[PRE REVIEW]: PyQMRI: An accelerated Python based Quantitative MRI Python toolbox #2718

whedon · 2020-10-02T18:52:28Z

Submitting author: @MaierOli2010 (Oliver Maier)
Repository: https://github.com/IMTtugraz/PyQMRI
Version: v0.3.1
Editor: @Kevin-Mattheus-Moerman
Reviewers: @grlee77, @agahkarakuzu, @DARSakthi
Managing EiC: Kevin M. Moerman

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Thanks for submitting your paper to JOSS @MaierOli2010. Currently, there isn't an JOSS editor assigned to your paper.

@MaierOli2010 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).

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

whedon · 2020-10-02T18:52:31Z

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

⚠️ JOSS reduced service mode ⚠️

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

whedon · 2020-10-02T18:52:45Z

PDF failed to compile for issue #2718 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/2718 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in collect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/lib/whedon/processor.rb:61:in find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/bin/whedon:119:in <top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

Kevin-Mattheus-Moerman · 2020-10-02T18:53:56Z

@whedon generate pdf

whedon · 2020-10-02T18:54:11Z

PDF failed to compile for issue #2718 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/2718 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in collect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/lib/whedon/processor.rb:61:in find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/bin/whedon:119:in <top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

Kevin-Mattheus-Moerman · 2020-10-02T18:56:53Z

@whedon generate pdf from branch JOSS_pub

whedon · 2020-10-02T18:56:56Z

Attempting PDF compilation from custom branch JOSS_pub. Reticulating splines etc...

whedon · 2020-10-02T18:57:08Z

PDF failed to compile for issue #2718 with the following error:

sh: 1: cd: can't cd to tmp/2718
/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/2718 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in collect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/lib/whedon/processor.rb:61:in find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/bin/whedon:119:in <top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

Kevin-Mattheus-Moerman · 2020-10-02T18:58:00Z

@openjournals/dev can you help troubleshoot why this paper is not compiling? Thanks

Kevin-Mattheus-Moerman · 2020-10-02T18:59:14Z

@whedon check repository

Kevin-Mattheus-Moerman · 2020-10-02T19:02:03Z

@whedon generate pdf from branch JOSS_pub

whedon · 2020-10-02T19:02:06Z

Attempting PDF compilation from custom branch JOSS_pub. Reticulating splines etc...

whedon · 2020-10-02T19:03:00Z

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

Kevin-Mattheus-Moerman · 2020-10-02T19:04:21Z

@openjournals/dev can you help troubleshoot why this paper is not compiling? Thanks

I think I fixed it by changing the repository link to be the repo itself not the branch

Kevin-Mattheus-Moerman · 2020-10-02T19:04:29Z

@whedon check repository

whedon · 2020-10-02T19:05:19Z

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.55 s (98.9 files/s, 38614.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          30           1662           3655           8461
C                                8            679            356           5650
reStructuredText                 9            134             98            231
DOS Batch                        1              8              1             27
Dockerfile                       1              7              1             27
YAML                             2              8             11             26
make                             1              4              6             10
INI                              1              0              0             10
Bourne Shell                     1              0              0              8
-------------------------------------------------------------------------------
SUM:                            54           2502           4128          14450
-------------------------------------------------------------------------------


Statistical information for the repository '2718' was gathered on 2020/10/02.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Maier, Oliver                  341        257592         241085           89.13
Oliver                          62         30982           6909            6.77
Oliver Maier                   131         16345           6600            4.10

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
Maier, Oliver             20463            7.9          7.4                4.81

MaierOli2010 · 2020-10-03T06:13:22Z

I would suggest hanayik as potential reviewer given his knowledge in MRI and Image Analysis and sbacchio for his knowledge in HPC and Iterative Linear Solvers. vitorsr, ulvgard, and stsievert might be suitable too given their background in optimization and image processing.

Kevin-Mattheus-Moerman · 2020-10-03T09:03:43Z

@whedon invite @jni as editor

whedon · 2020-10-03T09:03:47Z

@jni has been invited to edit this submission.

jni · 2020-10-03T10:46:24Z

@Kevin-Mattheus-Moerman unfortunately I don't have the bandwidth right now, especially since I'm about to go on leave. I will however additionally recommend grlee77 as an additional potential reviewer.

Kevin-Mattheus-Moerman · 2020-10-03T10:53:17Z

@whedon assign @Kevin-Mattheus-Moerman as editor

whedon · 2020-10-03T10:53:21Z

OK, the editor is @Kevin-Mattheus-Moerman

Kevin-Mattheus-Moerman · 2020-10-03T19:01:50Z

@grlee77, @JoshKarpel, @rljacobson, @mfroeling, @62442katieb, @agahkarakuzu, @mathieuboudreau, @spinicist, @imr-framework, @kerkelae , @DARSakthi, @ritagnunes

Would you be interested in reviewing this work for JOSS?

PyQMRI: An accelerated Python based Quantitative MRI Python toolbox
paper 👉 https://github.com/openjournals/joss-papers/blob/joss.02718/joss.02718/10.21105.joss.02718.pdf
software 👉 https://github.com/IMTtugraz/PyQMRI

JoshKarpel · 2020-10-04T02:38:04Z

Unfortunately I don't have time at the moment. Thanks for asking!

spinicist · 2020-10-04T10:22:58Z

Looks very interesting but I don't have access to a suitable GPU!

grlee77 · 2020-10-04T17:11:20Z

Sure, I am interested.

Kevin-Mattheus-Moerman · 2020-10-05T07:57:37Z

@whedon assign @grlee77 as reviewer

whedon · 2020-10-05T07:57:42Z

OK, @grlee77 is now a reviewer

62442katieb · 2020-10-05T14:10:37Z

@Kevin-Mattheus-Moerman looks like an interesting toolbox, but I don't have access to a GPU at the moment

agahkarakuzu · 2020-10-05T18:19:27Z

@Kevin-Mattheus-Moerman I've arranged GPU access, happy to help out!

mathieuboudreau · 2020-10-05T19:31:14Z

Since @agahkarakuzu and I are from the same lab, I yield to him and decline for myself.

DARSakthi · 2020-10-05T19:38:22Z

I can try to arrange for GPU access. If another reviewer is needed In general, and as an item of interest for the authors, GPUs are hard to come by -- including solutions like Google Collab - based scripts, which allows for free GPU access, could be valuable in expanding the user base. Let me know if no one else steps up @Kevin-Mattheus-Moerman. Looks like an interesting paper Cheers

…

On Mon, 5 Oct 2020 at 15:31, Mathieu Boudreau ***@***.***> wrote: Since @agahkarakuzu <https://github.com/agahkarakuzu> and I are from the same lab, I yield to him and decline for myself. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2718 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AL25BQ5BFPI6ARBHBXBKKFTSJINJHANCNFSM4SCBFCMQ> .

Kevin-Mattheus-Moerman · 2020-10-05T20:10:32Z

@whedon add @agahkarakuzu as reviewer

whedon · 2020-10-05T20:10:37Z

OK, @agahkarakuzu is now a reviewer

Kevin-Mattheus-Moerman · 2020-10-05T20:12:02Z

@DARSakthi if you are still interested I'd like to add you as a third reviewer, let me know. Thanks!

DARSakthi · 2020-10-06T02:32:47Z

Sure, I'll do it

…

On Mon, 5 Oct 2020 at 16:12, Kevin Mattheus Moerman < ***@***.***> wrote: @DARSakthi <https://github.com/DARSakthi> if you are still interested I'd like to add you as a third reviewer, let me know. Thanks! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2718 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AL25BQ6HERDLIY5OIVQIXKLSJISCHANCNFSM4SCBFCMQ> .

Kevin-Mattheus-Moerman · 2020-10-06T20:18:12Z

@whedon add @DARSakthi as reviewer

whedon · 2020-10-06T20:18:18Z

OK, @DARSakthi is now a reviewer

Kevin-Mattheus-Moerman · 2020-10-07T14:08:57Z

@whedon start review

whedon · 2020-10-07T14:09:02Z

OK, I've started the review over in #2727.

whedon added the pre-review label Oct 2, 2020

whedon added C Python Shell labels Oct 2, 2020

whedon assigned Kevin-Mattheus-Moerman Oct 3, 2020

whedon assigned grlee77 and Kevin-Mattheus-Moerman and unassigned Kevin-Mattheus-Moerman Oct 5, 2020

whedon assigned grlee77 and Kevin-Mattheus-Moerman and unassigned grlee77 and Kevin-Mattheus-Moerman Oct 5, 2020

whedon assigned DARSakthi, grlee77 and Kevin-Mattheus-Moerman and unassigned grlee77 and Kevin-Mattheus-Moerman Oct 6, 2020

whedon closed this as completed Oct 7, 2020

Kevin-Mattheus-Moerman mentioned this issue Oct 7, 2020

[REVIEW]: PyQMRI: An accelerated Python based Quantitative MRI Python toolbox #2727

Closed

60 tasks

[PRE REVIEW]: PyQMRI: An accelerated Python based Quantitative MRI Python toolbox #2718

[PRE REVIEW]: PyQMRI: An accelerated Python based Quantitative MRI Python toolbox #2718

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