[REVIEW]: mmappickle: A Python 3 library to store memory mappable objects into pickle-compatible files

[whedon]

Submitting author: @lfasnacht (Laurent Fasnacht)
Repository: https://github.com/UniNE-CHYN/mmappickle
Version: v1.0.0
Editor: @arfon
Reviewer: @glemaitre, @clemaitre58
Archive: 10.5281/zenodo.1291734

Status

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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) 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

@glemaitre & @clemaitre58, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @arfon know.

Review checklist for @glemaitre

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
• Version: Does the release version given match the GitHub release (v1.0.0)?
• Authorship: Has the submitting author (@lfasnacht) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @clemaitre58

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
• Version: Does the release version given match the GitHub release (v1.0.0)?
• Authorship: Has the submitting author (@lfasnacht) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @glemaitre, it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐ 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:

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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

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof 📄 <--

[glemaitre]

My item linked to the revision:

• functionality/scope of the project
• PEP8
• Version
• setup.py
• Install documentation
• Contributing guide
• General documentation comments
• Testing failure
• Test coverage
• Continuous integration

[lfasnacht]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof 📄 <--

[arfon]

@clemaitre58 - please complete your review when you get a chance.

[lfasnacht]

@glemaitre - Any news from your side? I think I've addressed all the issues you mentioned, but I'm waiting for your feedback/confirmation to close them, and also to make the 1.0.1 release once your review is finished...

I also think you could update the checkboxes in the checklist above, since a lot of these points have been addressed meanwhile.

Thanks a lot!

[glemaitre]

I'll do a pass at night.

…

On 7 May 2018 at 15:11, Laurent Fasnacht ***@***.***> wrote: @glemaitre <https://github.com/glemaitre> - Any news from your side? I think I've addressed all the issues you mentioned, but I'm waiting for your feedback/confirmation to close them, and also to make the 1.0.1 release once your review is finished... I also think you could update the checkboxes in the checklist above, since a lot of these points have been addressed meanwhile. Thanks a lot! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#651 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHG9PxBKoTruG7mUoS0EYBNl9lx6ewKBks5twEf7gaJpZM4S8zRh> .

-- Guillaume Lemaitre INRIA Saclay - Parietal team Center for Data Science Paris-Saclay https://glemaitre.github.io/

[lfasnacht]

@glemaitre - Great, thanks!

[clemaitre58]

@lfasnacht I think it could be nice to had a "getting started" section in your documentation in order to see quickly a basic example.

[clemaitre58]

Some links for the revision :
Code coverage

[lfasnacht]

@clemaitre58 After discussion with @glemaitre (UniNE-CHYN/mmappickle#9), it was decided to move the getting started to the front page of the documentation (http://mmappickle.readthedocs.io/en/latest/#quick-start), is it what you had in mind?

[glemaitre]

I find the quick start on the landing page better than in the a separate page.

[clemaitre58]

@lfasnacht Ok for the quick start.
But this first page is not referenced in the table of content on the left side. Is ti possible to add it?

[lfasnacht]

@clemaitre58 It was hard, but now it's done. It is indeed much better, thank you very much for the suggestion.

[arfon]

@glemaitre, @clemaitre58 - can you both confirm that we're good to accept here?

[glemaitre]

good on my side

[arfon]

@lfasnacht - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

[lfasnacht]

@whedon set 10.5281/zenodo.1291734 as archive

[whedon]

I'm sorry @lfasnacht, I'm afraid I can't do that. That's something only editors are allowed to do.

[lfasnacht]

@arfon It seems that you have to do that ;-) Thanks a lot!

[arfon]

@whedon set 10.5281/zenodo.1291734 as archive

[whedon]

OK. 10.5281/zenodo.1291734 is the archive.

[arfon]

@glemaitre, @clemaitre58 - many thanks for your reviews here ✨

@lfasnacht - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00651 ⚡ 🚀 💥

[whedon]

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

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[![DOI](http://joss.theoj.org/papers/10.21105/joss.00651/status.svg)](https://doi.org/10.21105/joss.00651)

This is how it will look in your documentation:

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[lfasnacht]

Dear all,

Thank you very much for your awesome work. I will definitely recommend submitting to JOSS to my colleagues, and will also consider submitting more of my work.

Kind regards,
Laurent