[REVIEW]: MiSTree: a Python package for constructing and analysing Minimum Spanning Trees

[whedon]

Submitting author: @knaidoo29 (Krishna Naidoo)
Repository: https://github.com/knaidoo29/mistree
Version: v1.2
Editor: @xuanxu
Reviewer: @melissawm, @zonca
Archive: 10.5281/zenodo.3495008

Status

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Markdown: [![status](https://joss.theoj.org/papers/461d79e9e5faf21029c0a7b1c928be28/status.svg)](https://joss.theoj.org/papers/461d79e9e5faf21029c0a7b1c928be28)

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.)

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

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✨ Please try and complete your review in the next two weeks ✨

Review checklist for @melissawm

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 (@knaidoo29) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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 @zonca

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 (@knaidoo29) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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. @melissawm, @zonca it looks like you're currently assigned to review this paper 🎉.

⭐ 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 😿

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@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[zonca]

Installation

• missing requirement on matplotlib Missing requirement knaidoo29/mistree#1
• package is not installable Package is not installable knaidoo29/mistree#2

Tests

• Tests are missing Tests are missing knaidoo29/mistree#3

Docs

• Expand statement of need Expand "statement of need" knaidoo29/mistree#4
• Add example notebook Add example notebook knaidoo29/mistree#5
• How to report issues How to report issues knaidoo29/mistree#6

[knaidoo29]

Just to keep everyone in the loop. I believe I have now addressed the installation issues addressed by @zonca. I've added matplotlib as a requirement and simplified the installation which is now done using pip (details are explained in the README and documentation). I've done some test on a few machines and this seems to be working smoothly so hopefully there are no longer any issues with this. I'm going to work on the testing in the next few days and will let you know once this is ready.

[zonca]

ok, @knaidoo29, anything related to software looks fine to me, now we'll focus on the paper: knaidoo29/mistree#7

[knaidoo29]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[melissawm]

Hello @knaidoo29 , I still haven't been able to install mistree, can you take a look at the two issues I just opened? Thanks!

[knaidoo29]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[knaidoo29]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[knaidoo29]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[zonca]

@xuanxu Accept

[xuanxu]

@zonca: Thanks! (There's some unchecked items in your review list, I guess you consider them done)

[melissawm]

@xuanxu Accepted, thanks.

[xuanxu]

Great, thanks @melissawm!

[knaidoo29]

Great to see that it's been accepted! Really appreciate all the help from both @zonca and @melissawm. I think the code and the paper are now much stronger.

@xuanxu is there anything I need to do before publication?

[xuanxu]

@whedon generate pdf

[xuanxu]

@whedon set 10.5281/zenodo.3495008 as archive

[whedon]

OK. 10.5281/zenodo.3495008 is the archive.

[xuanxu]

Everything looks ready 🎉
Pinging @openjournals/joss-eics for final acceptance

[Kevin-Mattheus-Moerman]

@openjournals/jose-eics does anybody know why for this paper the "matplotlib" project name is broken over 2 lines without a hyphen? is this because it is seen as a piece of code text? Since they use the `` symbols? i.e. the authors use

Dependencies for ``MiSTree`` include the ``Python`` modules ``numpy`` [@numpy], ``matplotlib`` [@Hunter:2007]

In the paper this is broken onto the next line like this:

Dependencies for MiSTree include the Python modules numpy (Oliphant, 2006), matplo
tlib (Hunter, 2007), ...

The authors have used code style formatting for all project names. If this is the issue then perhaps a simple quick fix is to use italic fonts rather then code fonts for project names.

[kyleniemeyer]

@Kevin-Mattheus-Moerman yes, that's probably what's going on. I wonder if adding a line break (\\) before the word would help?

[knaidoo29]

@Kevin-Mattheus-Moerman I'm happy to change this to italic font instead if that is the cause of the issue.

[Kevin-Mattheus-Moerman]

@knaidoo29 sure. Can you make that change and run @whedon generate pdf once you are done? Thanks.

[knaidoo29]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[knaidoo29]

Okay @Kevin-Mattheus-Moerman it looks like this has solved the issue.

[Kevin-Mattheus-Moerman]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

OK DOIs

- 10.1086/311146 is OK
- 10.1128/JCM.42.9.4230-4236.2004 is OK
- 10.1002/j.1538-7305.1957.tb01515.x is OK
- 10.1088/1748-0221/12/02/P02009 is OK
- 10.1093/mnras/stt2136 is OK
- 10.1111/j.1365-2966.2009.14508.x is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1504/IJCSE.2009.029165 is OK
- 10.2307/2033241 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof 👉 openjournals/joss-papers#1029

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1029, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[Kevin-Mattheus-Moerman]

@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.01721 joss-papers#1030
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01721
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...

[whedon]

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

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[Kevin-Mattheus-Moerman]

Congratulations @knaidoo29
Thanks @melissawm and @zonca for reviewing this work!!! 🎉
Thank you @xuanxu for editing this.

[knaidoo29]

Hi @Kevin-Mattheus-Moerman just noticed that the footnote starts with Naidoo, (3030). shouldn't this be Naidoo, (2019). or Naidoo, K. (2019).?

[Kevin-Mattheus-Moerman]

@openjournals/dev ☝️ is this fixable

[Kevin-Mattheus-Moerman]

@openjournals/dev @arfon 👋 is this fixable

[xuanxu]

@Kevin-Mattheus-Moerman @knaidoo29 There was a bug causing the 3030 in the footer, but it has been fixed and all the affected papers are recompiled now. Current paper should be OK.