def test_main(self):
rpkm_file = "rpkm_test.rpkm"
single_RPKM.main(tests.get_file("test_single_RPKM.count"), os.path.join(tests.get_test_dir(), rpkm_file ))
true_result = ["gene flag RPKM",
"ENSG1 0 5025125.62814",
"ENSG2 0 0.0"]
for true, test in zip(true_result, open(tests.get_file(rpkm_file))):
self.assertEqual(true.strip().split(), test.strip().split())
def test_wait_for_array_pbs(self):
commands = ['date', 'echo testing PBS']
job_name = 'test_qtools_submitter_wait_for_pbs'
submit_sh = '%s/%s.sh' % (tests.get_test_dir(), job_name)
sub = Submitter(queue_type='PBS',
sh_file=submit_sh,
command_list=commands,
job_name=job_name,
wait_for_array=['11111'])
job_id = sub.write_sh(submit=True,
nodes=1,
ppn=16,
queue='home-yeo',
walltime='0:01:00')
true_result_string = '''#!/bin/sh
#PBS -N test_qtools_submitter_wait_for_pbs
#PBS -o %s/test_qtools_submitter_wait_for_pbs.sh.out
#PBS -e %s/test_qtools_submitter_wait_for_pbs.sh.err
#PBS -V
#PBS -l walltime=0:01:00
#PBS -l nodes=1:ppn=16
#PBS -A yeo-group
#PBS -q home-yeo
#PBS -W depend=afterokarray:11111
# Go to the directory from which the script was called
cd $PBS_O_WORKDIR
date
echo testing PBS
''' % (tests.get_test_dir(), tests.get_test_dir())
true_result = true_result_string.split('\n')
# with open(submit_sh) as f:
# for x in f.readlines():
# print x,
for true, test in zip(true_result, open(submit_sh)):
self.assertEqual(true.strip().split(), test.strip().split())
# Make sure the job ID is a single (potentially multi-digit) integer
self.assertRegexpMatches(job_id, '^\d+$')
subprocess.Popen(["qdel", job_id], stdout=PIPE)
def test_main(self):
rpkm_file = "rpkm_test.rpkm"
single_RPKM.main(tests.get_file("test_single_RPKM.count"),
os.path.join(tests.get_test_dir(), rpkm_file))
true_result = [
"gene flag RPKM", "ENSG1 0 5025125.62814",
"ENSG2 0 0.0"
]
for true, test in zip(true_result, open(tests.get_file(rpkm_file))):
self.assertEqual(true.strip().split(), test.strip().split())
def test_wait_for_array_pbs(self):
commands = ['date', 'echo testing PBS']
job_name = 'test_qtools_submitter_wait_for_pbs'
submit_sh = '%s/%s.sh' % (tests.get_test_dir(), job_name)
sub = Submitter(queue_type='PBS', sh_file= submit_sh,
command_list=commands,
job_name=job_name, wait_for_array=['11111'])
job_id = sub.write_sh(submit=True, nodes=1, ppn=16,
queue='home-yeo', walltime='0:01:00')
true_result_string = '''#!/bin/sh
#PBS -N test_qtools_submitter_wait_for_pbs
#PBS -o %s/test_qtools_submitter_wait_for_pbs.sh.out
#PBS -e %s/test_qtools_submitter_wait_for_pbs.sh.err
#PBS -V
#PBS -l walltime=0:01:00
#PBS -l nodes=1:ppn=16
#PBS -A yeo-group
#PBS -q home-yeo
#PBS -W depend=afterokarray:11111
# Go to the directory from which the script was called
cd $PBS_O_WORKDIR
date
echo testing PBS
''' % (tests.get_test_dir(), tests.get_test_dir())
true_result = true_result_string.split('\n')
# with open(submit_sh) as f:
# for x in f.readlines():
# print x,
for true, test in zip(true_result, open(submit_sh)):
self.assertEqual(true.strip().split(), test.strip().split())
# Make sure the job ID is a single (potentially multi-digit) integer
self.assertRegexpMatches(job_id, '^\d+$')
subprocess.Popen(["qdel", job_id],
stdout=PIPE)
"""Test jpeg module."""
import shutil
from pathlib import Path
from typing import Tuple
from picopt.extern import ExtArgs
from picopt.formats import jpeg
from picopt.settings import Settings
from tests import IMAGES_DIR
from tests import get_test_dir
__all__ = () # hides module from pydocstring
TMP_ROOT = get_test_dir()
JPEG_SRC = IMAGES_DIR / "test_jpg.jpg"
TEST_OLD_JPEG = TMP_ROOT / "old.jpeg"
TEST_NEW_JPEG = TMP_ROOT / "new.jpeg"
def _setup_jpeg() -> Tuple[ExtArgs, Settings]:
TMP_ROOT.mkdir(exist_ok=True)
shutil.copy(JPEG_SRC, TEST_OLD_JPEG)
args = ExtArgs(str(TEST_OLD_JPEG), str(TEST_NEW_JPEG))
return args, Settings()
def _teardown(args: ExtArgs) -> None:
if TMP_ROOT.exists():
shutil.rmtree(TMP_ROOT)
"""Test png module."""
import shutil
from picopt.extern import ExtArgs
from picopt.formats.png import Png
from tests import IMAGES_DIR
from tests import get_test_dir
__all__ = () # hides module from pydocstring
TMP_DIR = get_test_dir()
TMP_OLD_PATH = TMP_DIR / "old.png"
TEST_SRC_PATH = IMAGES_DIR / "test_png.png"
TEST_SRC_PATH_16 = IMAGES_DIR / "test_png_16rgba.png"
def _setup(use_16: bool = False) -> ExtArgs:
if use_16:
src_path = TEST_SRC_PATH_16
else:
src_path = TEST_SRC_PATH
TMP_DIR.mkdir(exist_ok=True)
shutil.copy(src_path, TMP_OLD_PATH)
args = ExtArgs(str(TMP_OLD_PATH), str(TMP_OLD_PATH))
return args
def _teardown(args: ExtArgs) -> None:
if TMP_DIR.exists():
shutil.rmtree(TMP_DIR)