[fmt] Format topology module and tests #4849

RMeli · 2024-12-20T20:57:17Z

Format topology module and tests. Some files from active PRs might be excluded (see #4815).

📚 Documentation preview 📚: https://mdanalysis--4849.org.readthedocs.build/en/4849/

pep8speaks · 2024-12-20T20:57:46Z

Hello @RMeli! Thanks for opening this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file package/MDAnalysis/topology/ExtendedPDBParser.py:

Line 63:80: E501 line too long (80 > 79 characters)
Line 64:80: E501 line too long (80 > 79 characters)

In the file package/MDAnalysis/topology/FHIAIMSParser.py:

Line 103:80: E501 line too long (82 > 79 characters)

In the file package/MDAnalysis/topology/GMSParser.py:

Line 112:80: E501 line too long (139 > 79 characters)

In the file package/MDAnalysis/topology/LAMMPSParser.py:

Line 230:26: E203 whitespace before ':'
Line 452:55: E203 whitespace before ':'

In the file package/MDAnalysis/topology/PSFParser.py:

Line 270:9: E731 do not assign a lambda expression, use a def
Line 384:46: E203 whitespace before ':'

In the file package/MDAnalysis/topology/TOPParser.py:

Line 597:25: E203 whitespace before ':'
Line 664:43: E203 whitespace before ':'

In the file package/MDAnalysis/topology/guessers.py:

Line 164:80: E501 line too long (87 > 79 characters)
Line 343:59: E713 test for membership should be 'not in'

In the file package/MDAnalysis/topology/tpr/obj.py:

Line 191:38: E203 whitespace before ':'

In the file testsuite/MDAnalysisTests/topology/test_top.py:

Line 168:50: E203 whitespace before ':'
Line 920:80: E501 line too long (98 > 79 characters)

codecov · 2024-12-20T21:12:02Z

Codecov Report

Attention: Patch coverage is 91.87500% with 26 lines in your changes missing coverage. Please review.

Project coverage is 93.63%. Comparing base (4f143fd) to head (22dd13c).

Files with missing lines	Patch %	Lines
package/MDAnalysis/topology/GSDParser.py	16.66%	10 Missing ⚠️
package/MDAnalysis/topology/HoomdXMLParser.py	71.42%	2 Missing and 2 partials ⚠️
package/MDAnalysis/topology/ITPParser.py	93.10%	2 Missing and 2 partials ⚠️
package/MDAnalysis/topology/PSFParser.py	82.35%	3 Missing ⚠️
package/MDAnalysis/topology/CRDParser.py	90.90%	1 Missing ⚠️
package/MDAnalysis/topology/LAMMPSParser.py	97.72%	0 Missing and 1 partial ⚠️
package/MDAnalysis/topology/MOL2Parser.py	94.11%	1 Missing ⚠️
package/MDAnalysis/topology/PQRParser.py	91.66%	0 Missing and 1 partial ⚠️
package/MDAnalysis/topology/guessers.py	94.73%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4849      +/-   ##
===========================================
- 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

The web UI was really slow with this one. I hope all the review comments were saved.

RMeli · 2024-12-20T21:39:03Z

package/MDAnalysis/topology/tpr/setting.py

-    F_BONDS, F_G96BONDS, F_MORSE, F_CUBICBONDS,
-    F_CONNBONDS, F_HARMONIC, F_FENEBONDS, F_TABBONDS,
-    F_TABBONDSNC, F_RESTRBONDS, F_ANGLES, F_G96ANGLES, F_RESTRANGLES,
-    F_LINEAR_ANGLES, F_CROSS_BOND_BONDS, F_CROSS_BOND_ANGLES, F_UREY_BRADLEY,
-    F_QUARTIC_ANGLES, F_TABANGLES, F_PDIHS, F_RBDIHS, F_RESTRDIHS, F_CBTDIHS,
-    F_FOURDIHS, F_IDIHS, F_PIDIHS, F_TABDIHS,
-    F_CMAP, F_GB12, F_GB13, F_GB14,
-    F_GBPOL, F_NPSOLVATION, F_LJ14, F_COUL14,
-    F_LJC14_Q, F_LJC_PAIRS_NB, F_LJ, F_BHAM,
-    F_LJ_LR, F_BHAM_LR, F_DISPCORR, F_COUL_SR,
-    F_COUL_LR, F_RF_EXCL, F_COUL_RECIP, F_LJ_RECIP, F_DPD,
-    F_POLARIZATION, F_WATER_POL, F_THOLE_POL, F_ANHARM_POL,
-    F_POSRES, F_FBPOSRES, F_DISRES, F_DISRESVIOL, F_ORIRES,
-    F_ORIRESDEV, F_ANGRES, F_ANGRESZ, F_DIHRES,
-    F_DIHRESVIOL, F_CONSTR, F_CONSTRNC, F_SETTLE, F_VSITE1,
-    F_VSITE2, F_VSITE2FD, F_VSITE3, F_VSITE3FD, F_VSITE3FAD,
-    F_VSITE3OUT, F_VSITE4FD, F_VSITE4FDN, F_VSITEN,
-    F_COM_PULL, F_DENSITYFITTING, F_EQM, F_EPOT, F_EKIN,
-    F_ETOT, F_ECONSERVED, F_TEMP, F_VTEMP_NOLONGERUSED,
-    F_PDISPCORR, F_PRES, F_DHDL_CON, F_DVDL,
-    F_DKDL, F_DVDL_COUL, F_DVDL_VDW, F_DVDL_BONDED,
-    F_DVDL_RESTRAINT, F_DVDL_TEMPERATURE, F_NRE) = list(range(95))


Does formatting here has a special meaning?

RMeli · 2024-12-20T21:39:06Z

package/MDAnalysis/topology/tpr/setting.py

+    F_DVDL_RESTRAINT,
+    F_DVDL_TEMPERATURE,
+    F_NRE,
+) = list(range(95))

 #: Function types from ``<gromacs_dir>/src/gmxlib/tpxio.c``
 ftupd = [


Does formatting here has a special meaning?

RMeli · 2024-12-20T21:41:15Z

testsuite/MDAnalysisTests/topology/test_pdb.py

+        [
+            "N",
+            "C",
+            "C",
+            "O",
+            "C",
+            "C",
+            "O",
+            "N",
+            "H",
+            "H",
+            "H",
+            "H",
+            "H",
+            "H",
+            "H",
+            "H",
+            "Cu",
+            "Fe",
+            "Mg",
+            "Ca",
+            "S",
+            "O",
+            "C",
+            "C",
+            "S",
+            "O",
+            "C",
+            "C",
+        ],


Not great, not terrible.

RMeli · 2024-12-20T21:42:04Z

testsuite/MDAnalysisTests/topology/test_pdb.py

+        [
+            0,
+            0,
+            0,
+            0,
+            0,
+            0,
+            0,
+            -1,
+            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,


Not great, not terrible.

RMeli · 2024-12-20T21:43:02Z

testsuite/MDAnalysisTests/topology/test_top.py

+            [
+                "H",
+                "O",
+                "C",
+                "H",
+                "H",
+                "C",
+                "H",
+                "O",
+                "C",
+                "H",
+                "N",
+                "C",
+                "H",
+                "N",
+                "C",
+                "C",
+                "O",
+                "N",
+                "H",
+                "C",
+                "N",
+                "H",
+                "H",
+                "N",
+                "C",
+                "C",
+                "H",
+                "C",
+                "H",
+                "H",
+                "O",
+                "P",
+                "O",
+                "O",
+                "O",
+                "C",
+            ],


Not great, not terrible.

RMeli · 2024-12-20T21:47:20Z

testsuite/MDAnalysisTests/topology/test_tprparser.py

+        [
+            "O",
+            "H",
+            "H",
+            "",
+            "O",
+            "H",
+            "H",
+            "",
+            "O",
+            "H",
+            "H",
+            "",
+            "O",
+            "H",
+            "H",
+            "",
+            "Na",
+            "Na",
+            "Na",
+            "Na",
+        ],


Use the trick above?

RMeli · 2024-12-20T21:47:30Z

testsuite/MDAnalysisTests/topology/test_tprparser.py

-    @pytest.fixture(params=[TPR400, TPR402, TPR403, TPR404, TPR405, TPR406,
-                            TPR407, TPR450, TPR451, TPR452, TPR453, TPR454,
-                            TPR455, TPR502, TPR504, TPR505, TPR510, TPR2016,
-                            TPR2018, TPR2019B3, TPR2020, TPR2020Double,
-                            TPR2021, TPR2021Double, TPR2022RC1, TPR2023,
-                            TPR2024])


I don't mind, but not everyone will like this.

RMeli · 2024-12-20T21:47:37Z

testsuite/MDAnalysisTests/topology/test_tprparser.py

+            "H,C,H,H,C,H,H,H,C,H,H,H,C,O,N,H,C,H,C,H,H,C,H,C,H,H,H,C,H,H,"
+            "H,C,O,N,H,C,H,H,C,O,O,O,H,H,,O,H,H,,O,H,H,,O,H,H,,O,H,H,,O,H"
+            ",H,,O,H,H,,O,H,H,,O,H,H,,O,H,H,,O,H,H,,O,H,H,,O,H,H,,O,H,H,,"
+            "O,H,H"


This is a nice trick, could be applied elsewhere. Here just list("HCHHC") should work since they are all single-letter elements, but this will work elsewhere.

RMeli · 2024-12-20T21:47:51Z

testsuite/MDAnalysisTests/topology/test_tprparser.py

-    TPR400, TPR402, TPR403, TPR404, TPR405, TPR406, TPR407,
-    TPR450, TPR451, TPR452, TPR453, TPR454, TPR455, TPR455Double,
-    TPR460, TPR461, TPR502, TPR504, TPR505, TPR510, TPR510_bonded,
-    TPR2016, TPR2018, TPR2019B3, TPR2020B2, TPR2020, TPR2020Double,
-    TPR2021, TPR2021Double, TPR2022RC1, TPR2023, TPR2024,
-    TPR2016_bonded, TPR2018_bonded, TPR2019B3_bonded,
-    TPR2020B2_bonded, TPR2020_bonded, TPR2020_double_bonded,
-    TPR2021_bonded, TPR2021_double_bonded, TPR334_bonded,
-    TPR2022RC1_bonded, TPR2023_bonded, TPR2024_bonded,
-    TPR_EXTRA_2021, TPR_EXTRA_2020, TPR_EXTRA_2018,
-    TPR_EXTRA_2016, TPR_EXTRA_407, TPR_EXTRA_2022RC1,
-    TPR_EXTRA_2023, TPR_EXTRA_2024,


Is there some meaning here?

RMeli · 2024-12-20T21:48:03Z

testsuite/MDAnalysisTests/topology/test_top.py

+            [
+                "C",
+                "C",
+                "H",
+                "C",
+                "H",
+                "H",
+                "O",
+                "P",
+                "O",
+                "O",
+                "O",
+                "C",
+                "H",
+                "H",
+                "C",
+                "H",
+                "O",
+                "C",


If someone judge in terms of LOC, this is a win. =P

orbeckst

blanket LGTM — please merge when you're happy with it @RMeli

🎄 🎁

fmt topo

22dd13c

RMeli commented Dec 20, 2024

View reviewed changes

RMeli requested review from IAlibay and marinegor December 20, 2024 21:48

orbeckst assigned RMeli Dec 24, 2024

orbeckst approved these changes Dec 24, 2024

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[fmt] Format topology module and tests #4849

[fmt] Format topology module and tests #4849

RMeli commented Dec 20, 2024 •

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[fmt] Format topology module and tests #4849

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[fmt] Format topology module and tests #4849

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RMeli commented Dec 20, 2024 •

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