• Fixes to the labelling of network component graphs when using partial query graphs (#338)

Note this release fixes the TypeError: Population must be a sequence. For dicts or sets, use sorted(d). error

What's Changed

• Update from master by @nickjcroucher in #288
• Update graph summary processes by @nickjcroucher in #303
• Update from master branch by @nickjcroucher in #312
• Fix External Clusters csv being duplicated by @absternator in #324
• Small fixes to database pruning and updating by @nickjcroucher in #328
• Update plotting and network summary statistics by @nickjcroucher in #304
• Enable assignment & visualisation with partial query graphs by @nickjcroucher in #332

Full Changelog: v2.7.0...v2.7.1

Main additions are to remove the need for distance matrices (.dists.npy) in query assignment, and a formal stable nomenclature mode with --stable.

What's Changed

• Docs update by @samhorsfield96 in #318
• Replaced deprecated 'rU' with 'r' to make this work on recent python by @tgttunstall in #319
• PopPUNK 2.7.0 candidate by @johnlees in #320

New Contributors

• @tgttunstall made their first contribution in #319

Full Changelog: v2.6.7...v2.7.0

What's Changed

• Move call of sketchlibAssemblyQC in query assign by @absternator in #317

Full Changelog: v2.6.6...v2.6.7

Add more QC fail reporting for beebop

What's Changed

• Update cluster assign to write qcreport on qc failiures by @absternator in #315

New Contributors

• @absternator made their first contribution in #315

Full Changelog: v2.6.5...v2.6.6

Enables correct visualisation of external clustering.

Better DBSCAN fits and a fix to visualisation code

What's Changed

• Improvements to DBSCAN fitting by @nickjcroucher in #301
• Updates to DBSCAN fitting by @nickjcroucher in #302
• Avoid overwriting external clustering in visualise script by @nickjcroucher in #305

Full Changelog: v2.6.3...v2.6.4

Hotfix to fix some external cluster assigments #298
Also move docs to https://poppunk.bacpop.org/

What's Changed

• Update readthedocs config file to v2 by @johnlees in #291
• Add the roadmap to the docs by @johnlees in #292
• Add actions for docs build by @johnlees in #293
• Rename docs action by @johnlees in #294
• Use gha to publish docs by @johnlees in #295
• Remove permissions and add CNAME by @johnlees in #296
• Add permissions again by @johnlees in #297
• Poppunk assign fix by @samhorsfield96 in #298

Full Changelog: v2.6.2...v2.6.3

Hotfix for reference network name in poppunk_assign

What's Changed

• Update assign.py by @samhorsfield96 in #290

Full Changelog: v2.6.1...v2.6.2

Many small bug fixes

What's Changed

• Fix a broken error message in assign by @johnlees in #246
• Updates for GPU analysis + documentation by @nickjcroucher in #251
• Path fix for distance plot, update docs with new DB page by @johnlees in #252
• Increase default mandrake maxiter by 10x by @johnlees in #256
• Correct database content filenames by @HarryHung in #257
• Iterative PopPUNK updates by @BZhao95 in #259
• Fix for using visualise with indiv refine ref-db by @johnlees in #261
• Update Git Repository link by @HarryHung in #271
• Improve manual installation instruction by @HarryHung in #274
• Update CI to new mamba action by @johnlees in #272
• Fix overwrite, correct error messages by @HarryHung in #282
• API change in mpl380 ellipses by @johnlees in #285
• Allow overwrite if forced by @johnlees in #279
• Remove deprecated system packages from readthedocs build by @johnlees in #286

New Contributors

• @HarryHung made their first contribution in #257

Full Changelog: v2.6.0...v2.6.1