pyfive: A pure-Python HDF5 reader
pyfive: A pure-Python HDF5 reader - Published in JOSS (2026)
Science Score: 92.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 4 DOI reference(s) in README and JOSS metadata -
✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
5 of 12 committers (41.7%) from academic institutions -
✓Institutional organization owner
Organization ncas-cms has institutional domain (cms.ncas.ac.uk) -
✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords from Contributors
Repository
A pure Python HDF5 file reader
Basic Info
- Host: GitHub
- Owner: NCAS-CMS
- License: bsd-3-clause
- Language: Python
- Default Branch: main
- Homepage: https://pyfive.readthedocs.io
- Size: 2.44 MB
Statistics
- Stars: 94
- Watchers: 9
- Forks: 25
- Open Issues: 13
- Releases: 11
Metadata Files
README.md
pyfive : A pure Python HDF5 file reader
pyfive is an open source library for reading HDF5 files written using
pure Python (no C extensions). The package is still in development and not all
features of HDF5 files are supported.
pyfive aims to support the same API as h5py for reading files.
Cases where a file uses a feature that is supported by h5py but not pyfive are considered bugs
and should be reported in our Issues.
Writing HDF5 output is not a goal of pyfive and portions of the API which apply only to writing will not be implemented.
Dependencies
pyfive is tested against Python versions 3.10 to 3.14.
It may also work with other Python versions.
The only dependencies to run the software besides Python is numpy.
Install
pyfive can be installed using pip using the command::
pip install pyfive
conda packages are also available from conda-forge::
conda install -c conda-forge pyfive
To install from source in your home directory use::
pip install --user ./pyfive
The library can also be imported directly from the source directory.
Development
git
You can check out the latest pyfive souces with the command::
git clone https://github.com/NCAS-CMS/pyfive.git
testing
pyfive comes with a test suite in the tests directory.
These tests can be exercised using the pytest command from the root directory (requires installation of the pytest package).
Conda-forge feedstock
Package repository conda-forge feedstock
Codecov
Test coverage assessement is done using codecov
Documentation
Build locally with Sphinx:
$ sphinx-build -Ea doc doc/build
Owner
- Name: NCAS CMS
- Login: NCAS-CMS
- Kind: organization
- Location: UK
- Website: http://cms.ncas.ac.uk/
- Repositories: 10
- Profile: https://github.com/NCAS-CMS
Useful tools to support NERC weather and climate research
JOSS Publication
pyfive: A pure-Python HDF5 reader
Authors
National Center for Atmospheric Science (NCAS), United Kingdom., Department of Meteorology, University of Reading, Reading, United Kingdom.
Instituto de Física de Cantabria (IFCA), CSIC-Universidad de Cantabria, Santander, Spain.
European Synchrotron Radiation Facility (ESRF), Grenoble, France.
National Center for Atmospheric Science (NCAS), United Kingdom., Department of Meteorology, University of Reading, Reading, United Kingdom.
Astral Software Inc., USA.
Independent Researcher, USA.
NIST Center for Neutron Research, USA.
Institute of Geosciences, Meteorology Section, University of Bonn, Germany.
National Center for Atmospheric Science (NCAS), United Kingdom., Department of Meteorology, University of Reading, Reading, United Kingdom.
Editor
Richard Liu
Tags
Atmospheric Science Physics Climate Model Data EngineeringGitHub Events
Total
- Create event: 34
- Commit comment event: 4
- Release event: 2
- Delete event: 28
- Pull request event: 63
- Fork event: 3
- Issues event: 78
- Watch event: 11
- Issue comment event: 220
- Push event: 189
- Pull request review event: 88
- Pull request review comment event: 101
Last Year
- Create event: 25
- Commit comment event: 4
- Release event: 2
- Delete event: 16
- Pull request event: 49
- Fork event: 3
- Issues event: 43
- Watch event: 11
- Issue comment event: 145
- Push event: 142
- Pull request review comment event: 88
- Pull request review event: 76
Committers
Last synced: 5 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jonathan Helmus | j****s@g****m | 154 |
| Bryan Lawrence | b****e@n****k | 110 |
| Valeriu Predoi | v****i@g****m | 101 |
| David Hassell | d****l@n****k | 19 |
| Kai Mühlbauer | k****r@u****e | 18 |
| Bryan Lawrence | b****e@r****k | 10 |
| Brian Ben Maranville | b****e@n****v | 10 |
| Kai Mühlbauer | k****r@w****g | 7 |
| woutdenolf | w****f@u****t | 7 |
| zequihg50 | e****a@u****s | 3 |
| David Hassell | d****l@u****m | 1 |
| synaptic | s****w@h****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 9 days ago
All Time
- Total issues: 33
- Total pull requests: 30
- Average time to close issues: 9 months
- Average time to close pull requests: 16 days
- Total issue authors: 5
- Total pull request authors: 6
- Average comments per issue: 2.09
- Average comments per pull request: 2.43
- Merged pull requests: 13
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 15
- Pull requests: 24
- Average time to close issues: 19 days
- Average time to close pull requests: 1 day
- Issue authors: 3
- Pull request authors: 6
- Average comments per issue: 0.93
- Average comments per pull request: 2.5
- Merged pull requests: 10
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- bnlawrence (18)
- valeriupredoi (6)
- kmuehlbauer (5)
- davidhassell (3)
- jjhelmus (1)
Pull Request Authors
- valeriupredoi (11)
- davidhassell (7)
- kmuehlbauer (5)
- bnlawrence (4)
- zequihg50 (2)
- bmaranville (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
- Total downloads: unknown
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 3
conda-forge.org: pyfive
- Homepage: https://github.com/NCAS-CMS/pyfive
- License: BSD-3-Clause
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Latest release: 0.3.0
published over 3 years ago
Rankings
Dependencies
- actions/checkout v3 composite
- actions/setup-python v3 composite
- autodocsumm
- h5py
- netcdf4
- numpy >=2
- pytest
- pytest-cov
- pytest-rerunfailures
- python >=3.10
- sphinx
- sphinx_rtd_theme
- actions/checkout v4 composite
- actions/upload-artifact v4 composite
- openjournals/openjournals-draft-action master composite
- actions/checkout v4 composite
- actions/setup-python v4 composite
- pypa/gh-action-pypi-publish release/v1 composite
- numpy >=2