[REVIEW]: DBSP_DRP: A Python package for automated spectroscopic data reduction of DBSP data

[whedon]

Submitting author: @finagle29 (Milan Roberson)
Repository: https://github.com/finagle29/DBSP_DRP/
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @arfon
Reviewers: @crhea93, @arjunsavel
Archive: 10.5281/zenodo.6241526

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/8d33523aaa8283d0547994eb51b4407f"><img src="https://joss.theoj.org/papers/8d33523aaa8283d0547994eb51b4407f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/8d33523aaa8283d0547994eb51b4407f/status.svg)](https://joss.theoj.org/papers/8d33523aaa8283d0547994eb51b4407f)

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

@crhea93 & @arjunsavel, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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 ✨

Review checklist for @crhea93

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@finagle29) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• 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?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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?

Review checklist for @arjunsavel

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@finagle29) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• 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?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @crhea93, @arjunsavel it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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

@whedon commands

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

@whedon generate pdf

[whedon]

Wordcount for paper.md is 1158

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.12 s (496.0 files/s, 40014.8 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Python                           28            582            427           2333
reStructuredText                 11            163            212            246
Markdown                          2             31              0            197
YAML                              6             29             11            166
TeX                               1              0              0            119
Bourne Shell                      3             16              8             42
CSS                               2              4              0             34
DOS Batch                         1              8              1             26
Dockerfile                        1             11             11             26
JavaScript                        1              3              0             13
make                              1              4              7              9
Bourne Again Shell                1              0              7              7
TOML                              1              0              0              7
--------------------------------------------------------------------------------
SUM:                             59            851            684           3225
--------------------------------------------------------------------------------


Statistical information for the repository 'b6da3713d45f98e5f691e63c' was
gathered on 2021/08/13.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Milan Roberson                 184          5523           2220          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Milan Roberson             3303           59.8          5.2                8.39

[whedon]

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

OK DOIs

- 10.21105/joss.02308 is OK
- 10.1086/131027 is OK
- 10.3847/1538-4357/ab8943 is OK
- 10.3847/1538-4357/abbd98 is OK
- 10.3847/1538-4357/abaeec is OK
- 10.3847/1538-4357/abb45c is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[arfon]

@crhea93, @arjunsavel – 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.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. 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/3612 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.

[crhea93]

This is a very interesting-looking package! While the majority of the documentation is present, I think it would benefit from 3 sections that are currently missing:

• Functionality API
• Automated Testing
• Contributing Guidelines

I am particularly impressed with the post-install documentation! This is very handy indeed.

[arjunsavel]

I’ve completed my review!

Overall:
The contributors to DBSP_DRP have produced an extensive and useful data reduction pipeline. The degree of its automation is impressive, and the contributors’ effort is evident — and there is clear scientific merit, with application to a well-known instrument on a well-known telescope. As someone who’s been on observing runs (though I wouldn’t call myself an observer!) and worked on a reduction pipeline, I’m particularly interested in this code's quicklook capability this code has.

I've opened a few issues in the repository. Many of the items I've mentioned are related to grammar and consistency.

• Update testing instructions finagle29/DBSP_DRP#16
• Add community guidelines finagle29/DBSP_DRP#15
• Documentation edits finagle29/DBSP_DRP#14
• JOSS paper edits finagle29/DBSP_DRP#13

I also wanted to touch base about the authorship list — I only see the first author in the commit history.

The various installation routes worked well for me. However, I couldn't fully verify the code's functionality — when I tried to reduce the sample_data, the fact that the data didn’t have RA / Dec ended ups throwing an Astropy units type error. Is there different data I should use to verify that this works, or am I missing something?

In summary, this package looks great to me. I’ll sign off for acceptance pending the resolution of the above issues!

[arfon]

@crhea93, @arjunsavel – thanks for your feedback here ⚡! @finagle29 – please let us know when you've had a chance to respond to the reviewer feedback.

[whedon]

👋 @arjunsavel, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @crhea93, please update us on how your review is going (this is an automated reminder).

[arfon]

👋 @finagle29 – just checking in here to see how you're getting on responding to the reviewer feedback?

[finagle29]

Thanks for checking in!

I've been slowly working through the review issues that @arjunsavel opened. I've been a bit stuck on how to write contributing guidelines. Regarding the authorship list, Christoffer Fremling and Mansi Kasliwal were both substantial non-code contributors. The sample_data folder is slightly misnamed, it's intentionally broken FITS files that the unit tests rely on. I have put sample data to verify functionality here: https://drive.google.com/drive/folders/1HcbmItr50IN2D4GF37ycoZHa1Cco__6m?usp=sharing

I have two quick clarifying question for @crhea93. By functionality API, do you mean something like this automatically generated API documentation https://dbsp-drp.readthedocs.io/en/develop/dbsp_drp.html ? Also, could you elaborate on what Automated Testing documentation you would like to see?

[finagle29]

And a question for @arfon : I have changed institutional affiliations since completing the vast majority of my work on DBSP_DRP, should I use my previous affiliation on the paper? If so, is there some way I should note my current affiliation?

[arjunsavel]

Hi @finagle29 — thank you for addressing my issues, things are looking great! I've closed all the completed issues.

With regard to community guidelines, you could use the emcee package's CONTRIBUTING.md file as an example. In short, you'll need sections describing how to contribute to your package, how to report issues/bugs, and how to get help. Let me know if you have any specific questions about these!

Also, thanks for pointing me to some sample data — I'll be able to check that out in the next few days.

[arfon]

And a question for @arfon : I have changed institutional affiliations since completing the vast majority of my work on DBSP_DRP, should I use my previous affiliation on the paper? If so, is there some way I should note my current affiliation?

You can include multiple affiliations if you wish? Perhaps listing your current and previous ones? The example paper shows how to do this.

[arjunsavel]

Hi @finagle29 — sorry for the delay!

I've been able to run the sample_data that you provided for the blue arm, and everything looks great there! However, I'm not able to do so for the red arm; in this case, I run into a consistent issue with each file (no RA, Dec --> astropy throws a TypeError when trying to create SkyCoords).

[finagle29]

No worries, @arjunsavel !

I ran into that bug myself, and have just pushed a fix to the develop branch. If this error (or other errors) persists, we can take discussion over to https://github.com/finagle29/DBSP_DRP/discussions.

[arfon]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

Check final proof 👉 openjournals/joss-papers#3001

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3001, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03612 joss-papers#3002
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03612
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@crhea93, @arjunsavel – many thanks for your reviews here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@finagle29 – your paper is now accepted and published in JOSS ⚡🚀💥

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03612/status.svg)](https://doi.org/10.21105/joss.03612)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03612">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03612/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03612/status.svg
   :target: https://doi.org/10.21105/joss.03612

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[finagle29]

I just noticed a small issue: in the published version of the paper, there isn't a footnote after my name noting my present address/affiliation. When I use whedon to preview the paper on the main branch of the repo, the footnote is present.

[arfon]

I wonder if we're stripping this? As per the docs, the preferred way would be to write this as such:

authors:
  - name: Milan S. Roberson^[Present address: Department of Physics and Astronomy, University of California, Los Angeles.]
    orcid: 0000-0003-1118-3132
    affiliation: "1,2"
  - name: Christoffer Fremling
    orcid: 0000-0002-4223-103X
    affiliation: 2
  - name: Mansi M. Kasliwal
    orcid: 0000-0002-5619-4938
    affiliation: 2
affiliations:
  - name: Schmidt Academy of Software Engineering, California Institute of Technology
    index: 1
  - name: Division of Physics, Mathematics and Astronomy, California Institute of Technology
    index: 2
date: 26 October 2021
bibliography: paper.bib
nocite: |
  @Lunnan2020
---

@tarleb do you have any thoughts/suggestions here?

[tarleb]

I'm looking into it right now: we changed handling of author notes such that corresponding authors and equal contributors are handled better. That might have broken all other author notes. I think I can fix this.

[tarleb]

The note should now be rendered in the PDF in the same way it did before. I'm now checking how the note can be included in JATS output.

[finagle29]

Thanks @tarleb !!
Is it possible to rerender the PDF displayed at https://joss.theoj.org/papers/10.21105/joss.03612 ?

[tarleb]

I believe @arfon might be able to do that.

[finagle29]

@arfon could you rerender the published PDF?
I noticed this just now, but as a result of the footnote issue, the citation string on the JOSS website includes a open square bracket as the last character of my last name:
Roberson[ et al., (2022). DBSP_DRP: A Python package for automated spectroscopic data reduction of DBSP data. Journal of Open Source Software, 7(70), 3612, https://doi.org/10.21105/joss.03612

[arfon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03612 joss-papers#3076
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03612
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@arfon could you rerender the published PDF?

This looks to be fixed now @finagle29?

[finagle29]

Yes, everything looks great, thank you so much for your help!

[arfon]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#3576

[arfon]

@finagle29 – can you check this new PDF looks good? https://github.com/openjournals/joss-papers/blob/13c81ea7f6403838a32bbfbc9ae0835754b5e7d9/joss.03612/10.21105.joss.03612.pdf

[finagle29]

lgtm!