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Remove save() methods for v1.0 - Part 1#2487

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richardjgowers merged 10 commits intoMDAnalysis:developfrom
IAlibay:remove-saves-contacts
Feb 7, 2020
Merged

Remove save() methods for v1.0 - Part 1#2487
richardjgowers merged 10 commits intoMDAnalysis:developfrom
IAlibay:remove-saves-contacts

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@IAlibay
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@IAlibay IAlibay commented Jan 31, 2020

Addresses part of #1745 and #2443

Changes made in this Pull Request:

  • removed save() from contacts, diffusionmap, hole, lineardensity, and rms.
  • associated instances of filename used by save() methods has also been removed.

So I'm doing this PR in two parts, as there's quite a few small changes and it'd probably be easier to review if I don't try to cram everything in a single PR.

PR Checklist

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

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codecov bot commented Jan 31, 2020

Codecov Report

Merging #2487 into develop will not change coverage.
The diff coverage is n/a.

Impacted file tree graph

@@           Coverage Diff            @@
##           develop    #2487   +/-   ##
========================================
  Coverage    90.27%   90.27%           
========================================
  Files          169      169           
  Lines        23155    23155           
  Branches      3000     3000           
========================================
  Hits         20904    20904           
  Misses        1639     1639           
  Partials       612      612

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@IAlibay IAlibay mentioned this pull request Feb 2, 2020
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@IAlibay IAlibay mentioned this pull request Feb 4, 2020
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@fiona-naughton
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Looks good to me!

orbeckst pushed a commit that referenced this pull request Feb 6, 2020
* Partly addresses #1745 (completes save() removal with PR #2487 and PR #2486 )
* removes save methods
  - removes save method from psa.py
  - also minor change to test_hbonds.py
* deprecates hbond_analysis
  - close #2492
* updates changelog
@richardjgowers richardjgowers merged commit 0dede25 into MDAnalysis:develop Feb 7, 2020
@fiona-naughton fiona-naughton added maintainability deprecation Deprecated functionality to give advance warning for API changes. labels Sep 26, 2023
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