species QC to ChlRei (#1067)

* species QC to ChlRei
popsim-consortium · Nov 2, 2021 · 0fc1dbe · 0fc1dbe
1 parent cfd3bf8
commit 0fc1dbe
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Showing 2 changed files with 37 additions and 41 deletions.
diff --git a/stdpopsim/catalog/ChlRei/species.py b/stdpopsim/catalog/ChlRei/species.py
@@ -93,7 +93,7 @@
             reasons={stdpopsim.CiteReason.POP_SIZE},  # Quebec population
         ),
         stdpopsim.Citation(
-            author="Vitova et al.",
+            author="Vítová et al",
             year=2011,
             doi="https://doi.org/10.1007/s00425-011-1427-7",
             reasons={stdpopsim.CiteReason.GEN_TIME},

diff --git a/tests/test_ChlRei.py b/tests/test_ChlRei.py
@@ -21,68 +21,64 @@ def test_common_name(self):
     # independently referring to the citations provided in the
     # species definition, filling in the appropriate values
     # and deleting the pytest "skip" annotations.
-    @pytest.mark.skip("Population size QC not done yet")
     def test_qc_population_size(self):
-        assert self.species.population_size == -1
+        assert self.species.population_size == 1.4 * 1e-7
 
-    @pytest.mark.skip("Generation time QC not done yet")
     def test_qc_generation_time(self):
-        assert self.species.generation_time == -1
+        assert self.species.generation_time == 1 / 876
 
 
 class TestGenomeData(test_species.GenomeTestBase):
 
     genome = stdpopsim.get_species("ChlRei").genome
 
-    @pytest.mark.skip("Recombination rate QC not done yet")
     @pytest.mark.parametrize(
         ["name", "rate"],
         {
-            "1": -1,
-            "2": -1,
-            "3": -1,
-            "4": -1,
-            "5": -1,
-            "6": -1,
-            "7": -1,
-            "8": -1,
-            "9": -1,
-            "10": -1,
-            "11": -1,
-            "12": -1,
-            "13": -1,
-            "14": -1,
-            "15": -1,
-            "16": -1,
-            "17": -1,
+            "1": 1.21e-10,
+            "2": 1.49e-10,
+            "3": 1.52e-10,
+            "4": 1.47e-10,
+            "5": 1.70e-10,
+            "6": 1.17e-10,
+            "7": 8.66e-11,
+            "8": 1.39e-10,
+            "9": 1.12e-10,
+            "10": 1.97e-10,
+            "11": 1.63e-10,
+            "12": 9.15e-11,
+            "13": 1.43e-10,
+            "14": 1.90e-10,
+            "15": 3.93e-10,
+            "16": 1.71e-10,
+            "17": 1.83e-10,
         }.items(),
     )
     def test_recombination_rate(self, name, rate):
         assert rate == pytest.approx(
             self.genome.get_chromosome(name).recombination_rate
         )
 
-    @pytest.mark.skip("Mutation rate QC not done yet")
     @pytest.mark.parametrize(
         ["name", "rate"],
         {
-            "1": -1,
-            "2": -1,
-            "3": -1,
-            "4": -1,
-            "5": -1,
-            "6": -1,
-            "7": -1,
-            "8": -1,
-            "9": -1,
-            "10": -1,
-            "11": -1,
-            "12": -1,
-            "13": -1,
-            "14": -1,
-            "15": -1,
-            "16": -1,
-            "17": -1,
+            "1": 9.74e-10,
+            "2": 8.62e-10,
+            "3": 9.50e-10,
+            "4": 9.66e-10,
+            "5": 1.17e-09,
+            "6": 9.12e-10,
+            "7": 9.14e-10,
+            "8": 8.98e-10,
+            "9": 9.17e-10,
+            "10": 9.27e-10,
+            "11": 1.03e-09,
+            "12": 9.55e-10,
+            "13": 7.56e-10,
+            "14": 8.96e-10,
+            "15": 6.91e-10,
+            "16": 9.59e-10,
+            "17": 1.05e-09,
         }.items(),
     )
     def test_mutation_rate(self, name, rate):