[REVIEW]: EISPAC - The EIS Python Analysis Code #4914

editorialbot · 2022-11-07T21:41:51Z

Submitting author: @MJWeberg (Micah J. Weberg)
Repository: https://github.com/USNavalResearchLaboratory/eispac
Branch with paper.md (empty if default branch):
Version: v0.94.6
Editor: @mbobra
Reviewers: @nabobalis, @PaulJWright
Archive: 10.5281/zenodo.7949516

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/d41bb77616726ee7a4596edbb44968d1"><img src="https://joss.theoj.org/papers/d41bb77616726ee7a4596edbb44968d1/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/d41bb77616726ee7a4596edbb44968d1/status.svg)](https://joss.theoj.org/papers/d41bb77616726ee7a4596edbb44968d1)

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

@nabobalis & @PaulJWright, 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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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @mbobra 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 @PaulJWright

📝 Checklist for @nabobalis

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

editorialbot · 2022-11-07T21:41:53Z

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editorialbot · 2022-11-07T21:41:55Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.14 s (669.8 files/s, 94176.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          62           1325           3019           5176
reStructuredText                17            410            400           1002
Markdown                         4             74              0            284
YAML                             4             18             11            111
Jupyter Notebook                 2              0            861             91
TeX                              1              7              0             91
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            92           1846           4299           6790
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-11-07T21:41:57Z

Wordcount for eispac_paper.md is 863

editorialbot · 2022-11-07T21:42:54Z

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

OK DOIs

- 10.1007/s01007-007-0293-1 is OK
- 10.3847/1538-4357/ab4f7a is OK
- 10.5281/zenodo.5715161 is OK
- 10.1023/A:1005038224881 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-11-07T21:43:17Z

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

mbobra · 2022-11-07T21:46:07Z

👋 @nabobalis @PaulJWright Thank you so much for agreeing to review! You can find the article in the comment boxes above ⬆️ , and the software repository linked in the first comment box on this issue. To generate your checklist, use the following command:

@editorialbot generate my checklist

You can find reviewer guidelines here, together with all the review criteria. I think you're good to go. Again, JOSS is an open review process and we encourage communication between the reviewers, the submitting author @MJWeberg, and the editor (myself). Please feel free to ask me questions, I'm always around.

Can you please respond here (or give a thumbs up) so I know you're in the right place and found all the materials?

PaulJWright · 2022-11-07T21:48:28Z

Review checklist for @PaulJWright

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/USNavalResearchLaboratory/eispac?
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 (@MJWeberg) 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?

nabobalis · 2022-11-07T22:16:51Z

Review checklist for @nabobalis

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/USNavalResearchLaboratory/eispac?
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 (@MJWeberg) 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?

Comments

I've gone over the paper, the docs and ran some of the examples. I think Paul covered everything that I saw.

For me, this is good to go.
I left State of the field: unchecked since for me, there are no other packages doing this for EIS in Python.

PaulJWright · 2022-11-08T00:34:21Z

@mbobra @nabobalis, please let me know your opinions on this, but this open MR seems significant (USNavalResearchLaboratory/eispac#50). I would personally prefer this is merged and tested/documented before any approval.

Please let me know if this is out of scope.

MJWeberg · 2022-11-08T15:06:10Z

Hello @PaulJWright and @nabobalis, thanks for all the comments and feedback so far! I will work on addressing the issues raised, but I might not have the opportunity to get through all of them today. Please feel free to continue opening issues and/or add follow-up questions, I will answer them as soon as I can.

PaulJWright · 2022-11-08T16:03:23Z

Hello @PaulJWright and @nabobalis, thanks for all the comments and feedback so far! I will work on addressing the issues raised, but I might not have the opportunity to get through all of them today. Please feel free to continue opening issues and/or add follow-up questions, I will answer them as soon as I can.

Take your time, while it may look like a lot, the majority of changes I have requested should be low-effort.

mbobra · 2023-05-19T20:42:37Z

@editorialbot set v0.94.6 as version

editorialbot · 2023-05-19T20:42:39Z

Done! version is now v0.94.6

mbobra · 2023-05-19T20:42:51Z

@editorialbot recommend-accept

editorialbot · 2023-05-19T20:42:52Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-05-19T20:42:56Z

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

OK DOIs

- 10.1007/s01007-007-0293-1 is OK
- 10.3847/1538-4357/ab4f7a is OK
- 10.5281/zenodo.5715161 is OK
- 10.1023/A:1005038224881 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-05-19T20:43:55Z

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

\AA
   ^
unexpected control sequence \AA
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

editorialbot · 2023-05-19T20:44:42Z

👋 @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#4249, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

dfm · 2023-05-20T19:12:07Z

Thanks @nabobalis and @PaulJWright for your reviews! Thanks also to @mbobra for editing!

I'm going through the final editorial steps and I have just opened a small PR with some edits to the manuscript. Please take a look and then here are the remaining items:

@MJWeberg — Can you update the metadata for the Zenodo listing (there should be an "edit" button at the top right hand corner of this page if you're logged in) so that the title matches the manuscript?
@nabobalis — I see your comment about the "State of the Field" checkbox, but the "Data sharing" and "Reproducibility" boxes also seem to be unchecked. Did you have a reason for omitting those? Thanks!

nabobalis · 2023-05-20T20:07:45Z

@nabobalis — I see your comment about the "State of the Field" checkbox, but the "Data sharing" and "Reproducibility" boxes also seem to be unchecked. Did you have a reason for omitting those? Thanks!

Ah sorry! I actually misread the statement. They should be ticked.

dfm · 2023-05-23T10:53:59Z

Thanks @nabobalis - no worries at all!

Pinging @MJWeberg to take a look at the PR (USNavalResearchLaboratory/eispac#76) and my request above about updating the metadata so that I can finish the final processing! I know it's only been 3 days, but wanted to put this on your radar on a weekday :D

MJWeberg · 2023-05-23T15:38:41Z

@dfm, Thanks for the reminder and fixing the typos! We will get the Zenodo title changed as soon as possible (due to organizational policies, I am not the primary owner of the Zenodo archive).

MJWeberg · 2023-05-26T14:41:21Z

Zenodo deposit title updated! Please let us know if there are any other edits / changes required.

dfm · 2023-05-27T12:33:33Z

@editorialbot recommend-accept

editorialbot · 2023-05-27T12:33:34Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-05-27T12:33:37Z

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

OK DOIs

- 10.1007/s01007-007-0293-1 is OK
- 10.3847/1538-4357/ab4f7a is OK
- 10.5281/zenodo.5715161 is OK
- 10.1023/A:1005038224881 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-05-27T12:35:32Z

👋 @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#4270, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

dfm · 2023-05-27T12:38:07Z

@editorialbot accept

editorialbot · 2023-05-27T12:38:08Z

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

editorialbot · 2023-05-27T12:39:48Z

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: Weberg
  given-names: Micah J.
  orcid: "https://orcid.org/0000-0002-4433-4841"
- family-names: Warren
  given-names: Harry P.
  orcid: "https://orcid.org/0000-0001-6102-6851"
- family-names: Crump
  given-names: Nicholas
- family-names: Barnes
  given-names: Will
  orcid: "https://orcid.org/0000-0001-9642-6089"
contact:
- family-names: Weberg
  given-names: Micah J.
  orcid: "https://orcid.org/0000-0002-4433-4841"
doi: 10.5281/zenodo.7949516
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Weberg
    given-names: Micah J.
    orcid: "https://orcid.org/0000-0002-4433-4841"
  - family-names: Warren
    given-names: Harry P.
    orcid: "https://orcid.org/0000-0001-6102-6851"
  - family-names: Crump
    given-names: Nicholas
  - family-names: Barnes
    given-names: Will
    orcid: "https://orcid.org/0000-0001-9642-6089"
  date-published: 2023-05-27
  doi: 10.21105/joss.04914
  issn: 2475-9066
  issue: 85
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 4914
  title: EISPAC - The EIS Python Analysis Code
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.04914"
  volume: 8
title: EISPAC - The EIS Python Analysis Code

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 · 2023-05-27T12:39:53Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2023-05-27T12:39:54Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-05-27T12:39:54Z

🚨🚨🚨 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.04914 joss-papers#4271
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04914
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

dfm · 2023-05-27T12:45:13Z

Many thanks to @nabobalis and @PaulJWright for reviewing and to @mbobra for editing! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you!!

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

editorialbot · 2023-05-27T12:45:19Z

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reStructuredText:
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editorialbot added Python review Track: 1 (AASS) Astronomy, Astrophysics, and Space Sciences labels Nov 7, 2022

editorialbot assigned mbobra Nov 7, 2022

editorialbot mentioned this issue Nov 7, 2022

[PRE REVIEW]: EISPAC - The EIS Python Analysis Code #4907

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label May 19, 2023

dfm mentioned this issue May 20, 2023

JOSS: Fixing journal references, typos, undefined symbol USNavalResearchLaboratory/eispac#76

Merged

editorialbot added accepted published Papers published in JOSS labels May 27, 2023

dfm closed this as completed May 27, 2023

editorialbot mentioned this issue Jun 28, 2024

[PRE REVIEW]: amisrsynthdata: A Python package for generating synthetic data for the Advanced Modular Incoherent Scatter Radars #6938

Open

[REVIEW]: EISPAC - The EIS Python Analysis Code #4914

[REVIEW]: EISPAC - The EIS Python Analysis Code #4914

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Review checklist for @PaulJWright

Conflict of interest

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General checks

Functionality

Documentation

Software paper

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Review checklist for @nabobalis

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Comments

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