[REVIEW]: XRTpy : A Hinode X-Ray Telescope Python Package

[editorialbot]

Submitting author: @joyvelasquez (Joy velasquez)
Repository: https://github.com/HinodeXRT/xrtpy
Branch with paper.md (empty if default branch): main
Version: 0.4.1
Editor: @dfm
Reviewers: @dpshelio, @Cadair
Archive: 10.5281/zenodo.13157913

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/e8ae2a0f5cb2140907456c60f2c694ac/status.svg)](https://joss.theoj.org/papers/e8ae2a0f5cb2140907456c60f2c694ac)

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

@dpshelio & @Cadair, 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 @dfm 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 @Cadair

📝 Checklist for @dpshelio

[editorialbot]

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:

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.53 s (146.4 files/s, 17123.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          21            841            643           2741
reStructuredText                28            218            232            380
YAML                             9             65             13            364
TeX                              2             11              0            317
Jupyter Notebook                 7              0           2038            275
CSS                              2             44             78            208
Markdown                         3             48              0            138
TOML                             1             17              1            135
IDL                              2             20            169             41
DOS Batch                        1              8              1             26
HTML                             1              9              0             21
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            78           1285           3182           4655
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1222

[editorialbot]

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

OK DOIs

- 10.1146/annurev.astro.46.060407.145222 is OK
- 10.1086/191698 is OK
- 10.1007/s11207-007-0182-1 is OK
- 10.1007/s11214-007-9173-7 is OK
- 10.1007/s11214-007-9173-7 is OK
- 10.1007/s11207-007-9014-6 is OK
- 10.1086/337949 is OK
- 10.1007/s11207-010-9685-2 is OK
- 10.1007/s11207-013-0368-7 is OK
- 10.1088/0004-637X/755/1/33 is OK
- 10.1051/0004-6361/201424110 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[dfm]

@dpshelio, @Cadair, @joyvelasquez — This is the review thread for the paper. All of our correspondence will happen here from now on. Thanks again for agreeing to participate!

👉 Please read the "Reviewer instructions & questions" in the first comment above, and generate your checklists by commenting @editorialbot generate my checklist on this issue ASAP. 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 openjournals/joss-reviews#6396 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 try to make a start 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. Please get your review started as soon as possible!

[editorialbot]

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

[dfm]

@dpshelio, @Cadair — This is a ping to please get started with your reviews ASAP. Many thanks!

[Cadair]

Review checklist for @Cadair

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 https://github.com/HinodeXRT/xrtpy?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@joyvelasquez) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[dpshelio]

Review checklist for @dpshelio

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 https://github.com/HinodeXRT/xrtpy?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@joyvelasquez) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[dpshelio]

@dpshelio, @Cadair — This is a ping to please get started with your reviews ASAP. Many thanks!

Sorry for the delay. @dfm I've set a number of issues on xrtpy as shown above. I will be away till 1st of May, so unfortunately I won't be able to review any comments till then. In any case, most of the comments are simple to address, and I trust the authors to fulfil them and by completing that meta issue I created will be OK with me to check the missing checkboxes above.

[Cadair]

I have opened a couple of issues and one PR on XRTPy, and also agreed with some of @dpshelio's comments. I think all the things are pretty minor though. The package looks great and really useful. Would love to see it become SunPy affiliated as well.

[joyvelasquez]

Hi @Cadair,

First off, thank you for taking on the role of reviewer! Additionally, I appreciate the issues you've created and the feedback provided, regardless of their scale. They'll undoubtedly contribute to our improvement in attention to detail. I'll be addressing them promptly. Also, a special thanks for recognizing the potential for XRTpy to become a Sunpy affiliated package!

[dfm]

@joyvelasquez — I wanted to check in to see if you could update this thread with a summary of where things stand with respect to the recommended revisions. Thanks!!

[dfm]

@joyvelasquez — Any updates here? Let us know the status of your work addressing these comments.

[joyvelasquez]

@dfm, sorry for the late response. I'm almost done updating all the suggestions. I just have two more issues to address: XRTpy Issue #227 and Issue #229. I plan to finish them early next week. I'll make sure to let you know!

[dfm]

@joyvelasquez — Thanks for the update - sounds good!

[joyvelasquez]

Hi @dfm,
I have addressed most of the reviewers' suggestions/issues and merged them into the XRTpy Python package. However, I still need to cover one more topic: issue #227. The XRTpy team is working together to update this topic. It's difficult to judge how long it will take, but we're actively working on it. I will update you once complete.

[joyvelasquez]

Hi @dfm, the XRTpy team has made all the edits suggested by the reviewers, and all changes have been merged into
XRTpy. We are planning to release a update version of the package with all the JOSS-related changes and additional new features by the end of the month. I believe the XRTpy JOSS paper is ready for another review. How should we proceed from here?

[dfm]

Thanks for the update @joyvelasquez!

@dpshelio, @Cadair — Can you take another look in light of these changes? Thanks!

[dfm]

@dpshelio, @Cadair — A reminder to keep this on your radar. Thanks!

[Cadair]

Hi all,

I think it looks good to me. My remaining comment about the docs would be that I would like to see some kind of index of all the API to make it easier to find, but it is there if you click through so I am happy to tick all the boxes for the review.

[joyvelasquez]

Hello @Cadair,
Thank you for being a reviewer. Regarding the index suggestion, we do have one as you mentioned. However, we're working on making it more accessible.

[editorialbot]

Done! archive is now 10.5281/zenodo.13157913

[dfm]

@editorialbot set 0.4.1 as version

[editorialbot]

Done! version is now 0.4.1

[dfm]

@editorialbot check references

[dfm]

@editorialbot generate pdf

[editorialbot]

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

OK DOIs

- 10.1146/annurev.astro.46.060407.145222 is OK
- 10.21105/joss.02801 is OK
- 10.1051/aas:1997368 is OK
- 10.1051/aas:1997368 is OK
- 10.1086/191698 is OK
- 10.1007/s11207-007-0182-1 is OK
- 10.1007/s11214-007-9173-7 is OK
- 10.1088/0004-637X/800/1/54 is OK
- 10.1007/s11207-007-9014-6 is OK
- 10.1086/337949 is OK
- 10.1007/s11207-010-9685-2 is OK
- 10.1007/s11207-013-0368-7 is OK
- 10.1088/0004-637X/755/1/33 is OK
- 10.1051/0004-6361/201424110 is OK
- 10.3847/1538-4357/ab4f7a is OK
- 10.21105/joss.04914 is OK

MISSING DOIs

- No DOI given, and none found for title: CHIANTI - An Atomic Database for Emission Lines. P...
- No DOI given, and none found for title: The absolute coronal abundances of sulfur, calcium...

INVALID DOIs

- None

[editorialbot]

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

[dfm]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1146/annurev.astro.46.060407.145222 is OK
- 10.21105/joss.02801 is OK
- 10.1051/aas:1997368 is OK
- 10.1051/aas:1997368 is OK
- 10.1086/191698 is OK
- 10.1007/s11207-007-0182-1 is OK
- 10.1007/s11214-007-9173-7 is OK
- 10.1088/0004-637X/800/1/54 is OK
- 10.1007/s11207-007-9014-6 is OK
- 10.1086/337949 is OK
- 10.1007/s11207-010-9685-2 is OK
- 10.1007/s11207-013-0368-7 is OK
- 10.1088/0004-637X/755/1/33 is OK
- 10.1051/0004-6361/201424110 is OK
- 10.3847/1538-4357/ab4f7a is OK
- 10.21105/joss.04914 is OK

MISSING DOIs

- No DOI given, and none found for title: CHIANTI - An Atomic Database for Emission Lines. P...
- No DOI given, and none found for title: The absolute coronal abundances of sulfur, calcium...

INVALID DOIs

- None

[editorialbot]

⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

ID ref-DereU003A1997 already defined

[dfm]

@joyvelasquez — It looks like the Dere:1997 reference is defined twice in the bibliography. Can you remove one of those? Sorry I didn't catch this sooner!

[joyvelasquez]

Hi @dfm , I missed it too!
I've made the updated. May take a few minutes to run test. Change made to XRTpy's main branch. Would need me to do anything else after this?

[dfm]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1146/annurev.astro.46.060407.145222 is OK
- 10.21105/joss.02801 is OK
- 10.1051/aas:1997368 is OK
- 10.1086/191698 is OK
- 10.1007/s11207-007-0182-1 is OK
- 10.1007/s11214-007-9173-7 is OK
- 10.1088/0004-637X/800/1/54 is OK
- 10.1007/s11207-007-9014-6 is OK
- 10.1086/337949 is OK
- 10.1007/s11207-010-9685-2 is OK
- 10.1007/s11207-013-0368-7 is OK
- 10.1088/0004-637X/755/1/33 is OK
- 10.1051/0004-6361/201424110 is OK
- 10.3847/1538-4357/ab4f7a is OK
- 10.21105/joss.04914 is OK

MISSING DOIs

- No DOI given, and none found for title: CHIANTI - An Atomic Database for Emission Lines. P...
- No DOI given, and none found for title: The absolute coronal abundances of sulfur, calcium...

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5749, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[dfm]

@editorialbot accept

[editorialbot]

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

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Velasquez
  given-names: Joy
  orcid: "https://orcid.org/0009-0005-4804-0946"
- family-names: Murphy
  given-names: Nicholas A.
  orcid: "https://orcid.org/0000-0001-6628-8033"
- family-names: Reeves
  given-names: Katharine K.
  orcid: "https://orcid.org/0000-0002-6903-6832"
- family-names: Slavin
  given-names: Jonathan
  orcid: "https://orcid.org/0000-0002-7597-6935"
- family-names: Weber
  given-names: Mark
  orcid: "https://orcid.org/0000-0001-7098-7064"
- family-names: Barnes
  given-names: Will T.
  orcid: "https://orcid.org/0000-0001-9642-6089"
contact:
- family-names: Murphy
  given-names: Nicholas A.
  orcid: "https://orcid.org/0000-0001-6628-8033"
- family-names: Slavin
  given-names: Jonathan
  orcid: "https://orcid.org/0000-0002-7597-6935"
- family-names: Weber
  given-names: Mark
  orcid: "https://orcid.org/0000-0001-7098-7064"
doi: 10.5281/zenodo.13157913
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Velasquez
    given-names: Joy
    orcid: "https://orcid.org/0009-0005-4804-0946"
  - family-names: Murphy
    given-names: Nicholas A.
    orcid: "https://orcid.org/0000-0001-6628-8033"
  - family-names: Reeves
    given-names: Katharine K.
    orcid: "https://orcid.org/0000-0002-6903-6832"
  - family-names: Slavin
    given-names: Jonathan
    orcid: "https://orcid.org/0000-0002-7597-6935"
  - family-names: Weber
    given-names: Mark
    orcid: "https://orcid.org/0000-0001-7098-7064"
  - family-names: Barnes
    given-names: Will T.
    orcid: "https://orcid.org/0000-0001-9642-6089"
  date-published: 2024-08-09
  doi: 10.21105/joss.06396
  issn: 2475-9066
  issue: 100
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6396
  title: "XRTpy: A Hinode-X-Ray Telescope Python Package"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06396"
  volume: 9
title: "XRTpy: A Hinode-X-Ray Telescope Python Package"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot 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.06396 joss-papers#5750
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06396
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...

[dfm]

@dpshelio, @Cadair — 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!!

@joyvelasquez — Your paper is now accepted and published in JOSS! ⚡🚀💥

Note: It looks like the PDF isn't rendering (at least for me) at the DOI. This happens sometimes because of caching issues with our servers. Let's check back tomorrow if it doesn't resolve automatically.

[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.06396/status.svg)](https://doi.org/10.21105/joss.06396)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06396">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06396/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06396/status.svg
   :target: https://doi.org/10.21105/joss.06396

This is how it will look in your documentation:

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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:

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[Cadair]

Thanks @dfm always happy to review JOSS papers :)

[Cadair]

@joyvelasquez Thanks for writing XRTPy! Don't forget to add XRTPy to the list of sunpy affiliated packages :)