Merge pull request #367 from mcveanlab/disable-pongo

Remove PonPyg from the catalog temporarily.

Author: jeromekelleher

docs/catalog.rst

@@ -43,8 +43,6 @@ Then, if you feel ready, make an issue on our
 
 .. speciescatalog:: HomSap
 
-.. speciescatalog:: PonPyg
-
 .. speciescatalog:: DroMel
 
 .. speciescatalog:: AraTha

stdpopsim/catalog/pongo_pygmaeus.py

@@ -83,7 +83,11 @@
     population_size_citations=[
         _locke2011.because(stdpopsim.CiteReason.POP_SIZE)])
 
-stdpopsim.register_species(_species)
+
+# FIXME not registering this species because of the mixup with PonPyg
+# and PonAbe and the lack of clarity on how to deal with multi-species
+# population models. See #365 and #354.
+# stdpopsim.register_species(_species)
 
 
 ###########################################################

tests/test_pongo_pygmaeus.py

@@ -1,56 +1,58 @@
 import unittest
 
 
-import stdpopsim
+# import stdpopsim
 from stdpopsim import pongo_pygmaeus
 from tests import test_models
-from tests import test_species
+# from tests import test_species
 from qc import pongo_pygmaeus_qc
 
-
-class TestSpecies(unittest.TestCase, test_species.SpeciesTestMixin):
-    species = stdpopsim.get_species("PonPyg")
-
-    def test_basic_attributes(self):
-        self.assertEqual(self.species.population_size, 1.79*10**4)
-        self.assertEqual(self.species.generation_time, 20)
-
-
-class TestGenome(unittest.TestCase, test_species.GenomeTestMixin):
-    """
-    Tests for the Pongo pygmaeus genome.
-    """
-    genome = stdpopsim.get_species("PonPyg").genome
-
-    def test_basic_attributes(self):
-        self.assertEqual(len(self.genome.chromosomes), 24)
-
-    def test_chromosome_lengths(self):
-        genome = self.genome
-        self.assertEqual(genome.get_chromosome("chr1").length, 227913704)
-        self.assertEqual(genome.get_chromosome("chr2A").length, 109511694)
-        self.assertEqual(genome.get_chromosome("chr2B").length, 129937803)
-        self.assertEqual(genome.get_chromosome("chr3").length, 193656255)
-        self.assertEqual(genome.get_chromosome("chr4").length, 189387572)
-        self.assertEqual(genome.get_chromosome("chr5").length, 179185813)
-        self.assertEqual(genome.get_chromosome("chr6").length, 169501136)
-        self.assertEqual(genome.get_chromosome("chr7").length, 145408105)
-        self.assertEqual(genome.get_chromosome("chr8").length, 144036388)
-        self.assertEqual(genome.get_chromosome("chr9").length, 112206110)
-        self.assertEqual(genome.get_chromosome("chr10").length, 132178492)
-        self.assertEqual(genome.get_chromosome("chr11").length, 128122151)
-        self.assertEqual(genome.get_chromosome("chr12").length, 132184051)
-        self.assertEqual(genome.get_chromosome("chr13").length, 98475126)
-        self.assertEqual(genome.get_chromosome("chr14").length, 88963417)
-        self.assertEqual(genome.get_chromosome("chr15").length, 82547911)
-        self.assertEqual(genome.get_chromosome("chr16").length, 68237989)
-        self.assertEqual(genome.get_chromosome("chr17").length, 75914007)
-        self.assertEqual(genome.get_chromosome("chr18").length, 75923960)
-        self.assertEqual(genome.get_chromosome("chr19").length, 57575784)
-        self.assertEqual(genome.get_chromosome("chr20").length, 60841859)
-        self.assertEqual(genome.get_chromosome("chr21").length, 34683425)
-        self.assertEqual(genome.get_chromosome("chr22").length, 35308119)
-        self.assertEqual(genome.get_chromosome("chrX").length, 151242693)
+# FIXME commenting these out for now because PonPyg is removed from the
+# catalog and we can't use unittest.skip(). See #365
+
+# class TestSpecies(unittest.TestCase, test_species.SpeciesTestMixin):
+#     species = stdpopsim.get_species("PonPyg")
+
+#     def test_basic_attributes(self):
+#         self.assertEqual(self.species.population_size, 1.79*10**4)
+#         self.assertEqual(self.species.generation_time, 20)
+
+
+# class TestGenome(unittest.TestCase, test_species.GenomeTestMixin):
+#     """
+#     Tests for the Pongo pygmaeus genome.
+#     """
+#     genome = stdpopsim.get_species("PonPyg").genome
+
+#     def test_basic_attributes(self):
+#         self.assertEqual(len(self.genome.chromosomes), 24)
+
+#     def test_chromosome_lengths(self):
+#         genome = self.genome
+#         self.assertEqual(genome.get_chromosome("chr1").length, 227913704)
+#         self.assertEqual(genome.get_chromosome("chr2A").length, 109511694)
+#         self.assertEqual(genome.get_chromosome("chr2B").length, 129937803)
+#         self.assertEqual(genome.get_chromosome("chr3").length, 193656255)
+#         self.assertEqual(genome.get_chromosome("chr4").length, 189387572)
+#         self.assertEqual(genome.get_chromosome("chr5").length, 179185813)
+#         self.assertEqual(genome.get_chromosome("chr6").length, 169501136)
+#         self.assertEqual(genome.get_chromosome("chr7").length, 145408105)
+#         self.assertEqual(genome.get_chromosome("chr8").length, 144036388)
+#         self.assertEqual(genome.get_chromosome("chr9").length, 112206110)
+#         self.assertEqual(genome.get_chromosome("chr10").length, 132178492)
+#         self.assertEqual(genome.get_chromosome("chr11").length, 128122151)
+#         self.assertEqual(genome.get_chromosome("chr12").length, 132184051)
+#         self.assertEqual(genome.get_chromosome("chr13").length, 98475126)
+#         self.assertEqual(genome.get_chromosome("chr14").length, 88963417)
+#         self.assertEqual(genome.get_chromosome("chr15").length, 82547911)
+#         self.assertEqual(genome.get_chromosome("chr16").length, 68237989)
+#         self.assertEqual(genome.get_chromosome("chr17").length, 75914007)
+#         self.assertEqual(genome.get_chromosome("chr18").length, 75923960)
+#         self.assertEqual(genome.get_chromosome("chr19").length, 57575784)
+#         self.assertEqual(genome.get_chromosome("chr20").length, 60841859)
+#         self.assertEqual(genome.get_chromosome("chr21").length, 34683425)
+#         self.assertEqual(genome.get_chromosome("chr22").length, 35308119)
+#         self.assertEqual(genome.get_chromosome("chrX").length, 151242693)
 
 
 class TestPongo(unittest.TestCase, test_models.QcdCatalogDemographicModelTestMixin):