[REVIEW]: py2lispIDyOM: A Python package for IDyOM

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@xinyiguan@faroit<!--end-editor-- Reviewers: @AoifeHughes, @hayesall Archive: 10.5281/zenodo.7272236

Status

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Markdown: [![status](https://joss.theoj.org/papers/3f2e7b31cf9ee2f96ba631ff2617f8c5/status.svg)](https://joss.theoj.org/papers/3f2e7b31cf9ee2f96ba631ff2617f8c5)

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

@AoifeHughes & @hayesall, 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 @faroit 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 @hayesall

📝 Checklist for @AoifeHughes

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=0.09 s (955.6 files/s, 79729.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          11            461            333           1622
XML                              9              0              0            830
diff                             3              8             66            321
reStructuredText                46            298            255            257
Markdown                         3             70              0            164
YAML                             5             17             11            148
Jupyter Notebook                 4              0           2030            126
TeX                              1             10              0            103
make                             1              6              9             16
Lisp                             3              0              0             14
-------------------------------------------------------------------------------
SUM:                            86            870           2704           3601
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 1014

editorialbot commented 2 years ago

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

OK DOIs

- None

MISSING DOIs

- 10.1525/mp.2006.23.5.377 may be a valid DOI for title: Expectation in melody: The influence of context and learning
- 10.1525/mp.2005.22.4.663 may be a valid DOI for title: A model of melodic expectation
- 10.1016/j.cognition.2018.12.015 may be a valid DOI for title: Statistical learning and Gestalt-like principles predict melodic expectations
- 10.1016/j.cognition.2005.11.007 may be a valid DOI for title: Are we “experienced listeners”? A review of the musical capacities that do not depend on formal musical training
- 10.1177/102986490901300203 may be a valid DOI for title: Expectancy in Sami Yoiks revisited: The role of data-driven and schema-driven knowledge in the formation of melodic expectations
- 10.1016/j.concog.2010.07.004 may be a valid DOI for title: Incidental and online learning of melodic structure
- 10.1111/j.1756-8765.2012.01214.x may be a valid DOI for title: Auditory expectation: the information dynamics of music perception and cognition
- 10.1016/j.jecp.2020.105020 may be a valid DOI for title: Melodic expectations in 5-and 6-year-old children
- 10.1111/nyas.13654 may be a valid DOI for title: Statistical learning and probabilistic prediction in music cognition: mechanisms of stylistic enculturation

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:

faroit commented 2 years ago

👋🏼 @xinyiguan @AoifeHughes @hayesall 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 https://github.com/openjournals/joss-reviews/issues/4738 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 (@faroit) if you have any questions/concerns.

hayesall commented 2 years ago

Review checklist for @hayesall

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/xinyiguan/py2lispIDyOM?
[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 (@xinyiguan) 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?

AoifeHughes commented 2 years ago

Review checklist for @AoifeHughes

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/xinyiguan/py2lispIDyOM?
[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 (@xinyiguan) 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?

AoifeHughes commented 1 year ago

Hi, I would be happy to sign off on the publication of this project with one minor issue:

[x] Contribution guidelines

I think adding these are a requirement (ref reviewer checklist), and I think a small note on the README.md would facilitate this.

Once this point is addressed, I would support the publication.

xinyiguan commented 1 year ago

Hi @AoifeHughes 👋🏼

Thank you so much for your feedback. I just updated the how to contribute section on the documentation page and added a small note section of "contribution guideline" on the README.md.

AoifeHughes commented 1 year ago

Fantastic, thanks @xinyiguan for the quick response.

@faroit I can sign off on this now :)

hayesall commented 1 year ago

Thank you for your patience. I've opened some issues/PRs with recommendations.

I'd definitely like to see these points addressed:

If the first two items are more difficult than I expect, I will re-evaluate.

These points should probably be addressed, but I do not consider any of them to be blocking acceptance.

faroit commented 1 year ago

@hayesall thanks for your excellent review!

xinyiguan commented 1 year ago

Hi @hayesall 👋🏼,

Thank you so much for your valuable suggestions and recommendations to improve the package! I have made the corresponding adjustments and changes mentioned above and responded in the respective Issue post.

hayesall commented 1 year ago

Happy to help!

@faroit My review checklist is now complete. As mentioned in the respective issues: there are a few points that can be clarified/improved still, but this meets the core requirements.

xinyiguan commented 1 year ago

👋🏼 Hi, also updating in here. I have clarified and resolved all of the issues and points now :)

faroit 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:

faroit commented 1 year ago

The submission looks good now and we can move forward 👏 I just did check the paper again for grammar and spellings and created a tiny pull request that you can merge in if you like.

@xinyiguan when the paper is ready, please then please make a new release of the main repo that includes all of the changes that have resulted from the review. Please report the version number here.

Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive. For the archive version, please make sure that:

The title of the archive is the same as the JOSS paper title
The authors of the archive are the same as the JOSS paper authors

xinyiguan commented 1 year ago

Hi @faroit 👋🏼,

Thanks for the updates and the grammar check! I just merge the PR and made the new release.

The new release version is: v.1.0.2. The DOI of the Zenodo archive of the new release version is: 10.5281/zenodo.7272236

faroit commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1525/mp.2006.23.5.377 is OK
- 10.1525/mp.2005.22.4.663 is OK
- 10.1016/j.cognition.2018.12.015 is OK
- 10.1016/j.cognition.2005.11.007 is OK
- 10.1177/102986490901300203 is OK
- 10.1016/j.concog.2010.07.004 is OK
- 10.1111/j.1756-8765.2012.01214.x is OK
- 10.7554/eLife.51784 is OK
- 10.1016/j.jecp.2020.105020 is OK
- 10.1111/nyas.13654 is OK

MISSING DOIs

- None

INVALID DOIs

- None

faroit commented 1 year ago

@editorialbot set 10.5281/zenodo.7272236 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7272236

faroit commented 1 year ago

@editorialbot set v.1.0.2 as version

editorialbot commented 1 year ago

Done! version is now v.1.0.2

faroit commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1525/mp.2006.23.5.377 is OK
- 10.1525/mp.2005.22.4.663 is OK
- 10.1016/j.cognition.2018.12.015 is OK
- 10.1016/j.cognition.2005.11.007 is OK
- 10.1177/102986490901300203 is OK
- 10.1016/j.concog.2010.07.004 is OK
- 10.1111/j.1756-8765.2012.01214.x is OK
- 10.7554/eLife.51784 is OK
- 10.1016/j.jecp.2020.105020 is OK
- 10.1111/nyas.13654 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/sbcs-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/3679, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

oliviaguest commented 1 year ago

@editorialbot check references

oliviaguest commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1525/mp.2006.23.5.377 is OK
- 10.1525/mp.2005.22.4.663 is OK
- 10.1016/j.cognition.2018.12.015 is OK
- 10.1016/j.cognition.2005.11.007 is OK
- 10.1177/102986490901300203 is OK
- 10.1016/j.concog.2010.07.004 is OK
- 10.1111/j.1756-8765.2012.01214.x is OK
- 10.7554/eLife.51784 is OK
- 10.1016/j.jecp.2020.105020 is OK
- 10.1111/nyas.13654 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

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

OK DOIs

- 10.1525/mp.2006.23.5.377 is OK
- 10.1525/mp.2005.22.4.663 is OK
- 10.1016/j.cognition.2018.12.015 is OK
- 10.1016/j.cognition.2005.11.007 is OK
- 10.1177/102986490901300203 is OK
- 10.1016/j.concog.2010.07.004 is OK
- 10.1111/j.1756-8765.2012.01214.x is OK
- 10.7554/eLife.51784 is OK
- 10.1016/j.jecp.2020.105020 is OK
- 10.1111/nyas.13654 is OK

MISSING DOIs

- Errored finding suggestions for "The construction and evaluation of statistical mod...", please try later

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/sbcs-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/3695, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

oliviaguest commented 1 year ago

@editorialbot check references

oliviaguest commented 1 year ago

@faroit @xinyiguan sorry for this, I just need to make sure why it threw that error. Hopefully back very soon to publish this. 😊

oliviaguest commented 1 year ago

@editorialbot check references

xuanxu commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1525/mp.2006.23.5.377 is OK
- 10.1525/mp.2005.22.4.663 is OK
- 10.1016/j.cognition.2018.12.015 is OK
- 10.1016/j.cognition.2005.11.007 is OK
- 10.1177/102986490901300203 is OK
- 10.1016/j.concog.2010.07.004 is OK
- 10.1111/j.1756-8765.2012.01214.x is OK
- 10.7554/eLife.51784 is OK
- 10.1016/j.jecp.2020.105020 is OK
- 10.1111/nyas.13654 is OK

MISSING DOIs

- None

INVALID DOIs

- None

oliviaguest commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1525/mp.2006.23.5.377 is OK
- 10.1525/mp.2005.22.4.663 is OK
- 10.1016/j.cognition.2018.12.015 is OK
- 10.1016/j.cognition.2005.11.007 is OK
- 10.1177/102986490901300203 is OK
- 10.1016/j.concog.2010.07.004 is OK
- 10.1111/j.1756-8765.2012.01214.x is OK
- 10.7554/eLife.51784 is OK
- 10.1016/j.jecp.2020.105020 is OK
- 10.1111/nyas.13654 is OK

MISSING DOIs

- None

INVALID DOIs

- None

oliviaguest commented 1 year ago

@editorialbot recommend-accept

oliviaguest commented 1 year ago

@editorialbot recommend-accept

arfon commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1525/mp.2006.23.5.377 is OK
- 10.1525/mp.2005.22.4.663 is OK
- 10.1016/j.cognition.2018.12.015 is OK
- 10.1016/j.cognition.2005.11.007 is OK
- 10.1177/102986490901300203 is OK
- 10.1016/j.concog.2010.07.004 is OK
- 10.1111/j.1756-8765.2012.01214.x is OK
- 10.7554/eLife.51784 is OK
- 10.1016/j.jecp.2020.105020 is OK
- 10.1111/nyas.13654 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/sbcs-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/3709, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

oliviaguest commented 1 year ago

@editorialbot accept

openjournals / joss-reviews