v0.9.3

• Add extra error class for "unknown" (==unhandled) errors
• Wrap run function and have it optionally raise unhandled exceptions as TreeTimeUnknownError.
  This is mainly done to improve interaction with augur that uses TreeTime internals as a library.
  (both by @anna-parker with input from @victorlin)

PR #206
PR #208

0.9.2: bug fix

bug fix release:

• CLI now works for windows (thanks @corneliusroemer for the fix)
• fixes vcf parsing. haploid no-calls were not properly parsed and treated as reference (thanks @jodyphelan for the issue).
• fix file names in CLI output. (thanks @gtonkinhill)

0.9.1

Performance improvement and less greedy polytomy resolution

This release is mostly a bug-fix release and contains some additional safeguards against unwanted side-effects of greedy polytomy resolution.

• resolve polytomies only when significant LH gain can be achieved
• performance enhancement in pre-order iteration during marginal time tree estimate when hitting large polytomies.
• allow users to set branch specific rates (only when used as a library)

0.9.0: Uses FFT for convolution and ARG support

This release contains several major changes to how TreeTime calculates time scaled phylogenies.
Most of this is work by @anna-parker!

• implements convolutions needed for marginal time tree inference using FFT. Previously, these were calculated by explicit integration using optimized irregular grids. Using FFT requires regular (and hence much finer/larger) grids, but greatly reduces computational complexity from n^2 to n log(n), where n is the number of grid points. The FFT feature can be switched on an off with the use_fft attribute of the ClockTree class.
• Using FFT in convolutions required moving the contributions of the coalescent models from th branches to the nodes. This should not change the results in any way, but cleans up the code.
• The number concurrent of lineages determines the rate of coalescence. This can now optionally be calculated using the uncertainty of the timing of merger events, instead of the step functions used previously.
• Adds a subcommand to read in ancestral reassortment graphs of two segments produced by TreeKnit. This command takes two trees and a file with MCCs inferred by TreeKnit. See these docs for command line usage.

0.8.6

• optionally allow incomplete alignment PR #178
• reduce memory footprint through better clean up and optimizing types. PR #179

0.8.5

• bug fixes related to edge cases were sequences consist only of missing data
• bug fix when the CLI command treetime is run without alignment
• more robust behavior when parsing biopython alignments (id vs name of sequence records)
• drop python 3.5 support

re-release of 0.8.3.1 to avoid problems with distutils

v0.8.4

chore: rerelease

bug fix related to Bio.Seq.Seq now being bytearray

• Biopython changed the representation of sequences from strings to bytearraysin version 1.79. This caused crashes of mugration inference with more than 62 states as states than exceeded the ascii range. This fix now bypasses Bio.Seq in the mugration analysis.

update dependencies

v0.8.3

chore: version bump

bug fix release

v0.8.1

chore: release