search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
725 stars 38 forks source link

[REVIEW]: Variational Solvers for Irreversible Evolutionary Systems #6897

Open editorialbot opened 5 months ago

editorialbot commented 5 months ago

Submitting author: !--author-handle-->@kumiori<!--end-author-handle-- (Andrés A. León Baldelli) Repository: https://github.com/kumiori/irrevolutions Branch with paper.md (empty if default branch): andres-paper Version: v1 Editor: !--editor-->@majensen<!--end-editor-- Reviewers: @jorgensd, @jhale Archive: 10.5281/zenodo.14187154

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/bd8a379864dd513dcd8787c21ae4420c"><img src="https://joss.theoj.org/papers/bd8a379864dd513dcd8787c21ae4420c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/bd8a379864dd513dcd8787c21ae4420c/status.svg)](https://joss.theoj.org/papers/bd8a379864dd513dcd8787c21ae4420c)

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

@jorgensd & @jhale, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

Checklists

📝 Checklist for @jhale

📝 Checklist for @jorgensd

editorialbot commented 5 months ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

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

@editorialbot generate pdf
editorialbot commented 5 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=1.20 s (357.8 files/s, 91024.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
YAML                           280             76            102          28035
Python                          78           4266           2744          12863
Jupyter Notebook                31              0          44943          11933
TeX                              2             44              8           1202
XML                              1              0              0            720
GLSL                             4             27            459            498
CSV                              3              1              0            432
Markdown                         4            122              0            252
Dockerfile                       2             34              8             37
TOML                             1              6              8             22
JSON                            19              0              0             19
Bourne Shell                     2              0              4              7
INI                              1              1              0              4
-------------------------------------------------------------------------------
SUM:                           428           4577          48276          56024
-------------------------------------------------------------------------------

Commit count by author:

   259  andres
   155  Andrés A León Baldelli
    91  kumiori
    51  Andrés A León Baldelli
    23  Ayoub RHOUSNI
    22  SarahTACHET
     6  mbilynsky
     4  jaedong2019
     2  WissamY97
     1  assalaTrabelsi
     1  francoisfernet
     1  igorassist
     1  ueuzj
editorialbot commented 5 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.5281/zenodo.10447666 is OK
- 10.2172/2205494 is OK
- 10.1016/j.advwatres.2011.04.013 is OK
- 10.1007/s10589-008-9167-8 is OK

MISSING DOIs

- No DOI given, and none found for title: dolfiny: Python wrappers for DOLFINx
- 10.5802/crmeca.156 may be a valid DOI for title: La mécanique de l’endommagement au secours de la m...
- No DOI given, and none found for title: PETSc Web page
- No DOI given, and none found for title: PETSc Users Manual
- 10.1016/j.jmps.2011.03.010 may be a valid DOI for title: The issues of the uniqueness and the stability of ...
- No DOI given, and none found for title: The variational approach to fracture
- No DOI given, and none found for title: SLEPc: A scalable and flexible toolkit for the sol...
- 10.1016/s0022-5096(99)00028-9 may be a valid DOI for title: Numerical experiments in revisited brittle fractur...
- No DOI given, and none found for title: Numerical optimization
- No DOI given, and none found for title: Décomposition orthogonale d’un espace hilbertien s...

INVALID DOIs

- https://doi.org/10.1016/j.jmps.2021.104424 is INVALID because of 'https://doi.org/' prefix
editorialbot commented 5 months ago

Paper file info:

📄 Wordcount for paper.md is 1739

✅ The paper includes a Statement of need section

editorialbot commented 5 months ago

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

editorialbot commented 5 months ago

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

jhale commented 5 months ago

Review checklist for @jhale

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

jhale commented 5 months ago

GNU recommends/instructs that LGPLv3 files should be named COPYING and COPYING.LESSER.

majensen commented 4 months ago

@jorgensd how is your review coming along? Thank you

jorgensd commented 4 months ago

@jorgensd how is your review coming along? Thank you

I’ve been quite busy with conferences, but will start the review sometime next week.

jorgensd commented 4 months ago

Review checklist for @jorgensd

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

jorgensd commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

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

majensen commented 4 months ago

Thanks @jorgensd for your progress -

majensen commented 4 months ago

@jorgensd how is the review coming along? Let me know if I can help in any way. Thank you!

jorgensd commented 4 months ago

@jorgensd how is the review coming along? Let me know if I can help in any way. Thank you!

I’ve raised several issues that I haven’t gotten any response from the authors on. Without addressing these I don’t really want to move forward in the review process.

majensen commented 4 months ago

Thanks @jorgensd - @kumiori, can you please check your repo for the issues raised? 5 open issues here. Thank you

kumiori commented 3 months ago

Thank you for the reaching out. All issues have been addressed and commented. Best

On 26 Jul 2024, at 01:25, Mark Jensen @.***> wrote:

Thanks @jorgensd https://github.com/jorgensd - @kumiori https://github.com/kumiori, can you please check your repo for the issues raised? 5 open issues here https://github.com/kumiori/irrevolutions/issues. Thank you

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6897#issuecomment-2251562220, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAVLIEQHBG75MITNRNIP75DZOGCMZAVCNFSM6AAAAABJMTAG4WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENJRGU3DEMRSGA. You are receiving this because you were mentioned.

majensen commented 3 months ago

Thanks @kumiori ! @jorgensd would you mind taking another look?

jorgensd commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

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

jhale commented 3 months ago

Once the issues are addressed, I will be inclined towards recommending to the editors that the article is accepted.

majensen commented 3 months ago

Hi @kumiori - please have a look at @jhale 's issues 62-69 in your repo, as well as 52 and 53 for @jorgensd . Please let me know what your timeline looks like for addressing this, if you can. thanks!

kumiori commented 3 months ago

Hello @majensen, thanks for following up. Most of the issues have been addressed, the few remaining technical issues are being addressed in these days.

jorgensd commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

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

majensen commented 3 months ago

@kumiori how are your revisions progressing? It sounds like we are very close. Thanks

kumiori commented 2 months ago

Thank you @majensen for following up. Indeed! we are very close. Issues have been addressed with comments pointing out the edits. All technical points should be clarified, I am waiting for a follow up on some manuscript comments, cf. Issues #53 and #66. Best

jorgensd commented 2 months ago

@kumiori I think you have changed the access to your repo without meaning to. One can no longer comment on issues or open new issues: image image

jorgensd commented 2 months ago

I also cannot open Pull Request, for instance to fix your contributing file: image

kumiori commented 2 months ago

Sorry, I have been fiddling with access settings and inadvertently imposed temporary restrictions. It's reverted to normal, now. Thank you for pointing out, I corrected the links.

majensen commented 2 months ago

@kumiori @jorgensd how are the fixes coming along? @jhale, I see you still have some unchecked boxes on your review, can you advise? Thanks.

jorgensd commented 2 months ago

@kumiori @jorgensd how are the fixes coming along? @jhale, I see you still have some unchecked boxes on your review, can you advise? Thanks.

I have not been able to reproduce the figures from the paper, as mentioned in: https://github.com/kumiori/irrevolutions/issues/65

Other than that, I think some documentation is needed for some of the functions in the library: https://github.com/kumiori/irrevolutions/issues/78

Once those are fixed, I am happy with the state of the software.

majensen commented 1 month ago

@kumiori have you been able to respond to the suggestions? See https://github.com/openjournals/joss-reviews/issues/6897#issuecomment-2352143470. Thanks

jhale commented 1 month ago

This is nearly there; it would be good to see the authors make the final revisions so we can recommend accept!

majensen commented 1 month ago

@kumiori please let us know if you have been able to respond to the reviewers. We are very close! Thanks

jorgensd commented 1 month ago

Only very minor stuff left that @kumiori will fix very soon (on the reproducible figure part).

jorgensd commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

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

jorgensd commented 1 month ago

I guess once @jhale has reviewed the paper, changes, it should be change such that we do not see the diff with the old version

majensen commented 1 month ago

If I understand you @jorgensd - if @kumiori makes the suggested changes and pushes them to the code repo, a new "generate pdf" should create a PDF that has those changes. Old PDFs in this thread won't be recreated. Is that the question?

jorgensd commented 1 month ago

If I understand you @jorgensd - if @kumiori makes the suggested changes and pushes them to the code repo, a new "generate pdf" should create a PDF that has those changes. Old PDFs in this thread won't be recreated. Is that the question?

Currently there is striked out text in the generated pdf, as @kumiori has done this to easily indicate the changes for the reviewers. I am very happy he did this, but as at the paper from my end is approved, this highlighting should be removed, such that the paper is ready for publishing. I would just like @jhale to indicate that he is fine with the changes before we proceed.

majensen commented 1 month ago

@jorgensd - ah I see now. @jhale can you look at the changes in the PDF of https://github.com/openjournals/joss-reviews/issues/6897#issuecomment-2399757028, and comment here? If you approve, then @kumiori can proceed to clean up the paper for acceptance. Thank you!

kumiori commented 3 weeks ago

Hello, I am reaching out to inquire about the progress of our paper in review. Specifically, @jhale I wanted to check in regarding the two remaining open issues that were highlighted, on the licencing and the final paper issues.

majensen commented 3 weeks ago

@jhale have you communicated with @kumiori regarding issues above? Please let us know here either way. Much appreciated-

jhale commented 2 weeks ago

I've reviewed the licensing/copyright issues and the draft paper and I'm satisfied. Consequently I'm now happy to recommend to the editorial team that the paper be accepted for publication.

kumiori commented 2 weeks ago

@editorialbot commands

editorialbot commented 2 weeks ago

Hello @kumiori, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers
kumiori commented 1 week ago

@editorialbot generate pdf

kumiori commented 1 week ago

@editorialbot generate preprint