Increase testing parallelism #3620
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,101 @@ | ||
| import pytest | ||
| import os | ||
| import shutil | ||
| import hail as hl | ||
| import hail.expr.aggregators as agg | ||
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| @pytest.fixture(autouse=True) | ||
| def always_true(monkeypatch): | ||
| # FIXME: remove once test output matches docs | ||
| monkeypatch.setattr('doctest.OutputChecker.check_output', lambda a, b, c, d: True) | ||
| yield | ||
| monkeypatch.undo() | ||
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| @pytest.fixture(scope="session", autouse=True) | ||
| def init(doctest_namespace): | ||
| # This gets run once per process -- must avoid race conditions | ||
| print("setting up doctest...") | ||
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| olddir = os.getcwd() | ||
| os.chdir("docs/") | ||
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| doctest_namespace['hl'] = hl | ||
| doctest_namespace['agg'] = agg | ||
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| if not os.path.isdir("output/"): | ||
| try: | ||
| os.mkdir("output/") | ||
| except OSError: | ||
| pass | ||
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| files = ["sample.vds", "sample.qc.vds", "sample.filtered.vds"] | ||
| for f in files: | ||
| if os.path.isdir(f): | ||
| shutil.rmtree(f) | ||
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| ds = hl.read_matrix_table('data/example.vds') | ||
| doctest_namespace['ds'] = ds | ||
| doctest_namespace['dataset'] = ds | ||
| doctest_namespace['dataset2'] = ds.annotate_globals(global_field=5) | ||
| doctest_namespace['dataset_to_union_1'] = ds | ||
| doctest_namespace['dataset_to_union_2'] = ds | ||
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| v_metadata = ds.rows().annotate_globals(global_field=5).annotate(consequence='SYN') | ||
| doctest_namespace['v_metadata'] = v_metadata | ||
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| s_metadata = ds.cols().annotate(pop='AMR', is_case=False, sex='F') | ||
| doctest_namespace['s_metadata'] = s_metadata | ||
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| # Table | ||
| table1 = hl.import_table('data/kt_example1.tsv', impute=True, key='ID') | ||
| table1 = table1.annotate_globals(global_field_1=5, global_field_2=10) | ||
| doctest_namespace['table1'] = table1 | ||
| doctest_namespace['other_table'] = table1 | ||
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| table2 = hl.import_table('data/kt_example2.tsv', impute=True, key='ID') | ||
| doctest_namespace['table2'] = table2 | ||
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| table4 = hl.import_table('data/kt_example4.tsv', impute=True, | ||
| types={'B': hl.tstruct(B0=hl.tbool, B1=hl.tstr), | ||
| 'D': hl.tstruct(cat=hl.tint32, dog=hl.tint32), | ||
| 'E': hl.tstruct(A=hl.tint32, B=hl.tint32)}) | ||
| doctest_namespace['table4'] = table4 | ||
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| people_table = hl.import_table('data/explode_example.tsv', delimiter='\\s+', | ||
| types={'Age': hl.tint32, 'Children': hl.tarray(hl.tstr)}) | ||
| doctest_namespace['people_table'] = people_table | ||
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| # TDT | ||
| doctest_namespace['tdt_dataset'] = hl.import_vcf('data/tdt_tiny.vcf') | ||
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| ds2 = hl.variant_qc(ds) | ||
| doctest_namespace['ds2'] = ds2.select_rows(AF = ds2.variant_qc.AF) | ||
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| # Expressions | ||
| doctest_namespace['names'] = hl.literal(['Alice', 'Bob', 'Charlie']) | ||
| doctest_namespace['a1'] = hl.literal([0, 1, 2, 3, 4, 5]) | ||
| doctest_namespace['a2'] = hl.literal([1, -1, 1, -1, 1, -1]) | ||
| doctest_namespace['t'] = hl.literal(True) | ||
| doctest_namespace['f'] = hl.literal(False) | ||
| doctest_namespace['na'] = hl.null(hl.tbool) | ||
| doctest_namespace['call'] = hl.call(0, 1, phased=False) | ||
| doctest_namespace['a'] = hl.literal([1, 2, 3, 4, 5]) | ||
| doctest_namespace['d'] = hl.literal({'Alice': 43, 'Bob': 33, 'Charles': 44}) | ||
| doctest_namespace['interval'] = hl.interval(3, 11) | ||
| doctest_namespace['locus_interval'] = hl.parse_locus_interval("1:53242-90543") | ||
| doctest_namespace['locus'] = hl.locus('1', 1034245) | ||
| doctest_namespace['x'] = hl.literal(3) | ||
| doctest_namespace['y'] = hl.literal(4.5) | ||
| doctest_namespace['s1'] = hl.literal({1, 2, 3}) | ||
| doctest_namespace['s2'] = hl.literal({1, 3, 5}) | ||
| doctest_namespace['s3'] = hl.literal({'Alice', 'Bob', 'Charlie'}) | ||
| doctest_namespace['struct'] = hl.struct(a=5, b='Foo') | ||
| doctest_namespace['tup'] = hl.literal(("a", 1, [1, 2, 3])) | ||
| doctest_namespace['s'] = hl.literal('The quick brown fox') | ||
| doctest_namespace['interval2'] = hl.Interval(3, 6) | ||
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| print("finished setting up doctest...") | ||
| yield | ||
| os.chdir(olddir) |
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I think I figured why pytest was faster than nose -- we aren't running pytest with coverage enabled
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I always get error messages abt coverage not being available. I think this was on the cloud too. I can double check.