[PRE REVIEW]: nimCSO: A Nim package for Compositional Space Optimization

editorialbot commented 8 months ago

Submitting author: !--author-handle-->@amkrajewski@RMeli<!--end-editor-- Reviewers: @atzberg, @Henrium, @bdice Managing EiC: Arfon Smith

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editorialbot commented 8 months ago

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editorialbot commented 8 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (1878.4 files/s, 189250.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Nim                             14            222            393            925
TeX                              2             65             21            679
YAML                             9             31              0            259
Markdown                         3             89              0            207
Python                           2             16              0             76
CSV                              3              0              0             38
JSON                             1              1              0             27
Jupyter Notebook                 1              0            561             10
Dockerfile                       1              1              0              6
-------------------------------------------------------------------------------
SUM:                            36            425            975           2227
-------------------------------------------------------------------------------

Commit count by author:

   180  amkrajewski
   158  Adam M. Krajewski
     3  Zi-Kui Liu
     3  zikuiliu
     1  Arindam
     1  Arindam Debnath
     1  dovahkiin0022
     1  lukeamyers

editorialbot commented 8 months ago

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

OK DOIs

- 10.1002/adem.200300567 is OK
- 10.1016/j.msea.2003.10.257 is OK
- 10.1145/512274.512284 is OK
- 10.20517/jmi.2021.05 is OK
- 10.1557/jmr.2018.153 is OK
- 10.48550/arXiv.2402.00572 is OK

MISSING DOIs

- No DOI given, and none found for title: Nim Programming Language v2.0.0
- No DOI given, and none found for title: Efficient Generation of Grids and Traversal Graphs...
- 10.5860/choice.27-0936 may be a valid DOI for title: Genetic Algorithms in Search, Optimization and Mac...
- No DOI given, and none found for title: The Art of Computer Programming, Volume 4, Fascicl...
- No DOI given, and none found for title: Arraymancer v0.7.24: A fast, ergonomic and portabl...

INVALID DOIs

- https://dx.doi.org/10.2139/ssrn.4689687 is INVALID because of 'https://doi.org/' prefix

editorialbot commented 8 months ago

Paper file info:

📄 Wordcount for paper.md is 1923

✅ The paper includes a Statement of need section

editorialbot commented 8 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot commented 8 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

amkrajewski commented 8 months ago

@editorialbot check references

editorialbot commented 8 months ago

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

OK DOIs

- 10.1002/adem.200300567 is OK
- 10.1016/j.msea.2003.10.257 is OK
- 10.1145/512274.512284 is OK
- 10.20517/jmi.2021.05 is OK
- 10.2139/ssrn.4689687 is OK
- 10.1557/jmr.2018.153 is OK
- 10.48550/arXiv.2402.03528 is OK
- 10.5860/choice.27-0936 is OK
- 10.48550/arXiv.2402.00572 is OK

MISSING DOIs

- No DOI given, and none found for title: Nim Programming Language v2.0.0
- No DOI given, and none found for title: The Art of Computer Programming, Volume 4, Fascicl...
- No DOI given, and none found for title: Arraymancer v0.7.24: A fast, ergonomic and portabl...

INVALID DOIs

- None

arfon commented 8 months ago

@amkrajewski – thanks for your submission to JOSS. We're currently managing a large backlog of submissions and the editor most appropriate for your area is already rather busy.

For now, we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!

Also, while you're waiting, would you mind shortening your paper? As a rule, we're looking for papers to be ~1000 words long.

amkrajewski commented 8 months ago

@arfon - I understand, of course. Thanks for the clear and prompt information!

The word count of the manuscript body is 1373 which aligns with several similar recently published JOSS papers. Of course, I can reduce it if necessary. I think the automated count got especially inflated by markdown-formatted tables.

arfon commented 7 months ago

@editorialbot invite @RMeli as editor

:wave: @RMeli – would you be willing to edit this submission for JOSS?

editorialbot commented 7 months ago

Invitation to edit this submission sent!

arfon commented 7 months ago

@editorialbot query scope

@amkrajewski - apologies for not doing this earlier but I think this submission should go for a scope review with the broader editorial team as it's on the smaller-side of what we typically publish at JOSS.

This will likely take a week or two.

editorialbot commented 7 months ago

Submission flagged for editorial review.

amkrajewski commented 7 months ago

@arfon No problem! Please consider that (a) substantial effort was put into several iterations of optimizing the data structures and algorithms, as evidenced by commit history, and (2) the use of very concise Nim language plus metaprogramming made the codebase easily 2/3 times smaller in terms of LOCs compared to C++/Python.

Let me know if there are any questions!

arfon commented 7 months ago

@amkrajewski – thanks for the additional context. I'm happy to let this move forward to review. @RMeli – I'm going to assign you now. Thanks all!

arfon commented 7 months ago

@editorialbot assign @RMeli as editor

editorialbot commented 7 months ago

Assigned! @RMeli is now the editor

RMeli commented 7 months ago

@amkrajewski do you have suggestions for potential reviewers?

Unfortunately nim is not listed in the potential reviewers list, so we currently have no information on which volunteers know the language.

amkrajewski commented 7 months ago

@arfon Thanks! Great to hear that!

@RMeli Sure! There is an active sub-forum specific to scientific computing using nim. I should be able to find volunteers for JOSS there and report back.

In the meantime, based on internal reviews from my colleagues, I believe the codebase should be approachable for anyone familiar with natural sciences, fundamentals of low-level programming, and Python, since nim's syntax is very similar to recent Python versions (including type system as of 3.12). Looking at the JOSS reviewers list and their recent activities, here are some people who may be interested:

I believe ml-evs may also be interested and would be a great person to review this, especially in the context of nimCSO's target applications, but we are co-authors on a recent paper representing a possible COI. Although, there are almost 60 authors on it (arXiv:2402.00572) so perhaps that COI could be waived under JOSS policy.

RMeli commented 7 months ago

Hi @Henrium 👋

Would you be interested in reviewing this submission for JOSS (Journal of Open Source Software)?

You can find more information about the submission at the top of this Github issue #6455.

Thank you in advance!

RMeli commented 7 months ago

Hi @atzberg 👋

Would you be interested in reviewing this submission for JOSS (Journal of Open Source Software)?

You can find more information about the submission at the top of this Github issue #6455.

Thank you in advance!

RMeli commented 7 months ago

Thanks @amkrajewski for the suggestions.

I would tend to agree that co-autorship on a 60 authors paper might be waived as a COI. I see you work on different institutions. Would you mind expanding a bit more about your interactions with them during the project? In any case, let's see if we have other interested reviewers first.

atzberg commented 7 months ago

I would be happy to try to review. However, I should mention I am currently a bit over-subscribed on a few things and I would be available at the earliest June 3rd, if that works. -- Paul

On Thu, Apr 18, 2024 at 11:36 PM Rocco Meli @.***> wrote:

Henrium commented 7 months ago

Hi Dr. Meli, Thanks for inviting me, I'd be happy to review this submission, but busy with other things right now. I'll try to review in a month or so. Best, Henry

On Fri, Apr 19, 2024 at 1:33 AM Rocco Meli @.***> wrote:

RMeli commented 6 months ago

Thank you @atzberg and @Henrium for the fast replies! Ideally, I'd like the review to get started sooner rather than later. But if we will struggle to find other reviewers, I'll ping you again. Thank you a lot for the availability.

RMeli commented 6 months ago

Hi @csadorf 👋

Would you be interested in reviewing this submission for JOSS (Journal of Open Source Software)?

You can find more information about the submission at the top of this Github issue #6455.

Thank you in advance!

RMeli commented 6 months ago

Hi @lys-devel 👋

Would you be interested in reviewing this submission for JOSS (Journal of Open Source Software)?

You can find more information about the submission at the top of this Github issue #6455.

Thank you in advance!

RMeli commented 6 months ago

Hi @zeroset 👋

Would you be interested in reviewing this submission for JOSS (Journal of Open Source Software)?

You can find more information about the submission at the top of this Github issue #6455.

Thank you in advance!

amkrajewski commented 6 months ago

@RMeli, I just wanted to let you know that there is no pressure for a speedy review on my side. I understand that this is one of the busiest times of the year for most people in academia (myself included).

RMeli commented 6 months ago

Hi @bdice 👋

Would you be interested in reviewing this submission for JOSS (Journal of Open Source Software)?

You can find more information about the submission at the top of this Github issue #6455.

Thank you in advance!

RMeli commented 6 months ago

Hi @yangbai90 👋

Would you be interested in reviewing this submission for JOSS (Journal of Open Source Software)?

You can find more information about the submission at the top of this Github issue #6455.

Thank you in advance!

RMeli commented 6 months ago

Thank you @amkrajewski. If we can't find enough reviewers in the meantime, would you be OK with the timeline suggested by @atzberg and @Henrium, that is, review starting in the beginning of June?

amkrajewski commented 6 months ago

@RMeli The June timeline works fine for me. I hoped my submission would be reviewed before early August, so there should be plenty of time.

RMeli commented 6 months ago

@editorialbot add @atzberg as reviewer

editorialbot commented 6 months ago

@atzberg added to the reviewers list!

RMeli commented 6 months ago

@editorialbot add @Henrium as reviewer

editorialbot commented 6 months ago

@Henrium added to the reviewers list!

RMeli commented 6 months ago

Given the lack of response for other potential reviewers I added @atzberg and @Henrium as reviewers. Thank you for volunteering. Soon I will start the review issue, but as discussed we don't expect any activity until June.

bdice commented 6 months ago

Apologies for the late response. I briefly skimmed the paper and could be a reviewer, but (like the others) not until June.

RMeli commented 6 months ago

@editorialbot add @bdice as reviewer

Thank you @bdice for coming back to me, I realise people are very busy so no worries for late/no replies. I added you as a reviewer too, since you are also OK with the June timeline.

editorialbot commented 6 months ago

@bdice added to the reviewers list!

RMeli commented 6 months ago

Thank you @atzberg, @Henrium and @bdice for agreeing to review for JOSS. I'll soon start the review process, closing this PRE-REVIEW issue and opening a REVIEW issue for the actual review.

As discussed, the actual review will start in June. I'll mark the REVIEW issue as "PAUSED", and ping you again then.

If it's your first time reviewing for JOSS, please have a look at the following pages:

A good way to review is to open issues in the software repository, and link them to the (soon-to-be-open) review issue.

Do not hesitate to ping me with any questions you might have.

RMeli commented 6 months ago

@editorialbot start review

editorialbot commented 6 months ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6731.

openjournals / joss-reviews

[PRE REVIEW]: nimCSO: A Nim package for Compositional Space Optimization #6455

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