[REVIEW]: sacio: A library for Seismic Analysis Code data files

[whedon]

Submitting author: @savage13 (Brian Savage)
Repository: https://github.com/savage13/sacio
Version: v1.0.3
Editor: @danielskatz
Reviewers: @chad-iris, @mbegnaud
Archive: 10.5281/zenodo.5722418

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/46f90cf1fcfd3850e8a54ddd7f2af5d9"><img src="https://joss.theoj.org/papers/46f90cf1fcfd3850e8a54ddd7f2af5d9/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/46f90cf1fcfd3850e8a54ddd7f2af5d9/status.svg)](https://joss.theoj.org/papers/46f90cf1fcfd3850e8a54ddd7f2af5d9)

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

@chad-iris & @mbegnaud, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @danielskatz 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 ✨

Review checklist for @chad-iris

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@savage13) 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

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 and who the target audience is?
• 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?

Review checklist for @mbegnaud

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@savage13) 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

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 #3923

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 and who the target audience is?
• 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?

Review checklist for @jkmacc-LANL

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@savage13) 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

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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @chad-iris, @cja12, @jkmacc-LANL it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

[whedon]

Wordcount for paper.md is 506

[whedon]

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

OK DOIs

- 10.1007/s12517-008-0001-5 is OK
- doi:10.1029/2011GL047947 is OK
- 10.1785/0220160028 is OK
- 10.2172/110248 is OK
- 10.1785/0120110042 is OK
- 10.1002/jgrb.50146 is OK
- 10.1785/0120170145 is OK

MISSING DOIs

- 10.1111/j.1365-246x.2009.04429.x may be a valid DOI for title: Seismic tomography of the southern California crust based on spectral-element and adjoint methods

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.20 s (1131.7 files/s, 221181.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                           115            417           1044          13126
C                               17           1070           4695           9423
Bourne Shell                     8            724           1057           5513
JavaScript                      73            100            187           2043
CSS                              4            338             80           1664
C/C++ Header                     7            163           1019           1191
m4                               2             93             21            837
XML                              1              5              8            182
TeX                              1             11              0            125
Markdown                         2             40              0             93
make                             1             18              2             49
YAML                             1              1              0              3
-------------------------------------------------------------------------------
SUM:                           232           2980           8113          34249
-------------------------------------------------------------------------------


Statistical information for the repository '82b054a9e9c6aa7be10589c6' was
gathered on 2021/08/16.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Brian Savage                    75         23852           3876          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Brian Savage              19976           83.7          6.5               33.46

[whedon]

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

[danielskatz]

👋 @chad-iris and @cja12 and @jkmacc-LANL - Thanks for agreeing to review this submission.
This is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements. 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.

Please read the first couple of comments in this issue carefully, so that you can accept the invitation from JOSS and be able to check items, and so that you don't get overwhelmed with notifications from other activities in JOSS.

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, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#3619 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 reviews to be completed within about 2-4 weeks. Please let me know if either of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@danielskatz) if you have any questions/concerns.

[danielskatz]

@whedon check references

[whedon]

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

OK DOIs

- 10.1007/s12517-008-0001-5 is OK
- doi:10.1029/2011GL047947 is OK
- 10.1785/0220160028 is OK
- 10.2172/110248 is OK
- 10.1785/0120110042 is OK
- 10.1002/jgrb.50146 is OK
- 10.1785/0120170145 is OK

MISSING DOIs

- 10.1111/j.1365-246x.2009.04429.x may be a valid DOI for title: Seismic tomography of the southern California crust based on spectral-element and adjoint methods

INVALID DOIs

- None

[danielskatz]

👋 @savage13 - can you work on the possibly missing DOI that whedon suggests, but note that this may be incorrect. Please feel free to make changes to your .bib file, then use the command @whedon check references to check again, and the command @whedon generate pdf when the references are right to make a new PDF. Whedon commands need to be the first entry in a new comment.

[danielskatz]

@cja12 - I see you are trying to use the automated GitHub feature on the checklist - these issues you open are intentionally being closed by whedon. Please note the instructions at the top of your checklist:

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

and when you open an issue there, please mention openjournals/joss-reviews#3619 so that a link is created to this review issue and we can see if it is open or closed.

[danielskatz]

@cja12 - Did you see the instructions in #3619 (comment)? Right now, you are getting notifications for all JOSS reviews, and those instructions tell you how to turn this off, so you will only get notifications for this review. I hope that might solve your problem and let you keep working on this review, particularly since you already have started.

[savage13]

@whedon check references

[whedon]

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

OK DOIs

- 10.1007/s12517-008-0001-5 is OK
- doi:10.1029/2011GL047947 is OK
- 10.1785/0220160028 is OK
- 10.2172/110248 is OK
- 10.1785/0120110042 is OK
- 10.1002/jgrb.50146 is OK
- 10.1111/j.1365-246X.2009.04429.x is OK
- 10.1785/0120170145 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[savage13]

@whedon generate pdf

[whedon]

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

[whedon]

👋 @chad-iris, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @cja12, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @jkmacc-LANL, please update us on how your review is going (this is an automated reminder).

[danielskatz]

👋 @chad-iris, @cja12, @jkmacc-LANL - we're now about 3 weeks into the process. How is it going? I see some progress by @cja12, but no checked items from @chad-iris or @jkmacc-LANL

[jkmacc-LANL]

My apologies for the delay; my invitation has expired. Can it please be resent?

[danielskatz]

@whedon re-invite @jkmacc-LANL as reviewer

[whedon]

OK, the reviewer has been re-invited.

@jkmacc-LANL please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[jkmacc-LANL]

Documentation Issue submitted: savage13/sacio#1

[savage13]

Updated and fixed issues opened by mbegnaud. Sorry for the delay.

[danielskatz]

@mbegnaud - please take a look at the issues/responses when you get a chance, and check off more items, or let us know what else needs to be done in your opinion. Thanks!

[mbegnaud]

@danielskatz I have checked everything off. I think those are the only suggestions on my side.

[danielskatz]

Thanks @mbegnaud!

[danielskatz]

@savage13 - Next I'll proofread the paper, provide any comments, and provide instruction on archiving the software, which is what we need to proceed to acceptance.

[danielskatz]

@whedon check references

[whedon]

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

OK DOIs

- 10.1007/s12517-008-0001-5 is OK
- doi:10.1029/2011GL047947 is OK
- 10.1785/0220160028 is OK
- 10.2172/110248 is OK
- 10.1785/0120110042 is OK
- 10.1002/jgrb.50146 is OK
- 10.1111/j.1365-246X.2009.04429.x is OK
- 10.1785/0120170145 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[danielskatz]

@whedon generate pdf

[whedon]

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

[danielskatz]

@savage13 - I've suggested some minor changes in savage13/sacio#10 Overall, this looks good. Can you merge this?

Then, can you:

• Make a tagged release of your software, and list the version tag of the archived version here.
• Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
• Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
• Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

[savage13]

• Make a tagged release of your software, and list the version tag of the archived version here.
• Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
• Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
• Please list the DOI of the archived version here.

DOI of Archived Version at Zenodo: 10.5281/zenodo.5722418

[danielskatz]

@whedon set 10.5281/zenodo.5722418 as archive

[whedon]

OK. 10.5281/zenodo.5722418 is the archive.

[danielskatz]

@whedon set v1.0.3 as version

[whedon]

OK. v1.0.3 is the version.

[danielskatz]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1007/s12517-008-0001-5 is OK
- doi:10.1029/2011GL047947 is OK
- 10.1785/0220160028 is OK
- 10.2172/110248 is OK
- 10.1785/0120110042 is OK
- 10.1002/jgrb.50146 is OK
- 10.1111/j.1365-246X.2009.04429.x is OK
- 10.1785/0120170145 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2764

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2764, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[danielskatz]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03619 joss-papers#2765
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03619
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[danielskatz]

Congratulations to @savage13 (Brian Savage)!!

And thanks to @chad-iris and @mbegnaud for reviewing!
We couldn't do this without you

[whedon]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03619/status.svg)](https://doi.org/10.21105/joss.03619)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03619">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03619/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03619/status.svg
   :target: https://doi.org/10.21105/joss.03619

This is how it will look in your documentation:

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