Update HUNePi models

[ArtPoon]

• We are using two models, one to predict whether infections are increasing or decreasing, and a second to estimate the number of infections given increasing infections.
• I recently found that two terms in the regression model were not implemented correctly, so we need to upload new models to the server.
• Fortunately this does not seem to change predictions substantially - however the models become slightly more accurate.

[ArtPoon]

Something strange happened here:

>>> phy = Phylo.read("consensus.nwk", 'newick')
>>> tips = phy.get_terminals()
>>> target = 500
>>> while len(tips) > target:
...     tips = sorted(tips, key=lambda x: x.branch_length)
...     tip = tips[0]
...     parent = phy.prune(tip)
...     tips = tips[1:]
...     bad = [tip for tip in tips if tip.name is None]
...     if bad:
...         break
... 
>>> bad
[]
>>> len(tips)
500
>>> tips = phy.get_terminals()
>>> len(tips)
501
>>> bad = [tip for tip in tips if tip.name is None]
>>> bad
[Clade(branch_length=7.27065, confidence=0.5)]
>>> parent
Clade(branch_length=0.0, confidence=1.0)
>>> tip
Clade(branch_length=6.09403, name='1483')

[ArtPoon]

This seems to work:

>>> phy = Phylo.read("consensus.nwk", 'newick')
>>> tips = phy.get_terminals()
>>> while len(tips) > target:
...     tips = sorted(tips, key=lambda x: x.branch_length)
...     tip = tips[0]
...     parent = phy.prune(tip)
...     tips = phy.get_terminals()
... 
>>> tip
Clade(branch_length=6.09498, name='3592')
>>> parent
Clade(branch_length=0.0, confidence=1.0)
>>> len(tips)
500
>>> bad = [tip for tip in tips if tip.name is None]
>>> bad
[]
>>> bad = [tip for tip in phy.get_terminals() if tip.name is None]
>>> bad
[]

[ArtPoon]

I've updated the Bioplus repo, @GopiGugan can you please re-run with the new prunetree code?