[REVIEW]: MIRP: A Python package for standardised radiomics #6413

editorialbot · 2024-02-26T17:27:14Z

Submitting author: @alexzwanenburg (Alex Zwanenburg)
Repository: https://github.com/oncoray/mirp
Branch with paper.md (empty if default branch): paper
Version: v2.2.4
Editor: @emdupre
Reviewers: @surajpaib, @Matthew-Jennings, @drcandacemakedamoore, @theanega
Archive: 10.5281/zenodo.12493595

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/165c85b1ecad891550a21b12c8b2e577"><img src="https://joss.theoj.org/papers/165c85b1ecad891550a21b12c8b2e577/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/165c85b1ecad891550a21b12c8b2e577/status.svg)](https://joss.theoj.org/papers/165c85b1ecad891550a21b12c8b2e577)

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

@surajpaib & @Matthew-Jennings & @drcandacemakedamoore & @theanega, 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 @emdupre 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 @surajpaib

📝 Checklist for @Matthew-Jennings

📝 Checklist for @drcandacemakedamoore

📝 Checklist for @theanega

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

editorialbot · 2024-02-26T17:27:18Z

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 · 2024-02-26T17:27:33Z

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

OK DOIs

- 10.1038/s41571-022-00707-0 is OK
- 10.1038/nrclinonc.2016.162 is OK
- 10.1148/radiol.2020191145 is OK
- 10.1038/s41598-017-13448-3 is OK
- 10.1038/s41598-018-36938-4 is OK
- 10.1038/s41598-022-13967-8 is OK
- 10.1148/radiol.211604 is OK
- 10.1148/radiol.231319 is OK
- 10.1038/nrclinonc.2017.141 is OK
- 10.1038/s41467-023-44591-3 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-02-26T17:27:35Z

Software report:

github.com/AlDanial/cloc v 1.88  T=1.70 s (105.6 files/s, 31142.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         104           5692           4648          19852
HTML                            25           1334             75           7703
Markdown                        12           1193              0           5535
SVG                              2              1              1           2996
JavaScript                      12            131            221            880
CSS                              4            190             35            779
reStructuredText                 7            169            159            351
XML                              4              0            336            256
TeX                              1             19              0            236
R                                1             25              8             77
YAML                             3              6              4             57
TOML                             1              5              0             47
DOS Batch                        2              8              1             28
make                             1              4              7              9
Bourne Shell                     1              0              0              1
-------------------------------------------------------------------------------
SUM:                           180           8777           5495          38807
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2024-02-26T17:27:40Z

Wordcount for paper.md is 1025

editorialbot · 2024-02-26T17:28:37Z

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

emdupre · 2024-02-26T17:30:23Z

👋 Hi @surajpaib, @Matthew-Jennings, @drcandacemakedamoore, @theanega, and thank you again for agreeing to review this submission for MIRP !

The review will take place in this issue, and you can generate your individual reviewer checklists by asking editorialbot directly with @editorialbot generate my checklist.

In working through the checklist, you're likely to have specific feedback on MIRP. Whenever possible, please open relevant issues on the software repository (and cross-link them with this issue) rather than discussing them here. This helps to make sure that feedback is translated into actionable items to improve the software !

If you aren't sure how to get started, please see the Reviewing for JOSS guide -- and, of course, feel free to ping me with any questions !

surajpaib · 2024-02-26T17:41:26Z

Review checklist for @surajpaib

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/oncoray/mirp?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@alexzwanenburg) 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?

drcandacemakedamoore · 2024-02-27T08:34:09Z

Review checklist for @drcandacemakedamoore

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/oncoray/mirp?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@alexzwanenburg) 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?

Matthew-Jennings · 2024-02-27T09:02:58Z

Review checklist for @Matthew-Jennings

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/oncoray/mirp?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@alexzwanenburg) 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?

theanega · 2024-02-28T17:20:21Z

Review checklist for @theanega

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/oncoray/mirp?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@alexzwanenburg) 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?

alexzwanenburg · 2024-03-12T16:04:19Z

@editorialbot generate pdf

editorialbot · 2024-03-12T16:05:40Z

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

drcandacemakedamoore · 2024-03-15T10:58:33Z

@alexzwanenburg Can you please clarify if Sebastian Starke and Steffan Lock are the same person. I do not see any code contributions from a Steffan Lock. This may be fine if he helped make the package, but please clarify. Or maybe Steffan Leger as mentioned in the thank you at the bottom is the same as Steffan Lock?

alexzwanenburg · 2024-03-15T16:41:27Z

@drcandacemakedamoore Steffen Löck is my professor and advised on the paper and the package. Stefan Leger contributed to early in-house versions of MIRP, prior to moving GitHub. Sebastian Starke also made minor contributions to an earlier version of MIRP.

drcandacemakedamoore · 2024-03-17T09:50:21Z

@alexzwanenburg preferably module names should be all lower case (and super-best is single word or if no other choice with underscore). I notice you have modules that are camelcase. Different file systems have different case conventions. The real point is that it could be possible to import these modules in two different ways then cause problems on different files systems where case conventions are different. I will get to more substantial issues soon, but this already pops out for my eyes, before I even started the real review. But since I'm on superficial issues right now, some badges would not hurt (it's nice to have the pypi version badge and also Anaconda if you released it there, and I can't tell at first glance here.)

drcandacemakedamoore · 2024-03-17T10:56:09Z

@alexzwanenburg on a less superficial issue, I note there is no developer's documentation. Many people may want to tinker with what you have done, and hopefully even contribute to the package. I am looking for documentation somewhere that tells people how to run the testing, so they can test new stuff before sending it. I am also looking for this, because it is not clear if you have any automated testing that runs in CI (did I miss it?) so instead of figuring out how to run it from there I would need instructions to run your tests properly . Update: I see from my Windows machine it is python -m pytest but I have no idea what it will be from a Mac

emdupre · 2024-03-18T04:59:34Z

Thank you, @drcandacemakedamoore !

If you could please open subsequent review comments as issues on the MIRP repository, this will help to make sure there is sufficient space for follow-up discussion and that action items are trackable across reviewers. I know that @alexzwanenburg has started to respond in-thread, but we'll generally ask to keep only high-level discussions in the general review thread and re-direct all other comments to the project issue tracker.

If you have any other questions, of course, please don't hesitate to ask.

emdupre · 2024-03-25T21:00:18Z

👋 Hi everyone, happy Monday !

I just wanted to check-in on the status of this review and make sure that there weren't any current blockers in working through the reviewer checklists.

I did notice that @drcandacemakedamoore has opened oncoray/mirp#66, oncoray/mirp#67, and oncoray/mirp#68 -- thank you ! I'm cross-linking them here, so they're easier for myself (and other reviewers) to track.

theanega · 2024-03-26T11:58:33Z

Hello! Thank you very much for the invitation to review this paper. I will finalize the review later this week (only the "functionality" section is missing). For now, I've left my comments on issue #69 .
@emdupre Feel free to let me know if my comments are appropriate, this is my first time reviewing for JOSS so I'm learning, thanks!

emdupre · 2024-04-02T19:54:21Z

👋 Hi everyone ! Thank you for your comments on MIRP to date !

I just wanted to note that we have now passed the four week review window. If you could please work on finalizing your initial reviews as soon as possible, I would appreciate it.

Once you have finalized your initial reviews, you can let me know by responding directly in this thread. Of course, if you have any questions or blockers, please don't hesitate to let me know !

🙏 @surajpaib @Matthew-Jennings @drcandacemakedamoore @theanega

alexzwanenburg · 2024-07-04T06:38:19Z

@editorialbot generate pdf

editorialbot · 2024-07-04T06:39:57Z

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

emdupre · 2024-07-06T04:53:50Z

@editorialbot check references

editorialbot · 2024-07-06T04:54:16Z

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

OK DOIs

- 10.1038/s41571-022-00707-0 is OK
- 10.1038/nrclinonc.2016.162 is OK
- 10.1148/radiol.2020191145 is OK
- 10.1038/s41598-017-13448-3 is OK
- 10.1038/s41598-018-36938-4 is OK
- 10.1038/s41598-022-13967-8 is OK
- 10.1148/radiol.211604 is OK
- 10.1148/radiol.231319 is OK
- 10.1038/nrclinonc.2017.141 is OK
- 10.1038/s41467-023-44591-3 is OK
- 10.1158/0008-5472.CAN-17-0339 is OK
- 10.1002/mp.13046 is OK
- 10.1158/0008-5472.CAN-18-0125 is OK
- 10.1088/0031-9155/60/14/5471 is OK
- 10.1038/s41598-017-10371-5 is OK
- 10.1093/neuonc/now256 is OK

MISSING DOIs

- None

INVALID DOIs

- None

emdupre · 2024-07-06T04:57:11Z

Thank you, @alexzwanenburg ! I'm now happy to recommend mirp to the EiC team for publication in JOSS ✨🚀

Thank you, too, to @surajpaib, @Matthew-Jennings, @drcandacemakedamoore, and @theanega for your reviews and involvement throughout this process ! JOSS works because of your work 💐

emdupre · 2024-07-06T04:57:26Z

@editorialbot recommend-accept

editorialbot · 2024-07-06T04:57:28Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-07-06T04:57:55Z

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

OK DOIs

- 10.1038/s41571-022-00707-0 is OK
- 10.1038/nrclinonc.2016.162 is OK
- 10.1148/radiol.2020191145 is OK
- 10.1038/s41598-017-13448-3 is OK
- 10.1038/s41598-018-36938-4 is OK
- 10.1038/s41598-022-13967-8 is OK
- 10.1148/radiol.211604 is OK
- 10.1148/radiol.231319 is OK
- 10.1038/nrclinonc.2017.141 is OK
- 10.1038/s41467-023-44591-3 is OK
- 10.1158/0008-5472.CAN-17-0339 is OK
- 10.1002/mp.13046 is OK
- 10.1158/0008-5472.CAN-18-0125 is OK
- 10.1088/0031-9155/60/14/5471 is OK
- 10.1038/s41598-017-10371-5 is OK
- 10.1093/neuonc/now256 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-07-06T04:59:17Z

👋 @openjournals/bcm-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#5580, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

alexzwanenburg · 2024-07-11T17:01:29Z

Aside from an overly wide sentence on page 2 the proof looks fine from my perspective.

emdupre · 2024-07-12T15:24:08Z

@openjournals/bcm-eics, just re-pinging here in case this notification slipped through ! Thank you 🙏

Kevin-Mattheus-Moerman · 2024-07-17T08:12:58Z

@editorialbot set version as v2.2.4

editorialbot · 2024-07-17T08:13:00Z

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

Kevin-Mattheus-Moerman · 2024-07-17T08:13:21Z

@editorialbot set v2.2.4 as version

editorialbot · 2024-07-17T08:13:24Z

Done! version is now v2.2.4

Kevin-Mattheus-Moerman · 2024-07-17T08:18:27Z

@alexzwanenburg as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I have checked this review, your repository, the archive link, and the paper. Most seems in order, however the below are some points that require your attention:

European English is used throughout, except for one occurrence of standardized which should read standardised.
Please edit the Zenodo listed version tag to include the v so it will end up reading version v2.2.4 (I know it seems odd but the thing after the word version there should be the complete version tag as listed for your GitHub release tag, which has the v).

alexzwanenburg · 2024-07-17T08:32:22Z

@editorialbot generate pdf

editorialbot · 2024-07-17T08:34:00Z

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

alexzwanenburg · 2024-07-17T08:35:54Z

I made changed standardized to standardised in the paper, and updated the Zenodo listed version to v2.2.4.

Kevin-Mattheus-Moerman · 2024-07-17T20:52:25Z

@editorialbot accept

editorialbot · 2024-07-17T20:52:27Z

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

editorialbot · 2024-07-17T20:59:30Z

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: Zwanenburg
  given-names: Alex
  orcid: "https://orcid.org/0000-0002-0342-9545"
- family-names: Löck
  given-names: Steffen
  orcid: "https://orcid.org/0000-0002-7017-3738"
doi: 10.5281/zenodo.12493595
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Zwanenburg
    given-names: Alex
    orcid: "https://orcid.org/0000-0002-0342-9545"
  - family-names: Löck
    given-names: Steffen
    orcid: "https://orcid.org/0000-0002-7017-3738"
  date-published: 2024-07-17
  doi: 10.21105/joss.06413
  issn: 2475-9066
  issue: 99
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6413
  title: "MIRP: A Python package for standardised radiomics"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06413"
  volume: 9
title: "MIRP: A Python package for standardised radiomics"

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 · 2024-07-17T20:59:34Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-07-17T20:59:34Z

🚨🚨🚨 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.06413 joss-papers#5645
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06413
If everything looks good, then close this review issue.
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Kevin-Mattheus-Moerman · 2024-07-17T21:19:14Z

Congratulations on this JOSS publication @alexzwanenburg et al. !

Thanks for editing @emdupre !

And a special thank you to the reviewers: @surajpaib, @Matthew-Jennings, @drcandacemakedamoore, @theanega !!

editorialbot · 2024-07-17T21:19:15Z

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editorialbot added Python review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Feb 26, 2024

editorialbot assigned emdupre Feb 26, 2024

editorialbot mentioned this issue Feb 26, 2024

[PRE REVIEW]: MIRP: A Python package for standardised radiomics #6345

Closed

editorialbot added R TeX labels Feb 26, 2024

surajpaib mentioned this issue Mar 10, 2024

Software Paper Comments Thread oncoray/mirp#55

Closed

This was referenced Mar 18, 2024

Contributor instructions for testing and style oncoray/mirp#62

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PEP-8 compliant naming of files and modules oncoray/mirp#63

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editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jul 6, 2024

editorialbot added accepted published Papers published in JOSS labels Jul 17, 2024

Kevin-Mattheus-Moerman closed this as completed Jul 17, 2024

[REVIEW]: MIRP: A Python package for standardised radiomics #6413

[REVIEW]: MIRP: A Python package for standardised radiomics #6413

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editorialbot commented Feb 26, 2024 • edited Loading

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emdupre commented Feb 26, 2024

surajpaib commented Feb 26, 2024 • edited Loading

Review checklist for @surajpaib

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drcandacemakedamoore commented Feb 27, 2024 • edited Loading

Review checklist for @drcandacemakedamoore

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Matthew-Jennings commented Feb 27, 2024 • edited Loading

Review checklist for @Matthew-Jennings

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theanega commented Feb 28, 2024 • edited Loading

Review checklist for @theanega

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Software paper

alexzwanenburg commented Mar 12, 2024

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drcandacemakedamoore commented Mar 15, 2024 • edited Loading

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surajpaib commented Feb 26, 2024 •

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drcandacemakedamoore commented Feb 27, 2024 •

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Matthew-Jennings commented Feb 27, 2024 •

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theanega commented Feb 28, 2024 •

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drcandacemakedamoore commented Mar 15, 2024 •

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alexzwanenburg commented Mar 15, 2024 •

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drcandacemakedamoore commented Mar 17, 2024 •

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theanega commented Mar 26, 2024 •

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Kevin-Mattheus-Moerman commented Jul 17, 2024 •

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