Added the IPython extension. Updated examples and added a Jupyter notebook example.

Author: kudlicka

examples/coin.py

@@ -1,9 +1,5 @@
 #!/usr/bin/env python3
 
-import sys
-
-sys.path.append("..")
-
 import treeppl
 import matplotlib.pyplot as plt
 import seaborn as sns

examples/crbd.py

@@ -1,9 +1,5 @@
 #!/usr/bin/env python3
 
-import sys
-
-sys.path.append("..")
-
 import treeppl
 import numpy as np
 import pandas as pd

examples/crbd.tppl

@@ -30,7 +30,7 @@ function walk(node: Tree, time:Real, lambda: Real, mu: Real) {
   }
 }
 
-model function crbd(tree: Tree): Real[]  {
+model function crbd(tree: Tree): Real[] {
   assume lambda ~ Gamma(1.0, 1.0);
   assume mu ~ Gamma(1.0, 0.5);
   walk(tree.left, tree.age, lambda, mu);

examples/generative_crbd.py

@@ -1,24 +1,15 @@
 #!/usr/bin/env python3
 
-import sys
-
-sys.path.append("..")
-
 import treeppl
 from Bio import Phylo
 
 
-params = {
-    "time": 5.0,
-    "lambda": 1.0,
-    "mu": 0.1
-}
+params = {"time": 5.0, "lambda": 1.0, "mu": 0.1}
 
-with treeppl.Model(filename="generative_crbd.tppl", samples=1) as generative_simulate:
-    result = generative_simulate(**params)
+with treeppl.Model(filename="generative_crbd.tppl", samples=1) as generative_crbd:
+    result = generative_crbd(**params)
     tree = result.samples[0]
     tree = Phylo.BaseTree.Clade(
-        branch_length=params["time"] - tree.age,
-        clades=[tree.to_biopython()]
+        branch_length=params["time"] - tree.age, clades=[tree.to_biopython()]
     )
     Phylo.draw(tree)

examples/treeppl

@@ -0,0 +1 @@
+../treeppl