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[fmt] Format analysis module and tests #4848

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[fmt] Format analysis module and tests #4848

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@RMeli RMeli commented Dec 20, 2024 •
edited by github-actions bot
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Format most of the MDAnalysis/analysis module and corresponding test. Some files actives in current PRs are ignored and will be formatted once the corresponding PRs are merged (see #4815).

📚 Documentation preview 📚: https://mdanalysis--4848.org.readthedocs.build/en/4848/

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codecov bot commented Dec 20, 2024 •
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Codecov Report

Attention: Patch coverage is 93.57907% with 54 lines in your changes missing coverage. Please review.

Project coverage is 93.63%. Comparing base (4f143fd) to head (6a44252).

Files with missing lines Patch % Lines
...ckage/MDAnalysis/analysis/encore/confdistmatrix.py 60.00% 9 Missing and 1 partial ⚠️
...nalysis/analysis/hydrogenbonds/wbridge_analysis.py 92.43% 2 Missing and 7 partials ⚠️
package/MDAnalysis/analysis/encore/similarity.py 88.88% 1 Missing and 7 partials ⚠️
package/MDAnalysis/analysis/encore/utils.py 62.50% 4 Missing and 2 partials ⚠️
package/MDAnalysis/analysis/nuclinfo.py 88.46% 2 Missing and 4 partials ⚠️
...nalysis/analysis/hydrogenbonds/hbond_autocorrel.py 90.00% 2 Missing and 2 partials ⚠️
package/MDAnalysis/analysis/bat.py 93.33% 2 Missing and 1 partial ⚠️
...e/MDAnalysis/analysis/encore/clustering/cluster.py 84.61% 1 Missing and 1 partial ⚠️
.../dimensionality_reduction/reduce_dimensionality.py 84.61% 1 Missing and 1 partial ⚠️
package/MDAnalysis/analysis/rms.py 96.15% 2 Missing ⚠️
... and 2 more
Additional details and impacted files 
@@             Coverage Diff             @@
##           develop    #4848      +/-   ##
===========================================
- Coverage    93.65%   93.63%   -0.03%     
===========================================
  Files          177      189      +12     
  Lines        21779    22845    +1066     
  Branches      3064     3064              
===========================================
+ Hits         20398    21391     +993     
- Misses         929     1002      +73     
  Partials       452      452

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

RMeli
RMeli commented Dec 20, 2024
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testsuite/MDAnalysisTests/analysis/test_base.py Show resolved Hide resolved
testsuite/MDAnalysisTests/analysis/test_base.py Show resolved Hide resolved
package/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py
"SD",
"OG",
"OG1",
"OH",
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Trailing comma? Maybe it is just too long for 79 characters (to be checked).

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Too long indeed.

package/MDAnalysis/analysis/legacy/x3dna.py
Comment on lines +494 to +507
(
bp_shear,
bp_stretch,
bp_stagger,
bp_rise,
bp_shift,
bp_slide,
bp_buckle,
bp_prop,
bp_open,
bp_tilt,
bp_roll,
bp_twist,
) = ([], [], [], [], [], [], [], [], [], [], [], [])
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Refactor?

package/MDAnalysis/analysis/legacy/x3dna.py
Comment on lines +419 to +445
(
bp_shear,
bp_stretch,
bp_stagger,
bp_rise,
bp_shift,
bp_slide,
bp_buckle,
bp_prop,
bp_open,
bp_tilt,
bp_roll,
bp_twist,
) = (
np.array(bp_shear),
np.array(bp_stretch),
np.array(bp_stagger),
np.array(bp_rise),
np.array(bp_shift),
np.array(bp_slide),
np.array(bp_buckle),
np.array(bp_prop),
np.array(bp_open),
np.array(bp_tilt),
np.array(bp_roll),
np.array(bp_twist),
)
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?

testsuite/MDAnalysisTests/analysis/test_encore.py
Comment on lines -247 to -256
reference_cov = np.array([
[12.9122,-5.2692,3.9016,10.0663,-5.3309,3.8923,8.5037,-5.2017,2.6941],
[-5.2692,4.1087,-2.4101,-4.5485,3.3954,-2.3245,-3.7343,2.8415,-1.6223],
[3.9016,-2.4101,3.1800,3.4453,-2.6860,2.2438,2.7751,-2.2523,1.6084],
[10.0663,-4.5485,3.4453,8.8608,-4.6727,3.3641,7.0106,-4.4986,2.2604],
[-5.3309,3.3954,-2.6860,-4.6727,4.4627,-2.4233,-3.8304,3.0367,-1.6942],
[3.8923,-2.3245,2.2438,3.3641,-2.4233,2.6193,2.6908,-2.0252,1.5775],
[8.5037,-3.7343,2.7751,7.0106,-3.8304,2.6908,6.2861,-3.7138,1.8701],
[-5.2017,2.8415,-2.2523,-4.4986,3.0367,-2.0252,-3.7138,3.3999,-1.4166],
[2.6941,-1.6223,1.6084,2.2604,-1.6942,1.5775,1.8701,-1.4166,1.4664]])
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Can this be formatted more sensibly (one line per row)?

testsuite/MDAnalysisTests/analysis/test_encore.py
Comment on lines -265 to -274
reference_cov = np.array([
[39.0760,-28.5383,29.7761,37.9330,-35.5251,18.9421,30.4334,-31.4829,12.8712],
[-28.5383,24.1827,-25.5676,-29.0183,30.3511,-15.9598,-22.9298,26.1086,-10.8693],
[29.7761,-25.5676,28.9796,30.7607,-32.8739,17.7072,24.1689,-28.3557,12.1190],
[37.9330,-29.0183,30.7607,37.6532,-36.4537,19.2865,29.9841,-32.1404,12.9998],
[-35.5251,30.3511,-32.8739,-36.4537,38.5711,-20.1190,-28.7652,33.2857,-13.6963],
[18.9421,-15.9598,17.7072,19.2865,-20.1190,11.4059,15.1244,-17.2695,7.8205],
[30.4334,-22.9298,24.1689,29.9841,-28.7652,15.1244,24.0514,-25.4106,10.2863],
[-31.4829,26.1086,-28.3557,-32.1404,33.2857,-17.2695,-25.4106,29.1773,-11.7530],
[12.8712,-10.8693,12.1190,12.9998,-13.6963,7.8205,10.2863,-11.7530,5.5058]])
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Can this be formatted with one line per row?

testsuite/MDAnalysisTests/analysis/test_gnm.py
Comment on lines -67 to -79
assert_almost_equal(gen[0],
[7,-1,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0,-1,-1,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-1, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
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Leave original formatting or similar.

testsuite/MDAnalysisTests/analysis/test_gnm.py
Comment on lines -99 to -114
assert_almost_equal(gen[0],
[16.326744128018923, -2.716098853586913, -1.94736842105263, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, -0.05263157894736842, 0.0, 0.0, 0.0, -3.3541953679557905, 0.0, -1.4210526315789465, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, -1.0423368771244421, -1.3006649542861801, -0.30779350562554625, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -0.927172649945531, -0.7509392614826383,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, -2.263157894736841, -0.24333213169614382])
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Leave original formatting or similar.

testsuite/MDAnalysisTests/analysis/test_gnm.py
Comment on lines -125 to -136
assert_almost_equal(gen[0],
[303.0, -58.0, -37.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0,
0.0, 0.0, 0.0, -67.0, 0.0, -27.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -17.0, -15.0,
-6.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, -14.0, -15.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -43.0, -3.0])
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Leave original formatting or similar.

@RMeli RMeli requested review from IAlibay and marinegor December 20, 2024 22:16
orbeckst
orbeckst approved these changes Dec 24, 2024
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blanket LGTM

🎄 🎁

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@orbeckst orbeckst orbeckst approved these changes

@IAlibay IAlibay Awaiting requested review from IAlibay

@marinegor marinegor Awaiting requested review from marinegor

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