editorialbot commented 1 year ago

Submitting author: !--author-handle-->@OlivierBinette@osorensen<!--end-editor-- Reviewers: @Nikoletos-K, @ThomasHepworth Archive: 10.5281/zenodo.10086102

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/0d710193708360ea37298211961a4ab9/status.svg)](https://joss.theoj.org/papers/0d710193708360ea37298211961a4ab9)

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

@Nikoletos-K & @ThomasHepworth, 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 @osorensen 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 @Nikoletos-K

📝 Checklist for @ThomasHepworth

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=0.13 s (2254.5 files/s, 273575.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          34           1335           2363           2545
reStructuredText               231            622            572            691
Jupyter Notebook                 8              0          25647            379
Markdown                         3             53              0            146
make                             2             26              6             80
TeX                              1              7              0             79
YAML                             4             12             20             61
DOS Batch                        1              8              1             27
INI                              1              3              3             14
CSS                              1              0              1              4
-------------------------------------------------------------------------------
SUM:                           286           2066          28613           4026
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 596

editorialbot commented 1 year ago

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

OK DOIs

- 10.1126/sciadv.abi8021 is OK
- 10.14778/3137628.3137642 is OK
- 10.1145/3418896 is OK

MISSING DOIs

- 10.1080/00031305.2023.2191664 may be a valid DOI for title: Estimating the Performance of Entity Resolution Algorithms: Lessons Learned Through PatentsView.org

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:

osorensen commented 1 year ago

@editorialbot add @sonalgoyal as reviewer

editorialbot commented 1 year ago

@sonalgoyal added to the reviewers list!

Nikoletos-K commented 1 year ago

Review checklist for @Nikoletos-K

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/Valires/er-evaluation?
[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 (@OlivierBinette) 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?

Nikoletos-K commented 1 year ago

I have completed my review. ✅

I would like to make some comments/suggestions for @OlivierBinette:

Automated tests: You do have a test, but I believe that more tests and greater code coverage would be preferable. For automation, look at codecov and GitHub actions.
Example usage: I see notebooks with experiments using datasets like PatentsView, however it would be wonderful to have your software test some ER frameworks, in a notebook for example. pyJedAI would be ideal for this!✌️

OlivierBinette commented 1 year ago

@Nikoletos-K thank you for your comments. I agree with both points: deeper testing (beyond the current doctests) and more examples of evaluation of ER frameworks would be beneficial. I'll add this to my TODO list for the revision.

osorensen commented 1 year ago

Thanks for completing your review so quickly, @Nikoletos-K.

@OlivierBinette, you are welcome to start addressing the points raised by @Nikoletos-K already now, even though the other reviewers have not completed theirs yet. If you do, please report back here when the points have been addressed.

osorensen commented 1 year ago

@editorialbot remins reviewers in 2 weeks

editorialbot commented 1 year ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

osorensen commented 1 year ago

@editorialbot remind reviewers in 2 weeks

editorialbot commented 1 year ago

reviewers doesn't seem to be a reviewer or author for this submission.

osorensen commented 1 year ago

@editorialbot remind @ThomasHepworth in 2 weeks

editorialbot commented 1 year ago

Reminder set for @ThomasHepworth in 2 weeks

osorensen commented 1 year ago

@editorialbot remind @sonalgoyal in 2 weeks

editorialbot commented 1 year ago

Reminder set for @sonalgoyal in 2 weeks

ThomasHepworth commented 1 year ago

Review checklist for @ThomasHepworth

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/Valires/er-evaluation?
[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 (@OlivierBinette) 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?

ThomasHepworth commented 1 year ago

Heya and apologies for the delays. See above for my completed review.

I've run through all of the documentation and tried out the package on some synthetic data that we (the Ministry of Justice) have created. Everything works as expected and it produces some interesting insights.

My wider team are also all aware of the package and we're excited to dig into it and see how we can go about making use of it internally.

Some minor comments for @OlivierBinette:

I'd just like to echo Nikoletos's points, particularly around testing - https://github.com/openjournals/joss-reviews/issues/5619#issuecomment-1643791160.
I'd also like to add that it might make sense to lint some of the codebase and docs. Some of your code examples can run off the page in places. I'd recommend a combination of ruff and black.
You may want to clean up your root folder and hide some of the non-necessary files floating around.

I'll also leave a very minor comment about a link issue I found in the docs within the repo itself.

Thanks again! Tom

osorensen commented 1 year ago

Thanks a lot for completing your review, @ThomasHepworth!

editorialbot commented 1 year ago

:wave: @ThomasHepworth, please update us on how your review is going (this is an automated reminder).

editorialbot commented 1 year ago

:wave: @sonalgoyal, please update us on how your review is going (this is an automated reminder).

osorensen commented 1 year ago

@OlivierBinette, have you addressed the issues pointed out by @Nikoletos-K in the review above? If so, please let us know, so @Nikoletos-K can look at the changes and update his checklist.

OlivierBinette commented 1 year ago

@osorensen, I have not addressed the issues yet. I will be able to do so in October.

osorensen commented 1 year ago

Thanks @OlivierBinette. That's absolutely fine.

OlivierBinette commented 10 months ago

Hi @osorensen, I have addressed the reviewers comments. Specifically:

I have doctests for nearly all functions, and pytest doctests are incorporated in a Github Actions testing workflow.
I have added pytest unit tests to cover a broader range of behavior in foundational elements of the package, namely for data structures, error metrics, and data loading used throughout. Pytest of the distribution version is in my Github Actions workflow.
I formated code using Black (line-length=120), and linted with ruff.
I cleaned up many files and streamlined the package.
I made minor improvements to the documentation throughout.

I am planning to add more examples, tutorials, and tests as I finish the full methodology paper, but I think these changes might already satisfy the reviewer comments.

osorensen commented 10 months ago

Thanks @OlivierBinette!

@Nikoletos-K, you have one unchecked item in your review checklist. Could you please consider if the latest changes made by @OlivierBinette satisfies this?

osorensen commented 10 months ago

@Nikoletos-K, a gentle reminder about your JOSS review. Could you please check if the latest changes satisfy the last unranked item in your review checklist?

Nikoletos-K commented 10 months ago

Hi, yes I'll proceed to re-evaluation and I'll inform you by the end of the week. Is that ok?

osorensen commented 10 months ago

Thanks @Nikoletos-K, that would be fantastic!

Nikoletos-K commented 10 months ago

All done! Nice work @OlivierBinette!

osorensen commented 10 months ago

@editorialbot generate pdf

osorensen 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

- 10.1126/sciadv.abi8021 is OK
- 10.14778/3137628.3137642 is OK
- 10.1145/3418896 is OK

MISSING DOIs

- 10.1080/00031305.2023.2191664 may be a valid DOI for title: Estimating the Performance of Entity Resolution Algorithms: Lessons Learned Through PatentsView.org

INVALID DOIs

- None

osorensen commented 10 months ago

Thank you very much for your reviews @Nikoletos-K and @ThomasHepworth.

@OlivierBinette, I'll now read through the paper and let you know if there are some further issues.

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:

osorensen 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

- 10.1126/sciadv.abi8021 is OK
- 10.1080/00031305.2023.2191664 is OK
- 10.48550/arXiv.2301.03591 is OK
- 10.24963/ijcai.2022/552 is OK
- 10.14778/3137628.3137642 is OK
- 10.1145/3418896 is OK

MISSING DOIs

- None

INVALID DOIs

- None

osorensen commented 10 months ago

@editorialbot generate pdf

osorensen 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

osorensen commented 10 months ago

@OlivierBinette, can you please complete the author items in the checklist above, and report here when done?

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:

OlivierBinette commented 10 months ago

@osorensen I completed the author items in the checklist and made final edits to the paper (fixed formatting issues).

Released version with latest changes is version 2.2.1. DOI is 10.5281/zenodo.10086103.

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. VERSION 2.2.1
[x] Archive the release on Zenodo/figshare/etc and post the DOI here. DOI 10.5281/zenodo.10086103
[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.

osorensen commented 10 months ago

Thanks @OlivierBinette. Can you please change the title of the Zenodo archive so it matches the JOSS Paper?

OlivierBinette commented 10 months ago

@osorensen Done! Thank you: https://zenodo.org/records/10086103

osorensen commented 10 months ago

@editorialbot set 10.5281/zenodo.10086102 as archive

editorialbot commented 10 months ago

Done! archive is now 10.5281/zenodo.10086102

osorensen commented 10 months ago

@editorialbot set Version 2.2.1 as version

openjournals / joss-reviews

[REVIEW]: ER-Evaluation: End-to-End Evaluation of Entity Resolution Systems #5619

Status

Reviewer instructions & questions

Checklists

Review checklist for @Nikoletos-K

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @ThomasHepworth

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