def test_rename(self):
"""Renames file as expected """
# create temp file directory
with tempfile.TemporaryDirectory(".") as dirname:
# create temp filepath
dirname = pathlib.Path(dirname)
test_filepath = dirname / "Atomic_write_test"
# touch the filepath so it exists
f = open(test_filepath, "w").close()
self.assertTrue(exists(test_filepath))
# file should overwrite file if file already exists
with atomic_write(test_filepath, mode="w") as f:
f.write("abc")
def write(self, identifier, data):
relative_id = self.get_relative_identifier(identifier)
absolute_id = self.get_absolute_identifier(relative_id, from_relative=True)
if self._md5:
self._checksums[absolute_id] = get_text_hexdigest(data)
with atomic_write(str(relative_id), in_zip=self.source) as out:
out.write(data)
member = DataStoreMember(relative_id, self)
if relative_id not in self and relative_id.endswith(self.suffix):
self._members.append(member)
return member
def write(self, path, format="tsv", sep="\t"):
"""writes a flattened version to path
Parameters
----------
path : str
format
possible formats are 'rest'/'rst', 'markdown'/'md',
'latex', 'html', 'phylip', 'bedgraph', 'csv', 'tsv', or 'simple'
(default).
sep : str
used to split fields, will be inferred from path suffix if not
provided
"""
data = self.to_string(format=format, sep=sep)
with atomic_write(path, mode="wt") as outfile:
outfile.write(data)
def save_to_filename(alignment, filename, format, **kw):
"""Arguments:
- alignment: to be written
- filename: name of the sequence alignment file
- format: the multiple sequence file format
"""
if format is None:
raise FileFormatError("format not known")
with atomic_write(filename, mode="wt") as f:
try:
write_alignment_to_file(f, alignment, format, **kw)
except Exception:
try:
os.unlink(filename)
except Exception:
pass
raise
def write(self, identifier, data):
super().write(identifier, data)
id_suffix = identifier.split(".")[-1]
if id_suffix not in (self.suffix, "log"):
raise ValueError(
f"identifier does not end with required suffix {self.suffix}"
)
relative_id = self.get_relative_identifier(identifier)
absolute_id = self.get_absolute_identifier(relative_id, from_relative=True)
if self._md5:
self._checksums[absolute_id] = get_text_hexdigest(data)
with atomic_write(str(absolute_id), in_zip=False) as out:
out.write(data)
member = DataStoreMember(relative_id, self)
if relative_id not in self and relative_id.endswith(self.suffix):
self._members.append(member)
return member
def execute_ipynb(file_paths, exit_on_first, verbose):
failed = False
for test in file_paths:
path = pathlib.Path(test)
print()
print("=" * 40)
print(test)
with open(test) as f:
nb = nbformat.read(f, as_version=4)
ep = ExecutePreprocessor(timeout=600,
kernel_name="python3",
store_widget_state=True)
try:
ep.preprocess(nb, {"metadata": {"path": path.parent}})
except CellExecutionError:
failed = True
with atomic_write(test, mode="w") as f:
nbformat.write(nb, f)
if failed and exit_on_first:
raise SystemExit(
f"notebook execution failed in {test}, error saved "
"in notebook")
def write(self, filename):
with atomic_write(filename, mode="wt") as f:
for (score, tree) in self:
f.writelines(
self.scored_tree_format(
tree.get_newick(with_distances=True), str(score)))
