Joss-reviews: [PRE REVIEW]: PyQMRI: An accelerated Python based Quantitative MRI Python toolbox

Created on 2 Oct 2020 · 39Comments · Source: openjournals/joss-reviews

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

: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.

Author instructions

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).

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

C Python Shell pre-review

Source

whedon

Most helpful comment

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

agahkarakuzu on 5 Oct 2020

❤1 🎉1

All 39 comments

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

whedon on 2 Oct 2020

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:incollect!'
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:infind_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:inrun'
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:indispatch'
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 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

whedon on 2 Oct 2020

@whedon generate pdf

Kevin-Mattheus-Moerman on 2 Oct 2020

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

whedon on 2 Oct 2020

@whedon generate pdf from branch JOSS_pub

Kevin-Mattheus-Moerman on 2 Oct 2020

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

whedon on 2 Oct 2020

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:incollect!'
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:infind_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:inrun'
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:indispatch'
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 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

whedon on 2 Oct 2020

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

Kevin-Mattheus-Moerman on 2 Oct 2020

@whedon check repository

Kevin-Mattheus-Moerman on 2 Oct 2020

@whedon generate pdf from branch JOSS_pub

Kevin-Mattheus-Moerman on 2 Oct 2020

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

whedon on 2 Oct 2020

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

whedon on 2 Oct 2020

@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 on 2 Oct 2020

@whedon check repository

Kevin-Mattheus-Moerman on 2 Oct 2020

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

whedon on 2 Oct 2020

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.

MaierOli2010 on 3 Oct 2020

@whedon invite @jni as editor

Kevin-Mattheus-Moerman on 3 Oct 2020

@jni has been invited to edit this submission.

whedon on 3 Oct 2020

@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.

jni on 3 Oct 2020

👍1

@whedon assign @Kevin-Mattheus-Moerman as editor

Kevin-Mattheus-Moerman on 3 Oct 2020

OK, the editor is @Kevin-Mattheus-Moerman

whedon on 3 Oct 2020

@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 :point_right: https://github.com/openjournals/joss-papers/blob/joss.02718/joss.02718/10.21105.joss.02718.pdf
software :point_right: https://github.com/IMTtugraz/PyQMRI

Kevin-Mattheus-Moerman on 3 Oct 2020

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

JoshKarpel on 4 Oct 2020

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

spinicist on 4 Oct 2020

Sure, I am interested.

grlee77 on 4 Oct 2020

🎉1

@whedon assign @grlee77 as reviewer

Kevin-Mattheus-Moerman on 5 Oct 2020

OK, @grlee77 is now a reviewer

whedon on 5 Oct 2020

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

62442katieb on 5 Oct 2020

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

agahkarakuzu on 5 Oct 2020

❤1 🎉1

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

mathieuboudreau on 5 Oct 2020

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 notifications@github.com
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
https://github.com/openjournals/joss-reviews/issues/2718#issuecomment-703842156,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AL25BQ5BFPI6ARBHBXBKKFTSJINJHANCNFSM4SCBFCMQ
.

DARSakthi on 5 Oct 2020

@whedon add @agahkarakuzu as reviewer

Kevin-Mattheus-Moerman on 5 Oct 2020

OK, @agahkarakuzu is now a reviewer

whedon on 5 Oct 2020

👍1

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

Kevin-Mattheus-Moerman on 5 Oct 2020

Sure, I'll do it

On Mon, 5 Oct 2020 at 16:12, Kevin Mattheus Moerman <
[email protected]> 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
https://github.com/openjournals/joss-reviews/issues/2718#issuecomment-703862533,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AL25BQ6HERDLIY5OIVQIXKLSJISCHANCNFSM4SCBFCMQ
.

DARSakthi on 6 Oct 2020

@whedon add @DARSakthi as reviewer

Kevin-Mattheus-Moerman on 6 Oct 2020

OK, @DARSakthi is now a reviewer

whedon on 6 Oct 2020

@whedon start review

Kevin-Mattheus-Moerman on 7 Oct 2020

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2727.

whedon on 7 Oct 2020

Was this page helpful?

0 / 5 - 0 ratings

Related issues

[REVIEW]: PyGDH ("pigged"): Python Grid Discretization Helper

whedon · 11Comments

[REVIEW]: tidytext: Text Mining and Analysis Using Tidy Data Principles in R

whedon · 10Comments

[REVIEW]: hei: Calculate Healthy Eating Index (HEI) Scores

whedon · 12Comments

[REVIEW]: The Pulsar Signal Simulator: A Python package for simulating radio signal data from pulsars

whedon · 9Comments

[REVIEW]: Noisyopt

whedon · 6Comments