Contributors
Thanks to our contributors!
Accepted PRs from
- Gavin Huttley
- KatherineCaley
- Nick Shahmaras
- Xingjian Leng
Identified a Bug
- StephenRogers1
ENH
Significant refactor of composable apps. This is the backwards incompatible change we warned of in the last release! We now use a decorator `define_app` (on classes or functions) instead of class inheritance. Please see [the c3dev wiki](https://github.com/cogent3/cogent3/wiki/composable-functions) for examples on how to port from old-style to new-style composable apps.
We updated to the latest NCBI versions of genetic codes. Note, the name of genetic code 1 has changed from "Standard Nuclear" to "Standard".
BUG
- Fix progressive alignment bug when a guide-tree with zero edge lengths was encountered.
- Non-stationary independent tuple models can now be serialised.
DEP
- We have removed support for python 3.7.
- We have made scipy a dependency and begun deprecating statistical functions that are available in scipy. All deprecated functions have a warning that indicates the scipy replacement. The deprecated functions are: combinations, chi_high, chdtri, z_high, z_low function, chi_low, binomial_high, binomial_low, f_high, f_low, t_low and t_high.