[REVIEW]: A Short Introduction to PF: A C++ Library for Particle Filtering

whedon commented 4 years ago

Submitting author: @tbrown122387 (Taylor Brown) Repository: https://github.com/tbrown122387/pf Version: v1.0.3 Editor: @diehlpk Reviewer: @ziotom78, @andremrsantos Archive: 10.5281/zenodo.4068564

:warning: JOSS reduced service mode :warning:

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/8b4d434b0834c3cce76aaccd8e83ac9b"><img src="https://joss.theoj.org/papers/8b4d434b0834c3cce76aaccd8e83ac9b/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/8b4d434b0834c3cce76aaccd8e83ac9b/status.svg)](https://joss.theoj.org/papers/8b4d434b0834c3cce76aaccd8e83ac9b)

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

@ziotom78 & @andremrsantos, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
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 @diehlpk 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 @ziotom78

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 repository url?
[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 (@tbrown122387) 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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

Review checklist for @andremrsantos

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 repository url?
[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 (@tbrown122387) 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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

diehlpk commented 3 years ago

@tbrown122387 Congratulations to the acceptance of the paper. @ziotom78 and @andremrsantos thanks again for your reviews.

tbrown122387 commented 3 years ago

Terrific news! Thanks again everyone @diehlpk @ziotom78 @andremrsantos I'm very appreciative of all your time, and thank you for making this software better and helping it to reach more people!

tbrown122387 commented 3 years ago

Sorry for noticing just now, but there are a couple of typos that I might have fixed too late. Some were from before but might not have gotten picked up, and some are from just now. See my most recent commit https://github.com/tbrown122387/pf/commit/e5f9366480510d46fe1a880c818b314c8cdfa73b

diehlpk commented 3 years ago

You still can update typos in the paper. However, the typos will remain in the release. The paper for the actual publication will be compiled from master/branch.

kthyng commented 3 years ago

Version is up to date, and zenodo archive metadata looks good!

The paper looks good, except for the references, which have lost capitalization. @tbrown122387 can you go through your reference list in detail to preserve capitalization? You can do this by placing {} around the words in the .bib file that have capitalization that is not being preserved. {Markov} and {Monte Carlo} are what I've seen in a couple of the references, but I stopped looking so there may be more.

tbrown122387 commented 3 years ago

@kthyng okey dokey capitalization now matches titles.

kthyng commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

PDF failed to compile for issue #2599 with the following error:

/app/vendor/bundle/ruby/2.4.0/gems/octokit-4.8.0/lib/octokit/response/raise_error.rb:16:in on_complete': GET https://api.github.com/repos/openjournals/jose-reviews/issues/2599: 404 - Not Found // See: https://docs.github.com/rest/reference/issues#get-an-issue (Octokit::NotFound) from /app/vendor/bundle/ruby/2.4.0/gems/faraday-0.15.4/lib/faraday/response.rb:9:inblock in call' from /app/vendor/bundle/ruby/2.4.0/gems/faraday-0.15.4/lib/faraday/response.rb:61:in on_complete' from /app/vendor/bundle/ruby/2.4.0/gems/faraday-0.15.4/lib/faraday/response.rb:8:incall' from /app/vendor/bundle/ruby/2.4.0/gems/octokit-4.8.0/lib/octokit/middleware/follow_redirects.rb:73:in perform_with_redirection' from /app/vendor/bundle/ruby/2.4.0/gems/octokit-4.8.0/lib/octokit/middleware/follow_redirects.rb:61:incall' from /app/vendor/bundle/ruby/2.4.0/gems/faraday-0.15.4/lib/faraday/rack_builder.rb:143:in build_response' from /app/vendor/bundle/ruby/2.4.0/gems/faraday-0.15.4/lib/faraday/connection.rb:387:inrun_request' from /app/vendor/bundle/ruby/2.4.0/gems/faraday-0.15.4/lib/faraday/connection.rb:138:in get' from /app/vendor/bundle/ruby/2.4.0/gems/sawyer-0.8.2/lib/sawyer/agent.rb:94:incall' from /app/vendor/bundle/ruby/2.4.0/gems/octokit-4.8.0/lib/octokit/connection.rb:156:in request' from /app/vendor/bundle/ruby/2.4.0/gems/octokit-4.8.0/lib/octokit/connection.rb:19:inget' from /app/vendor/bundle/ruby/2.4.0/gems/octokit-4.8.0/lib/octokit/client/issues.rb:114:in issue' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/review.rb:21:inissue_body' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/bin/whedon:44:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/bin/whedon:131:in<top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

kthyng commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

kthyng commented 3 years ago

@tbrown122387 ok looks good!

kthyng commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1791

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1791, 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 commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

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

whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1792
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02599
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng commented 3 years ago

Congrats on your new paper @tbrown122387! Thank you to editor @diehlpk and to reviewers @ziotom78 and @andremrsantos — we couldn't do this process without your expertise and time!

whedon commented 3 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.02599/status.svg)](https://doi.org/10.21105/joss.02599)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02599">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02599/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02599/status.svg
   :target: https://doi.org/10.21105/joss.02599

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

tbrown122387 commented 3 years ago

@diehlpk @kthyng is there any chance we can re-publish this after I insert the following blurb somewhere?

The author acknowledges Research Computing at The University of Virginia for providing computational resources and technical support that have contributed to the results reported within this publication. URL: https://rc.virginia.edu

These folks had helped me out with some of the cmake issues that were raised here which was in response to some of the feedback given by @ziotom78 Sorry to make more work for you all. I had just stumbled upon a page on their site that requested attribution as a form of support.

diehlpk commented 3 years ago

@tbrown122387 I think you can add it to the paper and @arfon can reprocess the paper and replace the old version. Please wait for his instructions.

arfon commented 3 years ago

Sure thing! I've added this in https://github.com/openjournals/joss-papers/blob/d5a41afeb6cfbf928dfb18738fd6e74ab1768151/joss.02599/10.21105.joss.02599.pdf

tbrown122387 commented 3 years ago

Thanks very much @diehlpk and @arfon !

openjournals / joss-reviews