[REVIEW]: Shapelets: A Python package implementing shapelet functions and their applications #6058

editorialbot · 2023-11-13T17:02:42Z

Submitting author: @nasserma (Nasser Mohieddin Abukhdeir)
Repository: https://github.com/uw-comphys/shapelets
Branch with paper.md (empty if default branch): publications
Version: v1.0
Editor: @kyleniemeyer
Reviewers: @tbmiller-astro, @Anshuman5
Archive: 10.5281/zenodo.10819578

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/6242ad18d2e947c2e680aa0187d6003e/status.svg)](https://joss.theoj.org/papers/6242ad18d2e947c2e680aa0187d6003e)

Reviewers and authors:

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Reviewer instructions & questions

@tbmiller-astro & @Anshuman5, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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Checklists

📝 Checklist for @tbmiller-astro

📝 Checklist for @Anshuman5

The text was updated successfully, but these errors were encountered:

editorialbot · 2023-11-13T17:02:45Z

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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editorialbot · 2023-11-13T17:02:47Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (708.9 files/s, 72487.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                         3            131              0            220
TeX                              1             16              0            177
Python                           6            138            350            173
YAML                             1              1              0             18
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            12            286            350            591
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-11-13T17:02:49Z

Wordcount for paper.md is 2379

editorialbot · 2023-11-13T17:02:52Z

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

OK DOIs

- 10.1111/j.1365-2966.2005.09453.x is OK
- 10.1088/1361-6528/aaf353 is OK
- 10.1103/physreve.91.033307 is OK
- 10.1093/mnras/stz787 is OK
- 10.1088/2053-1591/3/8/082001 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1364/opex.12.005760 is OK
- 10.1007/s10827-008-0107-5 is OK
- 10.1152/jn.00498.2005 is OK
- 10.1088/0004-637x/813/2/102 is OK
- 10.1093/mnras/stu2611 is OK
- 10.1007/978-1-4612-2812-7_1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-11-13T17:04:40Z

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

tbmiller-astro · 2023-11-13T18:06:10Z

Review checklist for @tbmiller-astro

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/uw-comphys/shapelets?
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 (@nasserma) 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?

nasserma · 2023-11-16T00:00:41Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (708.9 files/s, 72487.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                         3            131              0            220
TeX                              1             16              0            177
Python                           6            138            350            173
YAML                             1              1              0             18
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            12            286            350            591
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

@AoifeHughes Could this software report be rerun, I am relatively sure it was using the publications branch of the repository, which did not have up-to-date code, I just merged it with the main branch and if the report is run now it will reflect the actual number of source files, lines of code, comments, etc.

AoifeHughes · 2023-11-21T08:15:21Z

@editorialbot check repository

editorialbot · 2023-11-21T08:15:23Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (703.1 files/s, 107182.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          15            485           1095            940
reStructuredText                 4            255             82            342
Markdown                         3            141              0            256
TeX                              1             16              0            177
YAML                             1              1              0             18
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            25            898           1177           1736
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-11-21T08:15:25Z

Wordcount for paper.md is 2379

AoifeHughes · 2023-12-04T08:46:36Z

@tbmiller-astro, @Anshuman5 how are the reviews coming along?

Anshuman5 · 2023-12-05T07:48:35Z

Review checklist for @Anshuman5

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/uw-comphys/shapelets?
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 (@nasserma) 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?

Anshuman5 · 2023-12-06T19:51:13Z

@AoifeHughes reviews will take another 2-3 weeks.

tbmiller-astro · 2023-12-06T19:55:06Z

@AoifeHughes I have some time the next few days and hope to be done the initial review by the end of the week

tbmiller-astro · 2023-12-06T21:07:23Z

Hi, I was actually able to get my initial review done this afternoon. The package overall looks great, well done @nasserma and the other authors.

There are a few issues I found. Two major ones to do with missing tests/ folder and need for more API documentation that I created issues for on the package's GitHub page.

mptino · 2023-12-06T23:34:36Z

Hi @tbmiller-astro - thanks for the comments. I closed one issue regarding the unit testing and shapelets-test entry point (which is now functional) and uploaded a set of minimal tests for basic functionality of the package. More unit tests will appear in the coming weeks.

nasserma · 2023-12-07T01:39:54Z

I closed one issue regarding the unit testing

@mptino I re-opened this issue, once @tbmiller-astro is satisfied we can close it.

nasserma · 2023-12-27T22:08:13Z

@tbmiller-astro @Anshuman5 We are working through these issues this week and should have most of the issues address by the end of the year, sorry for the wait!

nasserma · 2024-01-19T23:09:05Z

@tbmiller-astro @Anshuman5 We have addressed all of the issues that you have brought-up with the package, please see more detailed descriptions in the responses to those issues. Is there anything else we should address as part of the first round of review comments?

Anshuman5 · 2024-01-20T18:15:22Z

@nasserma thank you for fixing the issues. I do not have any additional comments. Also, I have updated the review checklist above.

nasserma · 2024-01-20T18:49:00Z

@nasserma thank you for fixing the issues. I do not have any additional comments. Also, I have updated the review checklist above.

@Anshuman5 thanks for your efforts!

tbmiller-astro · 2024-01-22T16:58:17Z

Well done @nasserma and the other authors, my checklist is completed now too and I have no further issues.

nasserma · 2024-01-22T18:30:57Z

Thanks @tbmiller-astro ! @AoifeHughes I think we addressed all of the reviewer comments, please let us know if anything else is needed, thanks.

nasserma · 2024-02-06T21:40:10Z

@AoifeHughes just checking in, are there any further actions on our part regarding the review?

editorialbot · 2024-03-14T23:26:55Z

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

OK DOIs

- 10.1111/j.1365-2966.2005.09453.x is OK
- 10.1088/1361-6528/ad1df4 is OK
- 10.1088/1361-6528/aaf353 is OK
- 10.1103/physreve.91.033307 is OK
- 10.1093/mnras/stz787 is OK
- 10.1088/2053-1591/3/8/082001 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1364/opex.12.005760 is OK
- 10.1007/s10827-008-0107-5 is OK
- 10.1152/jn.00498.2005 is OK
- 10.1088/0004-637x/813/2/102 is OK
- 10.1093/mnras/stu2611 is OK
- 10.1007/978-1-4612-2812-7_1 is OK

MISSING DOIs

- No DOI given, and none found for title: Shapelets—I. A method for image analysis
- No DOI given, and none found for title: High-precision timing of 42 millisecond pulsars wi...
- No DOI given, and none found for title: Advances in K-means clustering: a data mining thin...

INVALID DOIs

- None

kyleniemeyer · 2024-03-14T23:33:53Z

@nasserma it does look like DOIs might be available for two of those references, can you add?

Refregier 2003 paper on shapelets: 10.1046/j.1365-8711.2003.05901.x
Desvignes et al. 2016: 10.1093/mnras/stw483

No need to update the archive, just the paper.

nasserma · 2024-03-14T23:53:25Z

@editorialbot check references

editorialbot · 2024-03-14T23:53:41Z

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

OK DOIs

- 10.1046/j.1365-8711.2003.05901.x is OK
- 10.1111/j.1365-2966.2005.09453.x is OK
- 10.1088/1361-6528/ad1df4 is OK
- 10.1088/1361-6528/aaf353 is OK
- 10.1103/physreve.91.033307 is OK
- 10.1093/mnras/stz787 is OK
- 10.1088/2053-1591/3/8/082001 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1364/opex.12.005760 is OK
- 10.1007/s10827-008-0107-5 is OK
- 10.1152/jn.00498.2005 is OK
- 10.1088/0004-637x/813/2/102 is OK
- 10.1093/mnras/stu2611 is OK
- 10.1093/mnras/stw483 is OK
- 10.1007/978-3-642-29807-3 is OK
- 10.1007/978-1-4612-2812-7_1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

nasserma · 2024-03-14T23:54:12Z

@kyleniemeyer sorry for the oversights, they are corrected.

kyleniemeyer · 2024-03-17T19:54:58Z

@editorialbot recommend-accept

editorialbot · 2024-03-17T19:55:00Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-03-17T19:55:15Z

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

OK DOIs

- 10.1046/j.1365-8711.2003.05901.x is OK
- 10.1111/j.1365-2966.2005.09453.x is OK
- 10.1088/1361-6528/ad1df4 is OK
- 10.1088/1361-6528/aaf353 is OK
- 10.1103/physreve.91.033307 is OK
- 10.1093/mnras/stz787 is OK
- 10.1088/2053-1591/3/8/082001 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1364/opex.12.005760 is OK
- 10.1007/s10827-008-0107-5 is OK
- 10.1152/jn.00498.2005 is OK
- 10.1088/0004-637x/813/2/102 is OK
- 10.1093/mnras/stu2611 is OK
- 10.1093/mnras/stw483 is OK
- 10.1007/978-3-642-29807-3 is OK
- 10.1007/978-1-4612-2812-7_1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-03-17T19:56:44Z

👋 @openjournals/pe-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#5141, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kyleniemeyer · 2024-03-17T19:57:20Z

@editorialbot recommend-accept

editorialbot · 2024-03-17T19:57:21Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-03-17T19:57:37Z

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

OK DOIs

- 10.1046/j.1365-8711.2003.05901.x is OK
- 10.1111/j.1365-2966.2005.09453.x is OK
- 10.1088/1361-6528/ad1df4 is OK
- 10.1088/1361-6528/aaf353 is OK
- 10.1103/physreve.91.033307 is OK
- 10.1093/mnras/stz787 is OK
- 10.1088/2053-1591/3/8/082001 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1364/opex.12.005760 is OK
- 10.1007/s10827-008-0107-5 is OK
- 10.1152/jn.00498.2005 is OK
- 10.1088/0004-637x/813/2/102 is OK
- 10.1093/mnras/stu2611 is OK
- 10.1093/mnras/stw483 is OK
- 10.1007/978-3-642-29807-3 is OK
- 10.1007/978-1-4612-2812-7_1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-03-17T19:59:03Z

👋 @openjournals/pe-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#5142, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

nasserma · 2024-03-17T21:00:29Z

@kyleniemeyer could we have the rest of the day to go through the manuscript, just one last proof?

kyleniemeyer · 2024-03-17T21:01:59Z

@nasserma sure thing. I'll plan to finalize tomorrow

nasserma · 2024-03-18T03:01:57Z

@kyleniemeyer thanks, we have made many minor typographical and grammatical corrections, we think the manuscript is finalized.

kyleniemeyer · 2024-03-18T12:31:09Z

@editorialbot generate pdf

editorialbot · 2024-03-18T12:32:20Z

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

kyleniemeyer · 2024-03-18T12:33:29Z

looks good to me!

kyleniemeyer · 2024-03-18T12:34:25Z

@editorialbot accept

editorialbot · 2024-03-18T12:34:28Z

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

editorialbot · 2024-03-18T12:41:13Z

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: Tino
  given-names: Matthew Peres
  orcid: "https://orcid.org/0009-0005-6832-1761"
- family-names: Abdulaziz
  given-names: Abbas Yusuf
- family-names: Suderman
  given-names: Robert
- family-names: Akdeniz
  given-names: Thomas
- family-names: Abukhdeir
  given-names: Nasser Mohieddin
  orcid: "https://orcid.org/0000-0002-1772-0376"
contact:
- family-names: Abukhdeir
  given-names: Nasser Mohieddin
  orcid: "https://orcid.org/0000-0002-1772-0376"
doi: 10.5281/zenodo.10819578
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Tino
    given-names: Matthew Peres
    orcid: "https://orcid.org/0009-0005-6832-1761"
  - family-names: Abdulaziz
    given-names: Abbas Yusuf
  - family-names: Suderman
    given-names: Robert
  - family-names: Akdeniz
    given-names: Thomas
  - family-names: Abukhdeir
    given-names: Nasser Mohieddin
    orcid: "https://orcid.org/0000-0002-1772-0376"
  date-published: 2024-03-18
  doi: 10.21105/joss.06058
  issn: 2475-9066
  issue: 95
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6058
  title: "Shapelets: A Python package implementing shapelet functions
    and their applications"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06058"
  volume: 9
title: "Shapelets: A Python package implementing shapelet functions and
  their applications"

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 · 2024-03-18T12:41:17Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-03-18T12:41:18Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.06058 joss-papers#5145
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06058
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer · 2024-03-18T12:47:25Z

Congratulations @nasserma on your article's publication in JOSS! Please consider signing up as a reviewer if you haven't already.

Many thanks to @tbmiller-astro and @Anshuman5 for reviewing this.

editorialbot · 2024-03-18T12:47:27Z

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

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</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06058/status.svg
   :target: https://doi.org/10.21105/joss.06058

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editorialbot added Python review TeX Track: 3 (PE) Physics and Engineering labels Nov 13, 2023

editorialbot assigned AoifeHughes Nov 13, 2023

editorialbot mentioned this issue Nov 13, 2023

[PRE REVIEW]: Shapelets: A Python package implementing shapelet functions and their applications #5911

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Mar 17, 2024

editorialbot added accepted published Papers published in JOSS labels Mar 18, 2024

kyleniemeyer closed this as completed Mar 18, 2024

[REVIEW]: Shapelets: A Python package implementing shapelet functions and their applications #6058

[REVIEW]: Shapelets: A Python package implementing shapelet functions and their applications #6058

Comments

editorialbot commented Nov 13, 2023 • edited

Status

Reviewer instructions & questions

Checklists

editorialbot commented Nov 13, 2023

editorialbot commented Nov 13, 2023

editorialbot commented Nov 13, 2023

editorialbot commented Nov 13, 2023

editorialbot commented Nov 13, 2023

tbmiller-astro commented Nov 13, 2023 • edited

Review checklist for @tbmiller-astro

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

nasserma commented Nov 16, 2023

AoifeHughes commented Nov 21, 2023

editorialbot commented Nov 21, 2023

editorialbot commented Nov 21, 2023

AoifeHughes commented Dec 4, 2023

Anshuman5 commented Dec 5, 2023 • edited

Review checklist for @Anshuman5

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Anshuman5 commented Dec 6, 2023

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mptino commented Dec 6, 2023

nasserma commented Dec 7, 2023 • edited

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editorialbot commented Nov 13, 2023 •

edited

tbmiller-astro commented Nov 13, 2023 •

edited

Anshuman5 commented Dec 5, 2023 •

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nasserma commented Dec 7, 2023 •

edited

kyleniemeyer commented Mar 14, 2024 •

edited