editorialbot commented 4 months ago

Submitting author: !--author-handle-->@kkappler@diehlpk<!--end-editor-- Reviewers: @blsqr, @sinanozaydin Archive: 10.5281/zenodo.13334589

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/7d22a8379f812eb1fa42dd1a9bddad37"><img src="https://joss.theoj.org/papers/7d22a8379f812eb1fa42dd1a9bddad37/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/7d22a8379f812eb1fa42dd1a9bddad37/status.svg)](https://joss.theoj.org/papers/7d22a8379f812eb1fa42dd1a9bddad37)

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

@blsqr & @sinanozaydin, 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 @diehlpk 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 @sinanozaydin

📝 Checklist for @blsqr

editorialbot commented 4 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 4 months ago

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

OK DOIs

- 10.1016/j.cageo.2022.105270 is OK
- 10.1016/j.cageo.2015.09.015 is OK
- 10.1111/j.1365-246x.1997.tb05663.x is OK
- 10.1023/A:1015012821040 is OK
- 10.1111/rssa.12315 is OK
- 10.1190/geo2018-0679.1 is OK
- 10.1093/gji/ggz197 is OK
- 10.2481/dsj.ss_igy-009 is OK
- 10.3389/feart.2020.00296 is OK

MISSING DOIs

- No DOI given, and none found for title: BIRRP: Bounded influence, remote reference process...
- No DOI given, and none found for title: Continuous integration: improving software quality...
- No DOI given, and none found for title: Mod3DMT and EMTF: Free Software for MT Data Proces...
- No DOI given, and none found for title: Resistics: A versatile native Python 3 package for...
- No DOI given, and none found for title: The Magnetotelluric Method
- No DOI given, and none found for title: MTHotel

INVALID DOIs

- None

editorialbot commented 4 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.16 s (778.1 files/s, 278718.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          97           2503           5840           7867
XML                              2             22              0           2440
Jupyter Notebook                11              0          24668            848
JSON                             2              0              0            547
TeX                              1             14              0            138
Markdown                         1             44              0            103
reStructuredText                 8            112            136             73
CSV                              1              0              0             46
YAML                             2              1              4             32
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           127           2708          30656          12129
-------------------------------------------------------------------------------

Commit count by author:

  1187  Karl N. Kappler
    93  JP
    13  kkappler
    12  Lindsey Heagy
     9  Joseph Capriotti
     5  timronan
     3  Laura Keyson
     2  Karl Kappler
     1  Seogi Kang

editorialbot commented 4 months ago

Paper file info:

📄 Wordcount for paper.md is 1754

✅ The paper includes a Statement of need section

editorialbot commented 4 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot commented 4 months ago

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

sinanozaydin commented 4 months ago

Review checklist for @sinanozaydin

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/simpeg/aurora?
[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 (@kkappler) 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?

blsqr commented 4 months ago

Review checklist for @blsqr

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/simpeg/aurora?
[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 (@kkappler) 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?

diehlpk commented 3 months ago

Hi @blsqr, @sinanozaydin how is your review going?

blsqr commented 3 months ago

@diehlpk Thank you for checking in. I continued my review today and opened two issues in the Aurora repository:

sinanozaydin commented 3 months ago

Hi @blsqr, @sinanozaydin how is your review going?

Hello @diehlpk, as i mentioned before i can only start reviewing this after 11 July since I'm at fieldwork right now until then.

Cheers,

diehlpk commented 3 months ago

Hi @blsqr, @sinanozaydin how is your review going?

Hello @diehlpk, as i mentioned before i can only start reviewing this after 11 July since I'm at fieldwork right now until then.

Cheers,

Sorry, I forgot about that.

blsqr commented 2 months ago

@kkappler @diehlpk Sorry for not having continued with the review yet; I will do so next week.

sinanozaydin commented 2 months ago

@diehlpk I have opened an issue for my review:

https://github.com/simpeg/aurora/issues/337

diehlpk commented 2 months ago

@kkappler could you please have a look?

kkappler commented 2 months ago

Hi @diehlpk ,

I have started a branch fix_issue_337, and have a Draft PR in place to address Aurora issue 337. Currently I am working on documentation (making each module start with "This module contains ... ", and adding a descriptive sentence at the top of each method).

This response is started in a google doc. I will tag @sinanozaydin once all the comments are addressed. Lets give this a week or two for next status update.

kkappler commented 2 months ago

Hi @diehlpk , we have addressed @sinanozaydin 's review with inline responses here

sinanozaydin commented 2 months ago

Hello @diehlpk. With the revisions made by @kkappler (link above in their comment), I updated my checklist.

Cheers,

Sinan

blsqr 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:

diehlpk commented 2 months ago

@sinanozaydin thanks for finishing your review.

diehlpk commented 2 months ago

@blsqr could you please have a look if all your concerns were addressed?

blsqr commented 2 months ago

@diehlpk I have also concluded my checklist and support publication of the submitted software paper in JOSS.

The aurora package seems to address an important use case in magnetotelluric data processing, building on and extending the existing ecosystem. The submitted software paper gives a good overview of the main ideas and provides examples of how to use aurora for data analysis, starting from common dataset formats; while I'm not from this domain and probably can't assess shortcomings, the approaches taken seem convenient and well-implemented. Furthermore, it seems like this project is under very active development; the planned co-development of aurora with key packages of the domain seems like a very good idea.

Thanks to @kkappler for quickly addressing the issues raised during this review. If there are any other questions, feel free to reach out.

diehlpk commented 1 month ago

@blsqr, @sinanozaydin Thanks for finishing your review.

diehlpk commented 1 month ago

@editorialbot commands

editorialbot commented 1 month ago

Hello @diehlpk, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Add to this issue's reviewers list
@editorialbot add @username as reviewer

# Remove from this issue's reviewers list
@editorialbot remove @username from reviewers

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Assign a user as the editor of this submission
@editorialbot assign @username as editor

# Remove the editor assigned to this submission
@editorialbot remove editor

# Remind an author, a reviewer or the editor to return to a review after a 
# certain period of time (supported units days and weeks)
@editorialbot remind @reviewer in 2 weeks

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for version
@editorialbot set v1.0.0 as version

# Set a value for branch
@editorialbot set joss-paper as branch

# Set a value for repository
@editorialbot set https://github.com/organization/repo as repository

# Set a value for the archive DOI
@editorialbot set 10.5281/zenodo.6861996 as archive

# Mention the EiCs for the correct track
@editorialbot ping track-eic

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Recommends the submission for acceptance
@editorialbot recommend-accept

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Flag submission with questionable scope
@editorialbot query scope

# Get a link to the complete list of reviewers
@editorialbot list reviewers

# Creates a post-review checklist with editor and authors tasks
@editorialbot create post-review checklist

# Open the review issue
@editorialbot start review

diehlpk commented 1 month ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[ ] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
[ ] Check that the archive title, author list, version tag, and the license are correct
[ ] Set archive DOI with @editorialbot set <DOI here> as archive
[ ] Set version with @editorialbot set <version here> as version
[ ] Double check rendering of paper with @editorialbot generate pdf
[ ] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[ ] Recommend acceptance with @editorialbot recommend-accept

diehlpk commented 1 month ago

@kkappler if you are done with 346, please work on the Additional Author Tasks After Review is Complete above to proceed with the publication process.

kkappler commented 1 month ago

Hi @diehlpk ,

Re issue 346, as blsqr states, that task is on hold until the publication process is complete

The "Additional Author Tasks" have been addressed, can you please take a look?

Double check authors and affiliations (including ORCIDs)

We double checked ORCIDs and Affiliations

Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.

We made a special release of aurora, with the release tag joss_2024

Archive the release on Zenodo/figshare/etc and post the DOI here.

We Released on Zenodo with the following DOI: https://doi.org/10.5281/zenodo.13334589

Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.

The title, author list, and ORCIDs in the paper.pdf match those in the Zenodo archive.

Make sure that the license listed for the archive is the same as the software license.

Both Zenodo and aurora's github use the MIT license.

diehlpk commented 1 month ago

@editorialbot add joss_2024 as version

editorialbot commented 1 month ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

diehlpk commented 1 month ago

@editorialbot set joss_2024 as version

editorialbot commented 1 month ago

Done! version is now joss_2024

diehlpk commented 1 month ago

@editorialbot set 10.5281/zenodo.13334589 as archive

editorialbot commented 1 month ago

Done! archive is now 10.5281/zenodo.13334589

diehlpk commented 1 month ago

@editorialbot recommend-accept

editorialbot commented 1 month ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 month ago

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

✅ OK DOIs

- 10.1016/j.cageo.2022.105270 is OK
- 10.1016/j.cageo.2015.09.015 is OK
- 10.1111/j.1365-246x.1997.tb05663.x is OK
- 10.1023/A:1015012821040 is OK
- 10.1111/rssa.12315 is OK
- 10.5334/jors.148 is OK
- 10.1190/geo2018-0679.1 is OK
- 10.1093/gji/ggz197 is OK
- 10.2481/dsj.ss_igy-009 is OK
- 10.3389/feart.2020.00296 is OK
- 10.1190/1.9781560802686.ch8 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: BIRRP: Bounded influence, remote reference process...
- No DOI given, and none found for title: Continuous integration: improving software quality...
- No DOI given, and none found for title: Mod3DMT and EMTF: Free Software for MT Data Proces...
- No DOI given, and none found for title: Resistics: A versatile native Python 3 package for...
- No DOI given, and none found for title: MTHotel

❌ MISSING DOIs

- None

❌ INVALID DOIs

- https://doi.org/10.1016/j.cageo.2022.105102 is INVALID because of 'https://doi.org/' prefix

diehlpk commented 1 month ago

@kkappler please fix the invalid DOI and I will run the command again.

editorialbot commented 1 month ago

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

Element doi: [facet 'pattern'] The value 'https://doi.org/10.1016/j.cageo.2022.105102' is not accepted by the pattern '10\.[0-9]{4,9}/.{1,200}'.

diehlpk commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

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

✅ OK DOIs

- 10.1016/j.cageo.2022.105270 is OK
- 10.1016/j.cageo.2015.09.015 is OK
- 10.1111/j.1365-246x.1997.tb05663.x is OK
- 10.1023/A:1015012821040 is OK
- 10.1111/rssa.12315 is OK
- 10.5334/jors.148 is OK
- 10.1190/geo2018-0679.1 is OK
- 10.1093/gji/ggz197 is OK
- 10.2481/dsj.ss_igy-009 is OK
- 10.3389/feart.2020.00296 is OK
- 10.1190/1.9781560802686.ch8 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: BIRRP: Bounded influence, remote reference process...
- No DOI given, and none found for title: Continuous integration: improving software quality...
- No DOI given, and none found for title: Mod3DMT and EMTF: Free Software for MT Data Proces...
- No DOI given, and none found for title: Resistics: A versatile native Python 3 package for...
- No DOI given, and none found for title: MTHotel

❌ MISSING DOIs

- None

❌ INVALID DOIs

- https://doi.org/10.1016/j.cageo.2022.105102 is INVALID because of 'https://doi.org/' prefix

kkappler commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

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

✅ OK DOIs

- 10.1016/j.cageo.2022.105270 is OK
- 10.1016/j.cageo.2015.09.015 is OK
- 10.1111/j.1365-246x.1997.tb05663.x is OK
- 10.1023/A:1015012821040 is OK
- 10.1111/rssa.12315 is OK
- 10.5334/jors.148 is OK
- 10.1190/geo2018-0679.1 is OK
- 10.1016/j.cageo.2022.105102 is OK
- 10.1093/gji/ggz197 is OK
- 10.2481/dsj.ss_igy-009 is OK
- 10.3389/feart.2020.00296 is OK
- 10.1190/1.9781560802686.ch8 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: BIRRP: Bounded influence, remote reference process...
- No DOI given, and none found for title: Continuous integration: improving software quality...
- No DOI given, and none found for title: Mod3DMT and EMTF: Free Software for MT Data Proces...
- No DOI given, and none found for title: Resistics: A versatile native Python 3 package for...
- No DOI given, and none found for title: MTHotel

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

kkappler commented 1 month ago

@diehlpk The doi is fixed.

diehlpk commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

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

✅ OK DOIs

- 10.1016/j.cageo.2022.105270 is OK
- 10.1016/j.cageo.2015.09.015 is OK
- 10.1111/j.1365-246x.1997.tb05663.x is OK
- 10.1023/A:1015012821040 is OK
- 10.1111/rssa.12315 is OK
- 10.5334/jors.148 is OK
- 10.1190/geo2018-0679.1 is OK
- 10.1016/j.cageo.2022.105102 is OK
- 10.1093/gji/ggz197 is OK
- 10.2481/dsj.ss_igy-009 is OK
- 10.3389/feart.2020.00296 is OK
- 10.1190/1.9781560802686.ch8 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: BIRRP: Bounded influence, remote reference process...
- No DOI given, and none found for title: Continuous integration: improving software quality...
- No DOI given, and none found for title: Mod3DMT and EMTF: Free Software for MT Data Proces...
- No DOI given, and none found for title: Resistics: A versatile native Python 3 package for...
- No DOI given, and none found for title: MTHotel

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

diehlpk commented 1 month ago

@editorialbot recommend-accept

editorialbot commented 1 month ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 month ago

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

✅ OK DOIs

- 10.1016/j.cageo.2022.105270 is OK
- 10.1016/j.cageo.2015.09.015 is OK
- 10.1111/j.1365-246x.1997.tb05663.x is OK
- 10.1023/A:1015012821040 is OK
- 10.1111/rssa.12315 is OK
- 10.5334/jors.148 is OK
- 10.1190/geo2018-0679.1 is OK
- 10.1016/j.cageo.2022.105102 is OK
- 10.1093/gji/ggz197 is OK
- 10.2481/dsj.ss_igy-009 is OK
- 10.3389/feart.2020.00296 is OK
- 10.1190/1.9781560802686.ch8 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: BIRRP: Bounded influence, remote reference process...
- No DOI given, and none found for title: Continuous integration: improving software quality...
- No DOI given, and none found for title: Mod3DMT and EMTF: Free Software for MT Data Proces...
- No DOI given, and none found for title: Resistics: A versatile native Python 3 package for...
- No DOI given, and none found for title: MTHotel

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

openjournals / joss-reviews

[REVIEW]: Aurora: An open-source python implementation of the EMTF package for magnetotelluric data processing using MTH5 and mt_metadata #6832

Status

Reviewer instructions & questions

Checklists

Review checklist for @sinanozaydin

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @blsqr

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance