v3.3.2

Full Changelog: v3.3.1...v3.3.2

Full Changelog: v3.3.1...v3.3.2

🐋 Kaptive is containerized!

What's Changed

• Merge pull request #2 from klebgenomics/master by @tomdstanton in #69

Full Changelog: v3.3.0...v3.3.1

Database Decentralisation 📦

What's new?

Decentralised databases 📦

• Kaptive v3.3.0 fully decouples databases from the tool.
• Fully versioned databases.
• Only install the databases you need.
• Easier for curators to maintain their databases.

A new core 🍎

• Kaptive v3.3.0 is built around a new ultra fast API-first core.
• Allows for easier integration of new modules like plotting and annotation.
• Objects are structured with a data-oriented-design approach leveraging numpy for SoA (structure of arrays) batching.
• Designed for vectorised computation.
• Easier integration of machine learning in the future.
• Results are stored in frozen, slotted dataclasses - designed for efficiency, thread-safety and integration with web APIs.
• Extremely fast with numba!

Introduction of rammappy 🚀

• Kaptive is now 100% pip installable.
• No more background sub-processes, all computation happens directly in Kaptive.
• Safe for Web APIs.

Full Changelog: v3.2.2...v3.3.0

v3.2.2: fix: Rename inputf argument to input in cli.py

What's Changed

• Migrate to mkdocs. by @tomdstanton in #54
• Bump urllib3 from 2.6.3 to 2.7.0 by @dependabot[bot] in #57
• Bump tj-actions/changed-files from 42 to 46 in /.github/workflows by @dependabot[bot] in #60
• Bump idna from 3.11 to 3.15 by @dependabot[bot] in #59

New Contributors

• @dependabot[bot] made their first contribution in #57

Full Changelog: v3.2.1...v3.2.2

v3.2.1

What's Changed

• Remove dna features viewer by @tomdstanton in #52

Full Changelog: v3.2.0...v3.2.1

v3.2.0

What's Changed

• Add missing links to Outputs.rst by @pvanheus in #43
• Update annotations for KpSC K-locus genes by @tomdstanton in #49
• Update KpSC K logic allele names by @tomdstanton in #51

New Contributors

• @pvanheus made their first contribution in #43

Full Changelog: v3.1.0...v3.2.0

v3.1.0

What's Changed

• Kaptive 3 by @tomdstanton in #28
• • Bump to version 3.0.0b1 by @tomdstanton in #30
• Fixed TypingResult.from_dict class method when extra genes are pres… by @tomdstanton in #32
• Update to typing pipeline for close A.baumannii K-loci by @tomdstanton in #33
• Merge pull request #33 from klebgenomics/development by @tomdstanton in #34
• Bump to v3.0.0b4 for PyPI/Conda push by @tomdstanton in #35
• Bump to v3.0.0b5 by @tomdstanton in #36
• Update version to v3.1.0 by @tomdstanton in #41
• Bump to v3.1.0 by @tomdstanton in #42

New Contributors

• @tomdstanton made their first contribution in #28

Full Changelog: v2.0.9...v3.1.0

v3.0.0b6

• Fixes #37 and #39: thanks @katholt and @CorinYeatsCGPS!
• Removed the K. pnuemoniae variant database.

Full Changelog: v3.0.0b5...v3.0.0b6

v3.0.0b5

What's Changed

• Bump to v3.0.0b5 by @tomdstanton in #36

Full Changelog: v3.0.0b4...v3.0.0b5

v3.0.0b4

What's Changed

• Merge pull request #33 from klebgenomics/development by @tomdstanton in #34
• Bump to v3.0.0b4 for PyPI/Conda push by @tomdstanton in #35

Full Changelog: v3.0.0b3...v3.0.0b4