Joss-reviews: [REVIEW]: chronovise: Measurement-Based Probabilistic Timing Analysis framework

[whedon]

Submitting author: @federeghe (FEDERICO REGHENZANI)
Repository: https://github.com/federeghe/chronovise
Version: v1.0
Editor: @danielskatz
Reviewer: @lkosmid
Archive: 10.5281/zenodo.1404670

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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

@lkosmid, 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 @danielskatz know.

Review checklist for @lkosmid

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: Does the release version given match the GitHub release (v1.0)?
• [x] Authorship: Has the submitting author (@federeghe) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• [x] 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

• [x] Authors: Does the paper.md file include a list of authors with their affiliations?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] 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. @lkosmid it looks like you're currently assigned as the reviewer for this paper :tada:.

:star: Important :star:

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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1. 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 :page_facing_up: <--

[danielskatz]

@lkosmid - thanks for agreeing to do this review. You should start with the information at the top of the issue. Please let me know if you have questions.

[danielskatz]

@lkosmid - just a ping to see if everything is ok. I think you were out last week, but perhaps you will be able to start on this review this week?

[lkosmid]

@danielskatz - yes, indeed, everything is ok. I think I will be able to start reviewing at the end of this week.

[danielskatz]

@lkosmid - just a ping to see how the review is going

[lkosmid]

@danielskatz - review it's under way, prepared a clean environment to test the software

[lkosmid]

Two issues detected and need to be addressed:

Installation instructions (enhancement)
https://github.com/federeghe/chronovise/issues/9

Third party licensing attribution
https://github.com/federeghe/chronovise/issues/10

Btw, I won't be available next week, I will be able to continue the review at the end of next week, so it will be nice to have these issues resolved by then.

[danielskatz]

👋 @lkosmid - it looks like the issues you brought up have been addressed

Please confirm, and please continue your review

[lkosmid]

@danielskatz - Indeed, thanks @federeghe
I continue with the review

[lkosmid]

In general the short paper seems adequate. It motivates the need for Measurement Based Probabilistic Timing Analysis and in particular the need for an open source tool to compute pWCETs. However, I think that some important references are missing as well as the implementation of some of hte a state-of-the-art MBPTA features.

You can find more details comments here: https://github.com/federeghe/chronovise/issues/11

[federeghe]

@lkosmid Thank you for the detailed review. We'll work on that.

[federeghe]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[federeghe]

@lkosmid We updated the article and the code.

We replied inline to the issue federeghe/chronovise#11

Thank you again for the detailed review.

[lkosmid]

@federeghe Thank you for the updates in both the code and article.
I will continue with my review and let you know.

[lkosmid]

@federeghe Thank you for the updates in both the code and article.
I will continue with my review and let you know.

[lkosmid]

@federeghe I updated my comments on the short paper.
Some more minor changes are required.

[federeghe]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[lkosmid]

@federeghe thank you very much for your updates in the code and the manuscript.
We are almost there, some typos only need to be fixed, see my comments.
Regarding the code review, I have some imminent deadlines and back-to-back trips which might reduce my responsiveness and delay a bit the review, but I will try my best to finish it soon.

[federeghe]

@lkosmid Ok, thank you.

[federeghe]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[federeghe]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[danielskatz]

@lkosmid - can we get an update from you on where things are from your point of view?

[lkosmid]

@danielskatz the short paper has been thoroughly reviewed and after several iterations with @federeghe is ready.
From my side it is pending to review the software, its functionality, test environment and documentation (in fact the missing check boxes).
I have already installed the software and gave it a spin a while ago and it seems functional and according to the short paper, but I need to deeply review the code and compare its results with other software packages with similar functionality that I requested e.g. MBPTA-CV
However, as I mentioned I'm between back-to-back business trips and vacations will follow, so I'm afraid that I won't be able to complete those tasks before mid July. I apologise for the long review cycle...

[danielskatz]

👋 @lkosmid - Just checking to see if you are back...

[danielskatz]

👋 @lkosmid - Just checking again to see if you are back...

[lkosmid]

Hi @danielskatz I'm back trying to catch up. I will provide an update during the week.

[danielskatz]

Hi @lkosmid - Can I get an update about this review?

I see a bunch of stuff in https://github.com/federeghe/chronovise/issues/11 from a while ago, but it looks like they have all been addressed. Should that issue now be closed?

Are there other issues that have been raised?

[lkosmid]

Hi @danielskatz , all the issues regarding the content of the short paper paper have been addressed. I had forgotten to close the issue (although I had updated the corresponding checkboxes in the review page) soon after @federeghe updated it.

The only remaining (but time consuming) part from my side is to review the chronovise source code and documentation/examples to verify the claims of the short paper and be able to check the last remaining checkboxes to close the review. I want to make a comparison of some pWCET estimations computed with chronovise with at least MBPTA-CV, which is the reference open source tool in measurement based probabilistic timing analysis. This is necessary in order to make sure that the last claim of the paper, and one of the fundamental contributions of the paper (that the tool can be used by end users like engineers to obtain pWCET estimations with different EVT approaches and compare them) is correct. The problem is that my bandwidth is very limited at the moment, but I have it in high priority. Thank you both for bearing with me and I apologise for the long delay that this causes in the review process, but I think this extra step will ensure a high-quality review and increase the credibility and impact of the publication.

[danielskatz]

Thanks @lkosmid - I think there are likely some checkboxes in the review that could also be checked at this time (e.g., Authorship), and if you have a chance to do this so it's clear from the list what still needs to be done, that would be great, but is not strictly required - it can wait until you have time to do the code check.

[federeghe]

Dear @lkosmid,

To simplify your review and reduce your effort, I pushed a small example over 10000 samples generated from a normal distribution for MBPTA-CV together with a small bugfix. The example is called simple_hello_world_cv_2.cpp and in the samples folder you can find the original dataset (both in txt for R and in .h for chronovise).
I hope that this can be useful.

The result of the original MBPTA-CV R software is:

CV-Value = 0.981919
pWCET(10-6) = 42
pWCET(10-9) = 46

The result of chronovise is:

CV-Value = 0.986187
pWCET(10-6) = 42.8073
pWCET(10-9) = 46.9047

[danielskatz]

👋 @lkosmid - please let us know where you are

[lkosmid]

Hi @danielskatz and @federeghe , I was out of the office last week.
@federeghe thank you for the example you added, it definitely simplifies a lot my review.
I will be able to provide an update this week.

[lkosmid]

I think that the documentation is in a very good state. I only have a minor suggestion for improving the documentation (#16) and one small feature to be implemented (#15).

[federeghe]

@lkosmid Thank you for the suggestions and the detailed comments, issues federeghe/chronovise#15 and federeghe/chronovise#16 have been fixed.

[lkosmid]

@federeghe Thank you for applying the suggestions! I only have a very minor comment for #16

[lkosmid]

@federeghe Thank you for addressing all the comments. I don't have anything else, the review is complete. I have checked the last remaining item in the above checklist.
@danielskatz What are the next steps?

[danielskatz]

Thanks very much @lkosmid

@federeghe , please archive the current version of the repository in zenodo or similar, and let me know the DOI.

[federeghe]

Zenodo DOI: 10.5281/zenodo.1404670

Thank you

[danielskatz]

@whedon set 10.5281/zenodo.1404670 as archive

[whedon]

OK. 10.5281/zenodo.1404670 is the archive.

[danielskatz]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[danielskatz]

👋 @arfon, over to you to finish the acceptance

[arfon]

@lkosmid - many thanks for your review here and to @danielskatz for editing this submission ✨

@federeghe - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00711 :zap: :rocket: :boom:

[whedon]

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