more test fixes

Author: tristanpwdennis

tests/anoph/test_dipclust.py

@@ -80,10 +80,6 @@ def case_af1_sim(af1_sim_fixture, af1_sim_api):
     return af1_sim_fixture, af1_sim_api
 
 
-def case_adir1_sim(adir1_sim_fixture, adir1_sim_api):
-    return adir1_sim_fixture, adir1_sim_api
-
-
 @pytest.mark.parametrize("distance_metric", ["cityblock", "euclidean"])
 @parametrize_with_cases("fixture,api", cases=".")
 def test_plot_diplotype_clustering(

tests/anoph/test_fst.py

@@ -9,6 +9,7 @@
 
 from malariagen_data import af1 as _af1
 from malariagen_data import ag3 as _ag3
+from malariagen_data import adir1 as _adir1
 from malariagen_data.anoph.fst import AnophelesFstAnalysis
 
 
@@ -57,6 +58,24 @@ def af1_sim_api(af1_sim_fixture):
     )
 
 
+@pytest.fixture
+def adir1_sim_api(adir1_sim_fixture):
+    return AnophelesFstAnalysis(
+        url=adir1_sim_fixture.url,
+        public_url=adir1_sim_fixture.url,
+        config_path=_adir1.CONFIG_PATH,
+        major_version_number=_adir1.MAJOR_VERSION_NUMBER,
+        major_version_path=_adir1.MAJOR_VERSION_PATH,
+        pre=False,
+        gff_gene_type="protein_coding_gene",
+        gff_gene_name_attribute="Note",
+        gff_default_attributes=("ID", "Parent", "Note", "description"),
+        default_site_mask="dirus",
+        results_cache=adir1_sim_fixture.results_cache_path.as_posix(),
+        taxon_colors=_adir1.TAXON_COLORS,
+    )
+
+
 # N.B., here we use pytest_cases to parametrize tests. Each
 # function whose name begins with "case_" defines a set of
 # inputs to the test functions. See the documentation for

tests/anoph/test_g123.py

@@ -6,7 +6,6 @@
 
 from malariagen_data import af1 as _af1
 from malariagen_data import ag3 as _ag3
-from malariagen_data import adir1 as _adir1
 from malariagen_data.anoph.g123 import AnophelesG123Analysis
 
 
@@ -57,25 +56,6 @@ def af1_sim_api(af1_sim_fixture):
     )
 
 
-@pytest.fixture
-def adir1_sim_api(adir1_sim_fixture):
-    return AnophelesG123Analysis(
-        url=adir1_sim_fixture.url,
-        public_url=adir1_sim_fixture.url,
-        config_path=_adir1.CONFIG_PATH,
-        major_version_number=_adir1.MAJOR_VERSION_NUMBER,
-        major_version_path=_adir1.MAJOR_VERSION_PATH,
-        pre=False,
-        gff_gene_type="protein_coding_gene",
-        gff_gene_name_attribute="Note",
-        gff_default_attributes=("ID", "Parent", "Note", "description"),
-        default_site_mask="dirus",
-        results_cache=adir1_sim_fixture.results_cache_path.as_posix(),
-        taxon_colors=_adir1.TAXON_COLORS,
-        default_phasing_analysis="all",
-    )
-
-
 # N.B., here we use pytest_cases to parametrize tests. Each
 # function whose name begins with "case_" defines a set of
 # inputs to the test functions. See the documentation for
@@ -96,10 +76,6 @@ def case_af1_sim(af1_sim_fixture, af1_sim_api):
     return af1_sim_fixture, af1_sim_api
 
 
-def case_adir1_sim(adir1_sim_fixture, adir1_sim_api):
-    return adir1_sim_fixture, adir1_sim_api
-
-
 def check_g123_gwss(*, api, g123_params):
     # Run main gwss function under test.
     x, g123 = api.g123_gwss(**g123_params)