search

openjournals / joss-reviews

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

[PRE REVIEW]: Madym: A C++ toolkit for quantitative DCE-MRI analysis #3421

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @michaelberks (Michael Berks) Repository: https://gitlab.com/manchester_qbi/manchester_qbi_public/madym_cxx/ Version: v4.15.0 Editor: @emdupre Reviewers: @agahkarakuzu, @matteomancini Managing EiC: Arfon Smith

: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.

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e04f2517a022cc6d1de7681ecf147dae"><img src="https://joss.theoj.org/papers/e04f2517a022cc6d1de7681ecf147dae/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e04f2517a022cc6d1de7681ecf147dae/status.svg)](https://joss.theoj.org/papers/e04f2517a022cc6d1de7681ecf147dae)

Author instructions

Thanks for submitting your paper to JOSS @michaelberks. Currently, there isn't an JOSS editor assigned to your paper.

@michaelberks if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands
whedon commented 3 years ago

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

: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.

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

@whedon commands

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

@whedon generate pdf
arfon commented 3 years ago

@whedon generate pdf from branch JOSS_submission_4.15.0

whedon commented 3 years ago 
Attempting PDF compilation from custom branch JOSS_submission_4.15.0. Reticulating splines etc...
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1002/jmri.1880070113 is OK
- 10.1002/mrm.22005 is OK

MISSING DOIs

- 10.1038/nrclinonc.2012.2 may be a valid DOI for title: Dynamic contrast-enhanced MRI in clinical trials of antivascular therapies
- 10.1038/s41467-018-07174-1 may be a valid DOI for title: Plasma Tie2 is a tumor vascular response biomarker for VEGF inhibitors in metastatic colorectal cancer
- 10.1038/jcbfm.1983.1 may be a valid DOI for title: Graphical evaluation of blood-to-brain transfer constants from multiple-time uptake data
- 10.1002/mrm.28798 may be a valid DOI for title: A model selection framework to quantify microvascular liver function in gadoxetate-enhanced MRI: Application to healthy liver, diseased tissue, and hepatocellular carcinoma

INVALID DOIs

- https://doi.org/10.1002/mrm.27939 is INVALID because of 'https://doi.org/' prefix
whedon commented 3 years ago

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

whedon commented 3 years ago

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

whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=1.95 s (104.5 files/s, 280494.8 lines/s)
-----------------------------------------------------------------------------------
Language                         files          blank        comment           code
-----------------------------------------------------------------------------------
C++                                 94          42357         109980         273921
HTML                                 1           7301              0          45503
C/C++ Header                        73           9705          31461          20891
Qt                                   2              0              0           2302
Python                               9            441            830           1317
CMake                                8            176            161            799
Markdown                             4             56              0            181
YAML                                 2             10              5            142
TeX                                  1             11              0            114
Dockerfile                           3             16             10             87
Bourne Shell                         2              0              0             11
DOS Batch                            2              0              0             10
JSON                                 1              0              0              8
TOML                                 1              0              0              7
Windows Resource File                1              0              0              1
-----------------------------------------------------------------------------------
SUM:                               204          60073         142447         345294
-----------------------------------------------------------------------------------

Statistical information for the repository '7d49a16b858e5d907662e543' was
gathered on 2021/06/26.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Michael Berks                   23        169135           2774           94.43
michaelberks                    36          6883           3252            5.57
momeemb2                         1             3              1            0.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Michael Berks            469418          277.5          0.1               34.44
arfon commented 3 years ago

@michaelberks – thanks for your submission to JOSS. We're currently managing a large backlog of submissions and the editor most appropriate for your area is already rather busy.

For now, we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!

Kevin-Mattheus-Moerman commented 3 years ago

@arfon I'm currently handling 7 submissions but once I've processed a few and if this still needs an editor I might be able to help. I've handled quite a few MRI papers.

michaelberks commented 3 years ago

@arfon and @Kevin-Mattheus-Moerman . Thanks both for the information, I understand the situation.

Looking at the whedon auto summary on the references, shall I add the missing the DOIs it has found (and correct the invalidly formatted DOI) now? I'll make the edit paper.bib directly on the paper submission branch (JOSS_submission_4.1.5.0).

Kevin-Mattheus-Moerman commented 3 years ago

@michaelberks yes you can fix those issues and update the paper draft at any time by calling @whedon generate pdf.

arfon commented 3 years ago

@whedon invite @emdupre as editor

:wave: @emdupre – would you be willing to edit this submission for JOSS?

whedon commented 3 years ago

@emdupre has been invited to edit this submission.

emdupre commented 3 years ago

@whedon assign @emdupre as editor

whedon commented 3 years ago

OK, the editor is @emdupre

emdupre commented 3 years ago

Hi @michaelberks, thank you for submitting to JOSS ! I'll be acting as editor for this submission -- though thank you, @Kevin-Mattheus-Moerman, for offering your help, here !

If you have any recommendations for appropriate reviewers, please let us know.

emdupre commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

emdupre commented 3 years ago

Hi @oesteban :wave: Any chance you'd be available and willing to review this submission for the Journal of Open Source Software ?

emdupre commented 3 years ago

Hi @tianxzhu :wave: Any chance you'd be available and willing to review this submission for the Journal of Open Source Software ?

danielskatz commented 3 years ago

Hi @emdupre - I think you might be asking for reviewers, not editors?

emdupre commented 3 years ago

Ah sorry, yes ! That was an accident. Will fix now.

michaelberks commented 3 years ago

@emdupre great thank-you.

Can I check the policy re version increments (or point me in the direction of link on the JOSS wesbite - apologies if I've missed).

I've been maintaining Madym user automated semantic versioning. When I submitted a few weeks ago it was version 4.15.0. However a user found a small bug in the Dicom converter tool, which I've fixed, bumping the version to 4.15.1. I think I read one of the reviewer checks was to verify that the repo version matches the version given on the submission form, which is obviously no longer the case.

More generally, what I should I do if other fixes come up during the submission process (or I get round to adding some requested features).

emdupre commented 3 years ago

I can update the submitted software version with whedon if there's a particular verison that reviewer's should be aware of. There's not a specific check that the version matches the submitted version during review, as -- as you mention -- it might be incrementing.

More generally, then, fixes coming up during the submission process is expected -- and the sign of a good review ! After reviews, we'll ask that you create and archive a version of your software that will be associated with the publication. This is the version check that we will look at most carefully !

emdupre commented 3 years ago

Hi @agahkarakuzu :wave: Any chance you'd be available and willing to review this submission for the Journal of Open Source Software ?

agahkarakuzu commented 3 years ago

Hi @emdupre thank you for the invitation!

I am available next week onwards, if that makes a reasonable timeline, happy to review this submission.

emdupre commented 3 years ago

Thank you, @agahkarakuzu ! I'll add you as a reviewer on this submission now.

emdupre commented 3 years ago

@whedon add @agahkarakuzu as reviewer

whedon commented 3 years ago

OK, @agahkarakuzu is now a reviewer

emdupre commented 3 years ago

Hi @Lestropie @mfroeling @grlee77 @jdtournier @matteomancini :wave:

Would you be willing to review Madym: A C++ toolkit for quantitative DCE-MRI analysis for JOSS (the Journal of Open Source Software) ?

The review takes place on GitHub and focuses on the software and this short paper: https://github.com/openjournals/joss-papers/blob/joss.03421/joss.03421/10.21105.joss.03421.pdf

If you're available to review this work, please let me know and I'll add you as a reviewer. Once I have sufficient reviewers I'll open a dedicated review issue.

Thanks!

matteomancini commented 3 years ago

Hi @emdupre thanks for inviting me! I'd be glad to review this software/paper.

emdupre commented 3 years ago

Thank you, @matteomancini ! I'll add you as a reviewer on this submission now.

emdupre commented 3 years ago

@whedon add @matteomancini as reviewer

whedon commented 3 years ago

OK, @matteomancini is now a reviewer

grlee77 commented 3 years ago

I appreciate the offer, but do not have the bandwidth to do a solid review at the moment.

Lestropie commented 3 years ago

Eager to review for JOSS at some point, but am already behind schedule on a couple of others 😩

jdtournier commented 3 years ago

HI @emdupre, I'm sorry, I won't be able to review this, I'm about to go on leave. Do keep me in mind for future reviews though!

emdupre commented 3 years ago

Thank you @jdtournier @Lestropie and @grlee77 for letting me know !

emdupre commented 3 years ago

@agahkarakuzu @matteomancini Thanks again for agreeing to review this submission. I'll go ahead and start the review now !

emdupre commented 3 years ago

@whedon start review

whedon commented 3 years ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/3523.