added stem method

[fjaviersanchez]

This PR adds the stem derivative method as implemented by @nikosarcevic. For now, it is pretty barebones/non-optimized. Will be working on improving speed in the upcoming days.

[fjaviersanchez]

Will need to update the environment and install instructions to make this work. For reference, how I use it locally:

git clone [email protected]:nikosarcevic/Derivative-Calculator.git
ipython
import sys
sys.path.append('PATH-to-Derivative-Calculator')
from augur.analyze import Analyze
ao = Analyze('./examples/config_test.yaml')
ao.get_fisher_matrix(method='stem')

Note that this is currently very slow with the default number of parameters (12+ hours in my laptop).

[arthurmloureiro]

Will need to update the environment and install instructions to make this work. For reference, how I use it locally:

git clone [email protected]:nikosarcevic/Derivative-Calculator.git
ipython
import sys
sys.path.append('PATH-to-Derivative-Calculator')
from augur.analyze import Analyze
ao = Analyze('./examples/config_test.yaml')
ao.get_fisher_matrix(method='stem')

Note that this is currently very slow with the default number of parameters (12+ hours in my laptop).

Hi @fjaviersanchez !
I think we should avoid having to import more paths into augur.

Maybe we can ask @nikosarcevic if this derivative calculations can be packaged into pip or at least have a pip installable option?* Or maybe if @nikosarcevic can include her derivatives into augur?

• I see there's a PR already here which addresses this question. Maybe we should hold-on until it is merged so we can make the derivatives an easier dependency on augur?