[REVIEW]: LaMa: a thematic labelling web application #5135

editorialbot · 2023-02-08T16:52:28Z

Submitting author: @muctadir (Hossain Muhammad Muctadir)
Repository: https://github.com/muctadir/lama
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @fboehm
Reviewers: @kinow, @luxaritas
Archive: 10.5281/zenodo.7866236

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/f91f03787429efa115f1e3aa144254bc"><img src="https://joss.theoj.org/papers/f91f03787429efa115f1e3aa144254bc/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/f91f03787429efa115f1e3aa144254bc/status.svg)](https://joss.theoj.org/papers/f91f03787429efa115f1e3aa144254bc)

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

@kinow & @luxaritas, 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 @fboehm 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 @kinow

📝 Checklist for @luxaritas

The text was updated successfully, but these errors were encountered:

editorialbot · 2023-02-08T16:52:30Z

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

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editorialbot · 2023-02-08T16:52:35Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.35 s (754.7 files/s, 180996.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                            10              0              0          22644
TypeScript                     122           2797           6447          11967
Python                          37           1783           3358           6104
Sass                            33            512            534           2347
HTML                            35            206            658           1967
SQL                              1              0              0            448
Markdown                         4            120              0            255
YAML                             2              5              4             75
XML                              6              0              0             69
TeX                              1              5              0             66
Bourne Shell                     3              4              0             50
JavaScript                       1              1              6             43
PowerShell                       2              4              0             32
Dockerfile                       2             20              7             30
TOML                             1              6              0             17
SVG                              1              0              0              4
-------------------------------------------------------------------------------
SUM:                           261           5463          11014          46118
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-02-08T16:52:37Z

Wordcount for paper.md is 1173

editorialbot · 2023-02-08T16:52:47Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1080/0142159X.2020.1755030 is OK
- 10.1191/1478088706qp063oa is OK
- 10.1136/bmj.320.7227.114 is OK
- 10.1123/jtpe.2017-0084 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-02-08T16:54:08Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

kinow · 2023-02-08T16:59:28Z

Review checklist for @kinow

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/muctadir/lama?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@muctadir) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

luxaritas · 2023-02-09T15:27:45Z

Review checklist for @luxaritas

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/muctadir/lama?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@muctadir) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

kinow · 2023-02-09T15:36:12Z

@muctadir I finished an initial review, creating issues in the LaMa repository. If you could have a look at those issues, please. Once they are resolved I will proceed with the rest of the review checklist. Thanks!

luxaritas · 2023-02-12T23:04:03Z

Looking at the repository commit history, I don't see clear indications that the submitting author made "major" contributions to the software implementation itself - it looks like contributions were primarily made to a prior version of this application before it was rewritten? Comments on this would be appreciated!

fboehm · 2023-02-13T21:01:35Z

@muctadir - please feel free to respond to the comments and suggestions in this thread. Thanks!

muctadir · 2023-02-14T00:26:25Z

@kinow thanks for your comments. We noticed the issues that you opened and currently working to resolve them.

@luxaritas Your observation is indeed correct. In terms of commits, my contributions are limited. For example, I improved some implementations as you can see in PR#1. However, I contributed significantly at least in two major ways. First is the development of the prior version (as you already mentioned), which includes concepts such as collaborative labeling, conflict resolution, theming and so on. These features were replicated to LaMa although the implementation was done separately. Secondly, I closely supervised the development and influenced all the major decisions. For example, the choice of technologies, moving to service based architecture, the UI design and so on. The newly added features, the changes in architecture, and design are based on our research on the older version of the tool. Please, let me know if my explanation is sufficient.

luxaritas · 2023-02-14T01:04:02Z

@muctadir That explanation is sufficient to me - thank you!

muctadir · 2023-02-16T09:15:02Z

@kinow we resolved all the issues that you created except one. I am wondering if it would be possible to move on with the review as we resolve the remaining one.

kinow · 2023-02-16T09:34:35Z

Hi @muctadir. Excellent. I will have another look and review the issues resolved, updating the checklist appropriately, and also see if I can continue working on the other review points. Thanks!

kinow · 2023-02-16T18:38:14Z

Hi @muctadir

I've made good progress on the review today. Here's what's pending in my review:

Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?

Pending, muctadir/lama#11

State of the field: Do the authors describe how this software compares to other commonly-used packages?

Pending muctadir/lama#7

Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.

Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.

References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

The item before is related, about the state of the field, could change the rest of the article, including the references. So I will wait for that one to complete these ones 👍

That's me for now, ping me again in the issues or here if you have any updates, please.

Thank you!
-Bruno

fboehm · 2023-02-28T21:52:12Z

@muctadir - how are the revisions going? Have you had a chance to update the software to implement the reviewers' suggestions?

Thanks!

muctadir · 2023-03-01T07:08:40Z

@fboehm @kinow we investigated and identified what the problem with the automated test was. Shortly, we will update the repo with the necessary changes. Sorry for the delayed responses. Last week was carnival week in our region and I was on leave half of last week.

fboehm · 2023-04-30T16:17:58Z

@editorialbot set 10.5281/zenodo.7866236 as archive

editorialbot · 2023-04-30T16:18:00Z

Done! archive is now 10.5281/zenodo.7866236

fboehm · 2023-04-30T16:18:59Z

@editorialbot generate pdf

editorialbot · 2023-04-30T16:20:15Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

fboehm · 2023-04-30T16:24:01Z

@editorialbot check references

editorialbot · 2023-04-30T16:24:07Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1080/0142159X.2020.1755030 is OK
- 10.1191/1478088706qp063oa is OK
- 10.1136/bmj.320.7227.114 is OK
- 10.1123/jtpe.2017-0084 is OK

MISSING DOIs

- None

INVALID DOIs

- None

fboehm · 2023-04-30T16:24:46Z

@editorialbot recommend-accept

editorialbot · 2023-04-30T16:24:48Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-04-30T16:24:52Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1080/0142159X.2020.1755030 is OK
- 10.1191/1478088706qp063oa is OK
- 10.1136/bmj.320.7227.114 is OK
- 10.1123/jtpe.2017-0084 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-04-30T16:26:11Z

👋 @openjournals/sbcs-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4188, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

oliviaguest · 2023-05-08T13:01:59Z

@editorialbot recommend-accept

editorialbot · 2023-05-08T13:02:01Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-05-08T13:02:06Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1080/0142159X.2020.1755030 is OK
- 10.1191/1478088706qp063oa is OK
- 10.1136/bmj.320.7227.114 is OK
- 10.1123/jtpe.2017-0084 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-05-08T13:03:48Z

👋 @openjournals/sbcs-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4210, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

oliviaguest · 2023-05-08T13:20:35Z

@editorialbot accept

editorialbot · 2023-05-08T13:20:36Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2023-05-08T13:22:39Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Bogachenkova
  given-names: Victoria
- family-names: Martins
  given-names: Eduardo Costa
- family-names: Jansen
  given-names: Jarl
- family-names: Olteniceanu
  given-names: Ana-Maria
- family-names: Henkemans
  given-names: Bartjan
- family-names: Lavin
  given-names: Chinno
- family-names: Nguyen
  given-names: Linh
- family-names: Bradley
  given-names: Thea
- family-names: Fürst
  given-names: Veerle
- email: [email protected]
  family-names: Muctadir
  given-names: Hossain Muhammad
  orcid: "https://orcid.org/0000-0002-2090-4766"
- email: [email protected]
  family-names: Brand
  given-names: Mark
  name-particle: van den
  orcid: "https://orcid.org/0000-0003-3529-6182"
- email: [email protected]
  family-names: Cleophas
  given-names: Loek
  orcid: "https://orcid.org/0000-0002-7221-3676"
- email: [email protected]
  family-names: Serebrenik
  given-names: Alexander
  orcid: "https://orcid.org/0000-0002-1418-0095"
contact:
- email: [email protected]
  family-names: Muctadir
  given-names: Hossain Muhammad
  orcid: "https://orcid.org/0000-0002-2090-4766"
doi: 10.5281/zenodo.7866236
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Bogachenkova
    given-names: Victoria
  - family-names: Martins
    given-names: Eduardo Costa
  - family-names: Jansen
    given-names: Jarl
  - family-names: Olteniceanu
    given-names: Ana-Maria
  - family-names: Henkemans
    given-names: Bartjan
  - family-names: Lavin
    given-names: Chinno
  - family-names: Nguyen
    given-names: Linh
  - family-names: Bradley
    given-names: Thea
  - family-names: Fürst
    given-names: Veerle
  - email: [email protected]
    family-names: Muctadir
    given-names: Hossain Muhammad
    orcid: "https://orcid.org/0000-0002-2090-4766"
  - email: [email protected]
    family-names: Brand
    given-names: Mark
    name-particle: van den
    orcid: "https://orcid.org/0000-0003-3529-6182"
  - email: [email protected]
    family-names: Cleophas
    given-names: Loek
    orcid: "https://orcid.org/0000-0002-7221-3676"
  - email: [email protected]
    family-names: Serebrenik
    given-names: Alexander
    orcid: "https://orcid.org/0000-0002-1418-0095"
  date-published: 2023-05-08
  doi: 10.21105/joss.05135
  issn: 2475-9066
  issue: 85
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5135
  title: "LaMa: a thematic labelling web application"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05135"
  volume: 8
title: "LaMa: a thematic labelling web application"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2023-05-08T13:22:45Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2023-05-08T13:22:46Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-05-08T13:22:46Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05135 joss-papers#4211
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05135
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

oliviaguest · 2023-05-09T11:15:36Z

Big congratulations @muctadir! Also thank you to @fboehm for editing; and appreciation to the reviewers: @kinow, @luxaritas. 😊

editorialbot · 2023-05-09T11:15:38Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

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[![DOI](https://joss.theoj.org/papers/10.21105/joss.05135/status.svg)](https://doi.org/10.21105/joss.05135)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05135">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05135/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05135/status.svg
   :target: https://doi.org/10.21105/joss.05135

This is how it will look in your documentation:

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muctadir · 2023-05-15T09:47:49Z

@oliviaguest @fboehm
Thanks a lot for your help and support in the publication process. I just noticed that one of the authors name is spelled incorrectly in the generated bibtex on the joss website. It is spelled Mark Den van Brand, but the correct spelling is Mark van den Brand. I think there might be a mistake while extracting first and last name from the full name in the paper. Is it possible to get it fixed?

fboehm · 2023-05-15T23:23:08Z

@muctadir - Thanks for bringing this to our attention.

@oliviaguest - do you have ideas about how to fix this?

oliviaguest · 2023-05-16T15:45:18Z

Yes, this can be fixed. I will investigate what needs to be done! Thanks for spotting this.

editorialbot added Dockerfile Python review Shell Track: 4 (SBCS) Social, Behavioral, and Cognitive Sciences labels Feb 8, 2023

editorialbot assigned fboehm Feb 8, 2023

editorialbot mentioned this issue Feb 8, 2023

[PRE REVIEW]: LaMa: a thematic labelling web application #5094

Closed

kinow mentioned this issue Feb 9, 2023

[docs] Improve installation process and instructions for Linux muctadir/lama#9

Closed

kinow mentioned this issue Feb 16, 2023

[joss] Run automated tests with GH Actions? muctadir/lama#11

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Apr 30, 2023

editorialbot added accepted published Papers published in JOSS labels May 8, 2023

oliviaguest closed this as completed May 9, 2023

editorialbot mentioned this issue Aug 1, 2024

[PRE REVIEW]: Annotate-Lab: Simplifying Image Annotation #7065

Closed

[REVIEW]: LaMa: a thematic labelling web application #5135

[REVIEW]: LaMa: a thematic labelling web application #5135

Comments

editorialbot commented Feb 8, 2023 • edited Loading

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Reviewer instructions & questions

Checklists

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kinow commented Feb 8, 2023 • edited Loading

Review checklist for @kinow

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

luxaritas commented Feb 9, 2023 • edited Loading

Review checklist for @luxaritas

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

kinow commented Feb 9, 2023

luxaritas commented Feb 12, 2023

fboehm commented Feb 13, 2023

muctadir commented Feb 14, 2023 • edited Loading

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