[REVIEW]: NiaARM: A minimalistic framework for Numerical Association Rule Mining

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@zStupan@fabian-s<!--end-editor-- Reviewers: @diegomcarvalho, @fabian-s Archive: 10.5281/zenodo.7123879

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/c463434452b371917a2a169dbddecf32/status.svg)](https://joss.theoj.org/papers/c463434452b371917a2a169dbddecf32)

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

@diegomcarvalho & @timClicks, 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 @fabian-s 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 @diegomcarvalho

📝 Checklist for @timClicks

📝 Checklist for @fabian-s

editorialbot commented 2 years 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:

@editorialbot commands

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 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (1009.3 files/s, 69095.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          23            431            402           1265
Markdown                        11            220              0            523
reStructuredText                18            208            278            340
TeX                              2             15              0            219
SVG                              1              0              1             65
YAML                             2              7              0             60
JSON                             1              0              0             47
TOML                             1              6              0             34
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            61            899            689           2588
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

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

OK DOIs

- 10.1007/978-3-030-03493-1_9 is OK
- 10.1007/978-3-030-68154-8_19 is OK
- 10.48550/ARXIV.2010.15524 is OK
- 10.21105/joss.00613 is OK
- 10.1109/69.846291 is OK
- 10.1016/j.ins.2020.02.073 is OK
- 10.1007/978-3-030-62362-3_10 is OK
- 10.1007/s12652-019-01540-7 is OK
- 10.1007/978-981-33-4370-2_1 is OK
- 10.1007/s42979-021-00725-2 is OK
- 10.1016/j.asoc.2007.05.003 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

Wordcount for paper.md is 577

editorialbot commented 2 years ago

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

fabian-s commented 2 years ago

👋🏼 @zStupan @diegomcarvalho, @timClicks 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

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#REVIEW_NUMBER so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@fabian-s) if you have any questions/concerns.

diegomcarvalho commented 2 years ago

Review checklist for @diegomcarvalho

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/firefly-cpp/NiaARM?
[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 (@zStupan) 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

[ ] 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: 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?
[ ] 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?

fabian-s commented 2 years ago

@timClicks how much more time do you think you'll need for your review?

fabian-s commented 2 years ago

@zStupan to speed up this process, you could begin to adress some of the issues identified by @diegomcarvalho while we wait for @timClicks to review the paper.

If you have questions or comments about specific points of the review or what would be required to adress them, please create separate GH issues for them in your repository and link to them here so we can have focussed discussions about them there and not in one sprawling thread.

zStupan commented 2 years ago

@fabian-s I believe there are no issues to address. Everything on the checklist is present in the repository.

arfon commented 2 years ago

:wave: @fabian-s – it looks like the reviews might have stalled here?

fabian-s commented 2 years ago

@arfon yes, sorry, seems so. I lost track of this over the summer.

@zStupan very sorry for the delay. I tend to agree that the open points left in @diegomcarvalho checklist all seem to be present in the repo.

@diegomcarvalho please confirm that the items missing in your checklist are satisfied in the repo or open issues/provide some additional feedback on the specific points that you feel need additional work by the submitting authors

@timClicks are you still willing to do a review for JOSS for this work?

diegomcarvalho commented 2 years ago

Hi @fabian-s, all items are satisfied by the collection provided in the repository.

Cheers, d.c

fabian-s commented 2 years ago

@timClicks are you still willing to do this review for JOSS?

timClicks commented 2 years ago

Yes I am! Sorry for the lack of contact. Please give me 24h.

fabian-s commented 2 years ago

Yes I am! Sorry for the lack of contact. Please give me 24h.

@timClicks seems like 24h might have been too ambitious ... :smirk: Could you let us know what a realistic time frame for getting this done is, please?

fabian-s commented 2 years ago

@timClicks please respond

fabian-s commented 2 years ago

@editorialbot add @fabian-s as reviewer

editorialbot commented 2 years ago

@fabian-s added to the reviewers list!

fabian-s commented 2 years ago

Review checklist for @fabian-s

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/firefly-cpp/NiaARM?
[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 (@zStupan) 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?

fabian-s commented 2 years ago

@editorialbot commands

editorialbot commented 2 years ago

Hello @fabian-s, here are the things you can ask me to do:


# List all available commands
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@editorialbot add @username as reviewer

# Remove from this issue's reviewers list
@editorialbot remove @username from reviewers

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Assign a user as the editor of this submission
@editorialbot assign @username as editor

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@editorialbot remove editor

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# certain period of time (supported units days and weeks)
@editorialbot remind @reviewer in 2 weeks

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for version
@editorialbot set v1.0.0 as version

# Set a value for archive
@editorialbot set 10.21105/zenodo.12345 as archive

# Set a value for branch
@editorialbot set joss-paper as branch

# Set a value for repository
@editorialbot set https://github.com/organization/repo as repository

# Generates the pdf paper
@editorialbot generate pdf

# Recommends the submission for acceptance
@editorialbot recommend-accept

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Flag submission with questionable scope
@editorialbot query scope

# Get a link to the complete list of reviewers
@editorialbot list reviewers

# Open the review issue
@editorialbot start review

fabian-s commented 2 years ago

@editorialbot remove @timClicks from reviewers

editorialbot commented 2 years ago

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

@editorialbot commands

timClicks commented 2 years ago

Sorry once more for being unable to complete this task in a timely manner 😞 .

fabian-s commented 2 years ago

hi @zStupan, i'm filling in as the 2nd reviewer here, sorry again for the delays.

Almost everything seems fine, but please see firefly-cpp/NiaARM#66 for one small request to add a more explicit comparison to other packages to your statement of need section.

I also had to run import nltk; nltk.download('stopwords'); nltk.download('punkt') to get the textmining example to run, but I admittedly did not use poetry install as your docs recommend so maybe that was my own fault....

fabian-s commented 2 years ago

@editorialbot generate pdf

fabian-s commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

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

OK DOIs

- 10.1007/978-3-030-03493-1_9 is OK
- 10.1007/978-3-030-68154-8_19 is OK
- 10.48550/ARXIV.2010.15524 is OK
- 10.21105/joss.00613 is OK
- 10.1109/69.846291 is OK
- 10.1016/j.ins.2020.02.073 is OK
- 10.1007/978-3-030-62362-3_10 is OK
- 10.1007/s12652-019-01540-7 is OK
- 10.1007/978-981-33-4370-2_1 is OK
- 10.1007/s42979-021-00725-2 is OK
- 10.1016/j.asoc.2007.05.003 is OK
- 10.48550/arXiv.2010.10884 is OK

MISSING DOIs

- 10.1007/s00500-008-0323-y may be a valid DOI for title: KEEL: a software tool to assess evolutionary algorithms for data mining problems

INVALID DOIs

- None

fabian-s commented 2 years ago

@zStupan seems like we're finally almost there -- please add the missing DOI (see above) and then:

[x] Make a tagged release of your software, and list the version tag of the archived version here.
[x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[x] Check that your archival deposit (e.g., in Zenodo) 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] Please list the DOI of the archived version here.

I can then move forward with recommending acceptance of the submission.

zStupan commented 2 years ago

@fabian-s the version tag is 0.2.1 and the DOI is 10.5281/zenodo.7123879

fabian-s commented 2 years ago

@editorialbot check references

fabian-s commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

OK DOIs

- 10.1007/978-3-030-03493-1_9 is OK
- 10.1007/978-3-030-68154-8_19 is OK
- 10.48550/ARXIV.2010.15524 is OK
- 10.21105/joss.00613 is OK
- 10.1109/69.846291 is OK
- 10.1016/j.ins.2020.02.073 is OK
- 10.1007/978-3-030-62362-3_10 is OK
- 10.1007/s12652-019-01540-7 is OK
- 10.1007/978-981-33-4370-2_1 is OK
- 10.1007/s42979-021-00725-2 is OK
- 10.1016/j.asoc.2007.05.003 is OK
- 10.48550/arXiv.2010.10884 is OK
- 10.1007/s00500-008-0323-y is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

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

fabian-s commented 2 years ago

@editorialbot set 10.5281/zenodo.7123879 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.7123879

fabian-s commented 2 years ago

@editorialbot set 0.2.1 as version

editorialbot commented 2 years ago

Done! version is now 0.2.1

fabian-s commented 2 years ago

@editorialbot recommend-accept

(timClicks is still listed as a reviewer of this paper and could be removed, not sure if it matters)

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.1007/978-3-030-03493-1_9 is OK
- 10.1007/978-3-030-68154-8_19 is OK
- 10.48550/ARXIV.2010.15524 is OK
- 10.21105/joss.00613 is OK
- 10.1109/69.846291 is OK
- 10.1016/j.ins.2020.02.073 is OK
- 10.1007/978-3-030-62362-3_10 is OK
- 10.1007/s12652-019-01540-7 is OK
- 10.1007/978-981-33-4370-2_1 is OK
- 10.1007/s42979-021-00725-2 is OK
- 10.1016/j.asoc.2007.05.003 is OK
- 10.48550/arXiv.2010.10884 is OK
- 10.1007/s00500-008-0323-y is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3562, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

fabian-s commented 2 years ago

small issue:

(timClicks is still listed as a reviewer of this paper and could be removed, not sure if it matters)

arfon commented 2 years ago

Acknowledging that @fabian-s provided the second review here.

@zStupan – could you please merge this PR which removes the AAS-related stuff which doesn't apply here.

arfon commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.1007/978-3-030-03493-1_9 is OK
- 10.1007/978-3-030-68154-8_19 is OK
- 10.48550/ARXIV.2010.15524 is OK
- 10.21105/joss.00613 is OK
- 10.1109/69.846291 is OK
- 10.1016/j.ins.2020.02.073 is OK
- 10.1007/978-3-030-62362-3_10 is OK
- 10.1007/s12652-019-01540-7 is OK
- 10.1007/978-981-33-4370-2_1 is OK
- 10.1007/s42979-021-00725-2 is OK
- 10.1016/j.asoc.2007.05.003 is OK
- 10.48550/arXiv.2010.10884 is OK
- 10.1007/s00500-008-0323-y is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3568, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

openjournals / joss-reviews