Deprecated and slated for 2.0 removal #2739
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Let‘s get started. We‘ll have to figure out a way to do patches for 1.0 but it seems we can just do PRs against master at the moment and treat master as 1.x branch. We‘ll figure out a way to backport fixes from develop; I assume that if we do squash merges we get fairly clean diffs that we can cherry-pick or merge into master/1.x. |
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Also: remove six! |
This was referenced Jun 11, 2020
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* removes deprecated density code (part of #2739) * Removes density_from_Universe, density_from_PDB, Bfactor2RMSF, BfactorDensityCreator, and notwithin_coordinates_factory * Moves _set_user_grid to be a staticmethod of DensityAnalysis * Unused tests removed * Removal of six * some PEP8 string formatting changes * Adds a versionchanged for the removal * Adds changelog entry for deprecated density removal * Adds _set_user_grid to docs * Adds return entry
This was referenced Jun 14, 2020
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Towards #2739 ## Work done in this PR Removes the old helanal code in favour of helix_analysis
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* removes deprecated density code (part of MDAnalysis#2739) * Removes density_from_Universe, density_from_PDB, Bfactor2RMSF, BfactorDensityCreator, and notwithin_coordinates_factory * Moves _set_user_grid to be a staticmethod of DensityAnalysis * Unused tests removed * Removal of six * some PEP8 string formatting changes * Adds a versionchanged for the removal * Adds changelog entry for deprecated density removal * Adds _set_user_grid to docs * Adds return entry
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Towards MDAnalysis#2739 Removes the old helanal code in favour of helix_analysis
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…s#2913) * Move water bridge analysis from hbonds to hydrogenbonds (PR MDAnalysis#2913) * part of MDAnalysis#2739 * deprecate hydrogen bond analysis in water bridge in PR MDAnalysis#3111 * Update CHANGELOG Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
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@richardjgowers do you mind if I just move hbond_autocorrel to hydrogenbonds for this? |
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Yeah moving it is fine
…On Sun, May 2, 2021 at 14:07, Irfan Alibay ***@***.***> wrote:
@richardjgowers <https://github.com/richardjgowers> do you mind if I just
move hbond_autocorrel to hydrogenbonds for this?
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Fixes #2739 #3259 ## Work done in this PR * Moves hbond_autocorrel from hbonds to hydrogenbonds, stub will be removed in 3.0.0. * Removes deprecated hbonds.hbond_analysis code. * tests (note: tests were copied and we run full tests on the deprecated and the moved code, mainly to make sure that they can be called as expected; deprecation warnings are also tested) * make hydrogenbonds.hbond_autocorrel primary entry for docs * add entry for deprecated module at bottom of Hydrogen bonding docs * fixed doc in hydrogenbonds.wbridge_analysis * include the Gregoret 1991 reference (that was removed with the deprecated hbonds.hbond_analysis module) Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
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We have quite a lot of things that are slated for removal in 2.0:
With #2729 I guess we started 2.0 a little bit sooner than anticipated, so I thought I'd check that we are good at doing these removals before we go ahead and start cutting out code?
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