pandas-plink
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limix
replaced deprecated pandas lineterminator arg
Newer versions of pandas (2+) cause _write_bim and _write_fam to fail. This change ('line_terminator' -> 'lineterminator' in calls to pandas.DataFrame.to_csv) works for both new and old pandas versions.
Can you add a test to catch changes like this in future?
e.g.
def test_two():
import os
import tempfile
from pandas_plink import get_data_folder, read_plink1_bin, write_plink1_bin
tmp_path = tempfile.mkdtemp()
filename = "chr11.bed"
filename = os.path.join(get_data_folder(), filename)
G = read_plink1_bin(filename, verbose=False)
print(G)
write_plink1_bin(G, f"{tmp_path}/sample1.bed")
if __name__ == "__main__":
test_two()
Yeah, no problem. Importing the unittest module okay or keep it simpler?
On Tue, Dec 12, 2023 at 3:11 AM Dan Bolser @.***> wrote:
Can you add a test to catch changes like this in future?
e.g.
def test_two(): import os import tempfile
from pandas_plink import get_data_folder, read_plink1_bin, write_plink1_bin tmp_path = tempfile.mkdtemp() filename = "chr11.bed" filename = os.path.join(get_data_folder(), filename) G = read_plink1_bin(filename, verbose=False) print(G) write_plink1_bin(G, f"{tmp_path}/sample1.bed")if name == "main": test_two()
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Sounds great!
On Wed, Dec 13, 2023, 8:57 PM Richard Border @.***> wrote:
Yeah, no problem. Importing the
unittestmodule okay or keep it simpler?On Tue, Dec 12, 2023 at 3:11 AM Dan Bolser @.***> wrote:
Can you add a test to catch changes like this in future?
e.g.
def test_two(): import os import tempfile
from pandas_plink import get_data_folder, read_plink1_bin, write_plink1_bin
tmp_path = tempfile.mkdtemp() filename = "chr11.bed"
filename = os.path.join(get_data_folder(), filename)
G = read_plink1_bin(filename, verbose=False) print(G)
write_plink1_bin(G, f"{tmp_path}/sample1.bed")
if name == "main": test_two()
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