[REVIEW]: The MCAPL Framework including the Agent Infrastructure Layer and Agent JavaPathfinder

whedon commented 6 years ago

Submitting author: @louiseadennis (Louise Dennis) Repository: https://sourceforge.net/p/mcapl/mcapl_code/ci/master/tree/ Version: 2017 Editor: @danielskatz Reviewer: @BasTesterink, @fraimondi Archive: 10.5281/zenodo.1237635

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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 1 instructions & questions

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

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

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

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 (2017)?
[x] Authorship: Has the submitting author (@louiseadennis) 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)?

Reviewer 2 instructions & questions

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

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

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

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 (2017)?
[x] Authorship: Has the submitting author (@louiseadennis) 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. @BasTesterink 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:

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

watching

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

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

PDF failed to compile for issue #617 with the following error:

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danielskatz commented 6 years ago

@arfon - can you compile this paper again, as you did in https://github.com/openjournals/joss-reviews/issues/573

Can you also make sure both reviewers (Reviewer1: @BasTesterink; Reviewer2: @fraimondi) are invited and able to access the checklist?

danielskatz commented 6 years ago

I'm also just noting here that @fraimondi may need until April 20 to perform this review

arfon commented 6 years ago

@louiseadennis - I'm afraid I'm unable to download the code from the repository. The git clone operation keeps timing out. Also, browsing the files, I don't seem to be able to find the paper.md and paper.bib files. Could you please link to them here?

arfon commented 6 years ago

Can you also make sure both reviewers (Reviewer1: @BasTesterink; Reviewer2: @fraimondi) are invited and able to access the checklist?

Done.

louiseadennis commented 6 years ago

@arfon the paper.md and paper.bib files are in doc/joss_paper https://sourceforge.net/p/mcapl/mcapl_code/ci/master/tree/doc/joss_paper/paper.bib and https://sourceforge.net/p/mcapl/mcapl_code/ci/master/tree/doc/joss_paper/paper.md

I've no idea what is going on with sourceforge. I can't clone either, though I can fetch and push.

louiseadennis commented 6 years ago

@arfon as far as I can work out, cloning is failing because of a memory problem at the sourceforge end. I can't ssh into sourceforge at the moment to try the fixes suggested online (source forge says it has disable shell while it transitions to a new datacenter) and while there are some largish files in the repo (jars of libs etc.) I don't think I have loads of huge files that could be causing this. I'm a little stumped how to proceed here but will look into it further on Thursday when I have more time.

arfon commented 6 years ago

Thanks @louiseadennis - I've managed to compile the paper using the direct links you provided here: 10.21105.joss.00617.pdf

BasTesterink commented 6 years ago

I have very little to comment on this submission. Within minutes I was able to download and compile the framework on my Windows 10 machine with an Eclipse Oxygen installation. The examples that I tried (there are a lot of them) all ran without any errors on the first try. The code is well documented, clean and readable, both for the core Java code and the example agent-programming code. The manual contains extensive explanations of the kind of software this is and discusses the examples on the different application domains (those being the different agent programming languages that the framework supports).

I'm not sure what the expectations from JOSS are on community guidelines. There is no explicit guidelines sections in the readme for instance. I checked the review box because for me it seemed clear that any questions/suggestions should go to @loiseadennis or though the SF ticket system or mailing list.

In conclusion, I believe the contribution to be a valuable piece of software for agent-oriented programmers. The MCAPL project is one of the few up-to-date initiatives on agent program verification which gets more and more relevant now that AI & Ethics is attracting attention.

danielskatz commented 6 years ago

Thanks @BasTesterink

I'm not sure what the expectations from JOSS are on community guidelines. There is no explicit guidelines sections in the readme for instance. I checked the review box because for me it seemed clear that any questions/suggestions should go to @loiseadennis or though the SF ticket system or mailing list.

There should be an explicit guidelines section somewhere, likely in the README. It's useful for people new to open source to have some text that tells them how they can ask questions, or how they can make contributions (both in terms of mechanism and policy).

louiseadennis commented 6 years ago

Not 100% sure of the process here. But I've added a "Problems and Contributions" section to the README and pushed to the master branch.

danielskatz commented 6 years ago

For some reason, https://sourceforge.net/p/mcapl/mcapl_code/ci/master/tree/ isn't currently working

danielskatz commented 6 years ago

now it's back - not sure what happened...

louiseadennis commented 6 years ago

It was behaving strangely when @arfon was looking at it on Wednesday, throwing errors which implied a memory management problem at some level. I was going to look into it but then the problem went away so I assumed sourceforge had fixed it at their end.

danielskatz commented 6 years ago

Just adding a note that @fraimondi's review is expected the 20th of April - we'll be on hold until then.

fraimondi commented 6 years ago

I have done my review and I am happy with the repository, the documentation and the paper. The installation and examples all worked first time. In addition to Eclipse, I tried from the command line in Linux and Mac: no problem .

Very minor point (may be useful for bots?): the LICENSE file is called COPYING, is this OK?

danielskatz commented 6 years ago

The license file should be called LICENSE for consistency with general practices and user/developer expectations. @louiseadennis - can you fix this? Then we can move forward with acceptance.

danielskatz commented 6 years ago

and thanks @fraimondi !

danielskatz commented 6 years ago

👋 @louiseadennis - note this is waiting for a relatively small change from you.

louiseadennis commented 6 years ago

It's on the stack, we're just in the middle of project marking here. Should get to it this week or early next week at the very latest.

louiseadennis commented 6 years ago

Changed and pushed to the repository!

danielskatz commented 6 years ago

@fraimondi - I thought this was ready to be accepted, but my final look shows that there is one box left unchecked - yours on functionality.

Can you tell us what you think is needed?

fraimondi commented 6 years ago

Apologies, my mystake! The only thing that is needed is a new pair of glasses for the reviewer. I've now checked all the boxes, I think it is ready to be accepted. Thanks!

danielskatz commented 6 years ago

👋 @arfon - can we move this to acceptance now?

arfon commented 6 years ago

@louiseadennis - 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.

louiseadennis commented 6 years ago

I've added a new version to the existing Zenodo archive at https://doi.org/10.5281/zenodo.1237635

Is that sufficient or do I need to generate a new archive altogether?

arfon commented 6 years ago

Is that sufficient or do I need to generate a new archive altogether?

This should be good.

arfon commented 6 years ago

@whedon set 10.5281/zenodo.1237635 as archive

whedon commented 6 years ago

OK. 10.5281/zenodo.1237635 is the archive.

arfon commented 6 years ago

@BasTesterink, @fraimondi - many thanks for your reviews here and to @danielskatz for editing this submission ✨

@louiseadennis - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00617 ⚡️:rocket: :boom:

whedon commented 6 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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louiseadennis commented 6 years ago

I just noticed a typo in the title of the paper (an instead of and). I've fixed in the repository. Is there anyway this can be fixed online?

arfon commented 6 years ago

I just noticed a typo in the title of the paper (an instead of and). I've fixed in the repository. Is there anyway this can be fixed online?

I've just recompiled the paper so this should be fixed now.

louiseadennis commented 6 years ago

Thanks!

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