[REVIEW]: pyCSEP: A Python Package For Earthquake Forecast Developers #3658

whedon · 2021-08-25T15:23:23Z

Submitting author: @wsavran (William Savran)
Repository: https://github.com/SCECcode/pycsep
Version: v0.5.2
Editor: @kbarnhart
Reviewers: @nvanderelst, @mbarall
Archive: 10.5281/zenodo.5904124

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Review checklist for @nvanderelst

✨ 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. ✨

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General checks

Repository: Is the source code for this software available at the repository url?
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Contribution and authorship: Has the submitting author (@wsavran) 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?
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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 @mbarall

✨ 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 (@wsavran) 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?

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

whedon · 2021-08-25T15:23:27Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @nvanderelst 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:

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

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

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

@whedon generate pdf

whedon · 2021-08-25T15:23:43Z

PDF failed to compile for issue #3658 with the following error:

 Can't find any papers to compile :-(

whedon · 2021-08-25T15:23:50Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=3.01 s (32.6 files/s, 246647.9 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
XML                               5              0              0         717119
JSON                              9              0              0           7184
Python                           50           1999           3492           6769
YAML                             10            137             15           3482
reStructuredText                 14            476            395            851
Markdown                          3             69              0            183
Perl                              1             10             12             41
HTML                              2              4             11             22
Bourne Again Shell                1             16             28             19
make                              1              5              6             12
Jupyter Notebook                  1              0            180             10
Bourne Shell                      1              0              0              2
--------------------------------------------------------------------------------
SUM:                             98           2716           4139         735694
--------------------------------------------------------------------------------


Statistical information for the repository '0d8ef45d20f9efdd17e304bc' was
gathered on 2021/08/25.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
MH                               2             5              4            0.02
Pablo Iturrieta                  7           637            155            1.69
Philip Maechling                 1           386              0            0.82
Thomas Beutin ("tb")             4           103             18            0.26
William                         12            54             48            0.22
William Savran                 297         25334          16064           88.17
bayonato89                       2           104             27            0.28
khawajasim                      14          1161            131            2.75
pciturri                        20           810            333            2.43
tb                               6           124              6            0.28
wsavran                         32          1038            411            3.09

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
MH                            4           80.0          2.4               50.00
Pablo Iturrieta             592           92.9          5.7                9.46
Philip Maechling            155           40.2          0.0               54.84
Thomas Beutin ("tb")         29           28.2         16.5                0.00
William Savran            10100           39.9         18.9               14.90
bayonato89                  102           98.1          1.9                9.80
khawajasim                   35            3.0         18.2               11.43
pciturri                    440           54.3          9.2               19.09
wsavran                     803           77.4          4.6                9.59

kbarnhart · 2021-08-25T15:26:04Z

@nvanderelst - thanks for agreeing to review this submission to JOSS. In the prior comments there is a checklist that you can use to guide you through your review. There are also instructions to manage your github notifications so you don't get all notifications for all JOSS reviews.

We have an automatic reminder set up in two weeks to ask you how the review is going. At present we request that reviewers complete their reviews within 6 weeks. I know you indicated you would be able to get to this sometime in late September (totally fine). JOSS is trying to be mindful of changes people have experienced due to COVID-19.

As you work through your review, if there are any issues that come up, please make an issue in the PyCEP repository, and link to this issue (paste openjournals/joss-reviews/issues/3658 into the issue you create). That way most of the discussion can occur on in-repo issues.

If you have any questions, please let me know (tag me here or email [email protected]).

I plan to find a second reviewer for this submission and will manually edit this page to provide them a checklist once they have been identified.

kbarnhart · 2021-08-30T17:47:02Z

@whedon add @mbarall as reviewer

whedon · 2021-08-30T17:47:06Z

OK, @mbarall is now a reviewer

kbarnhart · 2021-08-30T17:50:22Z

@mbarall - thanks for agreeing to review this submission to JOSS. In the prior comments there is a checklist that you can use to guide you through your review. There are also instructions to manage your github notifications so you don't get all notifications for all JOSS reviews.

We have an automatic reminder set up in two weeks to ask you how the review is going. At present we request that reviewers complete their reviews within 6 weeks. You indicated to me that you expect your review to take a few weeks longer, which is totally fine. JOSS is trying to be mindful of changes people have experienced due to COVID-19. Please update me if anything else comes up.

As you work through your review, if there are any issues that come up, please make an issue in the PyCEP repository, and link to this issue (paste openjournals/joss-reviews/issues/3658 into the issue you create). That way most of the discussion can occur on in-repo issues.

Thanks again for contributing a review to JOSS.

kbarnhart · 2021-08-30T17:52:24Z

@whedon generate pdf from branch pycsep_joss

whedon · 2021-08-30T17:52:26Z

Attempting PDF compilation from custom branch pycsep_joss. Reticulating splines etc...

whedon · 2021-08-30T17:52:54Z

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

whedon · 2021-09-08T15:23:40Z

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

kbarnhart · 2021-09-08T15:39:16Z

@nvanderelst - no need to update now since you let me know ahead of time that you'd have availability to do this review closer to the end of September.

kbarnhart · 2021-09-22T14:11:53Z

@wsavran @nvanderelst @mbarall I wanted to let you know I'll be in the field with very limited internet access from Sept 24 through Sept 30. If any questions come up during that time, I'll respond when I return.

@nvanderelst, @mbarall I know that we are getting close (or are in) the time you expected to be able to do this review. Please let me know if you have any questions as you undertake your reviews. Thanks again for being willing to serve as a reviewer for JOSS.

kbarnhart · 2021-09-22T14:12:21Z

/ooo September 24 until September 30

kbarnhart · 2021-10-05T16:34:51Z

@nvanderelst, @mbarall - I wanted to check in and see how your reviews were going. Please let me know if you have any questions.

kbarnhart · 2021-10-22T14:16:01Z

@whedon re-invite @nvanderelst as reviewer

whedon · 2021-10-22T14:16:07Z

OK, the reviewer has been re-invited.

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

mbarall · 2021-11-18T17:49:12Z

@kbarnhart I have completed my review.

kbarnhart · 2021-11-19T18:46:35Z

@mbarall many thanks for your review!

@wsavran - I would recommend you comment on SCECcode/pycsep/issues/163 once you've addressed the issues outlined there. At that point, @mbarall and I can assess whether you have addressed those concerns.

It is up to you whether you want to address these concerns now, or wait until @nvanderelst has completed his review.

Let me know with any questions, comments, or concerns.

whedon · 2022-01-25T21:58:35Z

Attempting PDF compilation from custom branch pycsep_joss. Reticulating splines etc...

whedon · 2022-01-25T21:59:13Z

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

kbarnhart · 2022-01-25T23:58:47Z

@wsavran what's the final version number? v0.5.2, yes?

kbarnhart · 2022-01-25T23:59:34Z

@whedon set 10.5281/zenodo.5904124 as archive

whedon · 2022-01-25T23:59:38Z

OK. 10.5281/zenodo.5904124 is the archive.

wsavran · 2022-01-26T00:16:44Z

@kbarnhart yes, v0.5.2, is the latest release

kbarnhart · 2022-01-26T02:20:49Z

@whedon set v0.5.2 as version

whedon · 2022-01-26T02:20:54Z

OK. v0.5.2 is the version.

kbarnhart · 2022-01-26T02:21:11Z

@whedon recommend-accept

whedon · 2022-01-26T02:21:14Z

Attempting dry run of processing paper acceptance...

whedon · 2022-01-26T02:21:31Z

PDF failed to compile for issue #3658 with the following error:

 Can't find any papers to compile :-(

kbarnhart · 2022-01-26T02:22:38Z

@whedon recommend-accept from branch pycsep_joss

whedon · 2022-01-26T02:22:41Z

Attempting dry run of processing paper acceptance...

whedon · 2022-01-26T02:23:07Z

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

OK DOIs

- 10.1785/gssrl.78.1.7 is OK
- 10.1785/gssrl.78.1.17 is OK
- 10.1785/gssrl.78.1.30 is OK
- 10.1002/cpe.1519 is OK
- 10.4401/ag-5350 is OK
- 10.2478/s11600-011-0013-5 is OK
- 10.1785/0120090340 is OK
- 10.1785/0120120186 is OK
- 10.1785/0220180033 is OK
- 10.1785/0220180051 is OK
- 10.1785/0220180031 is OK
- 10.1785/0220180053 is OK
- 10.1093/gji/ggaa554 is OK
- 10.1785/0220170045 is OK
- 10.1785/0220180161 is OK
- 10.1785/0120200026 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/mcse.2007.55 is OK
-  10.25080/Majora-92bf1922-00a  is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2022-01-26T02:23:36Z

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

Check final proof 👉 openjournals/joss-papers#2909

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2909, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch pycsep_joss

kbarnhart · 2022-01-26T02:23:54Z

@wsavran I've recommended that this paper be accepted. One of the @openjournals/joss-eics will handle the submission from here. Congratulations on contributing a valuable piece of research software. Many thanks to @nvanderelst and @mbarall for your reviews.

wsavran · 2022-01-26T18:07:56Z

@kbarnhart Thanks for your help throughout this process! Also, thanks @mbarall and @nvanderelst for your reviews of the software. I think your suggestions have improved the documentation and user experience significantly.

arfon · 2022-01-29T00:22:14Z

@whedon accept deposit=true from branch pycsep_joss

whedon · 2022-01-29T00:22:17Z

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

whedon · 2022-01-29T00:23:24Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2022-01-29T00:23:25Z

🚨🚨🚨 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.03658 joss-papers#2913
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03658
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon · 2022-01-29T00:27:42Z

@nvanderelst, @mbarall – many thanks for your reviews here and to @kbarnhart for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@wsavran – your paper is now accepted and published in JOSS ⚡🚀💥

whedon · 2022-01-29T00:27:45Z

🎉🎉🎉 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.03658/status.svg)](https://doi.org/10.21105/joss.03658)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03658">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03658/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03658/status.svg
   :target: https://doi.org/10.21105/joss.03658

This is how it will look in your documentation:

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Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
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whedon added Perl 6 Python review Shell labels Aug 25, 2021

whedon assigned kbarnhart Aug 25, 2021

whedon mentioned this issue Aug 25, 2021

[PRE REVIEW]: pyCSEP: A Python Package For Earthquake Forecast Developers #3507

Closed

whedon unassigned kbarnhart Aug 30, 2021

whedon assigned kbarnhart Aug 30, 2021

whedon assigned mbarall Sep 2, 2021

whedon assigned nvanderelst Oct 23, 2021

kbarnhart mentioned this issue Nov 17, 2021

JOSS Review Thread SCECcode/pycsep#163

Closed

whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Jan 26, 2022

whedon added accepted published Papers published in JOSS labels Jan 29, 2022

arfon closed this as completed Jan 29, 2022

editorialbot mentioned this issue Jan 19, 2024

[PRE REVIEW]: FEDS-PEC: A Python Module for Streamlining NASA Fire Perimeter Comparisons to Alternative Mapping Methods #6249

Closed

editorialbot mentioned this issue Jun 26, 2024

[PRE REVIEW]: xesn: Echo state networks powered by xarray and dask #6933

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editorialbot mentioned this issue Oct 28, 2024

[PRE REVIEW]: geopolrisk-py: A Python-Based Library to Operationalize the Geopolitical Supply Risk Method for use in Life Cycle Assessment and Comparative Risk Assessment #7414

Closed

[REVIEW]: pyCSEP: A Python Package For Earthquake Forecast Developers #3658

[REVIEW]: pyCSEP: A Python Package For Earthquake Forecast Developers #3658

Comments

whedon commented Aug 25, 2021 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @nvanderelst

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @mbarall

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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