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alchemistry / alchemlyb

the simple alchemistry library
https://alchemlyb.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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Draft for a JOSS paper #328

Open xiki-tempula opened 1 year ago

xiki-tempula commented 1 year ago

@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 https://github.com/alchemistry/alchemlyb/pull/328#issuecomment-2123030068 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[bot] commented 1 year ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 98.83%. Comparing base (f40b89b) to head (2fca23e).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #328 +/- ## ======================================= Coverage 98.83% 98.83% ======================================= Files 28 28 Lines 1895 1895 Branches 407 407 ======================================= Hits 1873 1873 Misses 2 2 Partials 20 20 ```

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dotsdl commented 11 months ago

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 commented 11 months ago

@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 commented 11 months ago

@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 commented 9 months ago

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 commented 9 months ago

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

dotsdl commented 8 months ago

@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 commented 6 months ago

@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 commented 6 months ago

Thank @mrshirts for the comments.

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

dotsdl commented 6 months ago

@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 commented 6 months ago

@dotsdl Thanks!

mrshirts commented 3 months ago

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 commented 3 months ago

Thanks for the reminder.

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

xiki-tempula commented 3 months ago

I'm happy with the current state of the paper. I think I was waiting for @dotsdl to give green light and then this could be submitted. Do @orbeckst mind put yourself in the author list and the acknowledgement?

dotsdl commented 3 months ago

Just pushed minor edits @xiki-tempula; looking good. Doing a once-over on the checklist here and adding anything else I think may be appropriate. Timeboxing this to tonight to get it out the door.

dotsdl commented 3 months ago

Who would like to be the corresponding author?

dotsdl commented 3 months ago

I think the only outstanding pieces here are:

xiki-tempula commented 3 months ago

Thank @dotsdl For the review. I think we could put @orbeckst in the corresponding author and then submit this?

orbeckst commented 3 months ago

Great progress — let me do a proper read through before submitting, though. I’m currently travelling so won’t be able to do this this week. I’ll get my part done by Wed next week.

dotsdl commented 2 months ago

@orbeckst were you able to give the manuscript a read through?

mrshirts commented 2 months ago

Added a couple of more revisions. This is OK to go by me at a content level; as long as @xiki-tempula has gone through the checklist to make sure the requirements are all checked off, I'm OK with submission!

xiki-tempula commented 2 months ago

I think we meet all the checklist https://joss.readthedocs.io/en/latest/review_checklist.html Most of them are not about the paper but rather whether the repo is in good shape. Is @orbeckst happy?

orbeckst commented 2 months ago

I still have to go through some parts.

@davidlmobley is still missing as an author.

We had said in earlier email conversations that once we have a draft, we wanted to think about broadening authorship.

orbeckst commented 2 months ago

@mrshirts thanks for your edits. I did similar things independently (including the Mey 2020 reference). I merged everything.

@davidlmobley I also added you to the author list and the author contributions. Please check everything.

orbeckst commented 2 months ago

Call for contributing authors to JOSS paper

We drafted a paper on alchemlyb and are preparing to submit it to JOSS. We are inviting substantial contributors to alchemlyb to become authors on the paper.

Please read all the following carefully.

The deadline for responding (see below) is in 2 weeks, Tue June 4, 2024.

Substantial Contributors

We invite everyone listed here (and these are all the contributors to alchemlyb who are listed in AUTHORS and who aren't already on the paper, nobody was left out):

Authorship order

ZW and DLD contributed the majority of code and are currently driving the project or founded it. They share first authorship. DM, MRS, and OB conceptualized the project, provided funding, and also maintained it; OB is communicating author.

Additional contributing authors will be inserted after DLD in alphabetical order:

ZW, DLD, AA, BB, CC, ..., XX, ZZ, DM, MRS, OB

All contributing authors made substantial additions so alphabetical order seems to be one fair way to indicate this fact.

Conditions

As a substantial contributor you were responsible for major functional additions or fixes to the library and if you agree with and do the following, you will become an author on the paper:

  1. Confirm that you want to be an author by leaving a comment on this PR stating that you want to be an author on the paper.
  2. Read the manuscript (see Manuscript file) and provide comments/corrections if necessary within 2 weeks. At a minimum add your name and affiliation (see below under Contributing)
  3. Provide your email address — you can email obeckste@asu.edu if you do not want to provide it in a comment.
  4. Approve the manuscript draft within 2 weeks. (see below under Approval)
  5. As per JOSS Author Guidelines, co-authors agree to be accountable for all aspects of the work, and to notify JOSS if any retraction or correction of mistakes are needed after publication.

Do you not want to be an author?

If you do NOT want to be listed as an author then we want to list you in the acknowledgements as shown in the current manuscript.

Please confirm with a comment that you agree to being listed.

Manuscript file

Get the draft that has been approved by the main authors from the repo paper_joss_20240520.pdf; see annotations in this PDF about authors and acknowledgements.

Read the draft.

The manuscript itself is the markdown file paper.md that can be found under Files changed.

(You can also download the latest version of the PDF as an artifact from the draft-pdf GitHub action workflow. Select the latest run, under Artifacts at the bottom, look for paper, download paper.zip, and unzip to find paper.pdf. This PDF is rebuilt after every push to this branch.)

Contributing

You can contribute in any number of ways

Approval

Go to Files changed and leave a Review (green button); select Approve if you can.

In your review, state

I, FirstName LastName email@example.com, agree to be an author on this manuscript and I approve it.

Add anything else that you want to say. If you don't want to put your email address in there, email it separately to obeckste@asu.edu. We need to have a real way to contact you beyond just GitHub (and JOSS probably also wants email addresses of all authors).

IAlibay commented 2 months ago

Thanks so much for including me, I agree to being an author. I'll give things a review as soon as possible.

jhenin commented 2 months ago

Thank you for offering, I'll be happy to review and add small contributions to the manuscript.

DrDomenicoMarson commented 2 months ago

Thank you so much for including me, I gladly agree to be an author!

hl2500 commented 1 month ago

Thanks so much for including me! I'm happy to be a coauthor.

lee212 commented 1 month ago

It would be an honor to be listed as an author of alchemlyb paper.

xiki-tempula commented 1 month ago

@schlaicha, I think the name has been rendered well. You could see the pdf here https://github.com/alchemistry/alchemlyb/actions/runs/9271074281/artifacts/1544537769

ianmkenney commented 1 month ago

Thanks for including me. I'd be happy to be listed as an author on this paper!

EDIT: see #367

shuail commented 1 month ago

I, Shuai Liu (shuailiu25@gmail.com), agree to be an author on this manuscript and I approve it.

orbeckst commented 1 month ago

@brycestx could you please either edit the file to add yourself as an author with your appropriate affiliation (and ORCID if you have one) or leave a comment with this information here so that we can add you? Thanks!

A current PDF (2024-05-30) of the manuscript is in the repo.

orbeckst commented 1 month ago

@shuail could you please either edit the file to add yourself as an author with your appropriate affiliation (and ORCID if you have one) or leave a comment with this information here so that we can add you? Thanks!

A current PDF (2024-05-30) of the manuscript is in the repo.

vtlim commented 1 month ago

I’m happy to be listed as coauthor. My GitHub username needs to be corrected in the above list (vtlim, not vlim).

I, Victoria Lim limvt@uci.edu, agree to be an author on this manuscript and I approve it.

ORCID ID: https://orcid.org/0000-0003-4030-9312

Affiliated with University of California, Irvine

orbeckst commented 1 month ago

Thank you @vtlim , I added you to the paper. Apologies for getting the wrong GitHub handle, I also fixed it in https://github.com/alchemistry/alchemlyb/pull/328#issuecomment-2123030068 .

msoroush commented 1 month ago

I, first name: Mohammad, last name: Soroush Barhaghi, agree to be an author on this manuscript and I approve it.

xiki-tempula commented 1 month ago

@msoroush @brycestx @shuail Do you mind submit a PR or add a commit to

shuail commented 1 month ago

Hi I, Shuai Liu (shuailiu25@gmail.com), 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)

xiki-tempula commented 1 month ago

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

orbeckst commented 1 month ago

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

orbeckst commented 1 month ago

I submitted the paper to JOSS.

Please do not close or merge this branch.

Thank you to everyone!

orbeckst commented 1 month ago

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

orbeckst commented 1 day ago

Review was started in https://github.com/openjournals/joss-reviews/issues/6934