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Modernize print statements with str.format()

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This commit is contained in:
Nathan Baker
2020-05-28 20:31:03 -07:00
parent ba67f5149d
commit 87347a7d60
5 changed files with 70 additions and 59 deletions
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26
tests/test_basic_regression.py
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@@ -48,8 +48,9 @@ def get_test_dirs():
if test_path.is_dir():
path_dict[key] = test_path
else:
errstr = ("Can't find %s test files in %s"
% (key, [TEST_DIR / path, path]))
errstr = (
"Can't find {0:s} test files in {1:s}".format(
key, [TEST_DIR / path, path]))
raise FileNotFoundError(errstr)
return path_dict
@@ -65,8 +66,9 @@ def run_propka(options, pdb_path, tmp_path):
options += [str(pdb_path)]
args = propka.lib.loadOptions(options)
try:
_LOGGER.warning("Working in tmpdir %s because of PROPKA file output; "
"need to fix this.", tmp_path)
_LOGGER.warning(
"Working in tmpdir {0:s} because of PROPKA file output; "
"need to fix this.".format(str(tmp_path)))
cwd = Path.cwd()
os.chdir(tmp_path)
molecule = propka.molecular_container.Molecular_container(
@@ -93,7 +95,7 @@ def compare_output(pdb, tmp_path, ref_path):
ref_data.append(float(line))
test_data = []
pka_path = Path(tmp_path) / ("%s.pka" % pdb)
pka_path = Path(tmp_path) / ("{0:s}.pka".format(pdb))
with open(pka_path, "rt") as pka_file:
at_pka = False
for line in pka_file:
@@ -106,8 +108,9 @@ def compare_output(pdb, tmp_path, ref_path):
match = re.search(r'([0-9]+\.[0-9]+)', line)
value = float(match.group(0))
test_data.append(value)
errstr = ("Error exceeds maximum allowed value (%d decimal places)"
% MAX_ERR_DECIMALS)
errstr = (
"Error exceeds maximum allowed value ({0:d} decimal places)".format(
MAX_ERR_DECIMALS))
assert_almost_equal(
test_data, ref_data, decimal=MAX_ERR_DECIMALS, err_msg=errstr,
verbose=True)
@@ -126,17 +129,18 @@ def compare_output(pdb, tmp_path, ref_path):
def test_regression(pdb, options, tmp_path):
"""Basic regression test of PROPKA functionality."""
path_dict = get_test_dirs()
ref_path = path_dict["results"] / ("%s.dat" % pdb)
ref_path = path_dict["results"] / ("{0:s}.dat".format(pdb))
if ref_path.is_file():
ref_path = ref_path.resolve()
else:
_LOGGER.warning("Missing results file for comparison: %s", ref_path)
_LOGGER.warning("Missing results file for comparison: {0:s}".format(
str(ref_path)))
ref_path = None
pdb_path = path_dict["pdbs"] / ("%s.pdb" % pdb)
pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb))
if pdb_path.is_file():
pdb_path = pdb_path.resolve()
else:
errstr = "Missing PDB file: %s" % pdb_path
errstr = "Missing PDB file: {0:s}".format(pdb_path)
raise FileNotFoundError(errstr)
tmp_path = Path(tmp_path).resolve()