2.0.3

• Solves docker compatibility issues for pathogens other than SARS-CoV-2
• Adjusts how versions are printed out for demix --version

2.0.2

• adds covar for accelerated freyja covariants analyses
• adds barcode versioning for non-SARS-CoV-2 pathogens (which are in the freyja-barcodes repo)
• standardizes nomenclature schemes for barcodes and lineageyml for non-SC2 pathogens

2.0.1

Provides updates to 2.0.0. Thanks @ahmig for the help! These updates include:

1. control over the number threads being used (following introduction of corresponding parameters in cvxpy) in demix
2. verbose solver outputs for demix
3. explicit checking for possible issues in lineage hierarchy yml files
4. updates to the amplicon stat functionality, including bed file validation for amplicon seq data
5. minor bug fixes and updates to documentation

Closes #290

2.0.0

Freyja 2 release.

• expands Freyja analyses for pathogens beyond SARS-CoV-2, including seasonal and avian Flu, Dengue, MPXV, and Measles
• easier version checking
• barcode collapse updates to ensure correct grouping for other pathogens
• corresponding documentation, including for BarcodeForge
• some small bug fixes

1.5.3

• Adds flexibility and pandas robustness for freyja dash
• Handles VCF outputs from bcftools, and other variant callers
• Adds --autoadapt parameter for automatic selection of the --adapt parameter
• Fixes to freyja covariants
• Incorporation of multiple new pathogens, including H5N1 avian influenza

1.5.2

• Adds non-SARS-CoV-2 pathogen updating and demixing, via the --pathogen flag.
• Bug fixes, including np.float() error observed on some configurations

1.5.1

• changes default solver to clarabel, with options to use ecos and osqp
• improvements to the covariants function
• small bug fixes, plotting improvements
• switches barcodes to feather format, for faster loading and smaller file size.

1.5.0

• adds --depthcutoff features to account for available genome coverage, de-aliasing, and assignment of MRCAs
• enables both true and relaxed MRCA assignment
• incorporates collapsed MRCAs into summarization and plotting
• some small speed improvements
• option to set variants threshold above 0 for space constraints

1.4.9

Includes a series of updates:

• Improved error message reporting to prevent hard to understand fail cases
• Dash and plot changes to prevent labels/legend from being cut off
• spike (or arbitrary genome region) coverage estimates
• options to retain intermediate outputs via dash/plot
• lineage hierarchy input for demix, plot, dash, relgrowthrate

1.4.8

Bug fixes, plus beta version of adaptive regularization method.