search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
694 stars 36 forks source link

[REVIEW]: proteusPy: A Python Package for Protein Structure and Disulfide Bond Modeling and Analysis #6169

Open editorialbot opened 6 months ago

editorialbot commented 6 months ago

Submitting author: !--author-handle-->@suchanek<!--end-author-handle-- (Eric Suchanek) Repository: https://github.com/suchanek/proteusPy Branch with paper.md (empty if default branch): Version: v0.95.5 Editor: !--editor-->@Kevin-Mattheus-Moerman<!--end-editor-- Reviewers: @AnjaConev, @hmacdope Archive: Pending

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/45de839b48a550d6ab955c5fbbc508f2"><img src="https://joss.theoj.org/papers/45de839b48a550d6ab955c5fbbc508f2/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/45de839b48a550d6ab955c5fbbc508f2/status.svg)](https://joss.theoj.org/papers/45de839b48a550d6ab955c5fbbc508f2)

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

@JoaoRodrigues & @AnjaConev, 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 @richardjgowers 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 @AnjaConev

📝 Checklist for @hmacdope

editorialbot commented 6 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 6 months ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.80 s (179.7 files/s, 458701.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            44           7993              0          74213
Python                          43           2210           3215           5167
Jupyter Notebook                23              0         268221           2464
XML                              2             16              0            995
YAML                             6              5              7            925
Markdown                        12            232              0            901
TeX                              7             17             21            680
JavaScript                       3              9              9            120
Bourne Shell                     2             19              3             96
JSON                             1              0              0             38
TOML                             1              3              0             23
-------------------------------------------------------------------------------
SUM:                           144          10504         271476          85622
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 6 months ago

Wordcount for paper.md is 627

editorialbot commented 6 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 6 months ago

:warning: An error happened when generating the pdf. Problem with ORCID (0000-0000-0000-0000) for Adrian Price-Whelan. Invalid ORCID.

richardjgowers commented 6 months ago

@JoaoRodrigues @AnjaConev thanks for agreeing to review this. This issue will be used to track the review. There's instructions above for generating a checklist that should guide your review process. If/when you run into issues as part of your review I'd recommend raising these as issues in the github repo for the project. Let me know if you have any questions.

AnjaConev commented 6 months ago

Review checklist for @AnjaConev

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

AnjaConev commented 6 months ago

Here are some comments (I made related issues in the original repo):

Kevin-Mattheus-Moerman commented 5 months ago

@suchanek it looks like a reviewer provided some feedback for you to work on. Can you provide an update on related changes you will/have made?

@richardjgowers will you spur on this review again to make sure it keeps going? Thanks!

Kevin-Mattheus-Moerman commented 4 months ago

@richardjgowers :wave: please check in here if you can. Thanks

suchanek commented 4 months ago

Hi all, I've been commenting in the repo issues section directly, and have been addressing @AnjaConev comments...

suchanek commented 4 months ago

So far:

suchanek commented 4 months ago

Significant progress on all fronts. Pls have a look.

AnjaConev commented 4 months ago

Thank you for working on all these improvements - I will take a look at the pull requests today and get back to you!

AnjaConev commented 4 months ago

Great work - I think this package is a great contribution to the field. You have addressed all my concerns. There is just one more thing left from my list:

Can you add these guidelines to the README? In the meantime, I will also check the format of references in the text

suchanek commented 4 months ago

I've added these additions to the paper and the README. Thank you for your comments!

suchanek commented 4 months ago

I believe I have addressed the issues raised, please have a look.

richardjgowers commented 4 months ago

@JoaoRodrigues have you had time to start this?

JoaoRodrigues commented 4 months ago

Will get to it this week - was waiting for the previous rounds to finish not to overlap/overwhelm @suchanek. Incidentally, I'm also reviewing his PR in Biopython, which I'm pretty sure relates to this work :)

suchanek commented 4 months ago

Thank you João, you are correct. My PR is for this. Cheers!Eric G. Suchanek, PhD Astronomer at largeMonterey Institute for Research in Astronomy200 Eighth Street, Marina CA 93933(831-883-1000) Fax: 883-1031Dedicated to Research and Education in Astronomy for 50 Years.On Mar 5, 2024, at 11:54 AM, João Rodrigues @.***> wrote: Will get to it this week - was waiting for the previous rounds to finish not to overlap/overwhelm @suchanek. Incidentally, I'm also reviewing his PR in Biopython, which I'm pretty sure relates to this work :)

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: @.***>

Kevin-Mattheus-Moerman commented 3 months ago

@JoaoRodrigues, @AnjaConev are you able to resume/start your review? Thanks!

Kevin-Mattheus-Moerman commented 3 months ago

@richardjgowers please try to check in here about once a week if you can to spur on this review, thanks!

suchanek commented 3 months ago

Thank you. Eric G. Suchanek, PhD Astronomer at largeMonterey Institute for Research in Astronomy200 Eighth Street, Marina CA 93933(831-883-1000) Fax: 883-1031Dedicated to Research and Education in Astronomy for 50 Years.On Mar 31, 2024, at 4:11 AM, Kevin Mattheus Moerman @.***> wrote: @richardjgowers please try to check in here about once a week if you can to spur on this review, thanks!

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: @.***>

AnjaConev commented 3 months ago

Thanks @Kevin-Mattheus-Moerman for the reminder!

I just opened my final issue for @richardjgowers related to the references and the paper pdf https://github.com/suchanek/proteusPy/issues/9

That should be all on my side!

suchanek commented 3 months ago

All,I’ve had trouble getting the artifact (the paper) to drop correctly. Last workflow ran correctly. If you go to the actions for the repo you can grab it. Let me know if you have issues. Thank you!Eric G. Suchanek, PhD Astronomer at largeMonterey Institute for Research in Astronomy200 Eighth Street, Marina CA 93933(831-883-1000) Fax: 883-1031Dedicated to Research and Education in Astronomy for 50 Years.On Apr 2, 2024, at 12:36 PM, Anja Conev @.***> wrote: Thanks @Kevin-Mattheus-Moerman for the reminder! I just opened my final issue for @richardjgowers related to the references and the paper pdf suchanek/proteusPy#9 That should be all on my side!

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: @.***>

suchanek commented 2 months ago

All, I've dropped the latest draft manually into the repo under paper/paper.pdf. I am hopeful we can speed this along.

Cheers, Eric

richardjgowers commented 2 months ago

@JoaoRodrigues can I get you to start your review please?

suchanek commented 2 months ago

Is there some way we can move forward? I feel like we are stalled. I'd like to get this published so I can publish the analysis.

Thank you! Eric Suchanek

AnjaConev commented 2 months ago

Hi all - let me know if I can help in any way! All the things on my end from the review checklist look good. I would recommend accepting the work.

Again, please let me know if I can be of any help, it has been a long while since anyone looked at this!

richardjgowers commented 2 months ago

@openjournals/bcm-eics I've hit a bit of a problem with this review as only one reviewer has completed. I've gone through the review process and agree with the sole reviewer here. Could we move forward with one review?

richardjgowers commented 2 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

richardjgowers commented 2 months ago

@suchanek there's a few post-review tasks above, such as finalising the release and creating the (zenodo) DOI which we will need to finish this review too

richardjgowers commented 2 months ago

@editorialbot check references

richardjgowers commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.2174/092986708783330566 is OK
- 10.1016/0092-8674(92)90140-8 is OK
- 10.1021/bi00368a024 is OK
- 10.1021/bi00368a023 is OK
- 10.1021/bi00368a023 is OK
- 10.1021/bi0603064 is OK
- 10.1111/j.1538-7836.2010.03894.x is OK

MISSING DOIs

- No DOI given, and none found for title: proteusPy: A Package for Modeling and Analyzing Pr...
- No DOI given, and none found for title: proteusPy API
- No DOI given, and none found for title: Turtle Geometry: The computer as a medium for expl...

INVALID DOIs

- 10.1093/bioinformatics/btg2994 is INVALID
editorialbot commented 2 months ago

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

suchanek commented 2 months ago

I will work on getting the versions consistent and check references. Thanks for getting this moving again!Cheers,Eric G. Suchanek, PhD On May 3, 2024, at 2:03 PM, The Open Journals editorial robot @.***> wrote: 👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: @.***>

suchanek commented 2 months ago

OK i've added some verbiage, re-rendered and put paper.pdf into the repo. Current version is 0.95.5. I cleaned up the doi references as well. You'll want to officially re-render. I won't touch it now unless you see any typos.

suchanek commented 1 month ago

@richardjgowers can you kick off the remaining tasks?

richardjgowers commented 1 month ago

@editorialbot generate pdf

richardjgowers commented 1 month ago

@editorialbot set v0.95.5 as version

editorialbot commented 1 month ago

Done! version is now v0.95.5

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:

richardjgowers commented 1 month ago

@suchanek can you make a zenodo (or similar) archive of the 0.95.5 release and post the DOI here please?

suchanek commented 1 month ago

Apologies, I’m new to this lol. https://zenodo.org/doi/10.5281/zenodo.11148440

I believe this should do it. However, if i make any additional changes it will change, correct?

Thank you for your help Richard. :)

Cheers, Eric

On May 8, 2024, at 7:47 AM, Richard Gowers @.***> wrote:

@suchanek https://github.com/suchanek can you make a zenodo (or similar) archive of the 0.95.5 release and post the DOI here please?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6169#issuecomment-2100396762, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA7PYGU7PE6OUTFGD2NXP4LZBIGFFAVCNFSM6AAAAABA6SHF5WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBQGM4TMNZWGI. You are receiving this because you were mentioned.

suchanek commented 1 month ago

Current and last:

10.5281/zenodo.11148441

On May 8, 2024, at 9:33 AM, Dr Diogenes @.***> wrote:

Apologies, I’m new to this lol. https://zenodo.org/doi/10.5281/zenodo.11148440

I believe this should do it. However, if i make any additional changes it will change, correct?

Thank you for your help Richard. :)

Cheers, Eric

On May 8, 2024, at 7:47 AM, Richard Gowers @.***> wrote:

@suchanek https://github.com/suchanek can you make a zenodo (or similar) archive of the 0.95.5 release and post the DOI here please?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6169#issuecomment-2100396762, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA7PYGU7PE6OUTFGD2NXP4LZBIGFFAVCNFSM6AAAAABA6SHF5WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBQGM4TMNZWGI. You are receiving this because you were mentioned.

suchanek commented 1 month ago

Are we good to go Richard?Thanks!Eric G. Suchanek, PhD On May 8, 2024, at 7:47 AM, Richard Gowers @.***> wrote: @suchanek can you make a zenodo (or similar) archive of the 0.95.5 release and post the DOI here please?

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: @.***>

suchanek commented 1 month ago

@richardjgowers I think this is good to go?

Thanks! Eric

suchanek commented 1 month ago

@AnjaConev @richardjgowers -- friendly ping to check status. Please advise.

Thanks! Eric

suchanek commented 1 month ago

@richardjgowers Please let me know if there is anything needed on my end and if we are good to publish. I am now unable to push changes to the repository, and my development is on hold.

Thank you, Eric