[REVIEW]: Astronomical échelle spectroscopy data analysis with muler

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@gully@xuanxu<!--end-editor-- Reviewers: @bmorris3, @wtgee Archive: 10.5281/zenodo.6539458

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c889fa9eeb8a63103533494a1f0b0588"><img src="https://joss.theoj.org/papers/c889fa9eeb8a63103533494a1f0b0588/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c889fa9eeb8a63103533494a1f0b0588/status.svg)](https://joss.theoj.org/papers/c889fa9eeb8a63103533494a1f0b0588)

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

@bmorris3 & @wtgee, 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 @xuanxu 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 @wtgee

📝 Checklist for @bmorris3

editorialbot commented 2 years ago

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editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.13 s (382.7 files/s, 187077.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              5           1458           1268          12598
Python                          11            547            587           1621
Jupyter Notebook                15              0           4698            467
YAML                             5              9             10            169
Markdown                         4             45              0            120
reStructuredText                 5            106             62            116
DOS Batch                        1              8              1             26
make                             2              5             11             21
INI                              1              0              0              2
-------------------------------------------------------------------------------
SUM:                            49           2178           6637          15140
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

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

OK DOIs

- 10.1088/0004-637X/812/2/128 is OK
- 10.1117/12.2056431 is OK
- 10.1117/12.2312345 is OK
- 10.1117/12.317283 is OK
- 10.1117/12.395422 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3509134 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/ab40a7 is OK
- 10.1117/12.926102 is OK
- 10.1117/12.2056417 is OK
- 10.1117/12.2313835 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.5281/zenodo.845059 is OK
- 10.21105/joss.03095 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

Wordcount for paper.md is 1030

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:

wtgee commented 2 years ago

Review checklist for @wtgee

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/OttoStruve/muler?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@gully) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

bmorris3 commented 2 years ago

Review checklist for @bmorris3

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/OttoStruve/muler?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@gully) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

bmorris3 commented 2 years ago

@xuanxu I've completed my review, this submission looks fantastic. Excellent work, @gully et al.!

xuanxu commented 2 years ago

@bmorris3 great, thanks!

gully commented 2 years ago

Thank you all for the reviewing and editing process. We would like to add a coauthor who contributed code during the JOSS review process. I have made the coauthor addition on the paper.md in the main branch of the repo.

Thank you all again 🙏

wtgee commented 2 years ago

Thanks for addressing my issues @gully. I'll try to finish up my review today.

wtgee commented 2 years ago

@gully I finished off the review and added a few minor issues as well as https://github.com/OttoStruve/muler/issues/108, which prevents me from running two of the notebooks from a clean install. If I manually fix that issue the two notebooks don't have any other issues.

I've checked off all the boxes for my review but that Issue above should get fixed before final approval. The other minor grammatical issues don't affect the review.

wtgee commented 2 years ago

Thanks @gully, things look good on my end.

@xuanxu my review is complete as well. Thanks!

xuanxu commented 2 years ago

@wtgee Thank you!

xuanxu commented 2 years ago

@editorialbot generate pdf

xuanxu commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1088/0004-637X/812/2/128 is OK
- 10.1117/12.2056431 is OK
- 10.1117/12.2312345 is OK
- 10.1117/12.317283 is OK
- 10.1117/12.395422 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3509134 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/ab40a7 is OK
- 10.1117/12.926102 is OK
- 10.1117/12.2056417 is OK
- 10.1117/12.2313835 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.5281/zenodo.845059 is OK
- 10.21105/joss.03095 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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:

xuanxu commented 2 years ago

OK @gully, everything looks good, here are the next steps:

Please release a new tagged version from the current main branch so it includes all the changes made during the review process
Then archive that latest release in Zenodo or a similar service
Check the Zenodo deposit has the correct metadata: title and authors names should match the paper; you may also add authors' ORCIDs.

Once you do that please report here the version number and archive DOI

gully commented 2 years ago

Version number is v0.3.4, here is the link to Zenodo:

https://zenodo.org/record/6539458#.YnvVcy-B1pQ

xuanxu commented 2 years ago

@editorialbot set v0.3.4 as version

editorialbot commented 2 years ago

Done! version is now v0.3.4

xuanxu commented 2 years ago

@editorialbot set 10.5281/zenodo.6539458 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6539458

xuanxu commented 2 years ago

Thank you @gully. We're all set. Recommending for acceptance.

xuanxu commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.1088/0004-637X/812/2/128 is OK
- 10.1117/12.2056431 is OK
- 10.1117/12.2312345 is OK
- 10.1117/12.317283 is OK
- 10.1117/12.395422 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3509134 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/ab40a7 is OK
- 10.1117/12.926102 is OK
- 10.1117/12.2056417 is OK
- 10.1117/12.2313835 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.5281/zenodo.845059 is OK
- 10.21105/joss.03095 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/3210

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3210, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago

Doing it live! Attempting automated processing of paper acceptance...

editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 2 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/3212
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04302
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon commented 2 years ago

@bmorris3, @wtgee – many thanks for your reviews here and to @xuanxu for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@gully – your paper is now accepted and published in JOSS :zap::rocket::boom:

editorialbot commented 2 years ago

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reStructuredText:
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