fixes + fixing the model to include sampling time

stdpopsim/catalog/HomSap/demographic_models.py

@@ -1824,9 +1824,11 @@ def _ancient_europe():
             id="Pop0",
             description="1000GenomesEUR/BronzeAge/Neolithic/Anatolian/WestAsian/Basal",
         ),
-        stdpopsim.Population(id="Pop1", description="Yamnaya/CHG"),
-        stdpopsim.Population(id="Pop2", description="WHG/NorthernEuropean"),
-        stdpopsim.Population(id="Pop3", description="EHG"),
+        stdpopsim.Population(id="Pop1", description="Yamnaya/CHG", sampling_time=140),
+        stdpopsim.Population(
+            id="Pop2", description="WHG/NorthernEuropean", sampling_time=200
+        ),
+        stdpopsim.Population(id="Pop3", description="EHG", sampling_time=180),
     ]
     citations = [
         stdpopsim.Citation(

stdpopsim/qc/HomSap.py

@@ -1639,14 +1639,22 @@ def extended_pulse(
 
 
 def PearsonAncientEurope():
+    """
+    Demographic history of ancient Europe from Allentoft et al. 2022. It
+    describes population splits and migration pulses for four main branches
+    in Fig. S3i.1 in Supplementary Information (Part I) found at
+    https://www.biorxiv.org/content/10.1101/2022.05.04.490594v2.supplementary-material
+    The branches are colored (black, red, yellow and purple).
+    """
     id = "QC-AncientEurope_4A21"
     dgraph = demes.loads(_ancient_europe_demes_str)
     model = msprime.Demography.from_demes(dgraph)
     return stdpopsim.DemographicModel(
         id=id,
         description=id,
         long_description=id,
-        generation_time=None,
+        generation_time=29,  # TODO: not clear where this came from,
+        # but it is not necessary, given the times are in generations already
         model=model,
         mutation_rate=1.25e-8,
     )