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[REVIEW]: MSG: A software package for interpolating stellar spectra in pre-calculated grids #4602

Closed editorialbot closed 1 year ago

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@rhdtownsend<!--end-author-handle-- (Richard Townsend) Repository: https://github.com/rhdtownsend/msg Branch with paper.md (empty if default branch): joss Version: v1.0 Editor: !--editor-->@arfon<!--end-editor-- Reviewers: @AWehrhahn, @ivastar Archive: 10.5281/zenodo.7559319

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/fdb605600d48545f98dfb9f825dc833d"><img src="https://joss.theoj.org/papers/fdb605600d48545f98dfb9f825dc833d/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/fdb605600d48545f98dfb9f825dc833d/status.svg)](https://joss.theoj.org/papers/fdb605600d48545f98dfb9f825dc833d)

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

@AWehrhahn, 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 @arfon 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 @AWehrhahn

📝 Checklist for @ivastar

editorialbot commented 2 years 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 2 years ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.16 s (410.7 files/s, 247531.5 lines/s)
---------------------------------------------------------------------------------------
Language                             files          blank        comment           code
---------------------------------------------------------------------------------------
C                                        2           2105           9887          17931
Python                                  10            706           1056           2238
reStructuredText                        30            808           1040            703
Cython                                   1            196             27            256
TeX                                      2             21              0            190
Markdown                                 2             24              0            162
make                                     3             57             35            128
Jupyter Notebook                         1              0            475             67
Fortran 90                               1             34             14             61
Bourne Again Shell                       1             27             10             55
C/C++ Header                             1             17             20             54
Bourne Shell                             5             15              6             31
JSON                                     1              0              0             30
YAML                                     2              7             15             25
Windows Module Definition                1              0              0             17
CSS                                      1              6              5             16
---------------------------------------------------------------------------------------
SUM:                                    64           4023          12590          21964
---------------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 2 years ago

Wordcount for paper.md is 529

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.1051/0004-6361/201732484 may be a valid DOI for title: A collection of model stellar spectra for spectral types B to early-M
- 10.1051/0004-6361/201423945 may be a valid DOI for title: Determining stellar atmospheric parameters and chemical abundances of FGK stars with iSpec
- 10.1051/0004-6361/201219330 may be a valid DOI for title: The AMBRE project: A new synthetic grid of high-resolution FGKM stellar spectra
- 10.1051/0004-6361/201219058 may be a valid DOI for title: A new extensive library of PHOENIX stellar atmospheres and synthetic spectra
- 10.1086/660019 may be a valid DOI for title: Grids of ATLAS9 Model Atmospheres and MOOG Synthetic Spectra
- 10.1086/511270 may be a valid DOI for title: A Grid of NLTE Line-blanketed Model Atmospheres of Early B-Type Stars
- 10.1093/mnras/stt130 may be a valid DOI for title: On the interpolation of model atmospheres and high-resolution synthetic stellar spectra
- 10.1051/0004-6361/202038066 may be a valid DOI for title: Creating and using large grids of precalculated model atmospheres for a rapid analysis of stellar spectra

INVALID DOIs

- None
arfon commented 2 years ago

@AWehrhahn – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing: 

@editorialbot generate my checklist

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/4602 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

arfon commented 2 years ago

Note to all: I'm still on the look out for a second reviewer here.

editorialbot commented 2 years ago

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

AWehrhahn commented 2 years ago

Review checklist for @AWehrhahn

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

AWehrhahn commented 2 years ago

Here are some comments on the points in the checklist that I didn't check off yet

Installation instructions: Bad No python version given. Dependencies are given only by package name, no minimum versions requirement. No automated installation of dependencies either.

Example usage: Good Clear easy to run example of the software. Although I would like to see this example included as a script in the github and not only in the documentation.

Functionality documentation: OK The API is documented with explanations for the parameters. But without example input/outputs.

Automated tests: Ok (but not automated) Only manual guide in the documentation automatic tests (in the test directory) are missing (where not installed?)

Community guidelines: Bad No guidelines given (at least not as far as I could find them). Best guess is to use the default GitHub features.

State of the field: Kind of? They state that other packages exists, that have a different main focus. But do not discuss how their performance differs from this package.

AWehrhahn commented 2 years ago

Also please note that I have only tested the Python interface, not the C or Fortran APIs

arfon commented 2 years ago

@editorialbot add @ivastar as reviewer

editorialbot commented 2 years ago

@ivastar added to the reviewers list!

arfon commented 2 years ago

@ivastar - many thanks for agreeing to review this submission for JOSS!

Please take a look at the instructions above and let me know if you have any questions! https://github.com/openjournals/joss-reviews/issues/4602#issuecomment-1191517285

ivastar commented 2 years ago

Review checklist for @ivastar

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

arfon commented 2 years ago

:wave: @ivastar – just checking in here to see how you're getting on with your review?

ivastar commented 2 years ago

@arfon I've done the review. Do I write comments on the items I've left unchecked here?

arfon commented 2 years ago

@arfon I've done the review. Do I write comments on the items I've left unchecked here?

Yes please! Also, if you've opened issues on the repo (https://github.com/rhdtownsend/msg) that are related to these unchecked items then please link to them here too.

ivastar commented 2 years ago

Review completed. Most of my points agree with those of @AWehrhahn. I also only tested the Python interface. I added some comments to the issues that were already open and also added one more issue on the performance claims in handling large files.

arfon commented 2 years ago

Thanks @AWehrhahn and @ivastar! @rhdtownsend – please let us know when you've managed to review this feedback and make changes as appropriate to your submission.

rhdtownsend commented 2 years ago

Will do — thanks to both for their input. I’ve already fixed the issue with the tarball, and will respond to issues as I find time.

On Aug 23, 2022, at 1:09 AM, Arfon Smith @.**@.>> wrote:

Thanks @AWehrhahnhttps://github.com/AWehrhahn and @ivastarhttps://github.com/ivastar! @rhdtownsendhttps://github.com/rhdtownsend – please let us know when you've managed to review this feedback and make changes as appropriate to your submission.

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/4602#issuecomment-1223593294, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADIYU4A5HOWP5WN3HZHKAV3V2RTLPANCNFSM54HXQ2ZQ. You are receiving this because you were mentioned.Message ID: @.***>

arfon commented 1 year ago

:wave: @rhdtownsend – it's now three months since we heard from you on this submission. Could you re-confirm your interest in pursing this publication in JOSS?

rhdtownsend commented 1 year ago

Yes, I am still interested — been working on changes to address the referees' remarks.

cheers,

Rich

On Nov 27, 2022, at 6:29 AM, Arfon Smith @.***> wrote:

👋 @rhdtownsend – it's now three months since we heard from you on this submission. Could you re-confirm your interest in pursing this publication in JOSS? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

arfon commented 1 year ago

Thanks for getting back to us. Do you have an estimate of when you might wrap up the changes?

rhdtownsend commented 1 year ago

I hope to be submitting in a week or so — just putting some finishing touches in place.

On Dec 9, 2022, at 4:04 AM, Arfon Smith @.***> wrote:

Thanks for getting back to us. Do you have an estimate of when you might wrap up the changes? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

rhdtownsend commented 1 year ago

@editorialbot set v1.1 as version

editorialbot commented 1 year ago

I'm sorry @rhdtownsend, I'm afraid I can't do that. That's something only editors are allowed to do.

rhdtownsend commented 1 year ago

I'm ready for my changes to MSG to be reveiwed. In brief, here's how I've modified the project in response to the comments from @AWehrhahn:

And here's how I've modified the project in response to the comments from @ivastar:

I also bumped the version number to 1.1, to reflect the changes I made to the caching API.

Thanks to both reviewers for their helpful remarks!

rhdtownsend commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

rhdtownsend commented 1 year ago

Hi Arfon —

I committed my changes, and submitted responses to the referee’s remarks, last week. Is there anything else I need to do to effect a ‘resubmit’ of the paper?

cheers,

Rich

On Dec 9, 2022, at 9:07 AM, RICHARD H D TOWNSEND @.***> wrote:

I hope to be submitting in a week or so — just putting some finishing touches in place.

On Dec 9, 2022, at 4:04 AM, Arfon Smith @.***> wrote:

Thanks for getting back to us. Do you have an estimate of when you might wrap up the changes? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

danielskatz commented 1 year ago

@rhdtownsend - @arfon is off on a short break, but I'm sure he'll get back to you fairly soon when he returns

danielskatz commented 1 year ago

👋 @AWehrhahn, @ivastar - can you take a look at the changes thaat @rhdtownsend has made and see if you can make further progress on your reviews?

ivastar commented 1 year ago

@rhdtownsend thank you for making all these excellent changes!

I ran through the installation process again and it worked for me. One minor comments: the MESA Software Development Kit link in the documentation is incorrect (https://msg.readthedocs.io/en/stable/ref-guide/mesa-sdk)

I'm ready to sign off.

rhdtownsend commented 1 year ago

Thanks @ivastar for your response; I've committed a fix for the broken link, and it will appear when I tag a new patch release (1.1.1)

AWehrhahn commented 1 year ago

Hi, im on christmas Break right now, will look at it I'm January. Happy Holidays 😊

From: Rich Townsend @.> Sent: Friday, December 23, 2022 5:11:26 PM To: openjournals/joss-reviews @.> Cc: Ansgar Wehrhahn @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [REVIEW]: MSG: A software package for interpolating stellar spectra in pre-calculated grids (Issue #4602)

Thanks @ivastarhttps://github.com/ivastar for your response; I've committed a fix for the broken link, and it will appear when I tag a new patch release (1.1.1)

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/4602#issuecomment-1364081282, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AHRJM4AD4LTJWSSRW5FDWATWOXFK5ANCNFSM54HXQ2ZQ. You are receiving this because you were mentioned.Message ID: @.***>

rhdtownsend commented 1 year ago

Hi folks —

Following up on this — any progress on the review?

cheers,

Rich

On Dec 23, 2022, at 11:34 AM, Ansgar Wehrhahn @.***> wrote:

Hi, im on christmas Break right now, will look at it I'm January. Happy Holidays 😊

From: Rich Townsend @.> Sent: Friday, December 23, 2022 5:11:26 PM To: openjournals/joss-reviews @.> Cc: Ansgar Wehrhahn @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [REVIEW]: MSG: A software package for interpolating stellar spectra in pre-calculated grids (Issue #4602)

Thanks @ivastarhttps://github.com/ivastar for your response; I've committed a fix for the broken link, and it will appear when I tag a new patch release (1.1.1)

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/4602#issuecomment-1364081282, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AHRJM4AD4LTJWSSRW5FDWATWOXFK5ANCNFSM54HXQ2ZQ. You are receiving this because you were mentioned.Message ID: @.> — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.>

AWehrhahn commented 1 year ago

Hi, sorry I was a bit busy. Looked through the changes and everything is looking good now. Nice work

arfon commented 1 year ago

@rhdtownsend – At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

I can then move forward with accepting the submission.

rhdtownsend commented 1 year ago

Hi Arfon —

Done — the DOI is 10.5281/zenodo.7559319, and the full link is https://zenodo.org/record/7559319#.Y822CxPMLt0.

cheers,

Rich

On Jan 22, 2023, at 2:06 AM, Arfon Smith @.***> wrote:

@rhdtownsend – At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that: • The title of the archive is the same as the JOSS paper title • That the authors of the archive are the same as the JOSS paper authors I can then move forward with accepting the submission. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

rhdtownsend commented 1 year ago

@arfon any update on acceptance? I'd like to post the paper on arXiv, so I can start getting the word out to users.

arfon commented 1 year ago

@editorialbot set 10.5281/zenodo.7559319 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7559319

arfon commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1051/0004-6361/201732484 is OK
- 10.1051/0004-6361/201423945 is OK
- 10.1051/0004-6361/201732147 is OK
- 10.1088/0004-637X/812/2/128 is OK
- 10.1051/0004-6361/201219330 is OK
- 10.1051/0004-6361/201219058 is OK
- 10.1086/660019 is OK
- 10.1086/374373 is OK
- 10.1086/511270 is OK
- 10.1093/mnras/stt130 is OK
- 10.1051/0004-6361/202038066 is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 1 year ago

:wave: @openjournals/aass-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3914, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago 
Doing it live! Attempting automated processing of paper acceptance...
editorialbot commented 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 1 year ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘