[PRE REVIEW]: mednoise: a python package for medical image processing

[whedon]

Submitting author: @ravibandaru-lab (Ravi Bandaru) Repository: https://github.com/mednoise/mednoise Version: v.1.2.4 Editor: @osorensen Reviewers: @kasbohm, @ethanknights 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

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Markdown: [![status](https://joss.theoj.org/papers/e334cd1cbcdde8c9aa37254eb5c6bfec/status.svg)](https://joss.theoj.org/papers/e334cd1cbcdde8c9aa37254eb5c6bfec)

Author instructions

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

@ravibandaru-lab 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]

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]

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.12688/f1000research.29032.1 is OK
- 10.5281/zenodo.5043456 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.media.2020.101759 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.zemedi.2018.11.002 is INVALID because of 'https://doi.org/' prefix

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.05 s (208.4 files/s, 68974.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           6            483           1404           1546
Markdown                         2             32              0             75
TeX                              1              0              0             70
YAML                             1              2              3             19
TOML                             1              0              0              6
-------------------------------------------------------------------------------
SUM:                            11            517           1407           1716
-------------------------------------------------------------------------------

Statistical information for the repository '15b30f8b907e146b80d3b287' was
gathered on 2021/07/16.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Ravi Bandaru                    23          5974           2543          100.00

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
Ravi Bandaru               3433           57.5          0.0                4.54

[whedon]

PDF failed to compile for issue #3503 with the following error:

 ORCID looks to be the wrong length
/app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:155:in `block in check_orcids': Problem with ORCID (https://orcid.org/0000-0001-7109-9894) for Ravi Bandaru (RuntimeError)
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:153:in `each'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:153:in `check_orcids'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:90:in `initialize'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon/processor.rb:38:in `new'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon/processor.rb:38:in `set_paper'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/bin/whedon:58:in `prepare'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/bin/whedon:131:in `<top (required)>'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'

[ravibandaru-lab]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

[whedon]

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

OK DOIs

- 10.1016/j.media.2020.101759 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.12688/f1000research.29032.1 is OK
- 10.5281/zenodo.5043456 is OK
- 10.1016/j.zemedi.2018.11.002 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

@whedon commands

[ravibandaru-lab]

@whedon generate pdf

[whedon]

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

[ravibandaru-lab]

Hello! Thanks for processing my submission. Here are some potential reviewers I am thinking about:

1. sealhuang
2. oesteban
3. abhishekbajpayee
4. yxpd
5. glemaitre

[arfon]

@whedon invite @jni as editor

:wave: @jni – would you be able to edit this submission for us?

[whedon]

@jni has been invited to edit this submission.

[jni]

@arfon no rest for the wicked ey? 😂 I apologise, I must decline, as I am trying to close some loops before going on leave next month. 🙏 (The editor dashboard was down for me yesterday but I've made a note there now.)

[ravibandaru-lab]

@arfon Hello! 😄 Any luck on finding an editor?

[danielskatz]

👋 @ravibandaru-lab - sorry, but we're going to put this on our waiting list until a suitable editor is available

[kyleniemeyer]

@whedon invite @cMadan as editor

Hi @cMadan, could you edit this submission?

[Kevin-Mattheus-Moerman]

@cMadan :wave: Could you help handle this one?

[arfon]

@whedon invite @osorensen as editor

:wave: @osorensen - would you be willing to edit this submission for JOSS?

[whedon]

@osorensen has been invited to edit this submission.

[osorensen]

@whedon assign @osorensen as editor

[whedon]

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

@whedon commands

[osorensen]

@whedon assign @osorensen as editor

[whedon]

OK, the editor is @osorensen

[osorensen]

@sealhuang @oesteban @abhishekbajpayee @yxpd @glemaitre would any of you be interested in reviewing this submission to the Journal of Open Source Software?

[osorensen]

@ethanknights @fredrmag @markushs would any of you be interested in reviewing this submission to the Journal of Open Source Software? It seems to be within your areas of expertise.

[cMadan]

@kyleniemeyer @Kevin-Mattheus-Moerman, just seeing this now. It looks like whedon hadn't sent me an invitation email.

[osorensen]

@kasbohm, would you be interested in reviewing this submission to the Journal of Open Source Software?

[kasbohm]

Sure @osorensen!

[osorensen]

@whedon add @kasbohm as reviewer

[whedon]

OK, @kasbohm is now a reviewer

[osorensen]

Thanks @kasbohm, we'll wait for another potential reviewer to respond, and then you'll get instructions how to proceed.

[markushs]

@ethanknights @fredrmag @markushs would any of you be interested in reviewing this submission to the Journal of Open Source Software? It seems to be within your areas of expertise.

Sorry @osorensen, busy August

[osorensen]

No problem @markushs. Thanks for responding!

[ethanknights]

Sure @osorensen

[osorensen]

@whedon add @ethanknights as reviewer

[whedon]

OK, @ethanknights is now a reviewer

[osorensen]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/3597.