[REVIEW]: hillmaker: A Python package for occupancy analysis in discrete entity flow systems #6154

editorialbot · 2023-12-15T19:05:57Z

Submitting author: @misken (Mark Isken)
Repository: https://github.com/misken/hillmaker
Branch with paper.md (empty if default branch):
Version: v0.8.1
Editor: @mstimberg
Reviewers: @rerickson-usgs, @HLasse
Archive: 10.5281/zenodo.10530420

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/cd579f0843aedb47cea2ddc6cd2be666"><img src="https://joss.theoj.org/papers/cd579f0843aedb47cea2ddc6cd2be666/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/cd579f0843aedb47cea2ddc6cd2be666/status.svg)](https://joss.theoj.org/papers/cd579f0843aedb47cea2ddc6cd2be666)

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

@rerickson-usgs & @HLasse, 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 @mstimberg 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 @rerickson-usgs

📝 Checklist for @HLasse

The text was updated successfully, but these errors were encountered:

editorialbot · 2023-12-15T19:06:00Z

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:

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

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editorialbot · 2023-12-15T19:06:02Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.14 s (402.8 files/s, 159382.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          14           1049           1708           2364
Markdown                         7            185              0            430
Jupyter Notebook                11              0          14767            406
TOML                            11             71            102            196
TeX                              2             13              0            151
YAML                             7             30             40            139
reStructuredText                 2             28              6             58
Bourne Shell                     1              0             10             10
-------------------------------------------------------------------------------
SUM:                            55           1376          16633           3754
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-12-15T19:06:04Z

Wordcount for paper.md is 897

editorialbot · 2023-12-15T19:06:07Z

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

OK DOIs

- 10.1142/s0219622002000439 is OK
- 10.1007/s10729-010-9141-8 is OK
- 10.1023/A:1013034719088 is OK
- 10.2139/ssrn.2437936 is OK
- 10.1016/j.ejor.2010.06.021 is OK
- 10.1177/03611981221115086 is OK
- 10.4018/978-1-60960-872-9.ch019 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3509134 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.21105/joss.03021 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-12-15T19:07:24Z

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

mstimberg · 2023-12-15T19:12:01Z

👋🏼 @misken @, @rerickson-usgs, @HLasse this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains 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 and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6154 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within 6 weeks at the latest, but of course I understand that you might be away/not available during the holiday period at the end of the year. Please let me know if any of you require significantly more time. We can also use @editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@mstimberg) if you have any questions/concerns.

rerickson-usgs · 2023-12-15T19:20:22Z

Review checklist for @rerickson-usgs

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 https://github.com/misken/hillmaker?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@misken) 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
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.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
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

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, who the target audience is, and its relation to other work?
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?

HLasse · 2023-12-15T19:26:26Z

Review checklist for @HLasse

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 https://github.com/misken/hillmaker?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@misken) 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
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.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
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

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, who the target audience is, and its relation to other work?
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?

HLasse · 2024-01-05T12:30:00Z

My checklist is complete. The package works well and has very thorough documentation. Tests pass, and all the tutorials work as expected. The software seems to have been in use (in different forms) for a long time and sees use in multiple projects.

I've added a few minor PRs and issues for the authors to consider, but nothing major that should hold back the publication.

I recommend the paper for publication.

misken · 2024-01-05T14:43:40Z

Thank you, @HLasse. I much appreciate the PRs and Issues you raised and will get them incorporated. I responded to them individually just now.

rerickson-usgs · 2024-01-11T22:08:17Z

Thank you for inviting me to review this. I should have read the invite better before accepting.
I've done occupancy modeling in ecology (that is, imperfect detection of species), which is different than hospital occupancy (or patient use) modeling.

That being said, this package seems well done and I recommend accepting. As a feature request, I would to include the equation within the package and not just the supporting paper. I liked the documentation (like this file). An algorithm flow chart might also help.
Basically, something that would allow me to check the implementation of the numerical methods.
Something similar to https://hillmaker.readthedocs.io/en/latest/example_occupancy_analysis.html#step-2-process-each-scenario-with-hillmaker that explains how the main hillmaker function(s) work.
I also liked this page, https://hillmaker.readthedocs.io/en/latest/analysis_date_range.html, of documentation.

I was not able to install the package, but the problem is my work computer has an SSL intercept and conda is not working for me at the moment.

mstimberg · 2024-01-12T15:30:30Z

👋 @HLasse many thanks for your review and thanks @misken for incorporating the suggested changes.

mstimberg · 2024-01-12T15:40:47Z

👋 @rerickson-usgs Many thanks for your review – if you were mismatched for this review, this would also be my fault as an editor. I have to admit, I wasn't aware of the different uses of the term "occupancy modelling"… Do you feel that you are confident to recommend the paper for acceptance nevertheless? If not, I will find another reviewer that is familiar with the domain.

I was not able to install the package, but the problem is my work computer has an SSL intercept and conda is not working for me at the moment.

I am afraid that installing and running the package is a necessary condition for a review. If you don't think you'll be able to do so on your work machine, then this would be another reason for me to find another reviewer. In case it helps: if you can get your IT department to provide you with the certificates it uses, there are (non-trivial…) ways to make conda use them (https://docs.conda.io/projects/conda/en/latest/user-guide/configuration/non-standard-certs.html). An easier solution is to disable SSL verification (https://docs.conda.io/projects/conda/en/latest/user-guide/configuration/disable-ssl-verification.html) but of course this comes with a security risk.

Regardless of your answer to these questions, thanks again for volunteering to review and the time you spent on this 🙏!

rerickson-usgs · 2024-01-12T16:47:19Z

@mstimberg I am trying again on cloud based Jupyter Lab and it's working. It have worked before on my laptop, but just takes a looooong time. Perhaps a warning about slow install times might be helpful.

rerickson-usgs · 2024-01-12T17:00:43Z

@mstimberg I was able to complete my review. To put all of my feedback on one comments:

I could install and the tests passed
The package is well documented. Some suggestions I have to improve the documentation:
- As a feature request, I would to see the equations included within the package and not just the supporting paper. I liked the documentation (like this file).
- An algorithm flow chart might also help. Basically, something that would allow me to check the implementation of the numerical methods. Something similar to https://hillmaker.readthedocs.io/en/latest/example_occupancy_analysis.html#step-2-process-each-scenario-with-hillmaker that explains how the main hillmaker function(s) work.
- I also really liked this page, https://hillmaker.readthedocs.io/en/latest/analysis_date_range.html, of documentation.
The code seems well organized. I did not run a style check. But,
Please consider adding the style guide you're following to the CONTRIBUTING file

misken · 2024-01-12T18:08:07Z

Thanks for your review @rerickson-usgs. Glad you were able to install and run. hillmaker doesn't rely on conda, you can do a pip install and it only has a few dependencies. I've never had the install itself be slow, hmm, but I'll look into that.

Yes, I can certainly add more technical detail in terms of the algorithm to the docs. It's nothing terribly complex. We are in the process of writing a new hillmaker paper for Health Care Management Science and will be writing up all the technical details as part of that. I can adapt some of that for the docs.

I will modify the CONTRIBUTING file and my PyCharm settings to make sure my linter use is consistent and documented.

It's funny about the "occupancy modeling" confusion. When I do lit review related to occupancy modeling, I often get results related to the type of ecological occupancy modeling that you do. In addition, I've actually gotten involved in some ecology research with a stream ecologist colleague at Oakland University doing processing of massive amounts of temperature sensor data from loggers in streams. :)

misken · 2024-01-16T15:59:17Z

@rerickson-usgs I added some additional algorithmic details to the doc page on how occupancy is computed. Realized that there was a markdown table that wasn't being rendered to the html docs and fixed that - it illustrates the simple occupancy example on that page. I also added a link to the datetime.py file that does the heavy lifting on the occupancy computations - it's extremely thoroughly commented. Hopefully this will improve things until we get our next paper written and can use that a additional info on how hillmaker works.

mstimberg · 2024-01-16T16:20:40Z

Thanks for the updates @misken. Do these additions address your suggestions/concerns, @rerickson-usgs. In other words, would you recommend the paper/software for acceptance as it is? Thanks 🙏 !

mstimberg · 2024-01-26T15:05:14Z

@misken I made some minor changes in a PR (misken/hillmaker#79) – please merge if you are fine with all changes.

misken · 2024-01-26T18:08:43Z

Thanks, @mstimberg. Reviewed and merged. Let me know if anything else needed.

mstimberg · 2024-01-26T19:22:41Z

@editorialbot generate pdf

editorialbot · 2024-01-26T19:23:54Z

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

mstimberg · 2024-01-26T19:28:08Z

Everything is looking good from my side. For the final steps, I'll now hand things over to the track editor 🤝
Thanks again @HLasse and @rerickson-usgs for reviewing !

mstimberg · 2024-01-26T19:29:05Z

@editorialbot recommend-accept

editorialbot · 2024-01-26T19:29:06Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-01-26T19:29:24Z

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

OK DOIs

- 10.1142/s0219622002000439 is OK
- 10.1007/s10729-010-9141-8 is OK
- 10.1023/A:1013034719088 is OK
- 10.2139/ssrn.2437936 is OK
- 10.1016/j.ejor.2010.06.021 is OK
- 10.1177/03611981221115086 is OK
- 10.4018/978-1-60960-872-9.ch019 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.8180180 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.21105/joss.03021 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-01-26T19:30:47Z

👋 @openjournals/sbcs-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#4957, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

misken · 2024-01-30T13:03:26Z

@mstimberg is there something else I need to do here or is this on your end now?

mstimberg · 2024-01-30T13:11:14Z

@misken There is nothing to do from your side now. Please be patient and wait for the track editor to do the final checks and trigger the actual publication. I can ping them if they don't react within a few days, but given that I recommended the acceptance only two working days ago, I wouldn't do this just yet.

misken · 2024-01-30T15:53:29Z

Thanks @mstimberg, just wanted to make sure I wasn't missing some GitHub thing on my side that needed doing. No need to ping anyone, this isn't urgent.

oliviaguest · 2024-01-30T20:18:29Z

@editorialbot recommend-accept

editorialbot · 2024-01-30T20:18:32Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-01-30T20:18:50Z

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

OK DOIs

- 10.1142/s0219622002000439 is OK
- 10.1007/s10729-010-9141-8 is OK
- 10.1023/A:1013034719088 is OK
- 10.2139/ssrn.2437936 is OK
- 10.1016/j.ejor.2010.06.021 is OK
- 10.1177/03611981221115086 is OK
- 10.4018/978-1-60960-872-9.ch019 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.8180180 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.21105/joss.03021 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-01-30T20:19:54Z

👋 @openjournals/sbcs-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#4965, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

oliviaguest · 2024-01-30T20:21:02Z

@editorialbot accept

editorialbot · 2024-01-30T20:21:05Z

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

editorialbot · 2024-01-30T20:27:30Z

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: Isken
  given-names: Mark W.
  orcid: "https://orcid.org/0000-0001-8471-9116"
- family-names: Norman
  given-names: Jacob W.
doi: 10.5281/zenodo.10530420
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Isken
    given-names: Mark W.
    orcid: "https://orcid.org/0000-0001-8471-9116"
  - family-names: Norman
    given-names: Jacob W.
  date-published: 2024-01-30
  doi: 10.21105/joss.06154
  issn: 2475-9066
  issue: 93
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6154
  title: "hillmaker: A Python package for occupancy analysis in discrete
    entity flow systems"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06154"
  volume: 9
title: "hillmaker: A Python package for occupancy analysis in discrete
  entity flow systems"

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.

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editorialbot · 2024-01-30T20:27:33Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-01-30T20:27:34Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.06154 joss-papers#4967
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06154
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

oliviaguest · 2024-01-31T16:58:12Z

Huge thanks to the editor @mstimberg and the reviewers @rerickson-usgs, @HLasse! ✨ JOSS appreciates your work and effort. ✨ Also, big congratulations to the authors! 🥳 🍾

editorialbot · 2024-01-31T16:58:14Z

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

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misken · 2024-01-31T18:09:02Z

Thank you @editorialbot. I have made a donation and signed up to be a reviewer.

editorialbot · 2024-01-31T18:09:04Z

You are welcome

editorialbot added Jupyter Notebook Python review TeX Track: 4 (SBCS) Social, Behavioral, and Cognitive Sciences labels Dec 15, 2023

editorialbot assigned mstimberg Dec 15, 2023

editorialbot mentioned this issue Dec 15, 2023

[PRE REVIEW]: hillmaker: A Python package for occupancy analysis in discrete entity flow systems #6088

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openjournals deleted a comment from editorialbot Jan 26, 2024

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jan 26, 2024

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oliviaguest closed this as completed Jan 31, 2024

[REVIEW]: hillmaker: A Python package for occupancy analysis in discrete entity flow systems #6154

[REVIEW]: hillmaker: A Python package for occupancy analysis in discrete entity flow systems #6154

Comments

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rerickson-usgs commented Dec 15, 2023 • edited Loading

Review checklist for @rerickson-usgs

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

HLasse commented Dec 15, 2023 • edited Loading

Review checklist for @HLasse

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

HLasse commented Jan 5, 2024 • edited Loading

misken commented Jan 5, 2024

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editorialbot commented Dec 15, 2023 •

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rerickson-usgs commented Dec 15, 2023 •

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HLasse commented Dec 15, 2023 •

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HLasse commented Jan 5, 2024 •

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