[REVIEW]: pyfive: A pure-Python HDF5 reader

[editorialbot]

Submitting author: @bnlawrence (Bryan Lawrence)
Repository: https://github.com/ncas-cms/pyfive
Branch with paper.md (empty if default branch): joss_paper
Version: 1.1.0
Editor: @rich2355
Reviewers: @Zeitsperre, @ayenpure, @dostuffthatmatters
Archive: 10.5281/zenodo.18599472

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/406443bb95cff4ed1af6a6ba995b0b55/status.svg)](https://joss.theoj.org/papers/406443bb95cff4ed1af6a6ba995b0b55)

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

@Zeitsperre & @ayenpure & @dostuffthatmatters, 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/pre-2026-submission/reviewer_guidelines.html. Any questions/concerns please let @rich2355 know.

✨ Please start on your review when you are able; the expectation is that it will take 2-4 weeks to complete. ✨

Checklists

📝 Checklist for @ayenpure

📝 Checklist for @dostuffthatmatters

📝 Checklist for @Zeitsperre

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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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]

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

✅ OK DOIs

- 10.3389/fclim.2021.782909 is OK
- 10.1145/1966895.1966900 is OK
- 10.5281/zenodo.17550920 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: NetCDF-4: Software Implementing an Enhanced Data M...
- No DOI given, and none found for title: Chunking Data: Choosing Shapes

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Repository Analysis Report

Code breakdown

github.com/AlDanial/cloc v 1.98  T=0.09 s (1164.7 files/s, 154599.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          75           2067           1719           6012
XML                              1              0            203           1930
reStructuredText                13            261            263            466
Markdown                         3             61             12            165
YAML                             6             16             39            164
TOML                             1             12              7             96
TeX                              1              5              0             64
Text                             1              5              0             25
Bourne Shell                     1              0              2              5
SVG                              1             14             58              1
-------------------------------------------------------------------------------
SUM:                           103           2441           2303           8928
-------------------------------------------------------------------------------

Commit Count by Author

184	Bryan Lawrence
   178	Valeriu Predoi
   153	Jonathan Helmus
    33	Kai Mühlbauer
    23	bnlawrence
    21	David Hassell
    15	valeriupredoi
    11	zequihg50
     7	woutdenolf
     5	Brian Ben Maranville
     4	bbm
     1	Brian Benjamin Maranville
     1	Jonathan J. Helmus
     1	kmuehlbauer
     1	synaptic

Repository History

Repository age: First commit on April 20, 2016

GitHub Activity Metrics

Metric	Count
GitHub stars	94
Forks	24
GitHub contributors	9
Releases	10
Total issues	60
Total pull requests	106
Unique commenters/reviewers (excluding authors)	13

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1188

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

[editorialbot]

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

[rich2355]

Hi @bnlawrence, @Zeitsperre, @ayenpure, @dostuffthatmatters, it is so nice that we started the review right before the Christmas. Before we talk about the actual work, I want to firstly wish everyone a great holiday!

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#9688 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 about 2-4 weeks. I will also remind you if there is no reviewing activity for a while (say, one week). However, it is so close to holidays so I myself probably will also take sometime off 😄. Also, situations are always changing and please feel free to let me know if any of you requires some more time. For example, @dostuffthatmatters is free to start the review after Jan 15th next year, as requested.

Now the stage is both for the reviewers and the authors, but please feel free to ping me (@rich2355) if you have any questions/concerns within the review process.

Best wishes,
RL

[ayenpure]

Review checklist for @ayenpure

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/ncas-cms/pyfive?
• 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 (@bnlawrence) 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?