updated replace atoms.coordinates() with atoms.positions #3467

[manishsaini6421]

Fixes #

Changes made in this Pull Request:

PR Checklist

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

[codecov]

Codecov Report

Merging #3577 (5cdfd26) into develop (bf95f9c) will decrease coverage by 3.91%.
The diff coverage is 0.00%.

@@             Coverage Diff             @@
##           develop    #3577      +/-   ##
===========================================
- Coverage    94.20%   90.28%   -3.92%     
===========================================
  Files          190      181       -9     
  Lines        24668    23166    -1502     
  Branches      3313        0    -3313     
===========================================
- Hits         23238    20915    -2323     
- Misses        1384     2251     +867     
+ Partials        46        0      -46     

Impacted Files	Coverage Δ
package/MDAnalysis/analysis/encore/covariance.py	87.69% <0.00%> (ø)
package/MDAnalysis/converters/RDKitParser.py	14.39% <0.00%> (-81.82%)	⬇️
package/MDAnalysis/converters/RDKit.py	16.98% <0.00%> (-81.09%)	⬇️
package/MDAnalysis/analysis/hole2/hole.py	14.47% <0.00%> (-68.43%)	⬇️
package/MDAnalysis/converters/OpenMM.py	38.88% <0.00%> (-58.34%)	⬇️
package/MDAnalysis/converters/OpenMMParser.py	44.82% <0.00%> (-55.18%)	⬇️
package/MDAnalysis/analysis/hole2/utils.py	25.78% <0.00%> (-50.32%)	⬇️
package/MDAnalysis/analysis/psa.py	79.14% <0.00%> (-10.14%)	⬇️
package/MDAnalysis/topology/guessers.py	92.24% <0.00%> (-6.98%)	⬇️
package/MDAnalysis/core/selection.py	92.81% <0.00%> (-5.99%)	⬇️
... and 15 more

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[orbeckst]

@manishsaini6421 under normal circumstances we want you to continue working on one PR, namely on PR #3576 . Otherwise comments get lost. They way code review works is that you push work to your repository, it shows up in the PR, we comment, you read and address our comments, push more work, until the reviewers are happy.

Please

• close this PR
• reopen PR updated atoms.coordinates() with atoms.positions #3467 #3576
• make all your changes in PR updated atoms.coordinates() with atoms.positions #3467 #3576

Thanks.

[manishsaini6421]

Sir, how to change in same PR?

[orbeckst]

Make change in your code, add a commit, push changes to your shiny-new-feature branch. Because the PR is linked to the branch, the commit will show up in the PR.

[manishsaini6421]

@orbeckst Sir ,actually my first PR folder is deleted so please consider this one.

[hmacdope]

@manishsaini6421 we are going to close this PR and continue discussion in your previous PR, as we have already reviewed in that PR.

[orbeckst]

Now that this PR has been closed and PR #3576 has been reopened, you should be able to continue working on your code as before. Just keep pushing commits and they should show up in PR #3576.

Learning to work with git and GitHub takes some time. There is a lot of help available, e.g., https://docs.github.com/en/get-started#all-docs , but doing it in practice can still be daunting. One reason why we want GSOC applicants to submit code is so that they learn about the process as it is essential for being productive during GSOC.

[manishsaini6421]

@hmacdope Sir, please review this one because PR deleted by me from github due to lack of knoledge.
please sir reopen this one and close other one.

[hmacdope]

As stated above we will continue work in the old PR as it has a full record of our reviews and so on. Sorry about the inconvenience. :)