JOSS paper

[xiki-tempula]

@orbeckst I have made a quick draft of the JOSS paper.
I have only written the summary and the Statement of need and left other things as the template.
The guide line is here https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography

Co-authors

Substantial contributors to alchemlyb are invited to become authors of the paper. See #328 (comment) below for details.

Building the PDF

As part of the GitHub actions workflow, a full PDF version of the paper is built and you can download it as an artifact.

If you want to build the PDF locally you can use pandoc

pandoc --citeproc -o paper.pdf  paper.md

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.78%. Comparing base (8a361d5) to head (27caba8).

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #328   +/-   ##
=======================================
  Coverage   98.78%   98.78%           
=======================================
  Files          28       28           
  Lines        1978     1978           
  Branches      435      435           
=======================================
  Hits         1954     1954           
  Misses          2        2           
  Partials       22       22           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[dotsdl]

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?

[xiki-tempula]

@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.

[dotsdl]

@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.

[davidlmobley]

I just wanted to do a status check on this, since I’d been expecting to need to review mid-September…? Thanks.

…

On Aug 22, 2023, 8:17 AM -0700, David L. Dotson ***@***.***>, wrote: @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. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because your review was requested.Message ID: ***@***.***>

[xiki-tempula]

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

[dotsdl]

@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.

[xiki-tempula]

@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) ).

[xiki-tempula]

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.

[dotsdl]

@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.

[xiki-tempula]

@dotsdl Thanks!

[mrshirts]

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?

[orbeckst]

Thanks for the reminder.

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

[orbeckst]

@xiki-tempula can you please have a look at final JOSS todos openjournals/joss-reviews#6934 (comment) — we basically need a new release for alchemlyb #389.

[orbeckst]

Just as an update: We need to go through a final checklist (see openjournals/joss-reviews#6934 (comment) ) but at the moment the process is held up by zenodo not archiving our 2.3.2 release #393 .

[orbeckst]

The zenodo archiving issue was fixed a few days ago, just waiting for JOSS.

[orbeckst]

The last request from the JOSS editor is to add a CITATION.cff file #394 so that the author names in the zenodo archive correspond to the paper openjournals/joss-reviews#6934 (comment) when we make a new release #396 .

In PR #395 I am adding the citation file. Please check the PR and let me know as soon as possible if any changes need to be made.

[orbeckst]

We made a 2.4.0 release #396 and we now have a zenodo archive with a nicely formatted authors list with ORCIDs at https://doi.org/10.5281/zenodo.13774657 ... this should be it.

[orbeckst]

We were asked to ensure that the zenodo archive and the paper have the same title, so this requires #402 and making a quick 2.4.1 release #403 .

[orbeckst]

We should have everything:

• release 2.4.1
• zenodo DOI 10.5281/zenodo.13799342

Possibly one update to Acknowledgements so that everyone in the CITATION.cff (and on zenodo) is also somehow named in the paper.

[orbeckst]

We should be done ... openjournals/joss-reviews#6934 (comment)

[orbeckst]

The handling editor recommended the paper for acceptance & publication openjournals/joss-reviews#6934 (comment). 🎉

[dotsdl]

Thanks so much @orbeckst for shepherding this through and herding all the cats! 🐈

[orbeckst]

We're not there yet, sigh....

[orbeckst]

Paper is published https://joss.theoj.org/papers/10.21105/joss.06934

🎉 🎉 🎉 🎉 🎉 🎉 🎉 🎉 🎉 🎉 🎉 🎉 🎉 🎉 🎉 🎉 🎉 🎉 🎉 🎉 🎉 🎉

Thank you everyone for your great work!

[orbeckst]

With the paper published I will close the PR. We do not need to merge it.

[orbeckst]

Let's not delete the branch and keep it around, in case we want to recycle anything.

[mrshirts]

SOOO much work and so many iterations @orbeckst; thank you for shepherding it through!