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/9726590606/job/26845212202

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 (cfa4438) to head (e28a2a9).

❗ Current head e28a2a9 differs from pull request most recent head a76213f

Please upload reports for the commit a76213f to get more accurate results.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4518      +/-   ##
===========================================
- Coverage    93.60%   93.15%   -0.45%     
===========================================
  Files          171       12     -159     
  Lines        21235     1067   -20168     
  Branches      3933        0    -3933     
===========================================
- Hits         19876      994   -18882     
+ Misses         899       73     -826     
+ Partials       460        0     -460

☔ 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,
-)
-
+) 


package/MDAnalysis/coordinates/memory.py

package/MDAnalysis/topology/ParmEdParser.py

package/MDAnalysis/topology/core.py

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.

orbeckst

This is a nice clean-up PR. There's one issue that needs fixing and some minor comments – please see comments. Please ping me when you I can do a final review.

orbeckst · 2024-06-07T23:44:26Z

package/MDAnalysis/analysis/legacy/x3dna.py

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

 """
-import glob


Removing glob here is ok because it's imported when needed in the code.

orbeckst · 2024-06-07T23:47:44Z

package/MDAnalysis/coordinates/H5MD.py

 from MDAnalysis.lib.util import store_init_arguments
+from MDAnalysis.lib.mdamath import triclinic_box


Can we change these to relative imports like everything else?

Suggested change

from MDAnalysis.lib.util import store_init_arguments

from MDAnalysis.lib.mdamath import triclinic_box

from ..lib.util import store_init_arguments

from ..lib.mdamath import triclinic_box

orbeckst · 2024-06-07T23:49:39Z

package/MDAnalysis/coordinates/ParmEd.py

-from ..converters.ParmEd import (ParmEdConverter, ParmEdReader,
-                                 get_indices_from_subset, MDA2PMD,)


These MUST stay for compatibility reasons. The module will be removed in 3.0.0.

Just mark them to be ignored by the linter.

orbeckst · 2024-06-07T23:53:22Z

package/MDAnalysis/coordinates/core.py

@@ -38,8 +38,6 @@

 """

-from ..lib import util
-from ..lib.mdamath import triclinic_box, triclinic_vectors, box_volume


This is ok because we did NOT advertise these functions to be available in coordinates.core (https://docs.mdanalysis.org/stable/documentation_pages/coordinates/core.html#module-MDAnalysis.coordinates.core) but be careful when removing imports in top level __init__.py or in anything named core.py or base.py modules.

orbeckst · 2024-06-07T23:56:41Z

package/MDAnalysis/coordinates/DLPoly.py

@@ -31,7 +31,7 @@
 import numpy as np

 from . import base
-from . import core
+from ..lib.mdamath import triclinic_box


Do we like using triclinic_box() better than mdamath.triclinic_box()?

Personally, I generally prefer non-local objects to have at least one level of provenance attached to their name but I won't block over choosing the bare import.

Unless there are other reviewers that want to change to

from ..lib import mdamath ... mdamath.triclinic_box(...)

leave it as is, at least it's consistently used throughout.

orbeckst · 2024-06-08T00:00:14Z

package/MDAnalysis/lib/transformations.py

-from numpy.linalg import norm

-from .mdamath import angle as vecangle


Removal is ok because it wasn't documented to be present here.

... and if it doesn't break our tests then it should be fine.

orbeckst · 2024-06-08T05:35:37Z

testsuite/MDAnalysisTests/analysis/test_distances.py

@@ -29,8 +29,7 @@

 import MDAnalysis.analysis.distances

-from numpy.testing import (assert_equal, assert_array_equal, assert_almost_equal, 
-                           assert_array_almost_equal,assert_allclose)
+from numpy.testing import (assert_equal ,assert_allclose)


pep8 space and I don't think parentheses are needed

Suggested change

from numpy.testing import (assert_equal ,assert_allclose)

from numpy.testing import assert_equal, assert_allclose

orbeckst · 2024-06-08T05:36:34Z

testsuite/MDAnalysisTests/analysis/test_gnm.py

@@ -24,7 +24,7 @@
 from unittest.mock import patch

 import MDAnalysis as mda
-import MDAnalysis.analysis.gnm
+from MDAnalysis.analysis.gnm import (GNMAnalysis, closeContactGNMAnalysis)


not sure that this is strictly necessary — I am not a fan of bare imports

RMeli · 2024-06-29T20:05:32Z

@vachram97 I took the freedom to fix the conflicts for you, so that we can move forward and see how CI is faring.

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

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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

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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

orbeckst removed the close? Evaluate if issue/PR is stale and can be closed. label Jun 7, 2024

orbeckst requested changes Jun 8, 2024

View reviewed changes

Merge branch 'develop' into develop

a76213f

github-actions bot removed Component-Readers Component-Analysis Component-Core Component-lib Component-Topology Component-Converters labels Jun 29, 2024

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Enable Pylint warning unused-import #4518

Enable Pylint warning unused-import #4518

vachram97 commented Mar 18, 2024 •

edited by orbeckst

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RMeli commented Jun 29, 2024

		from MDAnalysis.lib.util import store_init_arguments
		from MDAnalysis.lib.mdamath import triclinic_box

		from ..converters.ParmEd import (ParmEdConverter, ParmEdReader,
		get_indices_from_subset, MDA2PMD,)

		from numpy.linalg import norm

		from .mdamath import angle as vecangle

	from numpy.testing import (assert_equal ,assert_allclose)
	from numpy.testing import assert_equal, assert_allclose

Enable Pylint warning unused-import #4518

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Enable Pylint warning unused-import #4518

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RMeli commented Jun 29, 2024

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