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dfm / emcee

The Python ensemble sampling toolkit for affine-invariant MCMC
https://emcee.readthedocs.io
MIT License
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Submitting a JOSS paper #316

Closed dfm closed 4 years ago

dfm commented 5 years ago

I've just pushed a draft of a paper for submission to JOSS in parallel with the release of version 3.0. I'd like to invite members of the community to join as an author on this paper if you're are interested. Please reply to this thread with your full name, affiliation, and (optionally) ORCID in the format needed by JOSS if you would like to join as an author. Pull requests or comments about the manuscript are also welcome! For example, my info is:

name: Daniel Foreman-Mackey
orcid: 0000-0003-0872-7098
affiliation: Center for Computational Astrophysics, Flatiron Institute

I'd like to submit this on 28 Oct 2019 so let me know if you're interested in joining, but need more time to decide.

Pinging committers with at least 10 lines (but others are also welcome if you feel that you have contributed!):

manodeep commented 5 years ago

@dfm Thanks! Yes, I would like to be listed as an author on the paper. 

name: Manodeep Sinha
orcid: 0000-0002-4845-1228
affiliation: "1, 2" 

affiliations:
 - name: Centre for Astrophysics & Supercomputing, Swinburne University of Technology
   index: 1
 - name: ARC Centre of Excellence for All Sky Astrophysics in 3 Dimensions (ASTRO 3D)
   index: 2
andyfaff commented 5 years ago

That's a very kind invitation, I would like to accept.

name: Andrew R. J. Nelson
orcid: 0000-0002-4548-3558
affiliation: "1" 

affiliations:
 - name: Australian Nuclear Science and Technology Organisation, NSW, Australia
   index: 1
terhardt commented 5 years ago

Thank you for the kind invitation and for drafting the paper. I'd feel honoured to accept.

name: Tobias Erhardt
orcid: 0000-0002-6683-6746
affiliation: Climate and Environmental Physics and Oeschger Center for Climate Change Research, University of Bern, Bern, Switzerland
jeremysanders commented 5 years ago

Thanks very much for the invitation! I feel like I haven't really provided anything significant for the code (just an example), so I don't think I'm justified becoming an author.

joezuntz commented 5 years ago

This is very kind of you, thank you very much. If you're happy to include me I'd be happy to accept.

name: Joe Zuntz
orcid: 0000-0001-9789-9646
affiliation: Institute for Astronomy, University of Edinburgh, Edinburgh, EH9 3HJ, UK
ipashchenko commented 5 years ago

Thank you, Dan. I would like to accept your kind invitation.

name: Ilya Pashchenko orcid: 0000-0002-9404-7023 affiliation: P.N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow, Russia

pkgw commented 5 years ago

Thanks for the invitation!

  - name: Peter K. G. Williams
    orcid: 0000-0003-3734-3587
    affiliation: "1, 2"
affiliations:
 - name: "Center for Astrophysics | Harvard & Smithsonian"
   index: 1
 - name: American Astronomical Society
   index: 2
farr commented 5 years ago

Thanks, Dan---I would be happy to be a co-author for v3. 

name: Will M. Farr
orcid: 0000-0003-1540-8562
affiliation: "1, 2"

affiliations:
 - name: "Department of Physics and Astronomy, Stony Brook University, Stony Brook NY 11794, United States"
   index: 1
 - name: "Center for Computational Astrophysics, Flatiron Institute, 162 5th Ave, New York NY 10010, United States"
   index: 2
migueldvb commented 5 years ago

Thanks for the invitation! My orcid and affiliation are:

  - name: Miguel de Val-Borro
    orcid: 0000-0002-0455-9384
    affiliation: Planetary Science Institute, 1700 East Fort Lowell Rd., Suite 106, Tucson, AZ 85719, USA
OriolAbril commented 5 years ago

Thank you so much for the invitation, it would be an honor.


- name: Oriol Abril Pla
  orcid: 0000-0002-1847-9481
  affiliation: Universitat Pompeu Fabra, Barcelona
davidwhogg commented 5 years ago

@dfm: This is too kind; I have done nothing for this update, except slow you down by creating obstacles in the rest of your life. I am perfectly happy to live in the acknowledgements. But if you want me in the author list I'm:

name: David W. Hogg
orcid: 0000-0003-2866-9403
affiliation: Center for Computational Astrophysics, Flatiron Institute
affiliation: Center for Cosmology and Particle Physics, Department of Physics, New York University
ericdill commented 5 years ago

That's a kind offer @dfm . The only thing I've done on this repo is a tiny bit of work on the CI parts. I hardly think that warrants inclusion on your manuscript. I'd like to let the folks who've contributed meaningfully to the code base get the credit they deserve.

jeremysanders commented 5 years ago

Thanks very much for the invitation! I feel like I haven't really provided anything significant for the code (just an example), so I don't think I'm justified becoming an author.

Well, if you think an example is good enough, then I'd be happy to be involved. My details are

name: Jeremy S. Sanders
orcid: 0000-0003-2189-4501
affiliation: Max Planck Institute for Extraterrrestrial Physics
Christopher-Bradshaw commented 5 years ago

Hey @dfm, I appreciate the offer, but my contribution was trivial and so I don't think I should be on the paper.

Thanks, and congrats!

simonrw commented 5 years ago

@dfm Similarly with me, I don't think I contributed to the code base in a meaningful way. Please feel free to not add me.

Thanks

dfm commented 5 years ago

@aarchiba: Would you like to be a co-author on this submission as well given your work on #319?

aarchiba commented 5 years ago

If I can get the code working and worth merging, and if you feel like it's a significant contribution, sure. I actually looked to see whether I hadn't added something to do with MPIPool but it doesn't show up in the history so probably I just hacked something together for my own use. I don't need to be "author n+1 who barely did anything" just because I fixed a bug, but I am willing to do some work on the paper text if that would help, so feel free to use your judgement as to who you want to include.

Also, because I bet you don't hear it enough and I know I don't say it enough: thank you for writing an extremely useful package! We used it in our test-of-gravity paper and it did sterling work under trying circumstances. I also took your advice to heart and released the entire source code, no matter how grotty: https://github.com/aarchiba/triplesystem

Anne

On Thu, 24 Oct 2019 at 14:42, Dan Foreman-Mackey notifications@github.com wrote:

@aarchiba https://github.com/aarchiba: Would you like to be a co-author on this submission as well given your work on #319 https://github.com/dfm/emcee/pull/319?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dfm/emcee/issues/316?email_source=notifications&email_token=AABBNIYDXOLZXIBIU6KRLCDQQGQ2VA5CNFSM4JB7HH5KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOECFCFQY#issuecomment-545923779, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABBNIY3XX5HBARC44AJIXDQQGQ2VANCNFSM4JB7HH5A .

terhardt commented 5 years ago

After reviewing what I actually contributed, I think I am more justified to reside in the acknowledgements. But I will leave that decision to you and I am happy to provide feedback on the draft though I have no experience with the format/content that JOSS requires.

dfm commented 5 years ago

@aarchiba: I think that contributing a bug fix is certainly an important contribution and I'd be happy to have you as a co-author, but it's up to you!

@terhardt: Same to you! The format for a JOSS paper is pretty simple: https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain and comments are definitely welcome!

@ all: I'm hoping to submit by the end of the day today (NYC time), but we'll be able to make changes during the review so please send along comments, questions, suggestions, etc.

davidwhogg commented 5 years ago

I'd like to directly encourage @aarchiba to join the paper. That was a non-trivial fix. Of course I am also just an amateur here, and all hail @dfm!

dfm commented 5 years ago

Agreed!!

I submitted the paper and it's now under review here: https://github.com/openjournals/joss-reviews/issues/1840

But please continue to send suggestions and/or your author info if you'd like to be a co-author! We can add names during the review.

aarchiba commented 4 years ago

Thank you, you're very kind, I'd like to accept.

name: Anne M. Archibald
orcid: 0000-0003-0638-3340
affiliation: University of Newcastle
dstndstn commented 4 years ago

Very kind of you to offer! I just looked at the contributions graphs, and I haven't done anything since 2012, so no need to include me. Congrats on the paper!

dfm commented 4 years ago

@ all: The JOSS review is just about finished so please let me know if you have any last comments about the paper or if you want to be added (or removed) from the author list. I'll try to get everything wrapped up for this review before tomorrow, but let me know if you need more time. Thanks!

dfm commented 4 years ago

PS the review is happening here: https://github.com/openjournals/joss-reviews/issues/1864

manodeep commented 4 years ago

@dfm Nothing from me. Thanks again for adding me to the author-list!

dfm commented 4 years ago

The paper has been accepted! Time to update our CVs:

https://joss.theoj.org/papers/10.21105/joss.01864

andyfaff commented 4 years ago

Great news

dfm commented 4 years ago

The paper has now been posted to arXiv: http://arxiv.org/abs/1911.07688

Let me know if you would like the password to claim ownership of the paper on arXiv.

farr commented 4 years ago

Hi Dan,

Just on general principles, I try to claim all my papers on the arXiv---so I'd like to claim ownership of this one.

Cheers, Will

On Mon, Nov 18, 2019 at 10:35 PM Dan Foreman-Mackey < notifications@github.com> wrote:

The paper has now been posted to arXiv: http://arxiv.org/abs/1911.07688

Let me know if you would like the password to claim ownership of the paper on arXiv.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dfm/emcee/issues/316?email_source=notifications&email_token=AAAV7QADJ27DGP2LNQCGYIDQUNNI5A5CNFSM4JB7HH5KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEMXTWA#issuecomment-555317720, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAV7QEXRQO3UEL4CXXHPLLQUNNI5ANCNFSM4JB7HH5A .

manodeep commented 4 years ago

@dfm Same here - will you please share the paper password.

jeremysanders commented 4 years ago

@dfm Password please too (and thanks!)

pkgw commented 4 years ago

@dfm Me too, please.

aarchiba commented 4 years ago

@dfm I'd like to claim it as well if you don't mind.