Treetime

* fix bug that omitted the inferred state of the root in the nexus export of the migration command
* add CLI flag and functionality to load sequence evolution models inferred and saved by TreeTime as human-readable text files. The flag is `--custom-gtr <filename>` and overwrites any arguments passed under the `--gtr` flag.
* explicitly specify the optimization method, brackets, bounds, and tolerances in calls of `scipy.optimize.minimize` to suppress scipy warning. Scipy had previously silently ignored bounds when the method wasn't explicitly set to `bounded`.

* avoid negative variance associated with branch lengths in tree regression. This could happen in rare cases when marginal time tree estimation returned short negative branch length and the variance was estimated as being proportional to branch length. Variances in the `TreeRegression` clock model are now always non-negative.
* downsample the grid during multiplication of distribution objects. This turned out to be an issue for trees with very large polytomies. In these cases, a large number of distributions get multiplied which resulted in grid sizes above 100000 points. Grid sizes are now downsampled to the average grid size.

* 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](https://github.com/neherlab/treetime/pull/206)
[PR 208](https://github.com/neherlab/treetime/pull/208)

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)

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)

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](https://github.com/PierreBarrat/TreeKnit.jl). This command takes two trees and a file with MCCs inferred by TreeKnit. See [these docs](https://treetime.readthedocs.io/en/latest/commands.html#arg) for command line usage.