[REVIEW]: bmm: Bayesian Map-matching

[whedon]

Submitting author: @SamDuffield (Samuel Duffield)
Repository: https://github.com/SamDuffield/bmm
Version: v1.3
Editor: @taless474
Reviewer: @georgiastuart, @matt-graham
Archive: 10.5281/zenodo.6023275

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/59abd48ba401a3256f38e635bebd3a64"><img src="https://joss.theoj.org/papers/59abd48ba401a3256f38e635bebd3a64/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/59abd48ba401a3256f38e635bebd3a64/status.svg)](https://joss.theoj.org/papers/59abd48ba401a3256f38e635bebd3a64)

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

@georgiastuart & @matt-graham, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @taless474 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 ✨

Review checklist for @georgiastuart

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@SamDuffield) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• 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 and who the target audience is?
• 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?

Review checklist for @matt-graham

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@SamDuffield) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• 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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @georgiastuart, @matt-graham it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Wordcount for paper.md is 745

[whedon]

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

OK DOIs

- doi.org/10.1016/j.compenvurbsys.2017.05.004 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.3946761 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1109/TITS.2013.2262376 is OK
- 10.1080/13658816.2017.1400548 is OK
- 10.1145/2093973.2094062 is OK
- 10.1145/1653771.1653818 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.93 s (38.7 files/s, 195675.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              1              0              0         176329
Python                          25            944           1137           2831
TeX                              1             26              0            185
Markdown                         2             44              0            138
reStructuredText                 4             49             28             55
DOS Batch                        1              8              1             26
YAML                             1              4              7             11
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            36           1079           1180         179584
-------------------------------------------------------------------------------


Statistical information for the repository '5718e75ec2cd059cd1d4afde' was
gathered on 2021/08/24.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Sam Duffield                    95         15624          13211           71.19
SamDuffield                     59          7081           4591           28.81

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Sam Duffield               4912           31.4         11.5                9.83

[whedon]

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

[georgiastuart]

I should be able to get to this next week.

[whedon]

👋 @matt-graham, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @georgiastuart, please update us on how your review is going (this is an automated reminder).

[georgiastuart]

I'm beginning my review, sorry for the delay!

[matt-graham]

Overall I think this a very nicely designed and useful package that represents a substantial effort by the author and has lots of positive aspects, including good documentation of the main API, a clear and readable Python codebase and a nice summary of the package and its functionality in the submitted paper.

There are a few minor issues I have raised that should be hopefully simple to fix - namely a lack of community guidelines for contributors / users (SamDuffield/bmm#10) and adding some more comparison to alternative software packages to the paper (SamDuffield/bmm#11).

I have also raised some issues which are intended more as suggestions for enhancements / nice-to-haves rather than blockers for acceptance (SamDuffield/bmm#7, SamDuffield/bmm#8).

The main area I think that needs improving is the coverage of the tests provided (SamDuffield/bmm#9). While there is a suite of tests using the unittest module from the Python standard library, the checks currently performed are quite minimal in some cases and several key functions do not have any associated tests. While I appreciate that the Monte Carlo algorithms being implemented here are inherently very complex and their stochastic nature makes writing tests for correctness difficult, I think there is still scope for adding various simple checks that would increase confidence both that the current implementation is correct and that it will remains so with any further updates.

[georgiastuart]

I will have my complete review next week. I apologize for the delay!

[taless474]

@georgiastuart how is the review going?

[georgiastuart]

My apologies, this fell off my radar. I will have my review up ASAP next week.

[taless474]

@whedon check references

[whedon]

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

OK DOIs

- doi.org/10.1016/j.compenvurbsys.2017.05.004 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.3946761 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1109/TITS.2013.2262376 is OK
- 10.1080/13658816.2017.1400548 is OK
- 10.1145/2093973.2094062 is OK
- 10.1145/1653771.1653818 is OK

MISSING DOIs

- 10.1109/tsp.2022.3141259 may be a valid DOI for title: Online Particle Smoothing with Application to Map-matching

INVALID DOIs

- None

[taless474]

@SamDuffield would you please take care of the missing DOI?

[SamDuffield]

@whedon check references

[whedon]

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

OK DOIs

- doi.org/10.1016/j.compenvurbsys.2017.05.004 is OK
- 10.1109/TSP.2022.3141259 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.3946761 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1109/TITS.2013.2262376 is OK
- 10.1080/13658816.2017.1400548 is OK
- 10.1145/2093973.2094062 is OK
- 10.1145/1653771.1653818 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[SamDuffield]

@taless474 looks all good now!

[taless474]

The next step is to issue a new tagged release of the software (if changed) and archive it (on Zenodo, figshare, as explained here.
Thank you, @SamDuffield, and thank you @matt-graham and @georgiastuart for all your effort.

[SamDuffield]

Archived version v1.3 on Zenodo at DOI: 10.5281/zenodo.6023275

Yes thank you @matt-graham and @georgiastuart for your efforts, and @taless474 for staying on top of things!

[taless474]

@SamDuffield LGTM! Would you please change the title in zanodo to match the title of your paper? Typically, these are the same for a JOSS-related paper. Note that you can manually change the metadata of the zenodo archive.

[taless474]

@whedon set v1.3 as version

[whedon]

OK. v1.3 is the version.

[SamDuffield]

@SamDuffield LGTM! Would you please change the title in zanodo to match the title of your paper? Typically, these are the same for a JOSS-related paper. Note that you can manually change the metadata of the zenodo archive.

Ok should have matching title now!

[taless474]

@whedon set 10.5281/zenodo.6023275 as archive

[whedon]

OK. 10.5281/zenodo.6023275 is the archive.

[taless474]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- doi.org/10.1016/j.compenvurbsys.2017.05.004 is OK
- 10.1109/TSP.2022.3141259 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.3946761 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1109/TITS.2013.2262376 is OK
- 10.1080/13658816.2017.1400548 is OK
- 10.1145/2093973.2094062 is OK
- 10.1145/1653771.1653818 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2943

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2943, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kthyng]

Amazing! Looks perfect.

[kthyng]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.03651 joss-papers#2947
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03651
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...

[kthyng]

Congratulations on your new publication @SamDuffield! Many thanks to editor @taless474 and reviewers @georgiastuart and @matt-graham for your time, hard work, and expertise!!

[whedon]

🎉🎉🎉 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.03651/status.svg)](https://doi.org/10.21105/joss.03651)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03651">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03651/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03651/status.svg
   :target: https://doi.org/10.21105/joss.03651

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss