PopPUNK Versions Save

Many small bug fixes

What's Changed

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

New Contributors

• @HarryHung made their first contribution in https://github.com/bacpop/PopPUNK/pull/257

Full Changelog: https://github.com/bacpop/PopPUNK/compare/v2.6.0...v2.6.1

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

New Contributors

• @BZhao95 made their first contribution in https://github.com/bacpop/PopPUNK/pull/216
• @samhorsfield96 made their first contribution in https://github.com/bacpop/PopPUNK/pull/226
• @tmaklin made their first contribution in https://github.com/bacpop/PopPUNK/pull/239

Full Changelog: https://github.com/bacpop/PopPUNK/compare/v2.5.0...v2.6.0

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

New Contributors

• @muppi1993 made their first contribution in https://github.com/bacpop/PopPUNK/pull/201
• @richfitz made their first contribution in https://github.com/bacpop/PopPUNK/pull/209

Full Changelog: https://github.com/bacpop/PopPUNK/compare/v2.4.0...v2.5.0

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

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

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)

• Update to sketchlib 1.4.0 (#90) (https://github.com/johnlees/pp-sketchlib/releases/tag/v1.4.0)
• Use faster, threaded matrix functions (#78, #80)
• Change from networkx to graph-tool (#83)
• Use sharedmem (#76)
• Add --lineage-clustering mode (#72)
• Better --refine-model default boundary (#94)

NB python >=3.8 is now required (#81, #76)

This accommodates updates to pp-sketchlib introduced since v1.1.0, mostly passing through new command line parameters (e.g. --use-gpu). See https://github.com/johnlees/pp-sketchlib/releases/tag/v1.3.0 for more info.

This is a major new release of PopPUNK, which uses a new 'backend' to do sketching and distance calculation, pp-sketchlib

This changes the input format and the API somewhat, will be incompatible with previous database versions, and generates slightly different distance results. If you need backwards compatibility the previous version can still be run by specifying --use-mash.

New features:

• Use pp-sketchlib as the backend. This is ~2x faster for sketching and 50-100x faster for distance calculations. Databases are ~1/4 of the size.
• Input data is now formatted as a tab separated file with name followed by any associated sequence. Sample names no longer have to be filenames. (Closes #43, #46)
• Read data can now be handled, including a filter to remove k-mers containing sequencing errors
• Faster database edits with prune_db and reference_pick
• Ability to use the previous sketching method and databases by specifying --use-mash

Bug fixes:

• Better error handling when creating visualisations, so output files are still produced if this fails

This adds:

• The ability to use a simple core threshold (#49)
• Use external clusters in generate viz mode (#55)

Other:

• Add scripts into package (#56)