[REVIEW]: HiddenMarkovModels.jl: generic, fast and reliable latent variable modeling

editorialbot commented 8 months ago

Submitting author: !--author-handle-->@gdalle@jbytecode<!--end-editor-- Reviewers: @DanielRivasMD, @dmbates Archive: 10.5281/zenodo.10931812

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/02568a7d960824132102d42439434b66"><img src="https://joss.theoj.org/papers/02568a7d960824132102d42439434b66/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/02568a7d960824132102d42439434b66/status.svg)](https://joss.theoj.org/papers/02568a7d960824132102d42439434b66)

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

@DanielRivasMD & @dmbates, 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 @jbytecode 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 @dmbates

📝 Checklist for @DanielRivasMD

editorialbot commented 8 months ago

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

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editorialbot commented 8 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.01 s (355.0 files/s, 169138.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              1              0              0           1968
TeX                              1             18              0            250
Markdown                         1             27              0             86
YAML                             2              0              5             28
-------------------------------------------------------------------------------
SUM:                             5             45              5           2332
-------------------------------------------------------------------------------

Commit count by author:

   127  Guillaume Dalle

editorialbot commented 8 months ago

Paper file info:

📄 Wordcount for paper.md is 1117

✅ The paper includes a Statement of need section

editorialbot commented 8 months ago

License info:

🔴 Failed to discover a valid open source license

editorialbot commented 8 months ago

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

OK DOIs

- 10.5281/zenodo.4454565 is OK
- 10.18637/jss.v098.i16 is OK
- 10.1137/141000671 is OK
- 10.1007/0-387-28982-8 is OK
- 10.48550/arXiv.1608.04295 is OK
- 10.21105/joss.03349 is OK
- 10.1016/S0006-3495(00)76441-1 is OK
- 10/cswph2 is OK
- 10.5281/ZENODO.4754896 is OK

MISSING DOIs

- 10.1109/icassp43922.2022.9746824 may be a valid DOI for title: GPU-Accelerated Forward-Backward Algorithm with Application to Lattic-Free MMI

INVALID DOIs

- None

editorialbot commented 8 months ago

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

jbytecode commented 8 months ago

@DanielRivasMD, @dmbates - thank you for accepting our invitation. Please, firstly create your checklist before starting your review. Thank you in advance

@gdalle - One of your citation entries in the BibTeX seems incorrect, could you please consider correcting it? Thank you.

gdalle commented 8 months ago

I'll take a look at the citation. The bot seems to expect that the paper is located on a branch where the rest of the code lives too. I'm gonna merge main into joss to fix it

jbytecode commented 8 months ago

@gdalle - As expressed at the top of the page, the default branch of your paper is joss.

gdalle commented 8 months ago

Yeah but there's no code on it, just the markdown, so that's why the bot can't find the license or get an accurate LOC count

gdalle commented 8 months ago

Also the version of the package is now 0.5.0

jbytecode commented 8 months ago

@editorialbot set v0.5.0 as version

editorialbot commented 8 months ago

Done! version is now v0.5.0

gdalle commented 8 months ago

@editorialbot commands

editorialbot commented 8 months ago

Hello @gdalle, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

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

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

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

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

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

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

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

gdalle commented 8 months ago

@editorialbot set joss2 as branch

editorialbot commented 8 months ago

Done! branch is now joss2

gdalle commented 8 months ago

@editorialbot check references

editorialbot commented 8 months ago

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

OK DOIs

- 10.5281/zenodo.4454565 is OK
- 10.18637/jss.v098.i16 is OK
- 10.1137/141000671 is OK
- 10.1007/0-387-28982-8 is OK
- 10.48550/arXiv.1608.04295 is OK
- 10.21105/joss.03349 is OK
- 10.1109/ICASSP43922.2022.9746824 is OK
- 10.1016/S0006-3495(00)76441-1 is OK
- 10/cswph2 is OK
- 10.5281/ZENODO.4754896 is OK

MISSING DOIs

- None

INVALID DOIs

- None

gdalle commented 8 months ago

@editorialbot check repository

editorialbot commented 8 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (1552.1 files/s, 151657.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           51            732            726           2524
SVG                              1              0              0           1968
TOML                            11            125              1            609
Markdown                         7            160              0            459
TeX                              2             20              0            283
YAML                             8              2             12            196
-------------------------------------------------------------------------------
SUM:                            80           1039            739           6039
-------------------------------------------------------------------------------

Commit count by author:

   140  Guillaume Dalle

editorialbot commented 8 months ago

Paper file info:

📄 Wordcount for paper.md is 1117

✅ The paper includes a Statement of need section

editorialbot commented 8 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

gdalle commented 8 months ago

@editorialbot generate pdf

gdalle commented 8 months ago

@jbytecode all good

editorialbot commented 8 months ago

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

dmbates commented 8 months ago

Review checklist for @dmbates

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/gdalle/HiddenMarkovModels.jl?
[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 (@gdalle) 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?

dmbates commented 8 months ago

The only question I have about the paper and the package is the form of citation in the paper for other Julia packages. Those like Makie.jl and ChainRules.jl that have recommended citation forms for the package are fine. Those that don't (HMMBase.jl, PythonCall.jl, and LogarithmicNumbers.jl) are cited by the author, year, package name, and package title. Those experienced with Julia packages may know to check at, e.g. https://juliahub.com/ui/packages, to determine the repository but a reader unfamiliar with Julia packages may not know this. How are registered Julia packages without citation info cited in other JOSS papers?

gdalle commented 8 months ago

I don't know, I pulled the information directly from the GitHub repository with Zotero whenever there was no CITATION.bib or Zenodo DOI available. If there's a better practice I'm curious too

gdalle commented 8 months ago

@jbytecode can we maybe get some guidance on this issue, so that @dmbates's review may be completed?

jbytecode commented 8 months ago

@dmbates, @gdalle - of course the best approach is to cite a journal article (that's why we have JOSS so now we can cite software in a straightforward way). Since every software package has not a journal paper, the second best approach is to find it has whether a Zenodo like archive or not, just because they provide a DOI which is a key on the citation issues. If this is not the case, the next approach is to find a CITATION.bib or a tagget release with a version number. Otherwise, all we at hand is the GitHub repo. Of course package's web page in the Juliahub can also be cited instead of GitHub repo.

dmbates commented 8 months ago

@gdalle There's this wonderful resource https://modernjuliaworkflows.github.io/ by G. Dalle et al. that mentions PkgCite.jl as a way to generate citations for the packages that you currently have loaded. It would suggest as a bibtex entry


@misc{PythonCall.jl,
 author        = {Rowley, Christopher},
 year          = {2022},
 url           = {https://github.com/JuliaPy/PythonCall.jl},
 title         = {PythonCall.jl: Python and Julia in harmony}
}

gdalle commented 8 months ago

I found out where the issue was: my Zotero settings had disabled URL export.

gdalle commented 8 months ago

I'll fix it tomorrow, thanks :)

gdalle commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

gdalle commented 8 months ago

@dmbates now the citations all have links, and I fixed a minor detail for benchmark reproducibility, which slightly changed the plots cause I re-ran them.

jbytecode commented 8 months ago

@DanielRivasMD - Sorry for pinging. One of our reviewers' report is almost done. It seems you haven't started your review, yet. Could you please start your review and update your status? Thank you in advance.

gdalle commented 7 months ago

@dmbates I saw that you checked the last remaining box, thank you! Is there anything else you need from me for your review?

dmbates commented 7 months ago

@gdalle No, nothing more required for the review. From me it looks good to go.

jbytecode commented 7 months ago

@DanielRivasMD - Sorry for pinging again. One of our reviewers' report has been finished. It seems you haven't started your review, yet. Could you please start your review and update your status? Thank you in advance.

jbytecode commented 7 months ago

@DanielRivasMD - Is it possible to generate your task list and start your review? Thank you in advance.

jbytecode commented 7 months ago

@gdalle - I regret to say that it seems one of our reviewers (@DanielRivasMD) is unable to find a proper time to respond. They haven't even created their task list. I believe we should look for another suitable reviewer at this point. Do you have any suggestions for reviewers?

gdalle commented 7 months ago

We can keep trying the suggestions here

https://github.com/openjournals/joss-reviews/issues/5874#issuecomment-1735023132

DanielRivasMD commented 7 months ago

  Hi, 

  I deeply apologize for the enormoys delay. Something urgent and personal came up that grab my focus for a couple of weeks. 

  I can get the review done tomorrow since I have already check the paper and make my own notes. I hope this is fine with you all. Please let me know. 

  Once again, I am sorry about the delay. 

  Cheers, 

  Daniel Rivas 

   On Monday, Apr 01, 2024 at 9:50 AM, Mehmet Hakan Satman ***@***.***> wrote: 

  @gdalle - I regret to say that it seems one of our reviewers ***@***.***) is unable to find a proper time to respond. They haven't even created their task list. I believe we should look for another suitable reviewer at this point. Do you have any suggestions for reviewers? 
  —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: ***@***.***> 
  ***@***.***": ***@***.***": "EmailMessage","potentialAction": ***@***.***": "ViewAction","target": "https://github.com/openjournals/joss-reviews/issues/6436#issuecomment-2030035230","url": "https://github.com/openjournals/joss-reviews/issues/6436#issuecomment-2030035230","name": "View Issue"},"description": "View this Issue on GitHub","publisher": ***@***.***": "Organization","name": "GitHub","url": "https://github.com"}}]

jbytecode commented 7 months ago

@DanielRivasMD - Thank you for your response. We are looking forward to hearing from you soon.

gdalle commented 7 months ago

@DanielRivasMD yes this is completely fine, no worries. Thanks for the update, and I hope everything is okay on your end. The personal stuff obviously comes first

DanielRivasMD commented 7 months ago

Hi again, where is the link to generate my checlist?

gdalle commented 7 months ago

@editorialbot commands

editorialbot commented 7 months ago

Hello @gdalle, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

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

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

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

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

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

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

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

openjournals / joss-reviews