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Remove Hydrogen isotopes in deprotonating #337

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merged 9 commits into from
Nov 8, 2023
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Ruibin-Liu
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@Ruibin-Liu Ruibin-Liu commented Aug 28, 2023

Hydrogen isotopes should also be removed. Also, the documentation was old/wrong and now it is updated.

Reference Issues/PRs

NA

What does this implement/fix? Explain your changes

Removing H atoms by element_symbol == "H" doesn't remove isotopes D or T.
Simply adding D and T to the list should work.

What testing did you do to verify the changes in this PR?

NA

Pull Request Checklist

  • Added a note about the modification or contribution to the ./CHANGELOG.md file (if applicable)
  • Added appropriate unit test functions in the ./graphein/tests/* directories (if applicable)
  • Modify documentation in the corresponding Jupyter Notebook under ./notebooks/ (if applicable)
  • Ran python -m py.test tests/ and make sure that all unit tests pass (for small modifications, it might be sufficient to only run the specific test file, e.g., python -m py.test tests/protein/test_graphs.py)
  • Checked for style issues by running black . and isort .

Hydrogen isotopes should also be removed. Also, the documentation was old/wrong and now it is updated.
@Ruibin-Liu
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What kinds of tests should I add?

@sonarcloud
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sonarcloud bot commented Aug 28, 2023

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@a-r-j
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a-r-j commented Sep 18, 2023

Thanks @Ruibin-Liu ! I think the tests you've added seem sufficient to me; anything you're unhappy with?

@Ruibin-Liu Ruibin-Liu marked this pull request as ready for review September 19, 2023 01:26
@Ruibin-Liu
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Thanks @Ruibin-Liu ! I think the tests you've added seem sufficient to me; anything you're unhappy with?

I think it's good to go, but I am not sure why some checks failed.

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sonarcloud bot commented Oct 5, 2023

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

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a-r-j commented Oct 25, 2023

Thanks @Ruibin-Liu ! I think the tests you've added seem sufficient to me; anything you're unhappy with?

I think it's good to go, but I am not sure why some checks failed.

Looks like there was some dependency drift. If you sync up to master I expect these tests will pass :)

@a-r-j a-r-j merged commit 6e3b1a0 into a-r-j:master Nov 8, 2023
4 of 11 checks passed
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sonarcloud bot commented Nov 8, 2023

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

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2 participants