Replaced numpy.testing.assert_almost_equal to numpy.testing.assert_allclose #4438

aditya292002 · 2024-01-24T09:11:31Z

Fixes #

Changes made in this Pull Request:

Replaced numpy.testing.assert_almost_equal to numpy.testing.assert_allclose for more consistent floating point comparisons. as mentioned in the issue #3743
Changes are made in mdanalysis/testsuite/MDAnalysisTests/analysis/test_align.py and /mdanalysis/package/MDAnalysis/visualization/streamlines_3D.py

PR Checklist

[Passed ] Tests
[ Not Updated] Docs?
[ Not Updated] CHANGELOG updated?
[ modernize testing code #3743] 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--4438.org.readthedocs.build/en/4438/

…tent floating point comparisons e.g. # assert_almost_equal(rms.rmsd(first_frame, first_frame), 0.0, 5, # err_msg="error: rmsd(X,X) should be 0") assert_allclose(rms.rmsd(first_frame, first_frame), 0.0, rtol=0, atol=1.5*1e-5, err_msg="error: rmsd(X,X) should be 0") 1.5 factor in atol bcz,in assert_almost_equal The test verifies that the elements of actual and desired satisfy. abs(desired-actual) < float64(1.5 * 10**(-decimal)) So, to keep behaviour consistent in assert_allclose introduced factor 1.5 in atol

pep8speaks · 2024-01-24T09:11:38Z

Hello @aditya292002! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file package/MDAnalysis/visualization/streamlines_3D.py:

Line 248:80: E501 line too long (83 > 79 characters)
Line 249:43: E127 continuation line over-indented for visual indent
Line 249:80: E501 line too long (111 > 79 characters)

In the file testsuite/MDAnalysisTests/analysis/test_align.py:

Line 200:80: E501 line too long (85 > 79 characters)
Line 207:80: E501 line too long (93 > 79 characters)
Line 210:80: E501 line too long (100 > 79 characters)
Line 210:101: W291 trailing whitespace
Line 320:80: E501 line too long (84 > 79 characters)
Line 360:44: E251 unexpected spaces around keyword / parameter equals
Line 360:46: E251 unexpected spaces around keyword / parameter equals
Line 396:35: E127 continuation line over-indented for visual indent
Line 439:80: E501 line too long (87 > 79 characters)
Line 446:29: E127 continuation line over-indented for visual indent
Line 454:29: E127 continuation line over-indented for visual indent

In the file testsuite/MDAnalysisTests/analysis/test_base.py:

Line 254:80: E501 line too long (81 > 79 characters)

In the file testsuite/MDAnalysisTests/analysis/test_contacts.py:

Line 265:80: E501 line too long (87 > 79 characters)
Line 282:80: E501 line too long (87 > 79 characters)
Line 307:80: E501 line too long (83 > 79 characters)
Line 367:61: E231 missing whitespace after ','
Line 367:80: E501 line too long (81 > 79 characters)
Line 413:80: E501 line too long (84 > 79 characters)
Line 435:80: E501 line too long (84 > 79 characters)

In the file testsuite/MDAnalysisTests/analysis/test_dihedrals.py:

Line 49:80: E501 line too long (84 > 79 characters)
Line 57:80: E501 line too long (84 > 79 characters)
Line 65:80: E501 line too long (84 > 79 characters)
Line 94:80: E501 line too long (81 > 79 characters)
Line 102:80: E501 line too long (87 > 79 characters)
Line 179:80: E501 line too long (89 > 79 characters)

In the file testsuite/MDAnalysisTests/analysis/test_encore.py:

Line 156:80: E501 line too long (98 > 79 characters)
Line 176:80: E501 line too long (103 > 79 characters)
Line 195:53: E231 missing whitespace after ','
Line 195:80: E501 line too long (93 > 79 characters)
Line 277:80: E501 line too long (88 > 79 characters)
Line 368:38: E231 missing whitespace after ','
Line 379:42: E231 missing whitespace after ','
Line 379:80: E501 line too long (83 > 79 characters)
Line 399:80: E501 line too long (87 > 79 characters)
Line 400:80: E501 line too long (85 > 79 characters)
Line 416:29: E127 continuation line over-indented for visual indent
Line 416:80: E501 line too long (128 > 79 characters)
Line 440:17: E251 unexpected spaces around keyword / parameter equals
Line 440:19: E251 unexpected spaces around keyword / parameter equals
Line 441:17: E251 unexpected spaces around keyword / parameter equals
Line 441:19: E251 unexpected spaces around keyword / parameter equals

Comment last updated at 2024-02-24 09:35:19 UTC

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 · 2024-01-24T09:13:48Z

Linter Bot Results:

Hi @aditya292002! Thanks for making this PR. We linted your code and found the following:

Some issues were found with the formatting of your code.

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codecov · 2024-01-24T09:21:55Z

Codecov Report

Attention: Patch coverage is 0% with 1 lines in your changes are missing coverage. Please review.

Project coverage is 93.37%. Comparing base (3a5339c) to head (e1f2f4e).

Files	Patch %	Lines
package/MDAnalysis/visualization/streamlines_3D.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4438      +/-   ##
===========================================
- Coverage    93.38%   93.37%   -0.01%     
===========================================
  Files          171      183      +12     
  Lines        21744    22823    +1079     
  Branches      4014     4014              
===========================================
+ Hits         20305    21311    +1006     
- Misses         952     1025      +73     
  Partials       487      487

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tylerjereddy

I had one or two comments, apart from those most cases seem to match this idiom:

Before: abs(desired-actual) < float64(1.5 * 10**(-decimal))
New: abs(desired-actual) < atol + rtol * abs(desired) with 0 for rtol reducing to abs(desired-actual) < atol, so you just set atol to 1.5 * 10**(-decimal) to match the original behavior.

I suppose that's hard to argue with in terms of being equivalent. There probably are some cases where you do want to allow an rtol, but I don't have a huge problem with the literal translations for now I suppose.

tylerjereddy · 2024-01-25T00:03:48Z

testsuite/MDAnalysisTests/analysis/test_align.py

@@ -167,7 +167,8 @@ def test_subselection_alignto(self, universe, reference, subselection, expectati

        with expectation:
            rmsd = align.alignto(universe, reference, subselection=subselection)
-            assert_almost_equal(rmsd[1], 0.0, decimal=9)
+            # assert_almost_equal(rmsd[1], 0.0, decimal=9)
+            assert_allclose(rmsd[1], 0.0, rtol=0, atol=1.5*1e-9)


I think we can remove the commented old version

tylerjereddy · 2024-01-25T00:05:39Z

testsuite/MDAnalysisTests/analysis/test_align.py


    def test_rmsd_custom_mass_weights(self, universe, reference):
        last_atoms_weight = universe.atoms.masses
        A = universe.trajectory[0]
        B = reference.trajectory[-1]
        rmsd = align.alignto(universe, reference,
-                             weights=reference.atoms.masses)
+                                weights=reference.atoms.masses)


some of the whitespace changes don't seem useful?

tylerjereddy · 2024-01-25T00:20:05Z

testsuite/MDAnalysisTests/analysis/test_align.py

+                        err_msg="assert_allclose failed for positions")
+        assert_allclose(avg.results.rmsd, rmsd,
+                        rtol=0, atol=1.5*(1e-4),
+                        err_msg="assert_allclose failed for rmsd")


fwiw, I don't think these custom messages are worth it in this context, but that may just be based on the style of the projects I usually maintain

tylerjereddy · 2024-01-25T00:21:41Z

testsuite/MDAnalysisTests/analysis/test_align.py

+                        rtol=0, atol=1.5*(1e-4),
+                        err_msg="assert_allclose failed for positions")
+        assert_allclose(avg.results.rmsd, rmsd,
+                        rtol=0, atol=1.5*(1e-4),


Don't you want 1e-7 since assert_almost_equal is using default arguments in the original here?

Yeah, that's a mistake. I will correct this.

- correction - removed unnecessary error messages

aditya292002 · 2024-01-25T07:38:42Z

Hi, @tylerjereddy, I've made all the suggested changes. Should I proceed with applying the same modifications to all the files? There are nearly 840 occurrences of just the 'assert_almost_close'. I'm thinking of creating a Python script to automate these changes. Should I go ahead with that approach?

Also, could you please explain why not all the test cases are passing? I didn't make any changes to the '/mdanalysis/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py' file, but the 'def test_creating_multiple_universe_without_offset(temp_xtc, ncopies=3)' test failed for Ubuntu with Python 3.12.

Thank you.

IAlibay · 2024-01-25T07:41:58Z

@aditya292002 this issue is really meant to be taken in small chunks and not all on one go. I would suggest doing a handful of files so that it's both manageable to yourself and reviewers.

Regarding the test failures, this is a known issue and not related to this PR.

…analysis

aditya292002 · 2024-01-25T09:52:09Z

@IAlibay, I've made additional changes to the files: test_base, test_bat, test_contracts, test_dihedrals, and test_encore.

Please review these modifications and merge this pull request for the time being. I'd like to further explore this project and address any other issues.
Thank you for your assistance.

aditya292002 · 2024-01-26T12:22:02Z

@IAlibay, I've made additional changes to the files: test_base, test_bat, test_contracts, test_dihedrals, and test_encore.

Please review these modifications and merge this pull request for the time being. I'd like to further explore this project and address any other issues. Thank you for your assistance.

IAlibay · 2024-01-26T17:57:14Z

@aditya292002 - whilst I appreciate your work here, I would like to ask for your patience. The MDAnalysis developers are not full time hired on the project and have their own separate jobs / lives. I will add this to my task list and will attempt to review, althoughtit may take at least a few days (there are already a few other reviews pending my attention).

aditya292002 · 2024-01-27T05:30:01Z

@aditya292002 - whilst I appreciate your work here, I would like to ask for your patience. The MDAnalysis developers are not full time hired on the project and have their own separate jobs / lives. I will add this to my task list and will attempt to review, althoughtit may take at least a few days (there are already a few other reviews pending my attention).

Apologies for any impatience displayed. I am currently a university student, and this marks my initial involvement in contributing to an open-source project. Rest assured, I will take note of this experience for future contributions.

IAlibay · 2024-01-31T02:18:04Z

I won't be able to get to reviewing this any time soon - can one of the current @MDAnalysis/coredevs take this on instead please?

orbeckst · 2024-01-31T14:10:57Z

@tylerjereddy would you be able review this PR, given that you already had some eyes on it?

tylerjereddy · 2024-02-01T02:00:36Z

@aditya292002 please remove the testsuite/MDAnalysisTests/analysis/__pycache__/test_gnm.cpython-310-pytest-7.4.4.pyc.1853 file from your branch, we don't want Python bytecode files under version control.

After you check that your diff only has the changes that are needed, feel free to ping me again and I'll take another look.

aditya292002 · 2024-02-02T10:40:10Z

@aditya292002 please remove the testsuite/MDAnalysisTests/analysis/__pycache__/test_gnm.cpython-310-pytest-7.4.4.pyc.1853 file from your branch, we don't want Python bytecode files under version control.

After you check that your diff only has the changes that are needed, feel free to ping me again and I'll take another look.

@tylerjereddy, I have removed the specified bytecode file.

tylerjereddy · 2024-02-03T00:49:01Z

testsuite/MDAnalysisTests/analysis/test_align.py

-        assert_almost_equal(rmsd, desired, decimal=5,
-                            err_msg="frame {0:d} of fit does not have "
-                                    "expected RMSD".format(frame))
+            fitted.trajectory[frame]


You still have unwanted whitespace changes here and elsewhere, please re-read the entire diff line-by-line and make sure those changes are not present (since I'm spending time doing the same).

orbeckst

Please fix any whitespace issues: if you didn't touch a line then it shouldn't change in the diff.
Write floats in engineering notation and not as products (see comment).
Remove assert_almost_equal from the import line in any file where you replaced it with assert_allclose.

orbeckst · 2024-02-10T01:45:06Z

package/MDAnalysis/visualization/streamlines_3D.py

-        np.testing.assert_almost_equal(array_cube_vertex_distances_from_centroid.min(),
-                                          array_cube_vertex_distances_from_centroid.max(), decimal=4,
+        np.testing.assert_allclose(array_cube_vertex_distances_from_centroid.min(),
+                                          array_cube_vertex_distances_from_centroid.max(), rtol=0, atol=1.5*(1e-4),


Write floats as 1.5e-4 and not as 1.5*(1e-4).

This applies to all floats with powers of ten throughout.

orbeckst · 2024-02-10T01:45:59Z

testsuite/MDAnalysisTests/analysis/test_align.py


        self._assert_rmsd(reference, fitted, 0, 0.0,
-                          weights=universe.atoms.masses)
+                            weights=universe.atoms.masses)


undo indent

orbeckst · 2024-02-10T01:46:03Z

testsuite/MDAnalysisTests/analysis/test_align.py

        self._assert_rmsd(reference, fitted, -1, 6.929083032629219,
-                          weights=universe.atoms.masses)
+                            weights=universe.atoms.masses)


undo indent

orbeckst · 2024-02-10T01:47:22Z

testsuite/MDAnalysisTests/analysis/test_base.py

@@ -27,7 +27,7 @@

 import numpy as np

-from numpy.testing import assert_equal, assert_almost_equal
+from numpy.testing import assert_equal, assert_almost_equal, assert_allclose


remove assert_almost_equal: the whole point of the PR is to get rid of it :-)

testsuite/MDAnalysisTests/analysis/test_align.py

aditya292002 · 2024-02-12T15:14:05Z

testsuite/MDAnalysisTests/analysis/test_encore.py

-        assert_almost_equal(result_value, expected_value, decimal=-3,
-                            err_msg="Unexpected value for Harmonic Ensemble Similarity: {0:f}. Expected {1:f}.".format(result_value, expected_value))
+        assert_allclose(result_value, expected_value, rtol=0, atol=1.5*(1e3),
+                        err_msg="Unexpected value for Harmonic Ensemble Similarity: {0:f}. Expected {1:f}.".format(result_value, expected_value))



please check if I have got this right

Yes, it's a very loose test!

aditya292002 · 2024-02-13T05:46:59Z

testsuite/MDAnalysisTests/analysis/test_encore.py

                            err_msg="Unexpected average value for bootstrapped samples in Clustering Ensemble similarity")
-        assert_almost_equal(stdev, expected_stdev, decimal=0,
+
+            assert_almost_equal(stdev, expected_stdev, decimal=0,
                            err_msg="Unexpected standard daviation  for bootstrapped samples in Clustering Ensemble similarity")


for this, "assert_almost_equal" statement
the value of parameter decimal = 0,

which means abs(x,y) should be < 1.5 (which i found by running some examples),

but, for assert_allclose(x,y, rtol=0, atol=0) means the abs(x-y) = 0,

To resolve this should I go ahead and replace the assert_almost_equal which a if condition.
Please suggest some alternate ways to handle it.

The equivalent for decimal=0 is atol=1.5e0 which is just atol=1.5:

assert_allclose(stdev, expected_stdev, rtol=0, atol=1.5)

Does the code above work?

Btw, can you please fix the spelling mistake: "daviation" --> "deviation"?

removed all the extra widespaces and correct the format for atol=1.5e-x

aditya292002 · 2024-02-17T04:39:50Z

@tylerjereddy, could you please take a look at the changes I made?

aditya292002 · 2024-02-20T05:54:46Z

@orbeckst , could you please take a look at the changes I made?

orbeckst

This looks almost done:

fix the last assert_almost_equal with decimal=0 (see comment)
add yourself to the AUTHORS file
add an entry to CHANGELOG:

"updated tests that used assert_almost_equal(..., decimal={N}) with equivalent assert_allclose(..., rtol=0, atol=1.5e-{N}) (issue modernize testing code #3743, PR Replaced numpy.testing.assert_almost_equal to numpy.testing.assert_allclose #4438)"

(Normally we don't include changes to the tests in CHANGELOG, but this one may make some tests fail and we want to have documentation that alerts us to the fact that we changed test evaluation.)

testsuite/MDAnalysisTests/analysis/test_align.py

orbeckst · 2024-02-20T22:22:07Z

testsuite/MDAnalysisTests/analysis/test_contacts.py

    assert_equal,
    assert_array_equal,
-    assert_array_almost_equal
+    assert_array_almost_equal,


assert_array_almost_equal() could also be replaced with assert_allclose().

orbeckst · 2024-02-20T22:23:05Z

testsuite/MDAnalysisTests/analysis/test_encore.py

-        assert_almost_equal(result_value, expected_value, decimal=-3,
-                            err_msg="Unexpected value for Harmonic Ensemble Similarity: {0:f}. Expected {1:f}.".format(result_value, expected_value))
+        assert_allclose(result_value, expected_value, rtol=0, atol=1.5*(1e3),
+                        err_msg="Unexpected value for Harmonic Ensemble Similarity: {0:f}. Expected {1:f}.".format(result_value, expected_value))



Yes, it's a very loose test!

orbeckst · 2024-02-20T22:33:01Z

testsuite/MDAnalysisTests/analysis/test_encore.py

                            err_msg="Unexpected average value for bootstrapped samples in Clustering Ensemble similarity")
-        assert_almost_equal(stdev, expected_stdev, decimal=0,
+
+            assert_almost_equal(stdev, expected_stdev, decimal=0,
                            err_msg="Unexpected standard daviation  for bootstrapped samples in Clustering Ensemble similarity")


The equivalent for decimal=0 is atol=1.5e0 which is just atol=1.5:

assert_allclose(stdev, expected_stdev, rtol=0, atol=1.5)

Does the code above work?

and - changed assert_array_almost_equal with assert_allclose

…equal to assert_allclose

orbeckst

Please fix CHANGELOG, otherwise looking good!

UPDATE: There are now tests that are failing. Please have a look at them and propose adjustments to the tolerances to make them pass again.

orbeckst · 2024-02-23T14:13:39Z

package/CHANGELOG

+24/02/23 aditya292002
+  * "updated tests that used assert_almost_equal(..., decimal={N}) with equivalent assert_allclose(..., rtol=0, atol=1.5e-{N}) (issue modernize testing code #3743, PR Replaced numpy.testing.assert_almost_equal to numpy.testing.assert_allclose #4438)"
+
+  /workspaces/mdanalysis/package/CHANGELOG


remove this line!

orbeckst · 2024-02-23T14:16:30Z

package/CHANGELOG

+24/02/23 aditya292002
+  * "updated tests that used assert_almost_equal(..., decimal={N}) with equivalent assert_allclose(..., rtol=0, atol=1.5e-{N}) (issue modernize testing code #3743, PR Replaced numpy.testing.assert_almost_equal to numpy.testing.assert_allclose #4438)"


Add information to the top of the file under 2.8.0.

add your handle after ??/??/?? IAlibay, HeetVekariya, marinegor, lilyminium

add the text under "Changes"

package/CHANGELOG

aditya292002 · 2024-02-24T13:11:04Z

@orbeckst Do I need to do anything more in this PR.

orbeckst · 2024-02-24T18:06:54Z

Congratulations on your first contribution @aditya292002 ! 🎉

aditya292002 added 2 commits January 24, 2024 07:36

added the deleted statements

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modernize testing code #3743

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made the changes as pointed by maintainer

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- correction - removed unnecessary error messages

Merge branch 'MDAnalysis:develop' into develop

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Corrected error with occured in last commit

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aditya292002 added 2 commits January 25, 2024 09:35

changed test_base, bat, contracts, dihedrals, encore under testsuite/…

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…analysis

corrected the error happened in last commit

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aditya292002 added 2 commits January 25, 2024 12:22

imported assert_allclose in the files

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corrected all the errors

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removed test_gnm.cpython-310-pytest-7.4.4.pyc.1853 bytecode file

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made all the changes as asked by the mainters

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removed all the extra widespaces and correct the format for atol=1.5e-x

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aditya292002 added 2 commits February 23, 2024 13:37

- updated authors file and changelog,

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and - changed assert_array_almost_equal with assert_allclose

updated authors file and changed log and changed assert_array_almost_…

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aditya292002 added 4 commits February 23, 2024 15:02

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		24/02/23 aditya292002
		* "updated tests that used assert_almost_equal(..., decimal={N}) with equivalent assert_allclose(..., rtol=0, atol=1.5e-{N}) (issue modernize testing code #3743, PR Replaced numpy.testing.assert_almost_equal to numpy.testing.assert_allclose #4438)"

Replaced numpy.testing.assert_almost_equal to numpy.testing.assert_allclose #4438

Replaced numpy.testing.assert_almost_equal to numpy.testing.assert_allclose #4438

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