Fix formatting for precommit

popsim-consortium · Oct 10, 2023 · b302533 · b302533
1 parent 5f16260
commit b302533
Showing 1 changed file with 65 additions and 62 deletions.
diff --git a/stdpopsim/qc/OrySat.py b/stdpopsim/qc/OrySat.py
@@ -3,16 +3,19 @@
 
 _species = stdpopsim.get_species("OrySat") 
 
+
 def _BottMig_3C07_qc():
     id = "QC-BottMig_3C07"
-
-    #populations
-    rufipogon = stdpopsim.Population(id = "RUF", description="O. rufipogon population")
-    indica = stdpopsim.Population(id = "IND", description="O. sativa indica population")
-    japonica = stdpopsim.Population(id = "TRJ", description="O. sativa tropical japonica population")
+
+    # populations
+    rufipogon = stdpopsim.Population(id="RUF", description="O. rufipogon population")
+    indica = stdpopsim.Population(id="IND", description="O. sativa indica population")
+    japonica = stdpopsim.Population(
+        id="TRJ", description="O. sativa tropical japonica population"
+    )
     populations = [rufipogon, indica, japonica]
 
-    # generation time of 1 year and a mutation rate of 3.2e-9 per bp per gen
+    # generation time of 1 year and a mutation rate of 3.2e-9 per bp per generation
     generation_time = 1
     mutation_rate = 3.2e-9
 
@@ -21,85 +24,85 @@ def _BottMig_3C07_qc():
 
     # Times
     T_1 = 12000  # time when domestication started
-    T_B = 9000  # (12000-3000), bottleneck lasted for 3000 years 
+    T_B = 9000  # (12000-3000), bottleneck lasted for 3000 years
 
     # Population sizes
-    N_anc = 150000 # Ancestral population size (12000 / (0.04 * 2))
+    N_anc = 150000  # Ancestral population size (12000 / (0.04 * 2))
     N_rufi = N_anc  # population size for rufipogon
     N_ind = 0.27 * N_anc  # population size for indica
     N_trj = 0.12 * N_anc  # population size for tropical japonica
-    N_B = (0.0055 * 150000) # bottleneck population size for both indica and tropical japonica
+    N_B = (
+        0.0055 * 150000
+    )  # bottleneck population size for both indica and tropical japonica
 
-    # Migration rates 
+    # Migration rates
     # to japonica = 0.42, to indica = 0.945, to rufipogon = 3.5
     m_ind = 0.945 / N_ind
     m_trj = 0.42 / N_trj
     m_rufi = 3.5 / N_rufi
     # they are symmetrical
-    
+
     migration_matrix = [
         [0, m_rufi, m_rufi],
         [m_ind, 0, m_ind],
         [m_trj, m_trj, 0],
-        ]
+    ]
 
     demographic_events = [
-            # There is migration between all populations:
-            # (forward in time, indexes are flipped because this is backwards)
-
-            # to rufipogon
-            # from indica to rufipogon 
-            msprime.MigrationRateChange(time = 0, rate = m_rufi, source = 0, dest = 1),
-            # from japonica to rufipogon
-            msprime.MigrationRateChange(time = 0, rate = m_rufi, source = 0, dest = 2),
-
-            # to indica
-            # from rufipogon to indica
-            msprime.MigrationRateChange(time = 0, rate = m_ind, source = 1, dest = 0),
-            # from japonica to indica
-            msprime.MigrationRateChange(time = 0, rate = m_ind, source = 1, dest = 2),
-
-            # to japonica
-            # from rufipogon to japonica
-            msprime.MigrationRateChange(time = 0, rate = m_trj, source = 2, dest = 0),
-            # from indica to japonica
-            msprime.MigrationRateChange(time = 0, rate = m_trj, source = 2, dest = 1),
-
-            # Independent bottlenecks at T_B for indica and japonica
-
-            # bottleneck for indica
-            msprime.PopulationParametersChange(time = T_B, initial_size = N_B, population_id = 1), 
-            # bottleneck for japonica
-            msprime.PopulationParametersChange(time = T_B, initial_size = N_B, population_id = 2),
-
-            # Migration stops before that
-            msprime.MigrationRateChange(time = T_B, rate = 0),
-
-            # Both merge onto rufipogon at T_1
-            # indica merges onto rufipogon
-            msprime.MassMigration(time = T_1, source = 1, destination = 0, proportion = 1.0),
-            # japonica merges onto rufipogon
-            msprime.MassMigration(time = T_1, source = 2, destination = 0, proportion = 1.0),
-        ]
+        # There is migration between all populations:
+        # (forward in time, indexes are flipped because this is backwards)
+        # to rufipogon
+        # from indica to rufipogon
+        msprime.MigrationRateChange(time=0, rate=m_rufi, source=0, dest=1),
+        # from japonica to rufipogon
+        msprime.MigrationRateChange(time=0, rate=m_rufi, source=0, dest=2),
+        # to indica
+        # from rufipogon to indica
+        msprime.MigrationRateChange(time=0, rate=m_ind, source=1, dest=0),
+        # from japonica to indica
+        msprime.MigrationRateChange(time=0, rate=m_ind, source=1, dest=2),
+        # to japonica
+        # from rufipogon to japonica
+        msprime.MigrationRateChange(time=0, rate=m_trj, source=2, dest=0),
+        # from indica to japonica
+        msprime.MigrationRateChange(time=0, rate=m_trj, source=2, dest=1),
+        # Independent bottlenecks at T_B for indica and japonica
+        # bottleneck for indica
+        msprime.PopulationParametersChange(time=T_B, initial_size=N_B, population_id=1),
+        # bottleneck for japonica
+        msprime.PopulationParametersChange(time=T_B, initial_size=N_B, population_id=2),
+        # Migration stops before that
+        msprime.MigrationRateChange(time=T_B, rate=0),
+        # Both merge onto rufipogon at T_1
+        # indica merges onto rufipogon
+        msprime.MassMigration(time=T_1, source=1, destination=0, proportion=1.0),
+        # japonica merges onto rufipogon
+        msprime.MassMigration(time=T_1, source=2, destination=0, proportion=1.0),
+    ]
 
     return stdpopsim.DemographicModel(
-        id = id,
-        description = id,
-        long_description = id,
-        generation_time = generation_time,
-        populations = populations,
-        population_configurations = [
-            msprime.PopulationConfiguration(initial_size = N_rufi, metadata = populations[0].asdict()
+        id=id,
+        description=id,
+        long_description=id,
+        generation_time=generation_time,
+        populations=populations,
+        population_configurations=[
+            msprime.PopulationConfiguration(
+                initial_size=N_rufi, metadata=populations[0].asdict()
             ),
-            msprime.PopulationConfiguration(initial_size = N_ind, metadata = populations[1].asdict()
+            msprime.PopulationConfiguration(
+                initial_size=N_ind, metadata=populations[1].asdict()
             ),
-            msprime.PopulationConfiguration(initial_size = N_trj, metadata = populations[2].asdict()
+            msprime.PopulationConfiguration(
+                initial_size=N_trj, metadata=populations[2].asdict()
             ),
         ],
-        migration_matrix = migration_matrix,
-        demographic_events = demographic_events,
-        mutation_rate = mutation_rate,
+        migration_matrix=migration_matrix,
+        demographic_events=demographic_events,
+        mutation_rate=mutation_rate,
     )
 
 
-_species.get_demographic_model("BottleneckMigration_3C07").register_qc(_BottMig_3C07_qc())
+_species.get_demographic_model("BottleneckMigration_3C07").register_qc(
+    _BottMig_3C07_qc()
+)