Pynteny: a Python package to perform synteny-aware, profile HMM-based searches in sequence databases

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