What's Changed * switch deploy to use trusted publisher rather than token/password by reece in https://github.com/biocommons/biocommons.seqrepo/pull/178 * Add shell script for autoupdate seqrepo by icebert in https://github.com/biocommons/biocommons.seqrepo/pull/124 * build: require typing_extensions by jsstevenson in https://github.com/biocommons/biocommons.seqrepo/pull/182
New Contributors * icebert made their first contribution in https://github.com/biocommons/biocommons.seqrepo/pull/124
What's Changed * style: apply updated style configs from template by jsstevenson in https://github.com/biocommons/biocommons.seqrepo/pull/141 * Do not preserve permissions when pulling an instance with rsync by theferrit32 in https://github.com/biocommons/biocommons.seqrepo/pull/144 * fix: resolve type errors/add type annotations by jsstevenson in https://github.com/biocommons/biocommons.seqrepo/pull/151 * docs: add description of store() by jsstevenson in https://github.com/biocommons/biocommons.seqrepo/pull/152 * refactor: use importlib instead of pkg_resources by jsstevenson in https://github.com/biocommons/biocommons.seqrepo/pull/149 * fix: remove unneeded __future__ imports by jsstevenson in https://github.com/biocommons/biocommons.seqrepo/pull/153 * chore: fix license classifier by jsstevenson in https://github.com/biocommons/biocommons.seqrepo/pull/154 * docs: add note about commit() by jsstevenson in https://github.com/biocommons/biocommons.seqrepo/pull/157 * fix: properly initialize file handler by jsstevenson in https://github.com/biocommons/biocommons.seqrepo/pull/160 * refactor: use Python 3 stdlib instead of six by jsstevenson in https://github.com/biocommons/biocommons.seqrepo/pull/164 * style: format with Ruff by jsstevenson in https://github.com/biocommons/biocommons.seqrepo/pull/158 * chore: add git ignore revs file by jsstevenson in https://github.com/biocommons/biocommons.seqrepo/pull/165 * build: require python>=3.10 by jsstevenson in https://github.com/biocommons/biocommons.seqrepo/pull/155 * refactor: resolve timezone-related python 3.12 deprecations by jsstevenson in https://github.com/biocommons/biocommons.seqrepo/pull/161 * chore: remove unused YAPF config by jsstevenson in https://github.com/biocommons/biocommons.seqrepo/pull/167 * feat: check rsync vs openrsync binary on CLI startup by jsstevenson in https://github.com/biocommons/biocommons.seqrepo/pull/172 * 176 resolve testing warnings by reece in https://github.com/biocommons/biocommons.seqrepo/pull/177
* fix: finish migrating from setup.cfg to pyproject.toml in order to install seqrepo cli by reece in https://github.com/biocommons/biocommons.seqrepo/pull/139
What's Changed * build: fix dynamic dependencies for newer setuptools versions by jsstevenson in https://github.com/biocommons/biocommons.seqrepo/pull/133 * feat(130): Introduces SEQREPO_FD_CACHE_MAXSIZE env var by kazmiekr in https://github.com/biocommons/biocommons.seqrepo/pull/131
New Contributors * jsstevenson made their first contribution in https://github.com/biocommons/biocommons.seqrepo/pull/133 * kazmiekr made their first contribution in https://github.com/biocommons/biocommons.seqrepo/pull/131
What's Changed * Update README.md by holtgrewe in https://github.com/biocommons/biocommons.seqrepo/pull/102 * docs: proposing to use default issue templates (110) by holtgrewe in https://github.com/biocommons/biocommons.seqrepo/pull/111 * 119: migrate to biocommons.example template by reece in https://github.com/biocommons/biocommons.seqrepo/pull/120 * Citation file by afrubin in https://github.com/biocommons/biocommons.seqrepo/pull/123 * Update README to support OSX users by dylan-myome in https://github.com/biocommons/biocommons.seqrepo/pull/122 * Thread safety for FastaDir file handle cache by theferrit32 in https://github.com/biocommons/biocommons.seqrepo/pull/117 * 112 make fastadir thread safe by reece in https://github.com/biocommons/biocommons.seqrepo/pull/118
New Contributors * holtgrewe made their first contribution in https://github.com/biocommons/biocommons.seqrepo/pull/102 * afrubin made their first contribution in https://github.com/biocommons/biocommons.seqrepo/pull/123 * dylan-myome made their first contribution in https://github.com/biocommons/biocommons.seqrepo/pull/122 * theferrit32 made their first contribution in https://github.com/biocommons/biocommons.seqrepo/pull/117
- Create thread-local seqrepo instance, which should lessen thread safety issues in pysam (specifically, races when seeking within files) - Soft-pin biocommons.seqrepo to >=0.6.6, which brings additional bug fixes