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[REVIEW]: Cutepeaks: A modern viewer for Sanger trace file #3457

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40 tasks done
whedon opened this issue Jul 7, 2021 · 42 comments
Closed
40 tasks done

[REVIEW]: Cutepeaks: A modern viewer for Sanger trace file #3457

whedon opened this issue Jul 7, 2021 · 42 comments
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accepted Inno Setup published Papers published in JOSS QMake recommend-accept Papers recommended for acceptance in JOSS. review TeX

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@whedon
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whedon commented Jul 7, 2021

Submitting author: @dridk (sacha schutz)
Repository: https://github.com/labsquare/CutePeaks
Version: v0.2.3
Editor: @lpantano
Reviewer: @tobiasrausch, @wdecoster
Archive: 10.5281/zenodo.5148809

⚠️ 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.

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/fe7efe76ee476b41dcd997fdbe8e19ec"><img src="https://joss.theoj.org/papers/fe7efe76ee476b41dcd997fdbe8e19ec/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/fe7efe76ee476b41dcd997fdbe8e19ec/status.svg)](https://joss.theoj.org/papers/fe7efe76ee476b41dcd997fdbe8e19ec)

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

@tobiasrausch & @wdecoster, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @lpantano 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

Review checklist for @tobiasrausch

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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@dridk) 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

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 and who the target audience is?
  • 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?

Review checklist for @wdecoster

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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@dridk) 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

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 and who the target audience is?
  • 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?
@whedon
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whedon commented Jul 7, 2021

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @tobiasrausch, @wdecoster it looks like you're currently assigned to review this paper 🎉.

⚠️ 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.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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
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whedon commented Jul 7, 2021

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

OK DOIs

- 10.1186/s12864-020-6635-8 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@whedon
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whedon commented Jul 7, 2021

Failed to discover a Statement of need section in paper

@whedon
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whedon commented Jul 7, 2021

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.04 s (1496.0 files/s, 148893.9 lines/s)
-----------------------------------------------------------------------------------
Language                         files          blank        comment           code
-----------------------------------------------------------------------------------
C++                                 24            819            234           2636
C/C++ Header                        23            316            243            788
Qt Linguist                          1              0              0            184
SVG                                  1              1              1            121
Markdown                             2             39              0             97
YAML                                 2              7             37             43
TeX                                  1              1              0             26
ProGuard                             1             20              5             24
Qt Project                           1             11              1             18
Windows Resource File                1              0              0              1
-----------------------------------------------------------------------------------
SUM:                                57           1214            521           3938
-----------------------------------------------------------------------------------


Statistical information for the repository 'cf5b7bbfc7f67a4bab82fa59' was
gathered on 2021/07/07.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Anne-Sophie Denommé-             5            39             35            0.06
Charles                          1           391              0            0.29
Olivier Gueudelot                1            78              5            0.06
dridk                          107         67049           3462           53.11
sacha schutz                    41          1252          60407           46.45
yschutz                          2            21             17            0.03

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
Anne-Sophie Denommé-         23           59.0         47.1                0.00
Olivier Gueudelot            37           47.4         49.6                0.00
dridk                      4961            7.4         44.4                9.94
yschutz                      15           71.4         41.5               40.00

@whedon
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whedon commented Jul 7, 2021

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

@tobiasrausch
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proof, line 27: The regular expression AC.+T should probably be AC+T

@wdecoster
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Hi @dridk, @tobiasrausch, and @lpantano

This is the first time I review for JOSS, so please let me know if I make a mistake. The process appears to be very clear though.

The installation instructions for Linux mention chmod +x cutepeaks-0.2.0-linux-x86_64.appimage, while the name of the binary is just cutepeaks-x86_64.AppImage.
Upon calling the executable (./cutepeaks-x86_64.AppImage) I get:

add font
./cutepeaks-x86_64.AppImage: symbol lookup error: /lib/x86_64-linux-gnu/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var

My operating system is Ubuntu 21.04.

Cheers,
Wouter

@dridk
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dridk commented Jul 8, 2021

@wdecoster sorry for that ! AppImage has been build on a previous system.
Here is a version for your system :
https://github.com/labsquare/CutePeaks/releases/download/0.2.3/cutepeaks-ubuntu_21-04-x86_64.AppImage

Should works ! I just tested it

@wdecoster
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Yes - I can confirm that works!

dridk added a commit to labsquare/CutePeaks that referenced this issue Jul 9, 2021
Update documentations ( community and license ) 
openjournals/joss-reviews#3457 (comment)
@wdecoster
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Hi @dridk, looking at the checklist both the paper and documentation miss a "statement of need", and the paper should additionally get a comparison to the "State of the field" - could you look into adding these sections?

dridk added a commit to labsquare/CutePeaks that referenced this issue Jul 20, 2021
@dridk
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dridk commented Jul 20, 2021

Hi @wdecoster ,
I reformulated a bit the paper to have the required section.
https://github.com/labsquare/CutePeaks/blob/master/paper/paper.md

Hi @tobiasrausch
I added the contributions section here :
https://github.com/labsquare/CutePeaks#contributions--bugs

About testing, I compile the code each time from github action
https://github.com/labsquare/CutePeaks/actions/workflows/c-cpp.yml.

Otherwise, it can be tested manually with example files available from the example folder.
https://github.com/labsquare/CutePeaks#usage

@whedon
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whedon commented Jul 21, 2021

👋 @tobiasrausch, please update us on how your review is going (this is an automated reminder).

@whedon
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whedon commented Jul 21, 2021

👋 @wdecoster, please update us on how your review is going (this is an automated reminder).

@tobiasrausch
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Hi @dridk, I think GitHub defaults to a contributing.md file in case you want to add this. Here is the link for your repo. Did you have a chance to check your regex in the paper? I believe this should be AC+T and not AC.+T from the examples you show afterwards.

dridk added a commit to labsquare/CutePeaks that referenced this issue Jul 21, 2021
dridk added a commit to labsquare/CutePeaks that referenced this issue Jul 21, 2021
@dridk
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dridk commented Jul 21, 2021

@tobiasrausch Oups.. didn't see your comment about regexp.. I just fixed it !

@tobiasrausch
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@whedon generate pdf

@whedon
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whedon commented Jul 22, 2021

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

@wdecoster
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I think for a tool like this the best automated testing is testing if it compiles - so I think that requirement is fulfilled.

@lpantano
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@whedon check references

@whedon
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whedon commented Jul 28, 2021

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

OK DOIs

- 10.1186/s12864-020-6635-8 is OK
- 10.7171/jbt.12-2303-004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@lpantano
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Hi @dridk, At this point could you:

  • Make a tagged release of your software, and list the version tag of the archived version here.
  • Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
  • Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
  • Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

@dridk
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dridk commented Jul 29, 2021

Hi @lpantano , here are the required informations

@dridk
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dridk commented Jul 29, 2021

@whedon generate pdf

@whedon
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whedon commented Jul 29, 2021

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

@lpantano
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@whedon set v0.2.3 as version

@whedon
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whedon commented Jul 30, 2021

OK. v0.2.3 is the version.

@lpantano
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@dridk, thank you for doing this. Can you make the zenodo has the same title than the paper? thanks

@dridk
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dridk commented Jul 30, 2021

@lpantano
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lpantano commented Aug 2, 2021

@whedon set 10.5281/zenodo.5148809 as archive

@whedon
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whedon commented Aug 2, 2021

OK. 10.5281/zenodo.5148809 is the archive.

@lpantano
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lpantano commented Aug 2, 2021

@whedon recommend-accept

@whedon
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whedon commented Aug 2, 2021

Attempting dry run of processing paper acceptance...

@whedon whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Aug 2, 2021
@whedon
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whedon commented Aug 2, 2021

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

OK DOIs

- 10.1186/s12864-020-6635-8 is OK
- 10.7171/jbt.12-2303-004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@whedon
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whedon commented Aug 2, 2021

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2489

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2489, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

@whedon
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whedon commented Aug 2, 2021

I'm sorry @dridk, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

@arfon
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arfon commented Aug 6, 2021

@whedon accept deposit=true

@whedon
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whedon commented Aug 6, 2021

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

@whedon whedon added accepted published Papers published in JOSS labels Aug 6, 2021
@whedon
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whedon commented Aug 6, 2021

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

@whedon
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whedon commented Aug 6, 2021

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03457 joss-papers#2502
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03457
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@arfon
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arfon commented Aug 6, 2021

@tobiasrausch, @wdecoster – many thanks for your reviews here and to @lpantano for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@dridk – your paper is now accepted and published in JOSS ⚡🚀💥

@arfon arfon closed this as completed Aug 6, 2021
@whedon
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whedon commented Aug 6, 2021

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03457/status.svg)](https://doi.org/10.21105/joss.03457)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03457">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03457/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03457/status.svg
   :target: https://doi.org/10.21105/joss.03457

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

@dridk
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dridk commented Aug 6, 2021

Thanks you all !
I was really impressed with your reviewing system which is very smart ! The markdown paper, the github issue system and your awesome whedon ! It would be nice if all scientific journals did the same !

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