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[REVIEW]: SAnTex: A Python-based Library for Seismic Anisotropy Calculation #6886

Open editorialbot opened 5 months ago

editorialbot commented 5 months ago

Submitting author: !--author-handle-->@utpal-singh<!--end-author-handle-- (Utpal Singh) Repository: https://github.com/utpal-singh/SAnTex Branch with paper.md (empty if default branch): main Version: v1.2 Editor: !--editor-->@rkurchin<!--end-editor-- Reviewers: !--reviewers-list-->@elena-pascal<!--end-reviewers-list-- Archive: Pending

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/aa2dd813064832aa84422d04abd0d5fc"><img src="https://joss.theoj.org/papers/aa2dd813064832aa84422d04abd0d5fc/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/aa2dd813064832aa84422d04abd0d5fc/status.svg)](https://joss.theoj.org/papers/aa2dd813064832aa84422d04abd0d5fc)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@elena-pascal & @SunilAnandatheertha, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @rkurchin know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @elena-pascal

📝 Checklist for @SunilAnandatheertha

editorialbot commented 5 months ago

Hello humans, 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:

@editorialbot commands

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

@editorialbot generate pdf
editorialbot commented 5 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/0191-8141(89)90042-4 is OK
- 10.1002/2016GC006705 is OK
- 10.3390/min11121322 is OK
- 10.1002/2017GL075647 is OK
- 10.1029/JB074i025p05961 is OK
- 10.1038/nature21359 is OK
- 10.1093/petrology/29.3.625 is OK
- 10.1029/2010GC003296 is OK
- 10.1144/M56-2020-16 is OK
- 10.1029/2019GC008289 is OK
- 10.1002/2015GC005964 is OK
- 10.1016/j.tecto.2006.02.011 is OK
- 10.1146/annurev.earth.36.031207.124120 is OK
- 10.1016/j.tecto.2015.07.026 is OK
- 10.1016/j.epsl.2005.01.024 is OK
- 10.1002/2016RG000552 is OK
- 10.1029/JB074i025p05973 is OK
- 10.1016/j.cageo.2012.05.031 is OK
- 10.1029/2003GC000614 is OK
- 10.1029/GD016p0111 is OK
- 10.1029/2018GC007931 is OK
- 10.1029/93GL02791 is OK
- 10.1029/98JB01489 is OK
- 10.1029/2000JB900041 is OK
- 10.1107/S1600576720011103 is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 5 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=1.20 s (50.1 files/s, 907314.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                             4              0              0           4408
Python                          34            772           1097           2355
TeX                              1             26              0            442
Jupyter Notebook                 6              0        1076485            321
reStructuredText                 9             70            131             89
Markdown                         2             36              0             82
YAML                             2              8              5             30
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            60            924        1077726           7762
-------------------------------------------------------------------------------

Commit count by author:

   155  utpal-singh
    17  Sinan Özaydın
     6  Utpal Singh
     3  usin8611
editorialbot commented 5 months ago

Paper file info:

📄 Wordcount for paper.md is 1114

✅ The paper includes a Statement of need section

editorialbot commented 5 months ago

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

editorialbot commented 5 months ago

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

elena-pascal commented 4 months ago

Review checklist for @elena-pascal

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

rkurchin commented 4 months ago

@SunilAnandatheertha, let me know if you have any questions about getting your review started!

SunilAnandatheertha commented 4 months ago

@editorialbot commands

On Mon, 1 Jul 2024 at 20:13, Rachel Kurchin @.***> wrote:

@SunilAnandatheertha, let me know if you have any questions about getting your review started!

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

-- Kind regards Sunil

SunilAnandatheertha commented 4 months ago

Thank you. Please provide me with some info on how to get started with the review. Eager to. Thanks.

On Mon, 1 Jul 2024 at 20:13, Rachel Kurchin @.***> wrote:

@SunilAnandatheertha https://github.com/SunilAnandatheertha, let me know if you have any questions about getting your review started!

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6886#issuecomment-2200848377, or unsubscribe https://github.com/notifications/unsubscribe-auth/APY25RX5VL7VDWQRNENLOPDZKGS67AVCNFSM6AAAAABJJE3N7WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMBQHA2DQMZXG4 . You are receiving this because you were mentioned.Message ID: @.***>

-- Kind regards Sunil

rkurchin commented 4 months ago

If you read the opening comment on this review issue, it has some basic instructions. Please don't hesitate to let me know what questions you have!

The general flow will be for you to generate your checklist and then work your way through it as you try out the code. Feel free to leave comments here and/or to file issues/PR's in the project repository related to the checklist items. If you do the latter, please link to this review issue for easy tracking (that way I won't have to hound for updates here if I can easily see that there's conversation going on in an issue/PR elsewhere 😉).

SunilAnandatheertha commented 4 months ago

Thank you.

SunilAnandatheertha commented 4 months ago

Review checklist for @SunilAnandatheertha

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

rkurchin commented 4 months ago

Hi reviewers @elena-pascal and @SunilAnandatheertha, checking in on review progress! Reminder that you should feel free to file issues/PR's in the project repo as part of your review, and please link to this issue for easy tracking if you do so!

elena-pascal commented 4 months ago

Hi @rkurchin sorry for being slow, it was busy times and then holiday times, I will be back at this next week. Thanks for being on top of this.

rkurchin commented 3 months ago

👋 Another friendly reviewer checkin for @SunilAnandatheertha and @elena-pascal!

elena-pascal commented 3 months ago

Hello, paper.md seems to have latex maths (md requires extra $ delimiters)? At least on my github it does not render. Can we have access to a copy with rendered maths? pdf would be fantastic.

rkurchin commented 3 months ago

Yes, the rendered one is accessible in the editorialbot comment above (and can be regenerated by running @editorialbot generate pdf): https://github.com/openjournals/joss-reviews/issues/6886#issuecomment-2166798638

rkurchin commented 3 months ago

@SunilAnandatheertha, any sense when you'll be able to get back to this review?

rkurchin commented 2 months ago

@elena-pascal, checking in with you about review progress here as well!

elena-pascal commented 2 months ago

Hi @rkurchin, I made an issue for the insufficient documentation, I would prefer to continue assessing the software with accessible documentation.

utpal-singh commented 2 months ago

Hi @elena-pascal,

Thank you for reviewing the paper. I wanted to confirm if the documentation you're requesting should be in the readthedocs format? Currently, we have it in PDF format, but I can create the readthedocs version if that's what's needed.

Best regards,
Utpal

elena-pascal commented 2 months ago

Hi @utpal-singh,

I left you an issue with more details. Is there a reason you choose your documentation to be in a pdf file? Git doesn't really deal well with binary files, additionally pdf is not a great way to store code snippets.

utpal-singh commented 2 months ago

Hi @elena-pascal

Thanks for the elaborated review issue. It seems I had missed the elaborated issue. Thanks for the feedback. The reason for providing the pdf file was a relatively quick look at the package contents. But, I will also prepare the documentation in the readthedocs too, not really much of an issue.

rkurchin commented 2 months ago

Hi @SunilAnandatheertha, checking in on review progress!

Also, @utpal-singh, I see that there's a ReadTheDocs live now and you're perhaps still actively committing updates to it, so perhaps ping here whenever you're ready for another look on that front!

rkurchin commented 2 months ago

Noting for the record that I've sent @SunilAnandatheertha an email as they seem unresponsive to GH notifications...

utpal-singh commented 1 month ago

Hi @elena-pascal ,

Thank you for elaborating the issue earlier, I have included the documentation which is live at https://santex.readthedocs.io/en/latest/, please let me know if its accessible now and easy to understand.

elena-pascal commented 1 month ago

Thanks @utpal-singh, for going above and beyond. I am a bit slow at the moment, as work is crazy but this is on my to do list and will get to it soon.

rkurchin commented 1 month ago

(emailed @SunilAnandatheertha again)

rkurchin commented 4 weeks ago

Checking in with @elena-pascal and @SunilAnandatheertha again about this review, thanks!

rkurchin commented 3 weeks ago

(emailed @SunilAnandatheertha, will find replacement reviewer if I don't hear back soon)

utpal-singh commented 2 weeks ago

(emailed @SunilAnandatheertha, will find replacement reviewer if I don't hear back soon)

Hi @rkurchin, Thank you for taking the time to find additional reviewers. Given that the review process has already extended over five months and we’re still seeking another reviewer, I’m wondering if there might be an option to proceed with just one. I ask because I have other work based on the SAnTex library that I’m hoping to publish and present at upcoming conference, and the timeline is a little challenging. Could you let me know if moving forward with a single reviewer might be possible in this case?

rkurchin commented 1 week ago

@utpal-singh, I do apologize for the slow pace on this review, but we do strongly prefer to have at least two reviewers, so I need to ask for your continued patience as we try to wrap this up as efficiently as possible.

rkurchin commented 1 week ago

@editorialbot remove @SunilAnandatheertha as reviewer

editorialbot commented 1 week ago

@SunilAnandatheertha removed from the reviewers list!

rkurchin commented 1 week ago

👋 @lfgmorales, @kilir, and/or @benholtzman, would you be 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

Because this is a replacement for a nonresponsive reviewer, we would appreciate an expedient review if at all possible, though of course understand that everyone has many demands on their time.

elena-pascal commented 1 week ago

Hello @utpal-singh, apologies for taking so long to get to this, work has been silly.

I am looking through the code and your notebooks. I think at this point, the paper and code is missing a way to validate its functionality. See the PRs. I cannot check the that you have automated tests that confirm the functionality of the code, since your tests only cover one or two (not clear) of the 5 functionalities. It would also be nice to have some information of where the values you assert against come from in tests. Especially because you have a lot of info in your notebooks, which are at the moment hidden, not really sure why they are part of this repo since you don't mention any of it in the paper.

Feel free to present the code and its results at the conference, and feel free to mention it is under review with JOSS. I don't see any conflict, or am I missing something?

rkurchin commented 5 days ago

(Emailed @lfgmorales, @kilir, and @benholtzman)

lfgmorales commented 5 days ago

Hi Rachel,

Thanks for the email

I am not entirely sure how to proceed here and what do we have to do, there was also an answer from Elena Pascal last week regarding this paper. Or this is not a paper “per se”, but just the code?

If you can clarify that, would be very helpful

all the best

Luiz

Luiz F. G. Morales ETH Zürich Structural Geology and Tectonics Group Scientific Center for Optical and Electron Microscopy (ScopeM) HPM C 57.3 Otto-Stern-Weg 3 8093 Zurich, Switzerland Phone +41 44 633 37 46 Email: @.***

On 13 Nov 2024, at 16:29, Rachel Kurchin @.***> wrote:

(Emailed @lfgmorales https://github.com/lfgmorales, @kilir https://github.com/kilir, and @benholtzman https://github.com/benholtzman)

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6886#issuecomment-2473950133, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALE5INZEMQFXVYSSHKZFBWT2ANV4ZAVCNFSM6AAAAABJJE3N7WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINZTHE2TAMJTGM. You are receiving this because you were mentioned.

rkurchin commented 5 days ago

Hi @lfgmorales! Our reviews primarily focus on the functionality of the software itself – you can read more about our review criteria here. They proceed via a checklist to ensure that all functional claims and best practices have been verified. Elena Pascal is the other reviewer for this software; our original second reviewer has become unresponsive; hence why I'm looking for another one relatively late in the process.

Please let me know if I can answer any other questions for you!

rkurchin commented 3 hours ago

Emailed @lfgmorales directly again to follow up...@utpal-singh, if you have other suggestions for alternative reviewers, definitely let me know as our database is a bit thin in this subject area.

elena-pascal commented 2 hours ago

Can I suggest @hakonanes ? I don't know if he will be available but he is an EBSD person and pretty active on github.