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

[editorialbot]

Submitting author: @gdalle (Guillaume Dalle)
Repository: https://github.com/gdalle/HiddenMarkovModels.jl
Branch with paper.md (empty if default branch): joss2
Version: v0.5.1
Editor: @jbytecode
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]

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]

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]

Paper file info:

📄 Wordcount for paper.md is 1117

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🔴 Failed to discover a valid open source license

[editorialbot]

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]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[jbytecode]

@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]

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]

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

[gdalle]

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]

Also the version of the package is now 0.5.0

[jbytecode]

@editorialbot set v0.5.0 as version

[editorialbot]

Done! version is now v0.5.0

[gdalle]

@editorialbot commands

[editorialbot]

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]

@editorialbot set joss2 as branch

[editorialbot]

Done! branch is now joss2

[gdalle]

@editorialbot check references

[editorialbot]

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]

@editorialbot check repository

[editorialbot]

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

[jbytecode]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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
- 10.1017/9781108917407 is OK
- 10.5281/zenodo.5881966 is OK

MISSING DOIs

- No DOI given, and none found for title: An Input Output HMM Architecture
- No DOI given, and none found for title: Dynamax:  State Space Models Library in JAX
- No DOI given, and none found for title: Machine Learning and Combinatorial Optimization Al...
- No DOI given, and none found for title: Hmmlearn: Hidden Markov Models in Python, with Sci...
- No DOI given, and none found for title: HMMBase.Jl:  Hidden Markov Models for Julia
- No DOI given, and none found for title: Probabilistic Machine Learning: Advanced Topics
- No DOI given, and none found for title: LogarithmicNumbers.Jl: A Logarithmic Number System...
- No DOI given, and none found for title: PythonCall.Jl: Python and Julia in Harmony
- No DOI given, and none found for title: Jmschrei/Pomegranate
- No DOI given, and none found for title: Pomegranate: Fast and Flexible Probabilistic Model...

INVALID DOIs

- None

[editorialbot]

⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

Element doi: [facet 'pattern'] The value '10/cswph2' is not accepted by the pattern '10\.[0-9]{4,9}/.{1,200}'.

[jbytecode]

@gdalle - The problem is about the DOI entry of the bibtex item

@article{rabinerTutorialHiddenMarkov1989,
  title = {A Tutorial on Hidden {{Markov}} Models and Selected Applications in Speech Recognition},
  author = {Rabiner, L.R.},
  date = {1989-02},
  journaltitle = {Proceedings of the IEEE},
  volume = {77},
  number = {2},
  pages = {257--286},
  issn = {1558-2256},
  doi = {10/cswph2},
  ...
}

Could you please fix it and then ping me again?

[jbytecode]

@openjournals/dev - Interestingly the doi is resolved by DOI.org however we get this error:

!! Invalid Crossref XML v5.3.1 in tmp/3a94f67f00ebb84ab56aec5ba38026f1/paper/paper.crossref. Errors: 1. 
  - 268:0: ERROR: Element {http://www.crossref.org/schema/5.3.1}doi: [facet pattern] The value 10/cswph2 is not accepted by the pattern 10.[0-9]{4,9}/.{1,200}.

[jbytecode]

@gdalle - using 10.1109/5.18626 instead may be fix that because the bibtex is reported as

@ARTICLE{18626,
  author={Rabiner, L.R.},
  journal={Proceedings of the IEEE}, 
  title={A tutorial on hidden Markov models and selected applications in speech recognition}, 
  year={1989},
  volume={77},
  number={2},
  pages={257-286},
  keywords={Tutorial;Hidden Markov models;Speech recognition},
  doi={10.1109/5.18626}}

[gdalle]

I just made the modification, anything to make our little bot happy ;)

@editorialbot generate pdf

[jbytecode]

@editorialbot check references

[editorialbot]

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
- 10.1109/5.18626 is OK
- 10.1017/9781108917407 is OK
- 10.5281/zenodo.5881966 is OK

MISSING DOIs

- No DOI given, and none found for title: An Input Output HMM Architecture
- No DOI given, and none found for title: Dynamax:  State Space Models Library in JAX
- No DOI given, and none found for title: Machine Learning and Combinatorial Optimization Al...
- No DOI given, and none found for title: Hmmlearn: Hidden Markov Models in Python, with Sci...
- No DOI given, and none found for title: HMMBase.Jl:  Hidden Markov Models for Julia
- No DOI given, and none found for title: Probabilistic Machine Learning: Advanced Topics
- No DOI given, and none found for title: LogarithmicNumbers.Jl: A Logarithmic Number System...
- No DOI given, and none found for title: PythonCall.Jl: Python and Julia in Harmony
- No DOI given, and none found for title: Jmschrei/Pomegranate
- No DOI given, and none found for title: Pomegranate: Fast and Flexible Probabilistic Model...

INVALID DOIs

- None

[jbytecode]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[jbytecode]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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
- 10.1109/5.18626 is OK
- 10.1017/9781108917407 is OK
- 10.5281/zenodo.5881966 is OK

MISSING DOIs

- No DOI given, and none found for title: An Input Output HMM Architecture
- No DOI given, and none found for title: Dynamax:  State Space Models Library in JAX
- No DOI given, and none found for title: Machine Learning and Combinatorial Optimization Al...
- No DOI given, and none found for title: Hmmlearn: Hidden Markov Models in Python, with Sci...
- No DOI given, and none found for title: HMMBase.Jl:  Hidden Markov Models for Julia
- No DOI given, and none found for title: Probabilistic Machine Learning: Advanced Topics
- No DOI given, and none found for title: LogarithmicNumbers.Jl: A Logarithmic Number System...
- No DOI given, and none found for title: PythonCall.Jl: Python and Julia in Harmony
- No DOI given, and none found for title: Jmschrei/Pomegranate
- No DOI given, and none found for title: Pomegranate: Fast and Flexible Probabilistic Model...

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/dsais-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5217, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[gdalle]

looks good to me

[arfon]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Dalle
  given-names: Guillaume
  orcid: "https://orcid.org/0000-0003-4866-1687"
doi: 10.5281/zenodo.10931812
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Dalle
    given-names: Guillaume
    orcid: "https://orcid.org/0000-0003-4866-1687"
  date-published: 2024-04-05
  doi: 10.21105/joss.06436
  issn: 2475-9066
  issue: 96
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6436
  title: "HiddenMarkovModels.jl: generic, fast and reliable state space
    modeling"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06436"
  volume: 9
title: "HiddenMarkovModels.jl: generic, fast and reliable state space
  modeling"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06436 joss-papers#5219
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06436
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@DanielRivasMD, @dmbates – many thanks for your reviews here and to @jbytecode for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@gdalle – your paper is now accepted and published in JOSS ⚡🚀💥

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06436/status.svg)](https://doi.org/10.21105/joss.06436)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06436">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06436/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06436/status.svg
   :target: https://doi.org/10.21105/joss.06436

This is how it will look in your documentation:

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