Merge pull request #870 from blankirigaya/master

Fix g123 test failures on Adir1/Amin1 by falling back to segregating sites when no phasing analysis is available

Author: jonbrenas

malariagen_data/amin1.py

@@ -105,7 +105,7 @@ def __init__(
             site_filters_analysis=site_filters_analysis,
             discordant_read_calls_analysis=discordant_read_calls_analysis,
             default_site_mask="minimus",
-            default_phasing_analysis="minimus_noneyet",
+            default_phasing_analysis=None,
             default_coverage_calls_analysis="minimus_noneyet",
             bokeh_output_notebook=bokeh_output_notebook,
             results_cache=results_cache,

malariagen_data/anoph/g123.py

@@ -153,7 +153,7 @@ def g123_gwss(
         self,
         contig: base_params.contig,
         window_size: g123_params.window_size,
-        sites: g123_params.sites = base_params.DEFAULT,
+        sites: g123_params.sites = g123_params.DEFAULT_SITE_PARAMETER,
         site_mask: Optional[base_params.site_mask] = base_params.DEFAULT,
         sample_sets: Optional[base_params.sample_sets] = None,
         sample_query: Optional[base_params.sample_query] = None,
@@ -172,9 +172,6 @@ def g123_gwss(
         # invalidate any previously cached data.
         name = "g123_gwss_v1"
 
-        if sites == base_params.DEFAULT:
-            assert self._default_phasing_analysis is not None
-            sites = self._default_phasing_analysis
         valid_sites = self.phasing_analysis_ids + ("all", "segregating")
         if sites not in valid_sites:
             raise ValueError(
@@ -259,7 +256,7 @@ def _g123_calibration(
     def g123_calibration(
         self,
         contig: base_params.contig,
-        sites: g123_params.sites = base_params.DEFAULT,
+        sites: g123_params.sites = g123_params.DEFAULT_SITE_PARAMETER,
         site_mask: Optional[base_params.site_mask] = base_params.DEFAULT,
         sample_query: Optional[base_params.sample_query] = None,
         sample_query_options: Optional[base_params.sample_query_options] = None,
@@ -279,6 +276,12 @@ def g123_calibration(
         # invalidate any previously cached data.
         name = "g123_calibration_v1"
 
+        valid_sites = self.phasing_analysis_ids + ("all", "segregating")
+        if sites not in valid_sites:
+            raise ValueError(
+                f"Invalid value for `sites` parameter, must be one of {valid_sites}."
+            )
+
         params = dict(
             contig=contig,
             sites=sites,
@@ -314,7 +317,7 @@ def plot_g123_gwss_track(
         self,
         contig: base_params.contig,
         window_size: g123_params.window_size,
-        sites: g123_params.sites = base_params.DEFAULT,
+        sites: g123_params.sites = g123_params.DEFAULT_SITE_PARAMETER,
         site_mask: Optional[base_params.site_mask] = base_params.DEFAULT,
         sample_sets: Optional[base_params.sample_sets] = None,
         sample_query: Optional[base_params.sample_query] = None,
@@ -417,7 +420,7 @@ def plot_g123_gwss(
         self,
         contig: base_params.contig,
         window_size: g123_params.window_size,
-        sites: g123_params.sites = base_params.DEFAULT,
+        sites: g123_params.sites = g123_params.DEFAULT_SITE_PARAMETER,
         site_mask: Optional[base_params.site_mask] = base_params.DEFAULT,
         sample_sets: Optional[base_params.sample_sets] = None,
         sample_query: Optional[base_params.sample_query] = None,

malariagen_data/anoph/g123_params.py

@@ -34,6 +34,8 @@
     """,
 ]
 
+DEFAULT_SITE_PARAMETER: sites = "segregating"
+
 min_cohort_size_default: base_params.min_cohort_size = 20
 
 max_cohort_size_default: base_params.max_cohort_size = 50

tests/anoph/conftest.py

@@ -2464,7 +2464,7 @@ def init_config(self):
             "DEFAULT_COHORTS_ANALYSIS": "20250710",
             "DEFAULT_DISCORDANT_READ_CALLS_ANALYSIS": "",
             "SITE_MASK_IDS": ["dirus"],
-            "PHASING_ANALYSIS_IDS": ["dirus_noneyet"],
+            "PHASING_ANALYSIS_IDS": [],
         }
         config_path = self.bucket_path / "v1.0-config.json"
         with config_path.open(mode="w") as f:
@@ -2786,7 +2786,7 @@ def init_config(self):
             "DEFAULT_COHORTS_ANALYSIS": "20251019",
             "DEFAULT_DISCORDANT_READ_CALLS_ANALYSIS": "",
             "SITE_MASK_IDS": ["minimus"],
-            "PHASING_ANALYSIS_IDS": ["minimus_noneyet"],
+            "PHASING_ANALYSIS_IDS": [],
         }
         config_path = self.bucket_path / "v1.0-config.json"
         with config_path.open(mode="w") as f:

tests/anoph/test_g123.py

@@ -6,6 +6,8 @@
 
 from malariagen_data import af1 as _af1
 from malariagen_data import ag3 as _ag3
+from malariagen_data import adir1 as _adir1
+from malariagen_data import amin1 as _amin1
 from malariagen_data.anoph.g123 import AnophelesG123Analysis
 
 
@@ -56,6 +58,44 @@ 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=None,
+    )
+
+
+@pytest.fixture
+def amin1_sim_api(amin1_sim_fixture):
+    return AnophelesG123Analysis(
+        url=amin1_sim_fixture.url,
+        public_url=amin1_sim_fixture.url,
+        config_path=_amin1.CONFIG_PATH,
+        major_version_number=_amin1.MAJOR_VERSION_NUMBER,
+        major_version_path=_amin1.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="minimus",
+        results_cache=amin1_sim_fixture.results_cache_path.as_posix(),
+        taxon_colors=_amin1.TAXON_COLORS,
+        default_phasing_analysis=None,
+    )
+
+
 # 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
@@ -76,6 +116,14 @@ 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 case_amin1_sim(amin1_sim_fixture, amin1_sim_api):
+    return amin1_sim_fixture, amin1_sim_api
+
+
 def check_g123_gwss(*, api, g123_params):
     # Run main gwss function under test.
     x, g123 = api.g123_gwss(**g123_params)
@@ -115,6 +163,10 @@ def test_g123_gwss_with_default_sites(fixture, api: AnophelesG123Analysis):
 
 @parametrize_with_cases("fixture,api", cases=".")
 def test_g123_gwss_with_phased_sites(fixture, api: AnophelesG123Analysis):
+    # Skip if this dataset has no phasing analyses (e.g., Adir1, Amin1).
+    if not api.phasing_analysis_ids:
+        pytest.skip("No phasing analyses available for this dataset.")
+
     # Set up test parameters.
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
     g123_params = dict(
@@ -182,6 +234,10 @@ def test_g123_gwss_with_bad_sites(fixture, api: AnophelesG123Analysis):
 
 @parametrize_with_cases("fixture,api", cases=".")
 def test_g123_calibration(fixture, api: AnophelesG123Analysis):
+    # Skip if this dataset has no phasing analyses (e.g., Adir1, Amin1).
+    if not api.phasing_analysis_ids:
+        pytest.skip("No phasing analyses available for this dataset.")
+
     # Set up test parameters.
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
     window_sizes = np.random.randint(100, 500, size=random.randint(2, 5)).tolist()