented Apr 11, 2022 • edited Loading

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mtiberti commented Apr 11, 2022 •

edited by orbeckst

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pep8speaks commented Apr 11, 2022 •

edited

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codecov bot commented Apr 11, 2022 •

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