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

whedon commented 3 years ago

Submitting author: @tobias-dv-lnu (Tobias Olsson) Repository: https://github.com/tobias-dv-lnu/s4rdm3x Version: v1.3 Editor: @gkthiruvathukal Reviewer: @kinow, @xirdneh Archive: 10.5281/zenodo.4475664

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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) 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:

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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?
[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 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

[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?
[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 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?

whedon commented 3 years ago

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.

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whedon commented 3 years ago

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

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kinow commented 3 years ago

@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 commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

kinow commented 3 years ago

Thanks!

gkthiruvathukal commented 3 years ago

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

whedon commented 3 years ago

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

whedon commented 3 years ago

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

kinow commented 3 years ago

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!

h0bb3 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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.

h0bb3 commented 3 years ago

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

gkthiruvathukal commented 3 years ago

@xirdneh Just checking on how things are coming along with your review. I'm definitely not trying to rush you but would like to see if we are getting closer.

@kinow Am I correct in interpreting your review as being complete and ready to recommend acceptance, or are their still issues requiring attention?

kinow commented 3 years ago

All good @gkthiruvathukal , review complete, article looking good, software built and tested locally. No other issues pending for me. Thanks!

xirdneh commented 3 years ago

@gkthiruvathukal I was able to test the code locally. Everything seems good. I am not able to edit the checklist. Should I just be able to edit the issue description?

arfon commented 3 years ago

@whedon re-invite @xirdneh as reviewer

whedon commented 3 years ago

The reviewer already has a pending invite.

@xirdneh please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

arfon commented 3 years ago

@xirdneh - please accept the repository invite above, this should then allow you to edit the checklist.

h0bb3 commented 3 years ago

@xirdneh please let me know if there is anything I can do to help you with the review :)

gkthiruvathukal commented 3 years ago

Thanks for the nudge on this @tobias-dv-lnu.

@xirdneh Can you let us know your timeframe for completing your review? It looks like @kinow has done a fairly thorough review. I would like to move forward with acceptance as soon as we have your input. Thanks!

xirdneh commented 3 years ago

Hi, sorry about this.

I will finish the review by tomorrow afternoon.

I already have everything written down just needed the invitation.

xirdneh commented 3 years ago

@whedon re-invite @xirdneh as reviewer

whedon commented 3 years ago

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

xirdneh commented 3 years ago

@gkthiruvathukal Sorry, could you send the invitation again? Seems like I didn't click it last time, I thought i did.

gkthiruvathukal commented 3 years ago

@whedon re-invite @xirdneh as reviewer

whedon commented 3 years ago

OK, the reviewer has been re-invited.

@xirdneh please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

gkthiruvathukal commented 3 years ago

@xirdneh I hope that works!

h0bb3 commented 3 years ago

@xirdneh Thanks, it seems to have worked! :)

@gkthiruvathukal What are the next steps for this? According to the instructions as I understand them:

"Upon successful completion of the review, authors will make a tagged release of the software, and deposit a copy of the repository with a data-archiving service such as Zenodo or figshare, get a DOI for the archive, and update the review issue thread with the version number and DOI. "

or is there something else you want me to do?

gkthiruvathukal commented 3 years ago

@tobias-dv-lnu We are close! I will follow up with a final checklist as soon as I get a response to the following.

@xirdneh Can you please confirm for us that you have no further issues to raise regarding this submission? I would like to move toward acceptance and give final instructions.

xirdneh commented 3 years ago

@gkthiruvathukal Yes, the submission is complete.

gkthiruvathukal commented 3 years ago

Thanks, @xirdneh

@tobias-dv-lnu Ok, I am ready now! Please do the following:

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo
[ ] Check the Zenodo deposit has the correct metadata, this includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it); you may also add the authors' ORCID.
[ ] List the Zenodo DOI of the archived version here.

h0bb3 commented 3 years ago

Thanks!

@gkthiruvathukal Think I'm all done :)

[x] Make a tagged release of your software, and list the version tag of the archived version here. release version tag: v1.3_archive URL: https://github.com/tobias-dv-lnu/s4rdm3x/tree/v1.3_archive
[x] Archive the reviewed software in Zenodo
[x] Check the Zenodo deposit has the correct metadata, this includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it); you may also add the authors' ORCID.
[x] List the Zenodo DOI of the archived version here. DOI: 10.5281/zenodo.4475664 URL: https://zenodo.org/record/4475664#.YBKnmjpKguU

kyleniemeyer commented 3 years ago

Thanks @tobias-dv-lnu @gkthiruvathukal, it looks like this is ready for acceptance so I can take it from here.

kyleniemeyer commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

kyleniemeyer commented 3 years ago

@whedon set 10.5281/zenodo.4475664 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4475664 is the archive.

kyleniemeyer commented 3 years ago

@whedon set v1.3 as version

whedon commented 3 years ago

OK. v1.3 is the version.

kyleniemeyer commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2077

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2077, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

whedon commented 3 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1145/3241403.3241456 is OK

MISSING DOIs

- 10.1016/j.infsof.2006.10.015 may be a valid DOI for title: Automated clustering to support the reflexion method
- 10.1109/wcre.2010.26 may be a valid DOI for title: Improving automated mapping in reflexion models using information retrieval techniques
- 10.1145/3344948.3344984 may be a valid DOI for title: Semi-automatic mapping of source code using naive Bayes
- 10.1145/3344948.3344997 may be a valid DOI for title: An exploration and experiment tool suite for code to architecture mapping techniques
- 10.1007/s11219-018-9404-z may be a valid DOI for title: Exploring the suitability of source code metrics for indicating architectural inconsistencies
- 10.1109/wcre.2012.35 may be a valid DOI for title: On the evolutionary nature of architectural violations

INVALID DOIs

- None

kyleniemeyer commented 3 years ago

@tobias-dv-lnu, it looks like DOIs may be available but missing for a number of your references. Can you please check these, and add if appropriate? I will then be able to accept the submission. Thanks!

gkthiruvathukal commented 3 years ago

Thanks, @kyleniemeyer for helping to bring this to closure! :)

h0bb3 commented 3 years ago

@kyleniemeyer Thanks! Just added the missing DOIs in the paper.bib file (whedon had made the correct guesses on the DOIs), everything should be ok now I hope :)

arfon commented 3 years ago

@whedon check references

whedon commented 3 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.infsof.2006.10.015 is OK
- 10.1109/WCRE.2010.26 is OK
- 10.1145/3344948.3344984 is OK
- 10.1145/3344948.3344997 is OK
- 10.1145/3241403.3241456 is OK
- 10.1007/s11219-018-9404-z is OK
- 10.1109/wcre.2012.35 is OK

MISSING DOIs

- None

INVALID DOIs

- None

openjournals / joss-reviews