diff options
Diffstat (limited to 'tests/test_serialization.py')
| -rw-r--r-- | tests/test_serialization.py | 66 |
1 files changed, 2 insertions, 64 deletions
diff --git a/tests/test_serialization.py b/tests/test_serialization.py index c856094..ab354e1 100644 --- a/tests/test_serialization.py +++ b/tests/test_serialization.py @@ -20,41 +20,12 @@ import tempfile from hypothesis import given, strategies as st from hypothesis.extra.numpy import arrays, array_shapes -from hypothesis.extra.pandas import column, columns, data_frames import pandas as pd from pytest import approx -from pyhegp.serialization import Summary, read_summary, write_summary, read_summary_headers, read_genotype, write_genotype, read_phenotype, write_phenotype, read_key, write_key -from pyhegp.utils import negate +from pyhegp.serialization import read_summary, write_summary, read_summary_headers, read_genotype, write_genotype, read_phenotype, write_phenotype, read_key, write_key -tabless_printable_ascii_text = st.text( - # Exclude control characters and tab. - st.characters(codec="ascii", - exclude_categories=("Cc",), - exclude_characters=("\t",)), - min_size=1) -chromosome_column = column(name="chromosome", - dtype="str", - elements=tabless_printable_ascii_text) -position_column = column(name="position", - dtype="int") -reference_column = column(name="reference", - dtype="str", - elements=st.text( - st.characters(codec="ascii", - categories=(), - include_characters=("A", "G", "C", "T")), - min_size=1)) - -@st.composite -def summaries(draw): - return Summary(draw(st.integers()), - draw(data_frames( - columns=([chromosome_column, position_column] - + ([reference_column] if draw(st.booleans()) else []) - + columns(["mean", "std"], - dtype="float64", - elements=st.floats(allow_nan=False)))))) +from helpers.strategies import * @given(summaries()) def test_read_write_summary_are_inverses(summary): @@ -95,22 +66,6 @@ def test_read_summary_headers_variable_whitespace(properties_and_whitespace): file.seek(0) assert properties == read_summary_headers(file) -def genotype_reserved_column_name_p(name): - return name.lower() in {"chromosome", "position", "reference"} - -sample_names = st.lists(tabless_printable_ascii_text - .filter(negate(genotype_reserved_column_name_p)), - unique=True) - -@st.composite -def genotype_frames(draw): - return draw(data_frames( - columns=([chromosome_column, position_column] - + ([reference_column] if draw(st.booleans()) else []) - + columns(draw(sample_names), - dtype="float64", - elements=st.floats(allow_nan=False))))) - @given(genotype_frames()) def test_read_write_genotype_are_inverses(genotype): with tempfile.TemporaryFile() as file: @@ -118,23 +73,6 @@ def test_read_write_genotype_are_inverses(genotype): file.seek(0) pd.testing.assert_frame_equal(genotype, read_genotype(file)) -def phenotype_reserved_column_name_p(name): - return name.lower() == "sample-id" - -phenotype_names = st.lists(tabless_printable_ascii_text - .filter(negate(phenotype_reserved_column_name_p)), - unique=True) - -@st.composite -def phenotype_frames(draw): - return draw(data_frames( - columns=([column(name="sample-id", - dtype="str", - elements=tabless_printable_ascii_text)] - + columns(draw(phenotype_names), - dtype="float64", - elements=st.floats(allow_nan=False))))) - @given(phenotype_frames()) def test_read_write_phenotype_are_inverses(phenotype): with tempfile.TemporaryFile() as file: |