replaced atoms.coordinates() with atoms.positions (Issue #3467)

[pranjii]

Fixes #3467

Changes made in this Pull Request:

PR Checklist

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

[orbeckst]

• Please change: .positions is an attibute not a method.
• Please remove the changes regarding units. We want to do 1 PR addressing 1 issue to keep things simple.

I approved running the tests – sorry, that's a current security measure. Please feel free to ping me @orbeckst if something is not moving along.

[pranjii]

• Please change: .positions is an attibute not a method.

  • Please remove the changes regarding units. We want to do 1 PR addressing 1 issue to keep things simple.

I approved running the tests – sorry, that's a current security measure. Please feel free to ping me @orbeckst if something is not moving along.

ohh sorry I am still new to github and python. I messed it up.

[codecov]

Codecov Report

Merging #3477 (e3e6664) into develop (5bf6359) will increase coverage by 3.59%.
The diff coverage is 0.00%.

@@             Coverage Diff             @@
##           develop    #3477      +/-   ##
===========================================
+ Coverage    90.15%   93.75%   +3.59%     
===========================================
  Files          176      176              
  Lines        23169    23169              
  Branches      3291     3297       +6     
===========================================
+ Hits         20889    21723     +834     
+ Misses        2280     1395     -885     
- Partials         0       51      +51     

Impacted Files	Coverage Δ
package/MDAnalysis/analysis/encore/covariance.py	87.69% <0.00%> (ø)
package/MDAnalysis/units.py	100.00% <ø> (ø)
package/MDAnalysis/coordinates/base.py	95.47% <0.00%> (+0.11%)	⬆️
package/MDAnalysis/coordinates/TRJ.py	97.88% <0.00%> (+0.46%)	⬆️
package/MDAnalysis/lib/util.py	90.55% <0.00%> (+0.56%)	⬆️
package/MDAnalysis/core/universe.py	97.95% <0.00%> (+3.62%)	⬆️
package/MDAnalysis/analysis/align.py	98.32% <0.00%> (+5.36%)	⬆️
package/MDAnalysis/core/selection.py	98.78% <0.00%> (+5.55%)	⬆️
package/MDAnalysis/topology/guessers.py	99.22% <0.00%> (+6.97%)	⬆️
package/MDAnalysis/analysis/psa.py	89.27% <0.00%> (+10.13%)	⬆️
... and 6 more

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[pranjii]

@orbeckst I mailed you my issue. It'd be great if you could help me out

[lilyminium]

@pranjii it's usually easier, faster and helps later viewers if you discuss problems here on the issue -- then all developers can pitch in and help.

[pranjii]

@pranjii it's usually easier, faster and helps later viewers if you discuss problems here on the issue -- then all developers can pitch in and help.

As I said I am new to github so I do not know the norms and I apologise for the troubles. I was not aware of how github worked and made changes to the already committed code unaware that any changes I made to my branch will also be made in the PR. So how do I reverse these changes keeping in mind that I made a small change in the code directly through github? Should I just close my pull request?

[orbeckst]

Hi @pranjii , don't worry – you're fine!!

There was no need to delete anything. I would have asked you to

• fix your code in your branch & push
• continue working on this PR

It's totally normal that you will change and rewrite the code in the PR in response to comments. It's actually really good to see your code so that we can comment early.

In short: you did everything correctly!

[pranjii]

@orbeckst thank u. I have closed this PR and will change the recommend things ASAP for a new PR and guess will dive a little bit deeper into git and github

[orbeckst]

Sure. Don't worry, learning the whole pull request/review workflow takes some time. Ask us before you delete anything, we can typically give guidance. Just be aware that we might not always be able to immediately respond — we are all pretty busy an it can sometimes take a day. As @lilyminium said, we discuss all issues in public. We also follow our Code of Conduct in conducting all these discussions respectfully.