[PRE REVIEW]: Re-Envisioning Numerical Information Field Theory (NIFTy.re): A Library for Gaussian Processes and Variational Inference #6382

editorialbot · 2024-02-19T20:07:12Z

Submitting author: @Edenhofer (Gordian Edenhofer)
Repository: https://github.com/nifty-ppl/nifty
Branch with paper.md (empty if default branch): paper
Version: v8.5
Editor: @dfm
Reviewers: @Abinashbunty, @apizzuto
Managing EiC: Dan Foreman-Mackey

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/9e0b78f8d981abdec4fc84605e46786a"><img src="https://joss.theoj.org/papers/9e0b78f8d981abdec4fc84605e46786a/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/9e0b78f8d981abdec4fc84605e46786a/status.svg)](https://joss.theoj.org/papers/9e0b78f8d981abdec4fc84605e46786a)

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The text was updated successfully, but these errors were encountered:

editorialbot · 2024-02-19T20:07:15Z

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

editorialbot · 2024-02-19T20:07:17Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (233.8 files/s, 106164.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1             30              0           1373
Python                           3             70             55            409
Markdown                         1             54              0            279
-------------------------------------------------------------------------------
SUM:                             5            154             55           2061
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2024-02-19T20:07:18Z

Wordcount for paper.md is 3216

editorialbot · 2024-02-19T20:07:18Z

Failed to discover a valid open source license

editorialbot · 2024-02-19T20:07:49Z

⚠️ An error happened when generating the pdf. Author (Reimar H. Leike) is missing affiliation.

dfm · 2024-02-19T20:08:22Z

@editorialbot set NIFTy_8 as branch

editorialbot · 2024-02-19T20:08:25Z

Done! branch is now NIFTy_8

editorialbot · 2024-02-19T20:08:28Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.00695 is OK
- 10.1046/j.1365-8711.2002.05881.x is OK
- 10.3847/1538-4365/ac4df7 is OK
- 10.1051/0004-6361/202141570 is OK
- 10.1051/0004-6361/202141249 is OK
- 10.48550/arXiv.2208.00211 is OK
- 10.48550/arXiv.2206.06143 is OK
- 10.48550/arXiv.2206.06205 is OK
- 10.3847/1538-4365/aafbea is OK
- 10.1086/498708 is OK
- 10.1088/0004-6256/140/6/1868 is OK
- 10.3847/1538-4357/ac1f96 is OK
- 10.48550/ARXIV.2206.10634 is OK
- 10.48550/arXiv.2308.01295 is OK
- 10.1371/journal.pone.0275011 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.48550/ARXIV.1901.11033 is OK
- 10.3390/e23070853 is OK
- 10.3390/psf2022005006 is OK
- 10.1109/TPAMI.2015.2448083 is OK
- 10.3847/1538-3881/aa9332 is OK
- 10.5281/zenodo.10463641 is OK
- 10.18637/jss.v076.i01 is OK
- 10.7717/peerj-cs.55 is OK
- 10.1086/670067 is OK
- 10.1093/mnras/staa278 is OK
- 10.5281/zenodo.8408702 is OK
- 10.48550/arXiv.1912.11554 is OK
- 10.1002/andp.201800290 is OK
- 10.1051/0004-6361/202243319 is OK
- 10.1051/0004-6361/202142846 is OK
- 10.1051/0004-6361/201834695 is OK
- 10.1051/0004-6361/201832832 is OK
- 10.1051/0004-6361/201730831 is OK
- 10.1093/mnras/sty3341 is OK
- 10.1051/0004-6361/202038708 is OK
- 10.1051/0004-6361/201833284 is OK
- 10.3847/2041-8213/ac67db is OK
- 10.1051/0004-6361/201628885 is OK
- 10.1051/0004-6361/202244784 is OK
- 10.1051/0004-6361/202141298 is OK
- 10.48550/arXiv.2204.11715 is OK
- 10.3847/1538-4357/ab5362 is OK
- 10.1093/mnras/sty1008 is OK
- 10.48550/arXiv.2303.03420 is OK
- 10.1051/0004-6361/201935765 is OK
- 10.1051/0004-6361/202142369 is OK
- 10.48550/arXiv.2303.09926 is OK
- 10.1051/0004-6361/201323195 is OK
- 10.48550/arXiv.2206.06710 is OK
- 10.1038/s41586-019-1874-z is OK
- 10.3847/1538-4365/abe465 is OK
- 10.3847/1538-3881/ab99c8 is OK
- 10.48550/arXiv.2206.05796 is OK
- 10.1038/s41550-021-01548-0 is OK
- 10.3847/1538-4357/ab2388 is OK
- 10.1051/0004-6361/202346851 is OK
- 10.48550/arXiv.2304.12350 is OK
- 10.1051/0004-6361/202346423 is OK
- 10.3847/1538-3881/acabc1 is OK
- 10.1051/0004-6361/202140486 is OK
- 10.1051/0004-6361/202243326 is OK
- 10.21105/joss.00695 is OK
- 10.21105/joss.01298 is OK
- 10.1086/427976 is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1051/0004-6361/201322068 is OK
- 10.1051/0004-6361/202243819 is OK
- 10.1103/PhysRevE.96.052104 is OK
- 10.1088/1475-7516/2021/04/071 is OK
- 10.48550/arXiv.2308.09176 is OK
- 10.3390/e25040652 is OK
- 10.3390/psf2022005033 is OK
- 10.1051/0004-6361/201935555 is OK

MISSING DOIs

- 10.1051/0004-6361/202038169 may be a valid DOI for title: Resolving nearby dust clouds

INVALID DOIs

- None

dfm · 2024-02-19T20:08:33Z

@editorialbot check repository

editorialbot · 2024-02-19T20:08:36Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.35 s (744.5 files/s, 141301.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         238           7079          11063          27373
SVG                              3              3              3           1067
Markdown                         4            178              0            610
reStructuredText                 8            330            235            605
YAML                             1             23              0            161
Dockerfile                       1              3              9             15
Bourne Shell                     1              4              0             12
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                           257           7620          11310          29846
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2024-02-19T20:08:38Z

Failed to discover a Statement of need section in paper

dfm · 2024-02-19T20:08:56Z

@editorialbot set paper as branch

editorialbot · 2024-02-19T20:08:58Z

Done! branch is now paper

dfm · 2024-02-19T20:10:04Z

@Edenhofer — Thanks for your submission! All the suitable JOSS editors are currently working at capacity so I'm going to "waitlist" this review until an editor with the relevant expertise is available to take it on. Thanks for your patience!

In the meantime, there are a few issues with your paper ☝️ Can you check the affiliations and make sure you have a "Statement of need" section in the paper?

Edenhofer · 2024-02-19T21:08:18Z

Thanks for opening the pre review issue so quickly!

I see that having the paper branch's history being unrelated to the main development branch's history is undesirable for JOSS. I merged both histories so that the paper and the code now share a history.

~~@editorialbot set paper_full as branch~~ (EDIT: I apparently can't change branches and thus force pushed over the paper branch)

The paper has a "statement of need" section and Reimar not having an affiliation was intentional. Reimar left academia and his contribution to this work are not related to his employer. I added a placeholder affiliation for now to make the bot happy :) I will discuss further with Reimar what we want to put there.

Edenhofer · 2024-02-19T21:49:34Z

I talked with Reimar and he prefers to have no affiliation. I thus added a new affiliation with "No Affiliation" as title. I hope this is acceptable.

P.S. I also fixed the DOI warning while at it.

dfm · 2024-02-20T01:35:53Z

Thanks! Our preferred notation for that is "Independent researcher", but otherwise all good.

dfm · 2024-02-20T01:37:00Z

@editorialbot generate pdf

editorialbot · 2024-02-20T01:38:20Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

editorialbot · 2024-02-20T01:39:00Z

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

Edenhofer · 2024-02-20T14:02:04Z

[...] if you have any suggestions for potential reviewers then please mention them here in this thread [...]

I think the following JOSS reviewers might be suitable for this submission

williamjameshandley
zhampel
dgerosa
Abinashbunty
thomaspinder
tbmiller-astro
apizzuto
prashjet (no collaboration but currently visiting the University of Vienna, prashjet's employer)

Edenhofer · 2024-03-12T12:45:16Z

I hate to bug you, but is there a rough ETA when this submission might be considered for review?

dfm · 2024-03-16T18:44:12Z

@Edenhofer — Thanks for checking in. Unfortunately there are quite a few submissions in the queue before this one (there was a big burst of submissions a month ago) and all the editors in this track are working at capacity. I expect it will still be a couple more weeks. Thanks for your patience!

Abinashbunty · 2024-03-21T01:45:48Z

@dfm I've been following the paper for a while and it's interesting for me to dive deeper and review it. 👍🏻

dfm · 2024-03-22T18:27:29Z

@Abinashbunty — Thanks for volunteering! Once an editor is assigned, they will follow up.

dfm · 2024-04-08T14:30:27Z

@editorialbot assign me as editor

Hi all — I'm now available to edit this submission. Thanks for your patience! I'll work on recruiting reviewers now, and once we have two, the main review will get started in a new thread.

editorialbot · 2024-04-08T14:30:30Z

Assigned! @dfm is now the editor

dfm · 2024-04-08T14:32:27Z

@editorialbot add @Abinashbunty as reviewer

@Abinashbunty — if your offer to review still stands, I've added you as a reviewer. If you don't have the capacity anymore, I'm happy to remove you. Either way, let me know and many thanks!!

editorialbot · 2024-04-08T14:32:29Z

@Abinashbunty added to the reviewers list!

dfm · 2024-04-08T14:36:11Z

👋 @williamjameshandley, @thomaspinder, @apizzuto — Would any of you be available and willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

Abinashbunty · 2024-04-08T14:37:01Z

@dfm I'm still available for the review. So it's fine. 👍🏻

I'll get started with the review already but will post my feedback in the new issue once that is initiated. 😄

apizzuto · 2024-04-08T14:41:30Z

I am also happy to review this submission!

dfm · 2024-04-09T13:15:09Z

@editorialbot add @apizzuto as reviewer

Thanks @apizzuto!!

I'll get the main review started in a new thread, and I'll have a lot more information for everyone over there. Thanks all!

editorialbot · 2024-04-09T13:15:11Z

@apizzuto added to the reviewers list!

dfm · 2024-04-09T13:15:19Z

@editorialbot start review

editorialbot · 2024-04-09T13:15:23Z

OK, I've started the review over in #6593.

editorialbot added pre-review Track: 1 (AASS) Astronomy, Astrophysics, and Space Sciences labels Feb 19, 2024

editorialbot added Python TeX labels Feb 19, 2024

editorialbot added the Dockerfile label Feb 19, 2024

dfm added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Feb 19, 2024

dfm removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Apr 8, 2024

editorialbot assigned dfm Apr 8, 2024

editorialbot assigned Abinashbunty Apr 8, 2024

editorialbot assigned apizzuto Apr 9, 2024

editorialbot closed this as completed Apr 9, 2024

[PRE REVIEW]: Re-Envisioning Numerical Information Field Theory (NIFTy.re): A Library for Gaussian Processes and Variational Inference #6382

[PRE REVIEW]: Re-Envisioning Numerical Information Field Theory (NIFTy.re): A Library for Gaussian Processes and Variational Inference #6382

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