distopia 0.3.0 compatibility changes #4734

hmacdope · 2024-10-15T10:24:39Z

Test implementation of distopia-0.3.0 distances API.

Changes made in this Pull Request:

Adds support for distopia 0.3.0 API

PR Checklist

Tests?
Docs?
CHANGELOG updated?
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--4734.org.readthedocs.build/en/4734/

pep8speaks · 2024-10-15T10:24:47Z

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

In the file package/MDAnalysis/lib/_distopia.py:

Line 64:80: E501 line too long (82 > 79 characters)
Line 90:80: E501 line too long (86 > 79 characters)
Line 96:80: E501 line too long (103 > 79 characters)
Line 98:80: E501 line too long (83 > 79 characters)
Line 102:80: E501 line too long (103 > 79 characters)
Line 105:80: E501 line too long (83 > 79 characters)
Line 109:80: E501 line too long (107 > 79 characters)
Line 111:80: E501 line too long (87 > 79 characters)
Line 113:1: E302 expected 2 blank lines, found 1
Line 114:80: E501 line too long (124 > 79 characters)
Line 116:80: E501 line too long (95 > 79 characters)
Line 118:1: E302 expected 2 blank lines, found 1
Line 119:80: E501 line too long (124 > 79 characters)
Line 121:80: E501 line too long (95 > 79 characters)
Line 123:1: E302 expected 2 blank lines, found 1
Line 130:80: E501 line too long (82 > 79 characters)
Line 132:80: E501 line too long (82 > 79 characters)
Line 134:1: E302 expected 2 blank lines, found 1
Line 135:80: E501 line too long (82 > 79 characters)
Line 137:80: E501 line too long (82 > 79 characters)
Line 139:1: E302 expected 2 blank lines, found 1
Line 144:1: E302 expected 2 blank lines, found 1
Line 149:1: E302 expected 2 blank lines, found 1
Line 153:1: W391 blank line at end of file

In the file package/MDAnalysis/lib/distances.py:

Line 77:53: W291 trailing whitespace
Line 344:1: W293 blank line contains whitespace
Line 348:44: W291 trailing whitespace
Line 374:80: E501 line too long (80 > 79 characters)
Line 457:44: W291 trailing whitespace
Line 483:80: E501 line too long (80 > 79 characters)
Line 1677:44: W291 trailing whitespace
Line 1703:80: E501 line too long (80 > 79 characters)
Line 1800:44: W291 trailing whitespace
Line 1827:80: E501 line too long (80 > 79 characters)
Line 1939:44: W291 trailing whitespace
Line 1963:80: E501 line too long (80 > 79 characters)

In the file testsuite/MDAnalysisTests/lib/test_distances.py:

Line 1095:32: E222 multiple spaces after operator
Line 1099:5: E303 too many blank lines (2)
Line 1106:32: E222 multiple spaces after operator

Comment last updated at 2025-01-06 18:00:18 UTC

github-actions · 2024-10-15T10:26:53Z

Linter Bot Results:

Hi @hmacdope! 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	✅ Passed

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/11344140762/job/31548247192

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

codecov · 2024-10-15T10:35:26Z

Codecov Report

Attention: Patch coverage is 90.14085% with 7 lines in your changes missing coverage. Please review.

Project coverage is 93.62%. Comparing base (536a390) to head (a865a46).
Report is 1 commits behind head on develop.

Files with missing lines	Patch %	Lines
package/MDAnalysis/lib/distances.py	88.57%	2 Missing and 2 partials ⚠️
package/MDAnalysis/lib/_distopia.py	91.66%	3 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4734      +/-   ##
===========================================
- Coverage    93.66%   93.62%   -0.04%     
===========================================
  Files          177      189      +12     
  Lines        21796    22918    +1122     
  Branches      3067     3079      +12     
===========================================
+ Hits         20415    21457    +1042     
- Misses         929     1007      +78     
- Partials       452      454       +2

☔ View full report in Codecov by Sentry.
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hmacdope · 2024-10-17T03:29:35Z

@orbeckst @richardjgowers this is ready for a first look over. The failing tests are for a 180 degree dihedral where numpy returns np.pi and distopia returns -np.pi (equivalent in polar coordinates). Are we ok to change the test to account for this? There are also options for changing in distopia but at the cost of a lot of performance improvement.

orbeckst · 2024-10-17T05:06:02Z

I'd be ok with changing tests but adding a note to docs.

package/MDAnalysis/lib/_distopia.py

orbeckst

I am not sure if the tests are actually run — if we can confirm that they run then I have no blockers.

ALso updated CHANGELOG, please.

package/MDAnalysis/lib/distances.py

package/MDAnalysis/lib/_distopia.py

orbeckst · 2024-10-18T21:45:28Z

FYI, upstream distopia 0.3.0 release is currently breaking all tests, see #4739 .

package/MDAnalysis/lib/distances.py

Co-authored-by: Oliver Beckstein <[email protected]>

…ompat

testsuite/MDAnalysisTests/lib/test_distances.py

package/MDAnalysis/lib/distances.py

package/MDAnalysis/lib/_distopia.py

package/MDAnalysis/lib/distances.py

orbeckst

With the astype required for distopia you may be creating a copy so that the top-level in-place operation is not actually in-place anymore. ... I think.

package/MDAnalysis/lib/distances.py

orbeckst · 2024-11-21T00:58:05Z

@hmacdope did you look further into the copy vs in-place issue?

hmacdope · 2024-12-02T21:06:57Z

@orbeckst I'll try get back to this over holidays, sorry for delay.

orbeckst · 2024-12-10T21:48:21Z

Ok! I think getting this one working will be important for a MDA paper.

orbeckst · 2024-12-10T22:04:57Z

@hmacdope I resolved the merge conflicts but please double-check that I didn't miss anything.

…s into distopia_0.3.0_compat

…ompat

hmacdope · 2025-01-02T09:20:37Z

@orbeckst this is probably ready for another look.

orbeckst · 2025-01-06T18:11:57Z

testsuite/MDAnalysisTests/lib/test_distances.py

    def test_selfdist(self, S_mol, box, tri_vec_box, backend):
        S_mol1, S_mol2 = S_mol
-        R_coords = distances.transform_StoR(S_mol1, box, backend=backend)
+        R_coords = distances.transform_StoR(S_mol1, box, backend="serial")


Why hard-code serial here instead of using backend?

Should the comment below apply to the R_coords line?

Maybe add a short comment.

orbeckst

Quick first look (sorry for brevity), see minor comments and below:

Could you please also make PEP8 happy?
Coverage?

orbeckst · 2025-01-06T18:13:32Z

testsuite/MDAnalysisTests/lib/test_distances.py

    def test_selfdist(self, S_mol, box, tri_vec_box, backend):
        S_mol1, S_mol2 = S_mol
-        R_coords = distances.transform_StoR(S_mol1, box, backend=backend)
+        R_coords = distances.transform_StoR(S_mol1, box, backend="serial")


Should the comment below apply to the R_coords line?

Maybe add a short comment.

orbeckst · 2025-01-06T18:13:54Z

testsuite/MDAnalysisTests/lib/test_distances.py

@@ -948,7 +961,7 @@ def test_selfdist(self, S_mol, box, tri_vec_box, backend):
        )

        # Do it again for input 2 (has wider separation in points)
-        R_coords = distances.transform_StoR(S_mol2, box, backend=backend)
+        R_coords = distances.transform_StoR(S_mol2, box, backend="serial")


Same questions as above – explain why backend="serial"

orbeckst · 2025-01-06T23:44:31Z

Something is not right with the macos-13 tests — they timed out at 55 mins and they are again taking much longer than all the other runners.

IAlibay · 2025-01-07T01:27:02Z

Something is not right with the macos-13 tests — they timed out at 55 mins and they are again taking much longer than all the other runners.

This is unrelated to this PR as far as I can tell (we probably should re-open #4781?). It's been a while but iirc the macos13 images had a sudden performance drop at some point in the last year-ish and it never was resolved. We could drop the tests to be "non optional deps only" that might help keep things a bit sane for now.

IAlibay

Couple things, apparent missing test coverage is the biggest thing, otherwise (assuming @orbeckst's comments are addressed), lgtm.

IAlibay · 2025-01-07T01:29:34Z

package/MDAnalysis/lib/_distopia.py

-    has_distopia_020 = all([hasattr(distopia, func) for func in needed_funcs])
-    if not has_distopia_020:
+    # check for compatibility: currently needs to be >=0.3.1,
+    # some versions of `distopia` don't have a version attribute


Are these versions known? I.e. if we know that this only affects a certain set of releases and they are all <0.3.1, then can we skip the warning altogther and just assume that this only happens in old versions we don't care about?

(intent: I'm trying to completly bypass the follow-up "there are no tests for line 50" with a blunt solution)

IAlibay · 2025-01-07T01:31:46Z

package/MDAnalysis/lib/_distopia.py

+    distopia.calc_bonds_triclinic(coords1, coords2, box, results=results)
+
+
+def calc_angle(


Has @RMeli lint lib? If so, could you run black on this file @hmacdope ?

IAlibay · 2025-01-07T01:43:37Z

package/MDAnalysis/lib/distances.py

@@ -353,6 +370,13 @@ def distance_array(
            backend=backend,
        )

+    if backend == 'distopia':


Not for this PR, but you do this pattern enough that I wonder if life might be easier if you moved this into a decorator (or even just straight up into check_coords?

IAlibay · 2025-01-07T01:44:26Z

package/MDAnalysis/lib/distances.py

+        # to float64, change for 3.0, see #3707
+        angles = angles.astype(np.float64)
+        if result is not None:
+            result[:] = angles


For here and dihedrals codecov is reporting no coverage, is that true/expected?

hmacdope added 6 commits October 15, 2024 16:02

start of docs

2ee12e5

improve distopia stup

9bf0cf7

add backend conditionals

f8d1295

fix wrong backend

badc778

shims

e97317b

working except for dihedrals

e0ce653

hmacdope added 3 commits October 16, 2024 21:07

move to 0.3.0

63162df

bump ci

0ec2057

bump ci

2392101

hmacdope marked this pull request as ready for review October 17, 2024 03:26

hmacdope requested review from orbeckst and richardjgowers October 17, 2024 03:30

IAlibay reviewed Oct 17, 2024

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orbeckst mentioned this pull request Oct 18, 2024

Pin to distopia < 0.3 ahead of v2.8.0 release #4739

Closed

orbeckst mentioned this pull request Oct 18, 2024

Deprecate encore #4737

Merged

5 tasks

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orbeckst mentioned this pull request Oct 18, 2024

pin distopia<0.3.0 #4740

Merged

8 tasks

hmacdope and others added 6 commits October 21, 2024 11:11

Update package/MDAnalysis/lib/distances.py

2cb04d2

Co-authored-by: Oliver Beckstein <[email protected]>

Merge remote-tracking branch 'upstream/develop' into distopia_0.3.0_c…

e4b8a10

…ompat

fix versioning

517c676

add version checking

36de301

remove erroneous triclinic note

b49b028

remove unnesecary import

d895d99

hmacdope commented Oct 24, 2024

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orbeckst self-assigned this Nov 21, 2024

Merge branch 'develop' into distopia_0.3.0_compat

2c070b7

add type for calc_bond_distance_ortho()

d4b9e9d

orbeckst added this to the Release 3.0 milestone Dec 12, 2024

hmacdope added 9 commits December 31, 2024 15:29

just stuff answers back in if we used a buffer

2621552

Merge branch 'distopia_0.3.0_compat' of github.com:hmacdope/mdanalysi…

154d389

…s into distopia_0.3.0_compat

add cram for distance array also

c75dce2

fix changelogs

02a3d93

Merge remote-tracking branch 'upstream/develop' into distopia_0.3.0_c…

07f1438

…ompat

black

9101d81

imporve mock test

447beac

fix typo

0a60016

add debug printing

730cee9

hmacdope requested a review from orbeckst January 2, 2025 07:43

Merge branch 'develop' into distopia_0.3.0_compat

a865a46

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distopia 0.3.0 compatibility changes #4734

distopia 0.3.0 compatibility changes #4734

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		distopia.calc_bonds_triclinic(coords1, coords2, box, results=results)


		def calc_angle(

distopia 0.3.0 compatibility changes #4734

Are you sure you want to change the base?

distopia 0.3.0 compatibility changes #4734

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