editorialbot commented 1 year ago

Submitting author: !--author-handle-->@daniellerch@mstimberg<!--end-editor-- Reviewers: @YassineYousfi, @ragibson Archive: 10.5281/zenodo.10497963

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Markdown: [![status](https://joss.theoj.org/papers/64b31ee2cb62898ab84706db83642354/status.svg)](https://joss.theoj.org/papers/64b31ee2cb62898ab84706db83642354)

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

@YassineYousfi & @ragibson, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

Checklists

📝 Checklist for @ragibson

📝 Checklist for @YassineYousfi

editorialbot commented 1 year ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

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

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editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (437.7 files/s, 89553.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          19           1370            477           3942
Markdown                         8            192              0            497
TeX                              1             20              0            160
Bourne Shell                     4             27              1             47
YAML                             1              1              0             18
-------------------------------------------------------------------------------
SUM:                            33           1610            478           4664
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1052

editorialbot commented 1 year ago

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

OK DOIs

- 10.1109/TIFS.2018.2871749 is OK
- 10.1007/11552055_12 is OK
- 10.1186/1687-417X-2014-1 is OK
- 10.5281/zenodo.4655945 is OK
- 10.1145/3335203.3335738 is OK
- 10.1109/tdsc.2022.3154967 is OK
- 10.1109/icip.2014.7025854 is OK
- 10.1007/3-540-45496-9_2 is OK
- 10.1109/WIFS49906.2020.9360897 is OK

MISSING DOIs

- 10.29327/226091 may be a valid DOI for title: Aletheia

INVALID DOIs

- None

editorialbot commented 1 year ago

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

mstimberg commented 1 year ago

👋🏼 @daniellerch, @YassineYousfi, @ragibson, this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

at the top of a new comment in this thread.

There are additional guidelines in the first comment of this issue.

Please don't hesitate to ping me (@mstimberg) if you have any questions/concerns.

ragibson commented 1 year ago

Review checklist for @ragibson

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 https://github.com/daniellerch/aletheia?
[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 (@daniellerch) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[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?

ragibson commented 1 year ago

(Apologies for originally pinging the wrong Daniel in this comment)

Finally getting around to this.

Just a quick note on the list of authors -- it seems the primary author @daniellerch wrote the software package and both authors collaborated on a few of the detection techniques used by the package (e.g., https://dl.acm.org/doi/10.1145/3335203.3335738 and https://ieeexplore.ieee.org/document/9722958), so the authors list looks good to me.

There are a handful of other contributors on the GitHub repository, but they're all much more minor.

ragibson commented 1 year ago

A note on the data sharing point -- the paper basically contains no original data since the examples are generic and I was able to effectively run them with my own local images.

Ditto on reproducibility of the examples in the paper.

ragibson commented 1 year ago

I would note that I ran into a few opaque errors in the simulators, but they look like research-grade code sourced from other authors/institutions (hence the requirement to accept secondary licenses and download the code from https://github.com/daniellerch/aletheia-external-resources). In these cases, the issues are external to the authors' work.

@daniellerch That said, I would like to see the secondary repository explicitly linked in the paper and/or READMEs of the package rather than just in aletheialib/utils.py.

ragibson commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

mstimberg commented 12 months ago

@ragibson Many thanks for your review and comments so far. @YassineYousfi, did you have any chance to look at the software/paper yet?

YassineYousfi commented 12 months ago

@mstimberg not yet, but I will check it out and review it this weekend!

YassineYousfi commented 11 months ago

Review checklist for @YassineYousfi

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 https://github.com/daniellerch/aletheia?
[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 (@daniellerch) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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)?
[ ] 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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[ ] 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?

YassineYousfi commented 11 months ago

Some notes to improve the submission:

The target audience for the software is not clearly stated in the documentation. I am assuming this software is geared towards researchers and enthusiasts.
How were the machine learning models trained? Very little detail is provided in https://github.com/daniellerch/aletheia/blob/master/aletheia-models/README.md. Note that some open source steganalysis training scripts exist (https://github.com/DDELab/deepsteganalysis), but weren't cited. can they be used to contribute more or better models?
DDE implementations are commonly used by researchers and should be cited https://dde.binghamton.edu/download/

mstimberg commented 11 months ago

:wave: @daniellerch I've seen that you have addressed and closes all the issues directly opened against your GitHub repository. Would you say that all the issues raised by the reviewers in the comments above have been addressed from your side or are you still working on it (updating the paper, for example)?

daniellerch commented 11 months ago

Thanks for checking in @mstimberg. I'm currently making some requested updates to the documentation and paper. Will keep you posted on the progress.

daniellerch commented 11 months ago

@YassineYousfi, thank you for your feedback. I have updated the README to better define the target audience. In addition, I've added more details about the training of Aletheia's machine learning models; there's a comprehensive article on this topic. Regarding DDELab's software, while it isn't directly integrated into Aletheia due to license incompatibilities, it is utilized by Aletheia and is available in an external repository. You can find the citation and acknowledgments there. Please refer to the 'External resources' section in the README.

daniellerch commented 11 months ago

Hi @mstimberg, I've finished updating the software and the documentation, thanks to the reviewers' helpful comments. Appreciate your patience and guidance. All set for a final review now.

mstimberg commented 11 months ago

Great, thanks @daniellerch. @ragibson and @YassineYousfi: do the updates address all your concerns/suggestions?

ragibson commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

ragibson commented 11 months ago

Checking off a few more items from my checklist:

Functionality documentation: I think this is good -- it's a bit of a strange case because a lot of the underlying tools are work from other authors, so they're not directly documented.
Automated tests: These do not exist since the testing scripts are apparently not meant for general use, but I'm willing to accept the program's help text on run and documentation examples as roughly verifying "the functionality of the software".
References: I have not thoroughly checked, but I'm not sure if all the open-source steganography/steganalysis tools are cited. However, their licenses are printed out by Aletheia itself when each one is downloaded for the first time, so I think this is okay.

Otherwise,

Community guidelines: As far as I can tell, guidelines on contributing/reporting issues/etc. do not exist.
State of the field: The paper does mention that Aletheia "stands out as the sole steganalysis tool currently available that incorporates the latest detection techniques." Does it need to / should it explicitly mention other commonly-used similar packages?
I know @YassineYousfi had some other papers that he wanted to see potentially cited.

mstimberg commented 10 months ago

:wave: Hi everyone, and a Happy New Year :sparkles: ! I hope you are all doing well and had a good break (assuming you took one, of course).

@daniellerch could you give us an update with respect to the remaining issues in @ragibson's comment above? @YassineYousfi do the changes mentioned in @daniellerch's earlier comment address all your concerns?

daniellerch commented 10 months ago

Hello everyone, and Happy New Year.

The latest changes I've made include adding the community guidelines.

On another note, if @ragibson is happy to accept the help of the program and the examples in the documentation instead of automated tests, I think the only thing left is the issue of references to other steganalysis software. As far as I know, there are software that implements some specific techniques, but no complete tool aimed at a more general user that allows for a comprehensive steganalysis using machine learning.

Of the tools that implement different steganalysis techniques, almost all come from the Digital Data Embedding Laboratory (https://dde.binghamton.edu/download/). Some of these are used by Aletheia and are cited at the time of download. There is also information about this in the "External resources" section. Of course, if you believe that these should also be cited in another part of the documentation, or in the paper, please let me know.

So, I think I have nothing pending. Please inform me if otherwise.

YassineYousfi commented 10 months ago

thanks @daniellerch @mstimberg, the changes address all my concerns. I updated my checklist.

ragibson commented 10 months ago

Thanks @daniellerch @mstimberg @YassineYousfi! It looks good to me now too 👍

mstimberg commented 10 months ago

Thank you very much @YassineYousfi @daniellerch for getting back to me, and thanks for your reviews in the first place, obviously.

@daniellerch since both reviewers have recommended the paper for acceptance, I will now proceed with the final checks before the final publishing steps. Could you please take care of the author tasks in the checklist below :point_down:

mstimberg commented 10 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[ ] Double check authors and affiliations (including ORCIDs)
[ ] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[ ] Archive the release on Zenodo/figshare/etc and post the DOI here.
[ ] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[ ] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
[x] Check the references in the paper for corrections (e.g. capitalization)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

mstimberg commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

daniellerch commented 10 months ago

Additional Author Tasks After Review is Complete

[x] Double check authors and affiliations (including ORCIDs)
[x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper. RELEASE: https://github.com/daniellerch/aletheia/releases/tag/v0.3
[x] Archive the release on Zenodo/figshare/etc and post the DOI here. ALL VERSIONS DOI: 10.5281/zenodo.4655944 RELEASE DOI: 10.5281/zenodo.10497963
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

mstimberg commented 10 months ago

Hi again @daniellerch, in addition to the points mentioned in the author checklist above, please have a look at the PR I just opened (daniellerch/aletheia#33). I made a few minor edits (mostly related to the formatting of the references and missing DOIs). Please merge it if you agree with all changes :pray:

daniellerch commented 10 months ago

@mstimberg Just made the merge. Thanks for the contributions!

mstimberg commented 10 months ago

@editorialbot set v0.3 as version

editorialbot commented 10 months ago

Done! version is now v0.3

mstimberg commented 10 months ago

@editorialbot set 10.5281/zenodo.10497963 as archive

editorialbot commented 10 months ago

Done! archive is now 10.5281/zenodo.10497963

mstimberg commented 10 months ago

Thanks for the updates @daniellerch. Regarding the Zenodo archive for v0.3, could you add the second author as an author there as well? If I understand correctly, they did not commit code directly, but supervised the development? In general, we prefer to have the same list of authors for the JOSS paper and the Zenodo archive, but if you have a strong reason to not have them be the same, please let me know! Also, please:

add the ORCID(s) to the Zenodo archive
add the license to the Zenodo archive
use the full title of the article as the title on Zenodo

Note that you can make all these changes manually on Zenodo, without releasing a new version

I think you used the automatic GitHub-Zenodo integration – if you want to make future releases have the complete metadata automatically, you can use a .zenodo.json file: https://developers.zenodo.org/#harvesting-with-multiple-filters

daniellerch commented 10 months ago

@mstimberg The second author didn't directly contribute code, yet their involvement has been recognized, and they are now included in the Zenodo archive. I believe everything is now in order. Thank you!

mstimberg commented 10 months ago

@daniellerch Many thanks for the changes. From your changes on Zenodo, I just realized that the affiliations concern three separate institutions (even though I assume they are all co-located). Could you update the paper in that regard, i.e. list them as ¹²³ as in the Zenodo archive (stating "Barcelona, Spain" each time – assuming this is correct, of course)? Thanks!

daniellerch commented 10 months ago

@editorialbot generate pdf

daniellerch commented 10 months ago

@mstimberg Thank you for pointing this out. The changes have been made to the paper, listing the affiliations as ¹²³ and stating 'Barcelona, Spain' for each, as per your suggestion. Thanks again!

editorialbot commented 10 months ago

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

mstimberg commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago

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

OK DOIs

- 10.1109/TIFS.2018.2871749 is OK
- 10.1145/1288869.1288872 is OK
- 10.1109/TIFS.2014.2312817 is OK
- 10.1007/11552055_12 is OK
- 10.1186/1687-417X-2014-1 is OK
- 10.1145/2482513.2482965 is OK
- 10.1145/3335203.3335738 is OK
- 10.1109/tdsc.2022.3154967 is OK
- 10.1109/icip.2014.7025854 is OK
- 10.1007/3-540-45496-9_2 is OK
- 10.1109/WIFS49906.2020.9360897 is OK

MISSING DOIs

- None

INVALID DOIs

- None

mstimberg commented 10 months ago

@editorialbot recommend-accept

All looking good from my side, handing things over to the topic editor for the final steps. Thanks again to everyone involved!

editorialbot commented 10 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 10 months ago

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

OK DOIs

- 10.1109/TIFS.2018.2871749 is OK
- 10.1145/1288869.1288872 is OK
- 10.1109/TIFS.2014.2312817 is OK
- 10.1007/11552055_12 is OK
- 10.1186/1687-417X-2014-1 is OK
- 10.1145/2482513.2482965 is OK
- 10.1145/3335203.3335738 is OK
- 10.1109/tdsc.2022.3154967 is OK
- 10.1109/icip.2014.7025854 is OK
- 10.1007/3-540-45496-9_2 is OK
- 10.1109/WIFS49906.2020.9360897 is OK

MISSING DOIs

- None

INVALID DOIs

- None

openjournals / joss-reviews

[REVIEW]: Aletheia: an open-source toolbox for steganalysis #5982

Status

Reviewer instructions & questions

Checklists

Review checklist for @ragibson

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @YassineYousfi

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

Additional Author Tasks After Review is Complete