Joss-reviews: [REVIEW]: s4rdm3x: A Tool Suite to Explore Code to Architecture Mapping Techniques

[whedon]

Submitting author: @tobias-dv-lnu (Tobias Olsson)
Repository: https://github.com/tobias-dv-lnu/s4rdm3x
Version: 1.2
Editor: @gkthiruvathukal
Reviewer: @kinow, @xirdneh
Archive: Pending

:warning: JOSS reduced service mode :warning:

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.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/f4301adc3e9121a10354c355d91b5c1f"><img src="https://joss.theoj.org/papers/f4301adc3e9121a10354c355d91b5c1f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/f4301adc3e9121a10354c355d91b5c1f/status.svg)](https://joss.theoj.org/papers/f4301adc3e9121a10354c355d91b5c1f)

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

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

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

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @gkthiruvathukal know.

✨ 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 @kinow

Conflict of interest

• [x] 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

• [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] Contribution and authorship: Has the submitting author (@tobias-dv-lnu) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] 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

• [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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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 @xirdneh

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 (@tobias-dv-lnu) 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: Do the authors clearly state 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. @kinow, @xirdneh it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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.

: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:

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

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

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

PDF failed to compile for issue #2791 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - 241d63aa7177374e42894fdd (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:incollect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/processor.rb:66:infind_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/bin/whedon:53:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/bin/whedon:131:in from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

[kinow]

@gkthiruvathukal hi, do you have karma to re-generate the article? I think the bot failed to do so, and I think I need it to complete the review checklist items for the paper. Please.

Thank you!

[arfon]

@whedon generate pdf

[whedon]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[kinow]

Thanks!

[gkthiruvathukal]

@gkthiruvathukal Sorry I didn't get to your request as fast as @arfon, @kinow. Looks like we're good now.

[whedon]

:wave: @kinow, please update us on how your review is going.

[whedon]

:wave: @xirdneh, please update us on how your review is going.

[kinow]

My review is complete @gkthiruvathukal :heavy_check_mark:

Even managed to test s4rdm3x with Apache Commons Imaging. I was going to use Apache Commons Lang, but I am currently working on Imaging. I didn't add all the relationships between packages, and the tool correctly highlighted the failed clusterings.

Didn't get fully familiar with the rest of the interface and metrics, but looks really useful for developers inspecting code bases, and getting familiar with new architectures.

I used IntelliJ's diagram builder to remind me of some of the relationships, but in the past I used Stan4J that would be a good tool to help users to create sysmdl files.

commons-imaging.sysmdl

name

Apache Commons Imaging

jar

commons-imaging-1.0-alpha2.jar

root-packages

org/apache/commons/imaging/

metrics file

commons-imaging-file-metrics.csv

modules

base
color
common
bmp
dcx
gif
icns
ico
jpeg
pcx
png
pnm
psd
rgbe
tiff
wbmp
xbm
xpm
icc
internal
palette

mapping

base org.apache.commons.imaging.color.[^.]*
color org.apache.commons.imaging.color.*
common org.apache.commons.imaging.common.*
bmp org.apache.commons.imaging.formats.bmp.*
dcx org.apache.commons.imaging.formats.dcx.*
gif org.apache.commons.imaging.formats.gif.*
icns org.apache.commons.imaging.formats.icns.*
ico org.apache.commons.imaging.formats.ico.*
jpeg org.apache.commons.imaging.formats.jpeg.*
pcx org.apache.commons.imaging.formats.pcx.*
png org.apache.commons.imaging.formats.png.*
pnm org.apache.commons.imaging.formats.pnm.*
psd org.apache.commons.imaging.formats.psd.*
rgbe org.apache.commons.imaging.formats.rgbe.*
tiff org.apache.commons.imaging.formats.tiff.*
wbmp org.apache.commons.imaging.formats.wbmp.*
xbm org.apache.commons.imaging.formats.xbm.*
xpm org.apache.commons.imaging.formats.xpm.*
icc org.apache.commons.imaging.formats.icc.*
internal org.apache.commons.imaging.formats.internal.*
palette org.apache.commons.imaging.formats.palette.*

relations

base icc
base common
common base
common internal
icc common
jpeg common
palette base
palette internal
color internal

Thank you for your patience and help with the issues found during the review @tobias-dv-lnu!

[tobias-dv-lnu]

Awesome! @kinow: Do you consider the sysmdl for commons imaging to be "correct"? If so would can I include it in the repo as an available system (always on the lookout for more data :) )

And thank you for the feedback and found problems!

[kinow]

Awesome! @kinow: Do you consider the sysmdl for commons imaging to be "correct"? If so would can I include it in the repo as an available system (always on the lookout for more data :) )

Not yet, but I will open a draft pull request. We can discuss how to improve it. I didn't understand how to use all the options and settings, and for the experiment.xml I simply used the same one from JebRef modifying the system loaded.

I've created a draft PR: https://github.com/tobias-dv-lnu/s4rdm3x/pull/14

[xirdneh]

Having some trouble testing a couple of things on the paper. I think it has to do with my local setup, I am currently tweaking some thing and will try to finish this over the weekend.
Sorry for the delay.

[tobias-dv-lnu]

@xirdneh: just let me know if I can help :)