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zip, pep8 and f-strings
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@lemieuxl
lemieuxl committed Mar 8, 2024
1 parent 345b8fe commit ab10308
Showing 1 changed file with 37 additions and 35 deletions.
72 changes: 37 additions & 35 deletions pyplink/tests/test_pyplink.py
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Expand Up @@ -33,7 +33,7 @@
import unittest
import zipfile
from io import UnsupportedOperation
from itertools import zip_longest as zip
from itertools import zip_longest
from shutil import which
from subprocess import PIPE, CalledProcessError, check_call
from tempfile import mkdtemp
Expand Down Expand Up @@ -116,6 +116,7 @@ def get_plink(tmp_dir):


class TestPyPlink(unittest.TestCase):
"""Class to test PyPlink."""

@classmethod
def setUpClass(cls):
Expand Down Expand Up @@ -244,8 +245,7 @@ def test_pyplink_bad_bed(self):
# This should raise an exception
with self.assertRaises(ValueError) as cm:
pyplink.PyPlink(new_prefix)
self.assertEqual("not a valid BED file: {}".format(new_bed),
str(cm.exception))
self.assertEqual(f"not a valid BED file: {new_bed}", str(cm.exception))

# Creating a new BED file with invalid second byte
new_bed = new_prefix + ".bed"
Expand All @@ -255,8 +255,7 @@ def test_pyplink_bad_bed(self):
# This should raise an exception
with self.assertRaises(ValueError) as cm:
pyplink.PyPlink(new_prefix)
self.assertEqual("not a valid BED file: {}".format(new_bed),
str(cm.exception))
self.assertEqual(f"not a valid BED file: {new_bed}", str(cm.exception))

# Creating a new BED file not in SNP-major format
new_bed = new_prefix + ".bed"
Expand All @@ -267,7 +266,7 @@ def test_pyplink_bad_bed(self):
with self.assertRaises(ValueError) as cm:
pyplink.PyPlink(new_prefix)
self.assertEqual(
"not in SNP-major format (please recode): {}".format(new_bed),
f"not in SNP-major format (please recode): {new_bed}",
str(cm.exception),
)

Expand All @@ -284,7 +283,7 @@ def test_missing_files(self):
os.remove(prefix + extension)
with self.assertRaises(IOError) as cm:
pyplink.PyPlink(prefix)
self.assertEqual("No such file: '{}'".format(prefix + extension),
self.assertEqual(f"No such file: '{prefix + extension}'",
str(cm.exception))
with open(prefix + extension, "w"):
pass
Expand Down Expand Up @@ -340,7 +339,9 @@ def test_get_bim(self):
self.assertTrue(set(bim.index.values) == set(self.markers))

# Checking the values for the markers
zipped = zip(self.markers, chromosomes, positions, cms, a1s, a2s)
zipped = zip_longest(
self.markers, chromosomes, positions, cms, a1s, a2s,
)
for marker, chrom, pos, cm, a1, a2 in zipped:
self.assertEqual(chrom, bim.loc[marker, "chrom"])
self.assertEqual(pos, bim.loc[marker, "pos"])
Expand Down Expand Up @@ -393,7 +394,7 @@ def test_get_fam(self):
)

# Checking the values
zipped = zip(fids, iids, fathers, mothers, genders, status)
zipped = zip_longest(fids, iids, fathers, mothers, genders, status)
for i, (fid, iid, father, mother, gender, s) in enumerate(zipped):
self.assertEqual(fid, fam.loc[i, "fid"])
self.assertEqual(iid, fam.loc[i, "iid"])
Expand Down Expand Up @@ -431,8 +432,8 @@ def test_get_fam_w_mode(self):
def test_generator(self):
"""Testing the class as a generator."""
# Zipping and checking
zipped = zip(
[i for i in zip(self.markers, self.genotypes)],
zipped = zip_longest(
[i for i in zip_longest(self.markers, self.genotypes)],
self.pedfile,
)
for (e_marker, e_geno), (marker, geno) in zipped:
Expand Down Expand Up @@ -479,8 +480,8 @@ def test_seek(self):
self.assertEqual(0, len(remaining))

# Seeking at the second position
zipped = zip(
[i for i in zip(self.markers[1:], self.genotypes[1:])],
zipped = zip_longest(
[i for i in zip_longest(self.markers[1:], self.genotypes[1:])],
self.pedfile,
)
self.pedfile.seek(1)
Expand All @@ -489,8 +490,8 @@ def test_seek(self):
np.testing.assert_array_equal(e_geno, geno)

# Seeking at the fourth position
zipped = zip(
[i for i in zip(self.markers[3:], self.genotypes[3:])],
zipped = zip_longest(
[i for i in zip_longest(self.markers[3:], self.genotypes[3:])],
self.pedfile,
)
self.pedfile.seek(3)
Expand All @@ -499,8 +500,8 @@ def test_seek(self):
np.testing.assert_array_equal(e_geno, geno)

# Seeking at the tenth position
zipped = zip(
[i for i in zip(self.markers[9:], self.genotypes[9:])],
zipped = zip_longest(
[i for i in zip_longest(self.markers[9:], self.genotypes[9:])],
self.pedfile,
)
self.pedfile.seek(9)
Expand Down Expand Up @@ -534,8 +535,8 @@ def test_seek_w_mode(self):

def test_iter_geno(self):
"""Tests the 'iter_geno' function."""
zipped = zip(
[i for i in zip(self.markers, self.genotypes)],
zipped = zip_longest(
[i for i in zip_longest(self.markers, self.genotypes)],
self.pedfile.iter_geno(),
)
for (e_marker, e_geno), (marker, geno) in zipped:
Expand All @@ -553,8 +554,8 @@ def test_iter_geno_w_mode(self):

def test_iter_acgt_geno(self):
"""Tests the 'iter_acgt_geno" function."""
zipped = zip(
[i for i in zip(self.markers, self.acgt_genotypes)],
zipped = zip_longest(
[i for i in zip_longest(self.markers, self.acgt_genotypes)],
self.pedfile.iter_acgt_geno(),
)
for (e_marker, e_geno), (marker, geno) in zipped:
Expand All @@ -580,8 +581,8 @@ def test_iter_geno_marker(self):
genotypes = [self.genotypes[i] for i in indexes]

# Zipping and comparing
zipped = zip(
[i for i in zip(markers, genotypes)],
zipped = zip_longest(
[i for i in zip_longest(markers, genotypes)],
self.pedfile.iter_geno_marker(markers),
)
for (e_marker, e_geno), (marker, geno) in zipped:
Expand Down Expand Up @@ -621,8 +622,8 @@ def test_iter_acgt_geno_marker(self):
genotypes = [self.acgt_genotypes[i] for i in indexes]

# Zipping and comparing
zipped = zip(
[i for i in zip(markers, genotypes)],
zipped = zip_longest(
[i for i in zip_longest(markers, genotypes)],
self.pedfile.iter_acgt_geno_marker(markers),
)
for (e_marker, e_geno), (marker, geno) in zipped:
Expand Down Expand Up @@ -665,8 +666,7 @@ def test_repr_r_mode(self):
nb_markers = len(i_file.read().splitlines())

# Creating the expected string representation
e_repr = "PyPlink({:,d} samples; {:,d} markers)".format(nb_samples,
nb_markers)
e_repr = f"PyPlink({nb_samples:,d} samples; {nb_markers:,d} markers)"

# Getting the observed string representation
o_repr = str(self.pedfile)
Expand Down Expand Up @@ -782,19 +782,19 @@ def test_write_binary(self):
# Writing the FAM file
with open(test_prefix + ".fam", "w") as o_file:
for i in range(7):
print("f{}".format(i+1), "s{}".format(i+1), "0", "0",
print(f"f{i+1}", f"s{i+1}", "0", "0",
random.choice((1, 2)), "-9", sep=" ", file=o_file)

# Writing the BIM file
with open(test_prefix + ".bim", "w") as o_file:
for i in range(3):
print(i+1, "m{}".format(i+1), "0", i+1, "T", "A", sep="\t",
print(i+1, f"m{i+1}", "0", i+1, "T", "A", sep="\t",
file=o_file)

# Reading the written binary file
with pyplink.PyPlink(test_prefix) as pedfile:
for i, (marker, genotypes) in enumerate(pedfile):
self.assertEqual("m{}".format(i+1), marker)
self.assertEqual(f"m{i+1}", marker)
np.testing.assert_array_equal(expected_genotypes[i], genotypes)

def test_write_binary_error(self):
Expand Down Expand Up @@ -825,7 +825,8 @@ def test_grouper_padding(self):
(9, 0, 0),
]
observed_chunks = pyplink.PyPlink._grouper(range(10), 3)
for expected, observed in zip(expected_chunks, observed_chunks):
for expected, observed in zip_longest(expected_chunks,
observed_chunks):
self.assertEqual(expected, observed)

def test_grouper_no_padding(self):
Expand All @@ -835,11 +836,12 @@ def test_grouper_no_padding(self):
(5, 6, 7, 8, 9),
]
observed_chunks = pyplink.PyPlink._grouper(range(10), 5)
for expected, observed in zip(expected_chunks, observed_chunks):
for expected, observed in zip_longest(expected_chunks,
observed_chunks):
self.assertEqual(expected, observed)

@unittest.skipIf(platform.system() not in {"Darwin", "Linux", "Windows"},
"Plink not available for {}".format(platform.system()))
f"Plink not available for {platform.system()}")
def test_with_plink(self):
"""Tests to read a binary file using Plink."""
# Checking if we need to skip
Expand Down Expand Up @@ -933,7 +935,7 @@ def test_with_plink(self):
self.assertEqual("", i_file.readline())

@unittest.skipIf(platform.system() not in {"Darwin", "Linux", "Windows"},
"Plink not available for {}".format(platform.system()))
f"Plink not available for {platform.system()}")
def test_with_plink_individual_major(self):
"""Tests to read a binary file (INDIVIDUAL-major) using Plink."""
# Checking if we need to skip
Expand Down Expand Up @@ -1099,7 +1101,7 @@ def test_dup_markers(self, pyplink_logger):
self.assertTrue(set(bim.index.values) == set(markers))

# Checking the values for the markers
zipped = zip(markers, chromosomes, positions, cms, a1s, a2s)
zipped = zip_longest(markers, chromosomes, positions, cms, a1s, a2s)
for marker, chrom, pos, cm, a1, a2 in zipped:
self.assertEqual(chrom, bim.loc[marker, "chrom"])
self.assertEqual(pos, bim.loc[marker, "pos"])
Expand Down

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