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[REVIEW]: RK-Opt: A package for the design of numerical ODE solvers #2514

Closed whedon closed 4 years ago

whedon commented 4 years ago

Submitting author: @ketch (David Ketcheson) Repository: https://github.com/ketch/RK-Opt Version: v1.0.3 Editor: @diehlpk Reviewers: @gardner48, @debdeepbh, @emconsta Archive: 10.5281/zenodo.4146740

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Markdown: [![status](https://joss.theoj.org/papers/9cb393c408b6ee3b6686fdb63a98ce74/status.svg)](https://joss.theoj.org/papers/9cb393c408b6ee3b6686fdb63a98ce74)

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

@gardner48 & @debdeepbh & @emconsta, 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 @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 ✨

Review checklist for @gardner48

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @debdeepbh

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @emconsta

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @gardner48, @debdeepbh 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.

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To fix this do the following two things:

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whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.2140/camcos.2012.7.247 is OK
- 10.1090/S0025-5718-09-02209-1 is OK
- 10.1137/120885899 is OK
- 10.1007/s10915-013-9796-7 is OK
- 10.1007/s10915-017-0560-2 is OK
- 10.1007/s10915-016-0195-8 is OK
- 10.1007/s10915-016-0195-8 is OK
- 10.1007/s10915-016-0195-8 is OK
- 10.1063/1.4992751 is OK
- 10.1137/07070485X is OK
- 10.1016/j.apnum.2008.03.034 is OK
- 10.1016/j.jcp.2009.11.006 is OK
- 10.1137/100818674 is OK
- 10.1137/10080960X is OK
- 10.1090/mcom/3115 is OK
- 10.1007/s10915-018-0664-3 is OK
- 10.1016/j.jcp.2019.01.003 is OK
- 10.1016/j.jcp.2020.109499 is OK
- 10.1007/978-1-84800-155-8_7 is OK
- 10.1007/s10915-019-00916-3 is OK

MISSING DOIs

- https://doi.org/10.1016/0378-4754(87)90083-8 may be missing for title: Solving ordinary differential equations I: Nonstiff Problems

INVALID DOIs

- None
diehlpk commented 4 years ago

@whedon add @emconsta as reviewer

whedon commented 4 years ago

OK, @emconsta is now a reviewer

diehlpk commented 4 years ago

Hi @emconsta @debdeepbh @gardner48 how is your review going? Please let me know if I can assist in any way.

diehlpk commented 4 years ago

Hi @emconsta @debdeepbh @gardner48 how is your review going? Please let me know if I can assist in any way.

debdeepbh commented 4 years ago

Hi @diehlpk I am unable to edit the checklist in place. Should I copy the markdown of the checklist to a new comment and edit there?

diehlpk commented 4 years ago

@arfon Could you might have a look?

arfon commented 4 years ago

@whedon re-invite @debdeepbh as reviewer

whedon commented 4 years ago

OK, the reviewer has been re-invited.

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

arfon commented 4 years ago

@arfon Could you might have a look?

Sure thing. Repository invitations expire on GitHub after a week or so. You can ask Whedon to re-invite reviewers like this ☝️

@debdeepbh - if you accept the invite you should now be able to edit the checklist.

debdeepbh commented 4 years ago

@arfon @diehlpk It works now. Thanks!

debdeepbh commented 4 years ago

Hi @ketch the full documentation link seems unreachable. Could you please update that?

ketch commented 4 years ago

@debdeepbh Thanks for catching that -- in fact, the whole server had gone down! It is back now and should be more reliable in the future.

emconsta commented 4 years ago

@ketch I am using a commercial Matlab license and do not have access to all toolboxes. In addition to required toolboxes, I believe parpool is in 'Parallel Computing Toolbox'. I think that should be listed as a requirement or optional requirement since it's not critical.

ketch commented 4 years ago

@emconsta You're right; thanks for pointing that out. I've added a note to the README in https://github.com/ketch/RK-Opt/commit/67e091630c727c2776696743bc1d0170bff5adf7.

diehlpk commented 4 years ago

Hi @emconsta @debdeepbh @gardner48 how is your review going? Please let me know if I can assist in any way.

diehlpk commented 4 years ago

Hi @emconsta @debdeepbh @gardner48 how is your review going? Please let me know if I can assist in any way.

diehlpk commented 4 years ago

Hi @emconsta @debdeepbh how is your review going? Please let me know if I can assist in any way.

diehlpk commented 4 years ago

@ketch Have you seen that @gardner48 opened a new issue?

diehlpk commented 4 years ago

Hi @emconsta @debdeepbh @gardner48 could you please let me know when you anticipate to finish your review?

gardner48 commented 4 years ago

@diehlpk Other than the issue I opened about running the examples I have finished my review.

ketch commented 4 years ago

@ketch Have you seen that @gardner48 opened a new issue?

Thanks; I think it is resolved now, along with @debdeepbh's issue.

diehlpk commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

diehlpk commented 4 years ago

Since we are quite close that the reviewers finished their review, I will do some editorial tasks on the paper. @ketch

  1. Affiliations: Please add the country
  2. Would it be possible to add the grant number for the AFOSR grant? Same for the DOE Computational Science Graduate Fellowship?
  3. Some citations use abbreviations (minority) for the journal name and some use the full name. Could you make this consistent?
  4. For some references the capitalization seems to be strange, e.g. In Proceedings of the european congress on computational methods in applied sciences and engineering. Could you check these? Adding {} to the title or journal name will keep the capitalization.
ketch commented 4 years ago
  1. Affiliations: Please add the country

Done.

  1. Would it be possible to add the grant number for the AFOSR grant? Same for the DOE Computational Science Graduate Fellowship?

There isn't a grant number for the CSGF. I've added the AFOSR number.

  1. Some citations use abbreviations (minority) for the journal name and some use the full name. Could you make this consistent?

Done.

  1. For some references the capitalization seems to be strange, e.g. In Proceedings of the european congress on computational methods in applied sciences and engineering. Could you check these? Adding {} to the title or journal name will keep the capitalization.

Done; I think I caught them all.

diehlpk commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

PDF failed to compile for issue #2514 with the following error:

Error reading bibliography ./paper.bib (line 80, column 9): unexpected "T" expecting space, ",", white space or "}" Error running filter pandoc-citeproc: Filter returned error status 1 Looks like we failed to compile the PDF

diehlpk commented 4 years ago

@ketch Could you please check why the paper does not compile?

diehlpk commented 4 years ago

Hi @emconsta @debdeepbh @gardner48 thanks for your review.

ketch commented 4 years ago

Sorry about that. I've fixed it and checked that it compiles now.

diehlpk commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

diehlpk commented 4 years ago

@ketch

diehlpk commented 4 years ago

@ketch I need this information to accept the publication. Could you might provide it soonish?

ketch commented 4 years ago

@diehlpk I've tried to do what you asked. The release version number is 1.0.1 and the DOI is 10.5281/zenodo.4138077. I don't see any author information or any way to set the author information on Zenodo.

Edit: I see on https://zenodo.org/record/4138077#.X5e6l1MzbUI that one author is missing, but I don't even know how that author list was generated so I'm unaware of how to fix it.

ranocha commented 4 years ago

I see on https://zenodo.org/record/4138077#.X5e6l1MzbUI that one author is missing

I've submitted a PR to RK-Opt to fix that: https://github.com/ketch/RK-Opt/pull/60

ketch commented 4 years ago

Thanks, @ranocha . I think everything is in order now. Here is the corrected information:

Release: 1.0.2 DOI: 10.5281/zenodo.4138949

diehlpk commented 4 years ago

@whedon commands

whedon commented 4 years ago

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

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@whedon list editors

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@whedon list reviewers

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@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom 
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

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# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

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@whedon accept

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@whedon check references

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@whedon check repository

EiC TASKS

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diehlpk commented 4 years ago

@whedon set v1.0.2 as version

whedon commented 4 years ago

OK. v1.0.2 is the version.

diehlpk commented 4 years ago

@ketch The title of the Zendo thingy has to match the paper's title (RK-Opt: A package for the design of numerical ODE solvers). You can edit/update the current version and change the title or rearrange authors. Note that the order of authors has to match the paper as well.

diehlpk commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

ranocha commented 4 years ago

I've submitted a PR to make the title on Zenodo match the title of the paper: https://github.com/ketch/RK-Opt/pull/62.

The order of authors looks to me identical on Zenodo and the paper (David I. Ketcheson; Matteo Parsani; Zachary J. Grant; Aron J. Ahmadia; Hendrik Ranocha).

diehlpk commented 4 years ago

Ok, perfect. Once I have the new release and the DOI. I can accept the paper. If you like to avoid having a new release, you can log in to Zendo and change the title there.

ketch commented 4 years ago

I couldn't find a way to change the title on Zenodo. Actually, it looks correct there already. But in case it's needed, I made another release.

New release: 1.0.3 DOI: 10.5281/zenodo.4146740