WIP: use random_region_str() for random region in GWSS function tests

malariagen · Dec 13, 2024 · d7a7698 · d7a7698
1 parent 95fb659
commit d7a7698
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Showing 4 changed files with 12 additions and 12 deletions.
diff --git a/tests/anoph/test_fst.py b/tests/anoph/test_fst.py
@@ -84,7 +84,7 @@ def test_fst_gwss(fixture, api: AnophelesFstAnalysis):
     cohort1_query = f"country == {countries[0]!r}"
     cohort2_query = f"country == {countries[1]!r}"
     fst_params = dict(
-        region=random.choice(api.contigs),
+        region=fixture.random_region_str(),
         sample_sets=all_sample_sets,
         cohort1_query=cohort1_query,
         cohort2_query=cohort2_query,

diff --git a/tests/anoph/test_g123.py b/tests/anoph/test_g123.py
@@ -101,7 +101,7 @@ def test_g123_gwss_with_default_sites(fixture, api: AnophelesG123Analysis):
     # Set up test parameters.
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
     g123_params = dict(
-        region=random.choice(api.contigs),
+        region=random.choice(api.contigs),  # FIXME: region=fixture.random_region_str(),
         sample_sets=[random.choice(all_sample_sets)],
         window_size=random.randint(100, 500),
         min_cohort_size=10,
@@ -116,7 +116,7 @@ def test_g123_gwss_with_phased_sites(fixture, api: AnophelesG123Analysis):
     # Set up test parameters.
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
     g123_params = dict(
-        region=random.choice(api.contigs),
+        region=random.choice(api.contigs),  # FIXME: region=fixture.random_region_str(),
         sites=random.choice(api.phasing_analysis_ids),
         sample_sets=[random.choice(all_sample_sets)],
         window_size=random.randint(100, 500),
@@ -132,7 +132,7 @@ def test_g123_gwss_with_segregating_sites(fixture, api: AnophelesG123Analysis):
     # Set up test parameters.
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
     g123_params = dict(
-        region=random.choice(api.contigs),
+        region=fixture.random_region_str(),
         sites="segregating",
         site_mask=random.choice(api.site_mask_ids),
         sample_sets=[random.choice(all_sample_sets)],
@@ -149,7 +149,7 @@ def test_g123_gwss_with_all_sites(fixture, api: AnophelesG123Analysis):
     # Set up test parameters.
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
     g123_params = dict(
-        region=random.choice(api.contigs),
+        region=fixture.random_region_str(),
         sites="all",
         site_mask=None,
         sample_sets=[random.choice(all_sample_sets)],
@@ -166,7 +166,7 @@ def test_g123_gwss_with_bad_sites(fixture, api: AnophelesG123Analysis):
     # Set up test parameters.
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
     g123_params = dict(
-        region=random.choice(api.contigs),
+        region=fixture.random_region_str(),
         sample_sets=[random.choice(all_sample_sets)],
         window_size=random.randint(100, 500),
         min_cohort_size=10,
@@ -185,7 +185,7 @@ def test_g123_calibration(fixture, api: AnophelesG123Analysis):
     window_sizes = np.random.randint(100, 500, size=random.randint(2, 5)).tolist()
     window_sizes = sorted([int(x) for x in window_sizes])
     g123_params = dict(
-        region=random.choice(api.contigs),
+        region=random.choice(api.contigs),  # FIXME: region=fixture.random_region_str(),
         sites=random.choice(api.phasing_analysis_ids),
         sample_sets=[random.choice(all_sample_sets)],
         min_cohort_size=10,

diff --git a/tests/anoph/test_h12.py b/tests/anoph/test_h12.py
@@ -105,7 +105,7 @@ def test_h12_calibration(fixture, api: AnophelesH12Analysis):
     window_sizes = np.random.randint(100, 500, size=random.randint(2, 5)).tolist()
     window_sizes = sorted(set([int(x) for x in window_sizes]))
     h12_params = dict(
-        region=random.choice(api.contigs),
+        region=fixture.random_region_str(),
         sample_sets=[random.choice(all_sample_sets)],
         window_sizes=window_sizes,
         min_cohort_size=5,
@@ -168,7 +168,7 @@ def test_h12_gwss_with_default_analysis(fixture, api: AnophelesH12Analysis):
     # Set up test parameters.
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
     h12_params = dict(
-        region=random.choice(api.contigs),
+        region=random.choice(api.contigs),  # FIXME: region=fixture.random_region_str(),
         sample_sets=[random.choice(all_sample_sets)],
         window_size=random.randint(100, 500),
         min_cohort_size=5,
@@ -236,7 +236,7 @@ def test_h12_gwss_multi_with_default_analysis(fixture, api: AnophelesH12Analysis
     cohort1_query = f"country == '{country1}'"
     cohort2_query = f"country == '{country2}'"
     h12_params = dict(
-        region=random.choice(api.contigs),
+        region=random.choice(api.contigs),  # FIXME: region=fixture.random_region_str(),
         sample_sets=all_sample_sets,
         window_size=random.randint(100, 500),
         min_cohort_size=1,
@@ -256,7 +256,7 @@ def test_h12_gwss_multi_with_window_size_dict(fixture, api: AnophelesH12Analysis
     cohort1_query = f"country == '{country1}'"
     cohort2_query = f"country == '{country2}'"
     h12_params = dict(
-        region=random.choice(api.contigs),
+        region=random.choice(api.contigs),  # FIXME: region=fixture.random_region_str(),
         sample_sets=all_sample_sets,
         window_size={
             "cohort1": random.randint(100, 500),

diff --git a/tests/anoph/test_h1x.py b/tests/anoph/test_h1x.py
@@ -143,7 +143,7 @@ def test_h1x_gwss_with_default_analysis(fixture, api: AnophelesH1XAnalysis):
     cohort1_query = f"country == '{country1}'"
     cohort2_query = f"country == '{country2}'"
     h1x_params = dict(
-        region=random.choice(api.contigs),
+        region=random.choice(api.contigs),  # FIXME: region=fixture.random_region_str(),
         sample_sets=all_sample_sets,
         window_size=random.randint(100, 500),
         min_cohort_size=1,