editorialbot commented 2 months ago

Submitting author: !--author-handle-->@aadya940@mooniean<!--end-editor-- Reviewers: @braniii, @MichalisPanayides Archive: 10.5281/zenodo.13305155

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/486cf1a43c0079e0628e044215168ad6"><img src="https://joss.theoj.org/papers/486cf1a43c0079e0628e044215168ad6/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/486cf1a43c0079e0628e044215168ad6/status.svg)](https://joss.theoj.org/papers/486cf1a43c0079e0628e044215168ad6)

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

@braniii & @MichalisPanayides, 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 @mooniean 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 @MichalisPanayides

📝 Checklist for @braniii

editorialbot commented 2 months 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:

@editorialbot generate pdf

editorialbot commented 2 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1034.0 files/s, 321988.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          14            390            397           1005
Jupyter Notebook                 6              0           7850            555
Markdown                         4             64              0            194
Cython                           5             33              0            137
YAML                             3             28              0            103
TeX                              1             15              0             73
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            35            542           8255           2102
-------------------------------------------------------------------------------

Commit count by author:

   102  aadya940
    50  Aadya Chinubhai

editorialbot commented 2 months ago

Paper file info:

📄 Wordcount for paper.md is 1301

✅ The paper includes a Statement of need section

editorialbot commented 2 months ago

License info:

✅ License found: BSD 2-Clause "Simplified" License (Valid open source OSI approved license)

editorialbot commented 2 months ago

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

OK DOIs

- None

MISSING DOIs

- No DOI given, and none found for title: Markov chain neural networks
- No DOI given, and none found for title: PyDTMC
- 10.1109/mcse.2010.118 may be a valid DOI for title: Cython: The best of both worlds
- No DOI given, and none found for title: Array programming with NumPy
- No DOI given, and none found for title: SciPy 1.0: fundamental algorithms for scientific c...
- No DOI given, and none found for title: Pytorch: An imperative style, high-performance dee...
- No DOI given, and none found for title: Numba: A llvm-based python jit compiler
- No DOI given, and none found for title: Convergence rates for Markov chains
- No DOI given, and none found for title: Regime switching models

INVALID DOIs

- None

editorialbot commented 2 months ago

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

mooniean commented 2 months ago

Hi @aadya940 and reviewers @braniii @MichalisPanayides 👋 ! - this is the review thread for the submission. All of our communications will happen here from now on.

Meanwhile, please check the post at the top of the issue for instructions on how to generate your own review checklist. As you go over the submission, please check any items that you feel have been satisfied. There are also 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 directly in the software repository. If you do so, please mention this thread so that a link is created (and I can keep an eye on what is happening). Please also feel free to comment and ask questions in this thread. It is often easier to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

Please feel free to ping me (@mooniean) if you have any questions or concerns. Thanks!

MichalisPanayides commented 2 months ago

Review checklist for @MichalisPanayides

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/aadya940/chainopy?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@aadya940) 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?

aadya940 commented 2 months ago

The changes have been made :+1:

aadya940 commented 2 months ago

Thanks @MichalisPanayides for the review :))

braniii commented 2 months ago

Review checklist for @braniii

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/aadya940/chainopy?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@aadya940) 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?

mooniean commented 1 month ago

Hi everyone! @braniii @MichalisPanayides and @aadya940

How is everything going? Just checking in to see if you need anything from me!

aadya940 commented 1 month ago

@mooniean Everything good from my side. Thanks for asking :))

braniii commented 1 month ago

@mooniean Thank you for asking. There are still some open issues regarding the documentation and the package management/installation process.

mooniean commented 1 month ago

@aadya940 hello! just checking you've seen the open issues that @braniii mentioned?

aadya940 commented 3 weeks ago

Hello @mooniean , Yes , Thanks :))

braniii commented 3 weeks ago

@editorialbot generate pdf

editorialbot commented 3 weeks ago

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

aadya940 commented 2 weeks ago

Hello! @mooniean @braniii @MichalisPanayides Looks like I'm done with all the issues raised in chainopy. Thanks :))

braniii commented 2 weeks ago

@editorialbot generate pdf

editorialbot commented 2 weeks ago

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

braniii commented 2 weeks ago

@mooniean There are still two open issues (make it installable via pip/pypi and add examples to the docs). Once these are fixed, I will check off the remaining boxes in my review.

Edit: @aadya940 fixed all issues.

mooniean commented 2 weeks ago

Hello everyone! I've checked that both reviewers have checked all the boxes. @braniii @MichalisPanayides are you happy to recommend the paper for publication in JOSS?

MichalisPanayides commented 2 weeks ago

Hello everyone! I've checked that both reviewers have checked all the boxes. @braniii @MichalisPanayides are you happy to recommend the paper for publication in JOSS?

Yes. I am happy with the changes

aadya940 commented 2 weeks ago

Thank You, really appreciate your feedbacks and the issues raised. :)) @MichalisPanayides @braniii

mooniean commented 1 week ago

Hi @aadya940 ! Before we do the post-review checklist, there's only a couple of small corrections for the paper (for consistency purposes in the most part):

There are some capitalisation inconsistencies: Line 29: writing pyDTMC while previous was PyDTMC (and afterwards too) Line 36: same with cython and python (Python has to be capitalised) Line 39: markov chains > Markov chains

And a small typo on line 115: should be packages ("we use the Pytest and PyDTMC packages)

aadya940 commented 1 week ago

Hello @mooniean , Thanks for the review. I've fixed the issues & can start with the post-review now. Please let me know what are the next steps :))

mooniean commented 1 week ago

@editorialbot generate pdf

editorialbot commented 1 week ago

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

mooniean commented 1 week 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 pull request)
[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

mooniean commented 1 week ago

@editorialbot check references

editorialbot commented 1 week ago

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

OK DOIs

- None

MISSING DOIs

- No DOI given, and none found for title: Markov chain neural networks
- No DOI given, and none found for title: PyDTMC
- No DOI given, and none found for title: simple-markov
- No DOI given, and none found for title: mchmm
- 10.1109/mcse.2010.118 may be a valid DOI for title: Cython: The best of both worlds
- No DOI given, and none found for title: Array programming with NumPy
- No DOI given, and none found for title: SciPy 1.0: fundamental algorithms for scientific c...
- No DOI given, and none found for title: Pytorch: An imperative style, high-performance dee...
- No DOI given, and none found for title: Numba: A llvm-based python jit compiler
- No DOI given, and none found for title: Convergence rates for Markov chains
- No DOI given, and none found for title: Regime switching models

INVALID DOIs

- None

aadya940 commented 1 week ago

@mooniean I already have a release made (v1.0.2):

https://github.com/aadya940/chainopy/releases/tag/v1.0.2

mooniean commented 1 week ago

@aadya940 can you check the DOIs missing on the comment above, please?

aadya940 commented 1 week ago

@editorialbot generate pdf

editorialbot commented 1 week ago

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

aadya940 commented 1 week ago

@editorialbot check references

editorialbot commented 1 week ago

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

OK DOIs

- 10.1109/MCSE.2010.118 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1145/2833157.2833162 is OK
- 10.1137/1037083 is OK
- 10.1057/9780230280830_23 is OK

MISSING DOIs

- No DOI given, and none found for title: Markov chain neural networks
- No DOI given, and none found for title: PyDTMC
- No DOI given, and none found for title: simple-markov
- No DOI given, and none found for title: mchmm
- No DOI given, and none found for title: Pytorch: An imperative style, high-performance dee...

INVALID DOIs

- None

aadya940 commented 1 week ago

@editorialbot generate pdf

editorialbot commented 1 week ago

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

aadya940 commented 1 week ago

@editorialbot generate pdf

editorialbot commented 1 week ago

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

aadya940 commented 1 week ago

@editorialbot check references

editorialbot commented 1 week ago

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

OK DOIs

- 10.1109/CVPRW.2018.00293 is OK
- 10.1109/MCSE.2010.118 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1145/2833157.2833162 is OK
- 10.1137/1037083 is OK
- 10.1057/9780230280830_23 is OK

MISSING DOIs

- No DOI given, and none found for title: PyDTMC
- No DOI given, and none found for title: simple-markov
- No DOI given, and none found for title: mchmm

INVALID DOIs

- 10.5555/3454287.3455008 is INVALID

aadya940 commented 1 week ago

@editorialbot generate pdf

editorialbot commented 1 week ago

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

aadya940 commented 1 week ago

@editorialbot check references

editorialbot commented 1 week ago

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

OK DOIs

- 10.1109/CVPRW.2018.00293 is OK
- 10.1109/MCSE.2010.118 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1145/3620665.3640366 is OK
- 10.1145/2833157.2833162 is OK
- 10.1137/1037083 is OK
- 10.1057/9780230280830_23 is OK

MISSING DOIs

- No DOI given, and none found for title: PyDTMC
- No DOI given, and none found for title: simple-markov
- No DOI given, and none found for title: mchmm

INVALID DOIs

- None

aadya940 commented 1 week ago

@mooniean I wasn't able to find the other DOIs, these likely don't exist. They're mostly just github repos and not proper publications.

aadya940 commented 1 week ago

The zenodo DOI for v1.0.3 (latest) is:

10.5281/zenodo.13305155

openjournals / joss-reviews

[REVIEW]: ChainoPy: A Python Library for Discrete Time Markov Chain based stochastic analysis #6880

Status

Reviewer instructions & questions

Checklists

Review checklist for @MichalisPanayides

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @braniii

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