Published March 3, 2023
| Version v1.0.0
Software
Open
Pynteny: a Python package to perform synteny-aware, profile HMM-based searches in sequence databases
- 1. Department of Microbiology. University of La Laguna. Spain.
Description
This is a release post-review after submitting the package at PyOpenSci. Additionally, the streamlit app has been removed (subcommand pynteny app) as it will be released later on in a different, pip-installable package (as an addon too pynteny). This changed has two motivations: 1) facilitate solving dependencies by conda and 2) streamline pynteny's code base.
What's Changed
- python >= 3.8 by @Robaina in https://github.com/Robaina/Pynteny/pull/36
- PyOpenSci REVIEW - Refactor code to meet PEP8 by @Robaina in https://github.com/Robaina/Pynteny/pull/40
- PyOpenSci REVIEW - extract nested functions in LabelledFASTA by @Robaina in https://github.com/Robaina/Pynteny/pull/47
- PyOpenSci REVIEW - minor updates by @Robaina in https://github.com/Robaina/Pynteny/pull/43
- PyOpenSci REVIEW - extract static classes and transfer to own modules by @Robaina in https://github.com/Robaina/Pynteny/pull/45
- PyOpenSci REVIEW - add setup to docs, add building docs to contributing by @Robaina in https://github.com/Robaina/Pynteny/pull/50
- change structure to adopt /src layout by @Robaina in https://github.com/Robaina/Pynteny/pull/54
- PyOpenSci REVIEW - config and download default directories by @Robaina in https://github.com/Robaina/Pynteny/pull/51
- PyOpenSci REVIEW - remove default location for PGAP download by @Robaina in https://github.com/Robaina/Pynteny/pull/57
- added config to install dir by @Robaina in https://github.com/Robaina/Pynteny/pull/58
- PyOpenSci REVIEW - 59 some more minor changes by @Robaina in https://github.com/Robaina/Pynteny/pull/60
- Chore/add qoc config by @Batalex in https://github.com/Robaina/Pynteny/pull/62
- Ensure file inputs are of type Path by @Robaina in https://github.com/Robaina/Pynteny/pull/63
- 29 deal with genome id when building peptide database by @Robaina in https://github.com/Robaina/Pynteny/pull/64
- add file name to files in fasta dir by @Robaina in https://github.com/Robaina/Pynteny/pull/68
- 69 download pfam database and split models into separate files by @Robaina in https://github.com/Robaina/Pynteny/pull/70
- update docs by @Robaina in https://github.com/Robaina/Pynteny/pull/72
- Adjacent repeated genes by @Robaina in https://github.com/Robaina/Pynteny/pull/73
- 74 optional prepend file name when multiple input files by @Robaina in https://github.com/Robaina/Pynteny/pull/75
- 77 Remove Streamlit App by @Robaina in https://github.com/Robaina/Pynteny/pull/81
- Requests + tqdm instead of python-wget by @Robaina in https://github.com/Robaina/Pynteny/pull/84
New Contributors
- @Batalex made their first contribution in https://github.com/Robaina/Pynteny/pull/62
Full Changelog: https://github.com/Robaina/Pynteny/compare/v0.0.5...v1.0.0
Notes
Files
Robaina/Pynteny-v1.0.0.zip
Files
(2.5 MB)
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md5:ee160a53e2c08d224a4978d68666f69a
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Additional details
Related works
- Is supplement to
- https://github.com/Robaina/Pynteny/tree/v1.0.0 (URL)