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

whedon commented 6 years ago

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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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 commented 6 years ago

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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whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

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

danielskatz commented 6 years ago

@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 commented 6 years ago

@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 commented 6 years ago

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

danielskatz commented 6 years ago

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

lkosmid commented 6 years ago

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

lkosmid commented 6 years ago

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 commented 6 years ago

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

Please confirm, and please continue your review

lkosmid commented 6 years ago

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

lkosmid commented 6 years ago

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 commented 6 years ago

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

federeghe commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

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

federeghe commented 6 years ago

@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 commented 6 years ago

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

lkosmid commented 6 years ago

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

lkosmid commented 6 years ago

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

federeghe commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

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

lkosmid commented 6 years ago

@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 commented 6 years ago

@lkosmid Ok, thank you.

federeghe commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

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

federeghe commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

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

danielskatz commented 6 years ago

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

lkosmid commented 6 years ago

@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 commented 6 years ago

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

danielskatz commented 6 years ago

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

lkosmid commented 6 years ago

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

danielskatz commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

👋 @lkosmid - please let us know where you are

lkosmid commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

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

lkosmid commented 6 years ago

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

lkosmid commented 6 years ago

@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 commented 6 years ago

Thanks very much @lkosmid

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

federeghe commented 6 years ago

Zenodo DOI: 10.5281/zenodo.1404670

Thank you

danielskatz commented 6 years ago

@whedon set 10.5281/zenodo.1404670 as archive

whedon commented 6 years ago

OK. 10.5281/zenodo.1404670 is the archive.

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