made universe for A and B to fix doctest fails #4023

Telomelonia · 2023-02-11T14:52:52Z

Changes made in this Pull Request:

a whole universe was defined to substitute A and B.
As discussed in the issue, the expected value should not be changed.

PR Checklist

Tests?
Docs?
CHANGELOG updated?
Issue raised/referenced?

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 the developer mailing list 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.

codecov · 2023-02-11T15:07:42Z

Codecov Report

Base: 93.52% // Head: 93.52% // No change to project coverage 👍

Coverage data is based on head (8a06938) compared to base (096f799).
Patch has no changes to coverable lines.

❗ Current head 8a06938 differs from pull request most recent head 7f6b504. Consider uploading reports for the commit 7f6b504 to get more accurate results

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #4023   +/-   ##
========================================
  Coverage    93.52%   93.52%           
========================================
  Files          190      190           
  Lines        25028    25028           
  Branches      3542     3542           
========================================
  Hits         23407    23407           
  Misses        1100     1100           
  Partials       521      521

Impacted Files	Coverage Δ
package/MDAnalysis/analysis/align.py	`96.38% <ø> (ø)`

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hmacdope

Looks good to me. Thanks for the contribution!
We ask that all first time contributors introduce themselves on the developer mailing list so we can get to know you. Please also add yourself to package/AUTHORS as part of this PR and then I can merge.

Telomelonia · 2023-02-13T18:54:28Z

@hmacdope
Sure ... will do that asap ✌️

orbeckst

Please fix the indicated issues.

Run doctest or at least copy&paste a python session that shows that the code worked: if someone copies your fixed code, it should run without errors.

Also add yourself to

your name to AUTHORS
your GitHub handle @Telomelonia to top of CHANGELOG under the current release in progress
confirm that you have introduced yourself on the developer mailing list (mention this PR/issue)

orbeckst · 2023-02-15T20:48:19Z

package/MDAnalysis/analysis/align.py

+    >>> A = mda.Universe('topol.tpr','traj.trr')
+    >>> B = mda.Universe('topol.tpr','traj.trr')


I suggest using A.copy()

Make B as a copy of A.

package/MDAnalysis/analysis/align.py

orbeckst · 2023-02-15T20:48:34Z

package/MDAnalysis/analysis/align.py

@@ -245,7 +245,8 @@ def rotation_matrix(a, b, weights=None):
    `R` can be used as an argument for
    :meth:`MDAnalysis.core.groups.AtomGroup.rotate` to generate a rotated
    selection, e.g. ::
-
+    >>> A = mda.Universe('topol.tpr','traj.trr')
+    >>> B = mda.Universe('topol.tpr','traj.trr')
    >>> R = rotation_matrix(A.select_atoms('backbone').positions,
    >>>                     B.select_atoms('backbone').positions)[0]


use ... instead of >>> to indicate line continuation

orbeckst · 2023-02-21T03:57:20Z

Hello @Telomelonia , are you still working on the PR? If so, please address my comments. Otherwise we will close the PR as stale.

Telomelonia · 2023-02-21T04:43:57Z

Hello @Telomelonia , are you still working on the PR? If so, please address my comments. Otherwise we will close the PR as stale.

@orbeckst
Sorry, I got engage into some work will see the changes

orbeckst

Please see comments and resolve the conflicts. Thanks!

package/MDAnalysis/analysis/align.py

orbeckst · 2023-02-21T18:28:52Z

package/MDAnalysis/analysis/align.py

+    >>> A = mda.Universe('topol.tpr','traj.trr')
+    >>> B = mda.Universe('topol.tpr','traj.trr')


Make B as a copy of A.

orbeckst

Please try out your code. Copy and paste the output from a Python session that demonstrates that your code is working.

package/CHANGELOG

orbeckst · 2023-02-24T15:46:13Z

package/MDAnalysis/analysis/align.py

@@ -245,9 +245,11 @@ def rotation_matrix(a, b, weights=None):
    `R` can be used as an argument for
    :meth:`MDAnalysis.core.groups.AtomGroup.rotate` to generate a rotated
    selection, e.g. ::
-
+    >>> from MDAnalysisTests.datafiles import TPR, TRR
+    >>> A = mda.Universe('topol.tpr','traj.trr')


Yeah. I am fixing this, but I am getting errors, and I don't know why, but I need time to understand before debugging

Show your code, then I can help.

@orbeckst, thanks, but I am currently having my semester exams 😄. So, I will try to continue after that ✌️

orbeckst · 2023-02-24T20:46:10Z

Please also resolve conflicts.

orbeckst · 2023-02-27T20:25:27Z

@Telomelonia , we just fixed #4044, which is important for your PR because it ensures that MDAnalysisTests is available for doctests. Please Resolve conflicts and while doing so, merge the current develop branch changes into your PR.

Then make sure that all the checks pass.

Telomelonia · 2023-02-28T02:50:58Z

Yea .. sure I will rebase it to develop branch

orbeckst · 2023-02-28T02:52:05Z

I think you can just use the "Resolve conflicts" button in the GH userinterface (but rebase also works).

orbeckst · 2023-03-09T20:48:49Z

@Telomelonia I hope your exams went well. Can you provide a date by when you'll be able to pick up the PR again?

Telomelonia · 2023-03-10T05:24:42Z

@Telomelonia I hope your exams went well. Can you provide a date by when you'll be able to pick up the PR again?

sure I will try to clear this PR by this weekend.

Telomelonia · 2023-03-10T05:39:08Z

@orbeckst
I am getting errors in this line of code ... even I had imported TPR and TRR
A = mda.Universe('topol.tpr','traj.trr')
FileNotFoundError: [Errno 2] No such file or directory: 'topol.tpr'
Is there any other test I could take a and b, or I can make my own with an arbitrary angle?

orbeckst · 2023-03-23T03:27:24Z

Sorry for the delayed response.

You need to import actual test files

from MDAnalysisTests.datafiles import TPR, TRR

and then use those.

Telomelonia · 2023-03-31T17:08:45Z

@HunterZ17
Due to some work, I won't be able to continue this PR

made universe for A and B

8a06938

github-actions bot added the Component-Analysis label Feb 11, 2023

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orbeckst requested changes Feb 15, 2023

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RMeli mentioned this pull request Feb 19, 2023

Failed doc examples in align.py #3365

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orbeckst added the close? Evaluate if issue/PR is stale and can be closed. label Feb 21, 2023

Telomelonia added 2 commits February 21, 2023 10:29

added author

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Update align.py

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Telomelonia added 2 commits February 22, 2023 16:58

Update align.py

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changelog updated

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orbeckst self-assigned this Feb 24, 2023

update changelog

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orbeckst added the close? Evaluate if issue/PR is stale and can be closed. label Mar 6, 2023

orbeckst removed the close? Evaluate if issue/PR is stale and can be closed. label Mar 23, 2023

Telomelonia closed this Mar 31, 2023

Telomelonia deleted the doctest_fix branch March 31, 2023 17:08

MohitKumar020291 mentioned this pull request Jun 29, 2023

DOCS: Align.py changes made #4182

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made universe for A and B to fix doctest fails #4023

made universe for A and B to fix doctest fails #4023

Telomelonia commented Feb 11, 2023 •

edited by orbeckst

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Telomelonia commented Mar 31, 2023

		>>> A = mda.Universe('topol.tpr','traj.trr')
		>>> B = mda.Universe('topol.tpr','traj.trr')

made universe for A and B to fix doctest fails #4023

made universe for A and B to fix doctest fails #4023

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