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[REVIEW]: sacio: A library for Seismic Analysis Code data files #3619

Closed whedon closed 2 years ago

whedon commented 3 years ago

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

:warning: JOSS reduced service mode :warning:

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

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

Code of Conduct

General checks

Functionality

Documentation

Software paper

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

Code of Conduct

General checks

Functionality

Documentation

Software paper

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

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

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 :tada:.

:warning: JOSS reduced service mode :warning:

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.

:star: Important :star:

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:

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whedon commented 3 years ago

Wordcount for paper.md is 506

whedon commented 3 years ago 
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 commented 3 years ago 
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 commented 3 years ago

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

danielskatz commented 3 years ago

👋 @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 commented 3 years ago

@whedon check references

whedon commented 3 years ago 
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 commented 3 years ago

👋 @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 commented 3 years ago

@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 commented 3 years ago

@cja12 - Did you see the instructions in https://github.com/openjournals/joss-reviews/issues/3619#issuecomment-899602160? 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 commented 3 years ago

@whedon check references

whedon commented 3 years ago 
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 commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

whedon commented 3 years ago

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

whedon commented 3 years ago

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

whedon commented 3 years ago

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

danielskatz commented 3 years ago

👋 @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 commented 3 years ago

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

danielskatz commented 3 years ago

@whedon re-invite @jkmacc-LANL as reviewer

whedon commented 3 years ago

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 commented 3 years ago

Documentation Issue submitted: https://github.com/savage13/sacio/issues/1

danielskatz commented 3 years ago

👋 @chad-iris, @cja12, @jkmacc-LANL - we're now about 6 weeks into the process. How is it going? I see some progress by @cja12 and @jkmacc-LANL, but no checked items from @chad-iris.

Are there things that you need from the author or me?

cja12 commented 3 years ago

Hi,

I informed you weeks ago that I was through using your system. I do not have any plans to continue this process. I found the interface too confusing and annoying - especially when it automated sending me dozens of irrelevant messages to me. For example, other than to me, I have no idea where this response is going. Ridiculous.

On Sep 29, 2021, at 1:55 PM, Daniel S. Katz @.***> wrote:

👋 @chad-iris, @cja12, @jkmacc-LANL - we're now about 6 weeks into the process. How is it going? I see some progress by @cja12 and @jkmacc-LANL, but no checked items from @chad-iris.

Are there things that you need from the author or me?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

================================i==================================== Charles J. Ammon, Department of Geosciences Penn State University / 440 Deike Bldg / University Park, PA 16802 VOICE: (814) 865 2310 / FAXES: (814) 863 7823 or (814) 863 8724 http://eqseis.geosc.psu.edu/~cammon/ http://www.personal.psu.edu/faculty/c/j/cja12/

danielskatz commented 3 years ago

Sorry. I'll remove you as a reviewer, and won't mention you again.

danielskatz commented 3 years ago

@whedon remove @cja12 as reviewer

whedon commented 3 years ago

OK, @cja12 is no longer a reviewer

danielskatz commented 3 years ago

👋 @jkmacc-LANL - how is this going at this point?

danielskatz commented 3 years ago

👋 @chad-iris - how is this going at this point?

danielskatz commented 3 years ago

👋 @jkmacc-LANL - how is this going at this point?

danielskatz commented 3 years ago

👋 @chad-iris - how is this going at this point?

danielskatz commented 3 years ago

I'm also emailing both reviewers now

chad-earthscope commented 3 years ago

@danielskatz My invitation expired as well, please re-send? I should be able to work on this right away.

danielskatz commented 3 years ago

@whedon re-invite @chad-iris As reviewer

whedon commented 3 years ago

OK, the reviewer has been re-invited.

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

chad-earthscope commented 3 years ago

Paper suggestions submitted: https://github.com/savage13/sacio/issues/2

chad-earthscope commented 3 years ago

Example code fix up: https://github.com/savage13/sacio/issues/3

chad-earthscope commented 3 years ago

Context for code in README/documentation: https://github.com/savage13/sacio/issues/4

chad-earthscope commented 3 years ago

Suggestion for paper Summary: https://github.com/savage13/sacio/issues/5

chad-earthscope commented 3 years ago

@danielskatz My review is complete. When the 4 issues I filed are addressed (https://github.com/savage13/sacio/issues) I recommend accepting the submission.

danielskatz commented 3 years ago

Thanks @chad-iris!

danielskatz commented 3 years ago

👋 @savage13 - any update on your progress on the issues opened by @chad-iris?

danielskatz commented 3 years ago

👋 @jkmacc-LANL - How is your review going? Are there any things blocking your progress?

danielskatz commented 3 years ago

I've had no response from @jkmacc-LANL here or via email in a month. I think I need to remove them and find another reviewer.

@savage13 & @kbarnhart (or @chad-iris) - do you have any suggestions?

danielskatz commented 3 years ago

👋 @mbegnaud - we seem to have lost the second reviewer in this review. Would you perhaps be able to step in and review it?

mbegnaud commented 3 years ago

Yes, I can review. When do you need it?

danielskatz commented 3 years ago

Ideally, as quickly as you can conveniently do it :) How long would you want/need?

I'm also going to update the checklists at the top to give you one, and change the reviewers in the system to remove @jkmacc-LANL and add you.

Thanks!!

danielskatz commented 3 years ago

@whedon remove @jkmacc-LANL as reviewer

whedon commented 3 years ago

OK, @jkmacc-LANL is no longer a reviewer