[REVIEW]: Castor: A C++ library to code "à la matlab"

[whedon]

Submitting author: @matthieuaussal (Matthieu Aussal)
Repository: https://github.com/leprojetcastor/castor
Branch with paper.md (empty if default branch):
Version: 1.0
Editor: @jbytecode
Reviewers: @mkitti, @pitsianis
Archive: 10.5281/zenodo.6360120

⚠️ JOSS reduced service mode ⚠️

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Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/758f31f8f400959b11a18cf5f7a5d04f"><img src="https://joss.theoj.org/papers/758f31f8f400959b11a18cf5f7a5d04f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/758f31f8f400959b11a18cf5f7a5d04f/status.svg)](https://joss.theoj.org/papers/758f31f8f400959b11a18cf5f7a5d04f)

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

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

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✨ 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 @mkitti

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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

• I confirm that I read and will adhere to the JOSS 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 (@matthieuaussal) 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 @pitsianis

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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

• I confirm that I read and will adhere to the JOSS 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 (@matthieuaussal) 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]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @mkitti, @junliu2050 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:

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

Wordcount for paper.md is 2074

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.19 s (421.7 files/s, 219330.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C/C++ Header                     7           3977           6283          22256
C++                             12            385            365           2080
reStructuredText                46           2015           2742           1332
Markdown                         2             63              0            239
CMake                            8             40             19            149
TeX                              1              9              0             58
YAML                             2              9              8             46
Python                           1              4              1             15
CSS                              1              2              0             11
make                             1              4              7             10
-------------------------------------------------------------------------------
SUM:                            81           6508           9425          26196
-------------------------------------------------------------------------------


Statistical information for the repository '0a6dc246b7c70f17d676860f' was
gathered on 2021/12/01.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
@marc.bakry                      1             8              8            0.04
Antoine RIDEAU                   1             1              1            0.00
Marc                             5           140              7            0.33
Matthieu Aussal                 33          4056           1918           13.29
Series Laurent                   5         35796           2680           85.58
U-INTRA\MB264355                 1           180              0            0.40
U-INTRA\mb264355                 7           135             31            0.37

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
@marc.bakry                   6           75.0         12.7              100.00
Antoine RIDEAU                1          100.0          4.8                0.00
Marc                        105           75.0         10.2                9.52
Matthieu Aussal            2667           65.8          9.6               27.78
Series Laurent            32503           90.8          0.5               18.13
U-INTRA\mb264355             84           62.2         11.9               23.81

[whedon]

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

[whedon]

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

OK DOIs

- None

MISSING DOIs

- 10.1145/2049662.2049663 may be a valid DOI for title: The University of Florida sparse matrix collection
- 10.1109/icme.2012.93 may be a valid DOI for title: Creating the Sydney York morphological and acoustic recordings of ears database
- 10.1109/38.865875 may be a valid DOI for title: Visualizing with VTK: a tutorial

INVALID DOIs

- None

[jbytecode]

Dear @mkitti and @junliu2050

• This is the review issue. Please ping me if you received this message.
• There are 20 checkbox items for each reviewer. Please follow them and click when you finish the corresping task.
• The review is live, so you can interact with the author(s) and me, open new issues in the software repo, and mention here.
• You can also contribute to software.
• Do not hesitate to ask me anything, anytime!

Thank you very much for accepting our invitation.

[jbytecode]

Dear @matthieuaussal

I have sent a pull request. It includes the missing DOIs that whedon suggests. Please apply the patch if you are agreed with me.

thank you in advance.

[jbytecode]

@whedon check references

[whedon]

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

OK DOIs

- 10.1145/2049662.2049663 is OK
- 10.1109/icme.2012.93 is OK
- 10.1109/38.865875 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[jbytecode]

@whedon generate pdf

[whedon]

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

[matthieuaussal]

@whedon <https://github.com/whedon> generate pdf

[whedon]

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

@whedon commands

[matthieuaussal]

@whedon generate pdf

…

Le 1 déc. 2021 à 13:09, whedon ***@***.***> a écrit : I'm sorry human, I don't understand that. You can see what commands I support by typing: @whedon commands — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3965 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHFHRGAETE5D5GCINFFJVB3UOYF6HANCNFSM5JDT4MGQ>. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[whedon]

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

[junliu2050]

Hi, after carefully reading through the paper, I feel I may not be very suitable for reviewing such a library since I do not use or develop a similar package by myself.
Hence you may assign Rodrigo Portugal as 2nd reviewer. Overall it is an interesting package, but the examples and comparison with similar packages can be improved.

[jbytecode]

@rosoport do you still want to review this submission?

[jbytecode]

@whedon remove @junliu2050 as reviewer

[whedon]

OK, @junliu2050 is no longer a reviewer

[editorialbot]

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

Check final proof 👉 openjournals/joss-papers#3058

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3058, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[jbytecode]

Thank you @mkitti and @pitsianis for consuming your valuable time for reviewing this submission, and thank you @matthieuaussal for sending your work and submission to JOSS. We have just completed the review and I recommended an acceptance. The Editor in Chief will have the final decision. Hope we will work in later projects and submissions!

[matthieuaussal]

dear all, many thanks for your very professional work, this 1st experience was a pleasure :-)

[kthyng]

Hi @matthieuaussal! I'll take over from here to wrap up.

Can you update the metadata for your Zenodo archive so the title and author list match your JOSS paper?

[kthyng]

@matthieuaussal your paper looks good, except please go through the capitalization in the references. For example, Jin et al has uncapitalized proper nouns. You can preserve capitalization in your .bib file by placing {} around words or phrases.

[matthieuaussal]

Hi @matthieuaussal! I'll take over from here to wrap up.

Can you update the metadata for your Zenodo archive so the title and author list match your JOSS paper?

Done, is it ok now?

[matthieuaussal]

@matthieuaussal your paper looks good, except please go through the capitalization in the references. For example, Jin et al has uncapitalized proper nouns. You can preserve capitalization in your .bib file by placing {} around words or phrases.

Could you precise me what is the correct rule, please?

[matthieuaussal]

@editorialbot generate pdf

[matthieuaussal]

@editorialbot generate pdf

[matthieuaussal]

@matthieuaussal your paper looks good, except please go through the capitalization in the references. For example, Jin et al has uncapitalized proper nouns. You can preserve capitalization in your .bib file by placing {} around words or phrases.

I think it's done, but I can't regenerate pdf to verify

[matthieuaussal]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

⚠️ An error happened when generating the pdf.

[kthyng]

Ok, that reference has capitalized proper nouns now. Let's proceed.

[kthyng]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03965 joss-papers#3066
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03965
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kthyng]

Congrats on your new publication @matthieuaussal! Many thanks to editor @jbytecode and reviewers @mkitti and @pitsianis for your time, hard work, and expertise!!

(I'll close this issue once the DOI resolves.)

[editorialbot]

🎉🎉🎉 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.03965/status.svg)](https://doi.org/10.21105/joss.03965)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03965">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03965/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03965/status.svg
   :target: https://doi.org/10.21105/joss.03965

This is how it will look in your documentation:

We need your help!

The 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:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[matthieuaussal]

@editorialbot generate pdf

…

Le 10 mars 2022 à 19:04, Matthieu Aussal ***@***.***> a écrit : @editorialbot generate pdf > Le 7 mars 2022 à 17:26, Mehmet Hakan Satman ***@***.*** ***@***.***>> a écrit : > > > Dear @matthieuaussal <https://github.com/matthieuaussal> > It seems our reviewers have just completed their major tasks. Please consider applying the latest minor suggestions, then I am going to start my editorial stuff. > > Thank you in advance. > > — > Reply to this email directly, view it on GitHub <#3965 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHFHRGE27XU5QR5PYNASYGLU6YU4JANCNFSM5JDT4MGQ>. > Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. > You are receiving this because you were mentioned. >

[editorialbot]

⚠️ An error happened when generating the pdf.

[arfon]

@matthieuaussal – curious what you're looking to accomplish here? Once a paper has been accepted it's not possible to generate PDF previews again like this sorry.

[matthieuaussal]

very curious, I did nothing, with no connection on github since months...