add tests for as1. add cnv flag to skip tests for classes without cnv data

Author: tristanpwdennis

docs/source/As1.rst

@@ -72,14 +72,6 @@ SNP data access
     biallelic_diplotypes
     biallelic_snps_to_plink
 
-Integrative genomics viewer (IGV)
----------------------------------
-.. autosummary::
-    :toctree: generated/
-
-    igv
-    view_alignments
-
 SNP frequency analysis
 ----------------------
 .. autosummary::
@@ -136,7 +128,6 @@ Diplotype clustering
     :toctree: generated/
 
     plot_diplotype_clustering
-    plot_diplotype_clustering_advanced
 
 Fst analysis
 ------------

tests/anoph/test_dipclust.py

@@ -4,6 +4,8 @@
 
 from malariagen_data import af1 as _af1
 from malariagen_data import ag3 as _ag3
+from malariagen_data import as1 as _as1
+
 from malariagen_data.anoph.dipclust import AnophelesDipClustAnalysis
 
 
@@ -63,6 +65,24 @@ def af1_sim_api(af1_sim_fixture):
     )
 
 
+@pytest.fixture
+def as1_sim_api(as1_sim_fixture):
+    return AnophelesDipClustAnalysis(
+        url=as1_sim_fixture.url,
+        public_url=as1_sim_fixture.url,
+        config_path=_as1.CONFIG_PATH,
+        major_version_number=_as1.MAJOR_VERSION_NUMBER,
+        major_version_path=_as1.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="stephensi",
+        results_cache=as1_sim_fixture.results_cache_path.as_posix(),
+        taxon_colors=_as1.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
@@ -83,6 +103,19 @@ def case_af1_sim(af1_sim_fixture, af1_sim_api):
     return af1_sim_fixture, af1_sim_api
 
 
+def case_as1_sim(as1_sim_fixture, as1_sim_api):
+    return as1_sim_fixture, as1_sim_api
+
+
+# Cases for tests that require CNV data (as1 fixture has no CNV data).
+def case_cnv_ag3_sim(ag3_sim_fixture, ag3_sim_api):
+    return ag3_sim_fixture, ag3_sim_api
+
+
+def case_cnv_af1_sim(af1_sim_fixture, af1_sim_api):
+    return af1_sim_fixture, af1_sim_api
+
+
 @pytest.mark.parametrize("sample_query", [None, "sex_call == 'F'"])
 @pytest.mark.parametrize("distance_metric", ["cityblock", "euclidean"])
 @parametrize_with_cases("fixture,api", cases=".")
@@ -201,7 +234,7 @@ def test_plot_diplotype_clustering_advanced_with_transcript(
 
 
 @pytest.mark.parametrize("sample_query", [None, "sex_call == 'F'"])
-@parametrize_with_cases("fixture,api", cases=".")
+@parametrize_with_cases("fixture,api", cases=".", prefix="case_cnv_")
 def test_plot_diplotype_clustering_advanced_with_cnv_region(
     fixture, api: AnophelesDipClustAnalysis, sample_query
 ):