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[REVIEW]: ParaMonte: A high-performance serial/parallel Monte Carlo simulation library for C, C++, Fortran #2741

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @shahmoradi (Amir Shahmoradi) Repository: https://github.com/cdslaborg/paramonte Version: v1.5.1 Editor: @VivianePons Reviewer: @milancurcic, @williamfgc Archive: 10.5281/zenodo.4749957

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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

@milancurcic & @williamfgc, 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 @VivianePons 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 @milancurcic

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @williamfgc

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

kyleniemeyer commented 3 years ago

Hello @shahmoradi, just checking in again. We are essentially ready to accept your submission, but just need you to make that change to your article.

shahmoradi commented 3 years ago

My Apologies for the delay, I have become fully occupied with some personal and family matters over the past month. Please give me until this weekend to fix the outstanding issues and resubmit this paper to JOSS. Thank you.

On Wed, Apr 14, 2021 at 12:50 PM Kyle Niemeyer @.***> wrote:

Hello @shahmoradi https://github.com/shahmoradi, just checking in again. We are essentially ready to accept your submission, but just need you to make that change to your article.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2741#issuecomment-819713800, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABDXNCPHVDRY7SH2UDA4ZETTIXIX3ANCNFSM4SMQE6OQ .

kyleniemeyer commented 3 years ago

@shahmoradi no problem, just let us know

shahmoradi commented 3 years ago

@whedon generate pdf

shahmoradi commented 3 years ago

Thank you for your patience and I apologize again for the delay. All DOIs should be now fixed. If there is anything else I have missed, please let me know. Best regards,

whedon commented 3 years ago

PDF failed to compile for issue #2741 with the following error: 

 Error reading bibliography file paper.bib:
(line 245, column 3):
unexpected "p"
expecting space, ",", white space or "}"
Looks like we failed to compile the PDF
shahmoradi 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:

VivianePons 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

- 10.3847/1538-4357/abb9b7 is OK
- 10.1088/0004-637x/766/2/111 is OK
- 10.1093/mnras/stv714 is OK
- 10.3847/1538-4357/abb9b7 is OK
- 10.1007/s11222-006-9438-0 is OK
- 10.1093/bioinformatics/btp162 is OK
- 10.18637/jss.v035.i04 is OK

MISSING DOIs

- 10.3847/1538-4357/abb9b7 may be a valid DOI for title: A Multilevel Empirical Bayesian Approach to Estimating the Unknown Redshifts of 1366 BATSE Catalog Long-Duration Gamma-Ray Bursts

INVALID DOIs

- None
VivianePons 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:

VivianePons commented 3 years ago

It seems that you have the same paper appearing twice in the bib file (A Multilevel Empirical Bayesian Approach to Estimating the Unknown Redshifts of 1366 BATSE Catalog Long-Duration Gamma-Ray Bursts)

shahmoradi commented 3 years ago

Fixed.

shahmoradi commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

PDF failed to compile for issue #2741 with the following error: 

 Error reading bibliography file paper.bib:
(line 146, column 1):
unexpected "%"
expecting space, white space or "}"
Looks like we failed to compile the PDF
shahmoradi 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:

VivianePons 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

- 10.3847/1538-4357/abb9b7 is OK
- 10.1088/0004-637x/766/2/111 is OK
- 10.1093/mnras/stv714 is OK
- 10.1007/s11222-006-9438-0 is OK
- 10.1093/bioinformatics/btp162 is OK
- 10.18637/jss.v035.i04 is OK

MISSING DOIs

- None

INVALID DOIs

- None
VivianePons commented 3 years ago

Thank you @shahmoradi for the fixes! Could you make an archive (on Zenodo, figshare, or other) of the software and give me the DOI? Be careful to use the same metadata as the paper (title and authors)

Thank you

shahmoradi commented 3 years ago

Here is the DOI (https://zenodo.org/record/4739757#.YJNelqFOnGp): 10.5281/zenodo.4739757 Sincerely,

shahmoradi 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:

VivianePons commented 3 years ago

Hi @shahmoradi it looks like you have archived the wrong thing. I see only the pdf paper and not the whole software repo.

shahmoradi commented 3 years ago

My apologies. I am not quite familiar with zenodo and other DOI granting websites. I have uploaded the repository to Zenodo. Does this look good? https://zenodo.org/record/4739775#.YJRg26FOnGo

VivianePons commented 3 years ago

Well, it's a bit weird because now you have the whole thing as a zip. The archive should be a direct copy of the repo, like you did in previous versions for example here: https://zenodo.org/record/4414285#.YJTwMiY69H4

shahmoradi commented 3 years ago

Could we then use the DOI you mentioned? This is DOI that I generated for the project last year. The new one that is troubling is the one that I tried to generate yesterday. If none work, I will retry fresh. Thank you for your patience.

VivianePons commented 3 years ago

We need a DOI with the current version of the software, including all changes made during the review so we can't use the old one

shahmoradi commented 3 years ago

@VivianePons I think the current zenodo DOI is automatically connected to the latest version of the software. See for example the history of the version of the package on this page: https://zenodo.org/record/4739775#.YJXr9aFOnGr I can remove the PDF of the paper that I added manually to the zenodo entry yesterday. If this does not help either, then I will create a DOI via figshare or some other platform as I am somewhat confused now on how Zenodo works and how to create new fresh entries of the same repository. Thank you

VivianePons commented 3 years ago

Hi @shahmoradi each DOI is linked to a specific version, I need the current version. The archive is like a picture of the current state of the software, which I need to finalize the publication, so that, in the future it is clear that the paper refers to this specific state of the software. Please either add a proper archive on the current zenodo or make a new one elsewhere.

shahmoradi commented 3 years ago

Here is the new Zenodo entry: https://zenodo.org/record/4749957#.YJrS7qFOnGo DOI: 10.5281/zenodo.4749957

Thank you Amir

VivianePons commented 3 years ago

@whedon set 10.5281/zenodo.4749957 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4749957 is the archive.

VivianePons commented 3 years ago

@whedon set v1.5.1 as version

whedon commented 3 years ago

OK. v1.5.1 is the version.

VivianePons commented 3 years ago

Thank you very much @shahmoradi we are now ready to accept the paper! Thanks to both reviewers @milancurcic and @williamfgc for their work

VivianePons commented 3 years ago

@whedon accept

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3847/1538-4357/abb9b7 is OK
- 10.1088/0004-637x/766/2/111 is OK
- 10.1093/mnras/stv714 is OK
- 10.1007/s11222-006-9438-0 is OK
- 10.1093/bioinformatics/btp162 is OK
- 10.18637/jss.v035.i04 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 3 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2301

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2301, 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 commented 3 years ago

👋 @shahmoradi - I'm the AEiC on duty currently, and I'll be proofreading this shortly, then either requesting changes, or proceeding to publication.

danielskatz commented 3 years ago

My suggested changes are in https://github.com/cdslaborg/paramonte/pull/14 - please merge this, or let me know what you disagree with, then we can proceed

shahmoradi commented 3 years ago

done. Thank you @danielskatz @VivianePons for your patience and edits, and special thanks again to both reviewers @milancurcic and @williamfgc for their variable suggestions.

danielskatz commented 3 years ago

@whedon accept

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 3 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2303

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2303, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3847/1538-4357/abb9b7 is OK
- 10.1088/0004-637x/766/2/111 is OK
- 10.1093/mnras/stv714 is OK
- 10.1007/s11222-006-9438-0 is OK
- 10.1093/bioinformatics/btp162 is OK
- 10.18637/jss.v035.i04 is OK

MISSING DOIs

- None

INVALID DOIs

- None
danielskatz commented 3 years ago

👋 @VivianePons - this paper is probably too long and too detailed, but I don't think it's worth cutting it at this point - this is just a thought of something to consider for other future papers

danielskatz commented 3 years ago

@whedon accept deposit=true