diff --git a/tests/anoph/test_fst.py b/tests/anoph/test_fst.py index f205a838..c52c832b 100644 --- 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 index 4bd5cb4a..4dc5e454 100644 --- 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 index 4e62def5..06fb5205 100644 --- 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 index 2a21fc85..ed1e21f9 100644 --- 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,