PopPUNK v2.6.5

Enables correct visualisation of external clustering.

PopPUNK v2.6.4

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

PopPUNK v2.6.3

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

PopPUNK v2.6.2

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

PopPUNK v2.6.1

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

PopPUNK v2.6.0

Main changes:

• Lineage fits now use reciprocal best match with --reciprocal-only, --count-unique-distances and --max-search-depth, which gives better results.
• Fixes for threshold model assignment

What's Changed

• Update parsing fixes branch with new master by @nickjcroucher in #195
• Update with recent changes to master by @nickjcroucher in #205
• Integrate changes from V250 candidate by @nickjcroucher in #206
• Small fixes for beebop by @muppi1993 in #217
• Update poppunk_iterate.py by @BZhao95 in #216
• Read the docs sphinx version by @johnlees in #215
• Adds poppunk_distribute_fit.py by @samhorsfield96 in #226
• Update with changes to master by @nickjcroucher in #230
• Patch for relative paths in plot fit by @johnlees in #236
• Fix option names for k-mer range min/max and k-mer step. by @tmaklin in #239
• Fix for assign with threshold models by @johnlees in #240
• Lineage model fitting - PopPUNK changes by @nickjcroucher in #232
• Remove blas by @johnlees in #244
• Proceed with update-db on QC failure by @johnlees in #245

New Contributors

• @BZhao95 made their first contribution in #216
• @samhorsfield96 made their first contribution in #226
• @tmaklin made their first contribution in #239

Full Changelog: v2.5.0...v2.6.0

PopPUNK v2.5.0

Minimum sketchlib version for this release is v2.0.0

New features:

• Dendropy replaced with faster & more reliable alternatives #203
• A new logo #202
• Improve iterative PopPUNK code
• Documentation update and improvements #191
• Deal better with name clash when querying #190
• Make manual start a bit easier to use #174
• Replace t-SNE with mandrake
• Output .microreact files, and allow direct creation of Microreact instances with an API key
• Various QC additions to help with multi-cluster merges #194

Bug fixes:

• Various fixes to cytoscape visualisation #185 #196 #210
• Hide progress bars when using --plot-fit
• Stop always checking query-query dists when clustering (and potential bug adding them to network twice)
• Fix N QC when working with reads #207

What's Changed

• Upgrade of GPU refinement by @nickjcroucher in #164
• Remove start_point concept from refine fit by @johnlees in #168
• Upgrades to refinement functions by @nickjcroucher in #175
• Update MST calculation documentation by @nickjcroucher in #177
• Move the extend algorithm into the C++ extension by @johnlees in #178
• Multi-boundary method by @johnlees in #180
• Bacpop 17 by @muppi1993 in #201
• Add rapidnj to docker image by @muppi1993 in #212
• Release for v2.5.0 by @johnlees in #204
• pip installable poppunk, almost by @richfitz in #209

New Contributors

• @muppi1993 made their first contribution in #201
• @richfitz made their first contribution in #209

Full Changelog: v2.4.0...v2.5.0

PopPUNK v2.4.0

Minimum sketchlib version for this release is v1.7.0

To use --gpu-graph requires cudf and cugraph to be installed from the nvidia conda channel, which is not part of the standard installation)

New features:

• Adds minimum spanning tree computation and visualisation #141 #148
• Add two new network scores based on betweenness #146
• Move boundary code into a C++ extension in this package #146 #158
• Adds GPU accelerated graphs #87 #148
• Adds a docker container which is used for web.poppunk.net #151 #162
• New github actions for testing and building the web API #151
• Add progress bars in for model assignment #155
• Parallelise model assignment #155
• Adds the VLKC terminology, and 'unword' cluster names #161

Bug fixes:

• Correctly specify thread count with rapidnj #139
• Regenerate random match changes after --update-db #149
• Fix issue with label order when using --update-db more than once #152
• Update some scripts/ to work with newer versions of numpy and scikit-learn #160
• Keep hyphens in sample names in trees #159
• Fix a plot name #158
• Pin some package versions #140 #142

PopPUNK v2.3.0

This is a major (API-breaking) update which moves the assign and visualisation functions into their own programs, to make the program more modular. The minimum version of pp-sketchlib required is 1.6.0.

New features:

• Lineage assign mode uses matrix code in pp-sketchlib #108
• New algorithm for clique pruning #110
• Visualisation and query moved out of main, and into their own programs #112 #115 #129
• Simpler CLI defaults #125
• Updated documentation #122
• Add edge weights to graph #123
• Add API for use of poppunk_assign with a http server #124 #131
• Add corrected/uncorrected distances when plotting k-mer fits #136

Bug fixes:

• More stable generation of documentation #132
• Fixes continue mode for QC function #134
• Fixes long length QC fail #137

PopPUNK v2.2.0

The first bug fix will affect many results, and all users are encouraged to upgrade

New features:

• More thorough sample QC using pp-sketchlib features (#101)
• Update to pp-sketchlib v1.5.1 (#104)

Bug fixes:

• Misordered labels with older versions of pp-sketchlib (#95)
• TypeError with visualisations (#99)
• networkx still used in reference prune program (#97)