Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.83%. Comparing base (584588c) to head (7a2b140).

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  Coverage   98.83%   98.83%           
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  Files          28       28           
  Lines        1895     1895           
  Branches      407      407           
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  Hits         1873     1873           
  Misses          2        2           
  Partials       20       20           

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Hey @xiki-tempula, thanks for getting this started!

How would you like me (and others) to engage? Do you mind if I push directly to this branch as I work on this with you?

@dotsdl I think you can just commit to the branch. But it would be nice to keep the commit history simple so there won't be a millions of fix typo commit.

@xiki-tempula understood, thanks. Will do the best I can to avoid commit spam. I think once we're ready to merge we can do it as a squash to avoid adding noise to master.

@dotsdl Do you have any thing to add. I will try to do another update on this later this month.

@xiki-tempula not at this time, no.

Apologies, it's renewals season for me and so I've had to divert attention elsewhere again. I will be able to devote some effort to this late November, so can operate on anything you put in between now and then. Feel free to leave sections you'd prefer I'd write so the load isn't all on you.

@dotsdl @orbeckst Finally had some time to work on this during the Xmas. The word count should be between 250-1000 and we are currently roughly 900. Do you guys mind have a look?
I have also add a new github action that renders the draft into a pdf and it shall be available as artifact of the corresponding action (.github/workflows/draft-pdf.yml / Paper Draft (push) ).

Thank @mrshirts for the comments.

• The alchemcial-analysis is only mentioned in one paragraph in the Statement of need section.
• The big paragraph of ABFE is removed and one sentence has been added to the end of how to expand the solvation free energy to ABFE.
• I didn't make a figure for solvation free energy as it is kind of awkward thing to discuss. If I only give a high-level description like I did here. Then I don't really need a figure. If I dig into more detail then it might not really be necessary as the reader might not expect that in JOSS.

Do @mrshirts mind to also add yourself to the relevant section in the Acknowledgements, please? Thank you.

@xiki-tempula sorry for the delay, I haven't forgotten about this. Will get you a proper review as soon as I can, and will add in content if I see obvious gaps.

@dotsdl Thanks!

What's the current status on this? It would be nice to get this submitted in the next month or so - I can allocate some time to help get it happen. How can I help?

Thanks for the reminder.

Let's try to get this ready by the end of the month.

Hi I, Shuai Liu ([email protected]), agree to be an author on this manuscript and I approve it. Affiliated with Silicon Therapeutics LLC, Boston, USA (when most of the contribution happens)

@shuail Do you mind supply the ORCID as well, please? Thanks.

I am doing a final read through and will submit in the next few hours.

I submitted the paper to JOSS.

Please do not close or merge this branch.

Thank you to everyone!

The JOSS Pre-Review issue is openjournals/joss-reviews#6845 .