This update is not backwards compatible. A configuration file update is nescessary. New features Added a new Snakefile for parameter space exploration. Basically acts as a wrapper around the foodme benchmark workflow for parameter grid search using snakemake's Paramspcae utility. Non backward compatible changes Flattened the parameter structure in the configuration. This is more compatible with the --config CLI argument and was required for the implementation of the parameter space exploration workflow. This requires users to update their configurations. Documentation Added documentation for the paramspace workflow
Notable changes, fixes, and additions since the previous release (1.5.1) are listed below. Changes ...
Since the previous release (1.6.1), there should be no changes that affect existing code, only addit...
When updating PlanetProfile via pip, conda, or git pull, new entries added to the config file would ...
1.5.0 This update is not backwards compatible. A configuration file update is nescessary. New featu...
1.5.1 Bug fix Added missing parameters to meat config file Fix dtype parsing in confusion matrix ca...
Bug fix Added missing pandas dependency in taxidTools environment Moved log directive to top of pyt...
Bug fix Moved the benchmark module form a rule to a workflow. THis allows to ignore the benchmark a...
Bug fix Fixed handling of last common node calculation in confusion matrix where last common anceso...
Bug fix Fixed header in consensus-table.tsv Fixed a bash synthax misuse in the calculation of VSear...
1.6.5 Fixes BLAST rule now correctly uses the threads_sample parameter instead of threads. This res...
Updated documentation (moved config documentation into readme). This is an intermediate release that...
What's Changed Reverts name of an argument to MixingParameters to restore backwards compatibility U...
Fixes Corrects parsing of the trim_primers_3end parameter (#64) Added a primer disambiguation step ...
1.6.4 Benchmarking paper for 16S Metabarcoding of meat products is online: Denay, G.; Preckel, L.; P...
[installation]: Downgraded scipy (scipy<1.9) in order to handle (https://github.com/biocore/scikit-b...
Notable changes, fixes, and additions since the previous release (1.5.1) are listed below. Changes ...
Since the previous release (1.6.1), there should be no changes that affect existing code, only addit...
When updating PlanetProfile via pip, conda, or git pull, new entries added to the config file would ...
1.5.0 This update is not backwards compatible. A configuration file update is nescessary. New featu...
1.5.1 Bug fix Added missing parameters to meat config file Fix dtype parsing in confusion matrix ca...
Bug fix Added missing pandas dependency in taxidTools environment Moved log directive to top of pyt...
Bug fix Moved the benchmark module form a rule to a workflow. THis allows to ignore the benchmark a...
Bug fix Fixed handling of last common node calculation in confusion matrix where last common anceso...
Bug fix Fixed header in consensus-table.tsv Fixed a bash synthax misuse in the calculation of VSear...
1.6.5 Fixes BLAST rule now correctly uses the threads_sample parameter instead of threads. This res...
Updated documentation (moved config documentation into readme). This is an intermediate release that...
What's Changed Reverts name of an argument to MixingParameters to restore backwards compatibility U...
Fixes Corrects parsing of the trim_primers_3end parameter (#64) Added a primer disambiguation step ...
1.6.4 Benchmarking paper for 16S Metabarcoding of meat products is online: Denay, G.; Preckel, L.; P...
[installation]: Downgraded scipy (scipy<1.9) in order to handle (https://github.com/biocore/scikit-b...
Notable changes, fixes, and additions since the previous release (1.5.1) are listed below. Changes ...
Since the previous release (1.6.1), there should be no changes that affect existing code, only addit...
When updating PlanetProfile via pip, conda, or git pull, new entries added to the config file would ...