Enable Pylint warning unused-import #4518

vachram97 · 2024-03-18T21:37:34Z

Contributes to #1295 (unused-import)

Changes made in this Pull Request:

unused-import check was enabled for pylint
unnecessary imports were removed
2 imports were shadowed since they are internal for library part

PR Checklist

Tests?
some tests are skipped on local machine
Docs?
no changes are needed to docs
CHANGELOG updated?
as no new functionality/bug fixes were introduced, there is nothing to add to changelog
Issue raised/referenced?

Developers certificate of origin

I certify that this contribution is covered by the LGPLv2.1+ license as defined in our LICENSE and adheres to the Developer Certificate of Origin.

📚 Documentation preview 📚: https://mdanalysis--4518.org.readthedocs.build/en/4518/

github-actions

Hello there first time contributor! Welcome to the MDAnalysis community! We ask that all contributors abide by our Code of Conduct and that first time contributors introduce themselves on GitHub Discussions so we can get to know you. You can learn more about participating here. Please also add yourself to package/AUTHORS as part of this PR.

github-actions · 2024-03-18T21:40:03Z

Linter Bot Results:

Hi @vachram97! Thanks for making this PR. We linted your code and found the following:

Some issues were found with the formatting of your code.

Code Location	Outcome
main package	⚠️ Possible failure
testsuite	⚠️ Possible failure

Please have a look at the darker-main-code and darker-test-code steps here for more details: https://github.com/MDAnalysis/mdanalysis/actions/runs/9375246198/job/25812975007

Please note: The black linter is purely informational, you can safely ignore these outcomes if there are no flake8 failures!

…kage

codecov · 2024-03-19T00:02:34Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.15%. Comparing base (347a0c0) to head (e28a2a9).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4518      +/-   ##
===========================================
- Coverage    93.59%   93.15%   -0.44%     
===========================================
  Files          168       12     -156     
  Lines        21104     1067   -20037     
  Branches      3919        0    -3919     
===========================================
- Hits         19752      994   -18758     
+ Misses         894       73     -821     
+ Partials       458        0     -458

☔ View full report in Codecov by Sentry.
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RMeli

Hi @vachram97, thanks for your contribution. The linters failure appears to be un-related to this PR.

LGTM, but given the size of the changes, we will need a few more eyes on this.

Note to self: once this is squashed-merged, the commit will need to be added to .git-blame-ignore-revs.

RMeli

Please add yourself in the AUTHORS file. And I would still add an entry in the CHANGELOG.

IAlibay

Very quickly review, apologies please take the brief comments as me only having a few minutes to review and not a reflection on the quality of the work (thank you so much for taking this task!) - @RMeli feel free to discard my review once the big things have been addressed (parmed mostly)

IAlibay · 2024-03-24T22:59:46Z

package/MDAnalysis/analysis/legacy/x3dna.py

@@ -117,7 +117,6 @@
 .. autoexception:: ApplicationError

 """


We have no tests for this module - I would suggest not touching imports here

IAlibay · 2024-03-24T23:00:49Z

package/MDAnalysis/analysis/psa.py

@@ -61,8 +61,7 @@
    Path,
    PSAPair,
    PSAnalysis,
-)
-
+) 


here and everywhere else this is done, please don't remove this extra blank line - it's there for pep8 reasons

IAlibay · 2024-03-24T23:01:03Z

package/MDAnalysis/analysis/waterdynamics.py

    WaterOrientationalRelaxation,
    AngularDistribution,
    MeanSquareDisplacement,
    SurvivalProbability,
-)
-
+) 


IAlibay · 2024-03-24T23:03:14Z

package/MDAnalysis/coordinates/memory.py


 from . import base
-from .timestep import Timestep


If I remember correctly, this is an intentional import that isn't used - we import Timestep here to not break the API since we used to have Timestep defined here (if I remember correctly? it's been a while since that happened - the plan was to remove in 3.0)

To be clear to @vachram97 : do not remove the import

IAlibay · 2024-03-24T23:04:53Z

package/MDAnalysis/topology/ParmEdParser.py

@@ -21,7 +21,6 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 import warnings
-from ..converters.ParmEdParser import ParmEdParser, squash_identical


This is an intentional import, the class moved but we're keeping the import here for backwards compatibility

To be clear to @vachram97 : do not remove the import

IAlibay · 2024-03-24T23:06:24Z

package/MDAnalysis/topology/core.py

-
-# Local imports
-from . import tables
-from .guessers import (


I'm not sure if these are imported as part of the expected API, someone else would have to double check

topology.tables seems to be expected to be present as part of the API https://docs.mdanalysis.org/stable/documentation_pages/topology/tables.html ; we can change it for 3.0 but for this PR, these imports need to stay

I am not 100% sure about guessers — usage in https://docs.mdanalysis.org/stable/documentation_pages/topology/guessers.html seems ambiguous or indicative that it's not required. I also don't see examples in the User Guide under Guessing using mda.topology.guess_*() @lilyminium do you happen to know if we are promising anywhere that mda.topology.guess_*() exists? Could we remove these imports? I'd be in favor of removing them right now if they are not in the API.

I don't think we promise this as an official recommendation of how to use it, although people may still be using the guesser functions and they are publically available. In addition, with #3753 these functions will go away anyway (as they'll come under the DefaultGuesser class) so I am in favour of removing them here.

Thanks!

So then please do the following @vachram97

Keep from . import tables

Remove from .guessers import ( ... )

orbeckst · 2024-03-25T19:41:55Z

@RMeli can you please shepherd this PR? Thank you!

orbeckst · 2024-03-26T00:24:07Z

@vachram97 I edited your issue text so that we don't accidentally close the parent issue #1295 .

orbeckst · 2024-05-31T00:53:33Z

@vachram97 do you still have time to work on this PR? If so, please respond to the reviews.

add back no_copy_shim import in transformations

orbeckst · 2024-05-31T00:59:06Z

I merged and accidentally removed a new import in transformations.py. I added it back in 4cbe32c and hopefully that's now ok.

vachram97 · 2024-06-06T20:22:22Z

I have updated the PR with all comments were addressed as requested and last version MDAnalysis/develop was merged into PR.

Tests fail on the testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py test with time limit error and seems to be not related to this PR.

vachram97 added 2 commits March 17, 2024 19:33

updated package with unused_import pylint setting

9d285ef

updated test files for pylint unused-imports warnings

7c7cd98

github-actions bot added Component-Analysis Component-Converters Component-Core Component-lib Component-Readers Component-Topology labels Mar 18, 2024

github-actions bot reviewed Mar 18, 2024

View reviewed changes

vachram97 added 2 commits March 18, 2024 23:19

returned due imports with pylint shadowing as part of due part of pac…

48d7386

…kage

bug fixes

76c50fe

RMeli approved these changes Mar 24, 2024

View reviewed changes

RMeli requested changes Mar 24, 2024

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IAlibay requested changes Mar 24, 2024

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orbeckst assigned RMeli Mar 25, 2024

orbeckst mentioned this pull request Mar 26, 2024

Enable Pylint warnings #1295

Open

38 tasks

orbeckst added 2 commits May 30, 2024 17:54

Merge branch 'develop' into develop

14a2a23

fixed partially botched merge

4cbe32c

add back no_copy_shim import in transformations

orbeckst added the close? Evaluate if issue/PR is stale and can be closed. label May 31, 2024

vachram97 added 3 commits June 4, 2024 22:30

returning imports for API compablity/API

3703d3a

Merge remote-tracking branch 'upstream/develop' into develop

c809024

returned import im legacy x3dna, CHANGELOG & AUTH

e28a2a9

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Enable Pylint warning unused-import #4518

Enable Pylint warning unused-import #4518

vachram97 commented Mar 18, 2024 •

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Enable Pylint warning unused-import #4518

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Enable Pylint warning unused-import #4518

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vachram97 commented Mar 18, 2024 • edited by orbeckst

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