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

editorialbot commented 7 months ago

Submitting author: !--author-handle-->@joyvelasquez@dfm<!--end-editor-- Reviewers: @dpshelio, @Cadair Archive: 10.5281/zenodo.13157913

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e8ae2a0f5cb2140907456c60f2c694ac"><img src="https://joss.theoj.org/papers/e8ae2a0f5cb2140907456c60f2c694ac/status.svg"></a>
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 commented 7 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 7 months ago

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 commented 7 months ago

Wordcount for paper.md is 1222

editorialbot commented 7 months ago

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 commented 7 months ago

@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 commented 7 months ago

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

dfm commented 6 months ago

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

Cadair commented 6 months ago

Review checklist for @Cadair

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/HinodeXRT/xrtpy?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

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

dpshelio commented 6 months ago

Review checklist for @dpshelio

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/HinodeXRT/xrtpy?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[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?
[ ] 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).
[ ] 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?
[ ] 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, who the target audience is, and its relation to other work?
[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)?
[ ] 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 commented 6 months ago

@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 commented 6 months ago

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 commented 5 months ago

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 commented 5 months ago

@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 commented 4 months ago

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

joyvelasquez commented 4 months ago

@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 commented 4 months ago

@joyvelasquez — Thanks for the update - sounds good!

joyvelasquez commented 4 months ago

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 commented 4 months ago

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 commented 3 months ago

Thanks for the update @joyvelasquez!

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

dfm commented 3 months ago

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

Cadair commented 3 months ago

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 commented 3 months ago

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.

joyvelasquez commented 2 months ago

Hello @dfm , I hope all is well! The XRTpy team is looking forward to your review. Thanks in advance!

dfm commented 2 months ago

@joyvelasquez — Thanks for checking in! I've gone back to @dpshelio's comment above and it looks like it should be fine to continue without a full checklist. I'm sorry for missing that!

I have a few last processing steps for you to do now. Can you first update the two references to \ssr in the biblography file:

-   journal = {\ssr},
+   journal = {Space Science Reviews},

Once you've done that:

Comment @editorialbot generate pdf on this thread and take one last read through the manuscript to make sure that you're happy with it (it's harder to make changes later!), especially the author names and affiliations. I've taken a pass and it looks good to me!
Increment the version number of the software and report that version number back here.
Create an archived release of that version of the software (using Zenodo or something similar). Please make sure that the metadata (title and author list) exactly match the paper. Then report the DOI of the release back to this thread.

dfm commented 2 months ago

And also: a big thank you to @dpshelio for @Cadair your reviews of this submission!!

joyvelasquez commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

joyvelasquez commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

joyvelasquez commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

joyvelasquez commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

joyvelasquez commented 2 months ago

Hello @dfm ,

I'm also most done and soon to publish on Zendo, working on metadata at the moment. However, I was able to generate/reserve a DOI tag from Zendo.

The version number of the software has been incremented to 0.4.1. The DOI for the archived release is 10.5281/zenodo.13157914.

dfm commented 2 months ago

Thanks @joyvelasquez! It looks like that DOI doesn't resolve. Please share the DOI once you have one with the metadata set up and then the final processing will be quick. Thanks!

joyvelasquez commented 1 month ago

Hello @dfm , I managed to finish up metadata on Zenodo, and published XRTpy. The DOI for the archived release is : https://zenodo.org/records/13157914

joyvelasquez commented 1 month ago

Hello Dan, Stuart, & David,

I want to express my deepest gratitude to all of you for your invaluable contributions to the review and publication of XRTpy in JOSS. Your thoughtful feedback, constructive suggestions, and attention to detail have significantly improved the quality of the package and its documentation. @dfm, your guidance as the editor was instrumental in navigating the submission process smoothly. @Cadair and @dpshelio, your insightful reviews have provided new perspectives and helped shape XRTpy into a more robust and user-friendly tool.

I am truly thankful as I speak on behalf of the XRTpy team, for the time and effort you have each dedicated to this project, and I’m excited to see how XRTpy will benefit the solar physics community.

dfm commented 1 month ago

@editorialbot set 10.5281/zenodo.13157913 as archive