add more element valence

[Aunity]

• Fix some bugs #302 PROPKA fails with "AttributeError: 'NoneType' object has no attribute 'group_type'" #140
• Add more element valence

[orbeckst]

Sorry, I am travelling/at conferences so reviewing this PR may take a while. Please feel free to ignore me if I am not able to review in time.

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On Sep 23, 2023, at 11:31 AM, Nathan Baker ***@***.***> wrote: @sobolevnrm <https://github.com/sobolevnrm> requested your review on: #169 <#169> add more element valence.

[speleo3]

Please reference your issue #163 from the description.

Tests would be great. Here is a simple test for issue #140: speleo3@8e5121a

[speleo3]

@Aunity do you need help with the changes I proposed?

[Aunity]

@speleo3 Sorry, it's been busy lately. Now it's fixed, please check again.

[speleo3]

Getting close, thanks @Aunity for the updates. There is a syntax error that needs fixing, see https://github.com/jensengroup/propka/actions/runs/6492041705/job/17653467393?pr=169

[codecov]

Codecov Report

Attention: 9 lines in your changes are missing coverage. Please review.

Comparison is base (fd7b155) 73.08% compared to head (0243462) 73.05%.
Report is 2 commits behind head on master.

❗ Current head 0243462 differs from pull request most recent head 7e243e6. Consider uploading reports for the commit 7e243e6 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #169      +/-   ##
==========================================
- Coverage   73.08%   73.05%   -0.04%     
==========================================
  Files          25       25              
  Lines        3972     3989      +17     
==========================================
+ Hits         2903     2914      +11     
- Misses       1069     1075       +6     

Files	Coverage Δ
propka/molecular_container.py	92.52% <100.00%> (-0.07%)	⬇️
propka/conformation_container.py	84.97% <85.71%> (-0.05%)	⬇️
propka/energy.py	90.12% <33.33%> (-1.51%)	⬇️
propka/protonate.py	86.63% <33.33%> (-1.64%)	⬇️

... and 2 files with indirect coverage changes

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[speleo3]

Thanks for the final fix.

Please don't reformat entire files in your pull requests. It adds noise and controversy to your valuable contribution. In my opinion, if reformatting is desired, it should be discussed with the development team first and done in a separate pull request, and ideally be implemented with a commit hook or CI job which enforces the new style in the future.

[Aunity]

@speleo3 Thank you for reminding me. I have revoked the previous commit and made some modifications again.