def init_dir(adir: PathLike, exist_ok=False, parents=False, rmtree=False):
adir = Path(adir)
if adir.is_dir():
if rmtree:
shutil.rmtree(adir)
adir.mkdir(exist_ok=exist_ok, parents=parents)
return adir
def find_root_with_reason(
criterion,
start: _PathLike = None) -> _typing.Tuple[_pathlib.Path, str]:
"""
Find directory matching root criterion with reason.
Recursively search parents of start path for directory
matching root criterion with reason.
"""
# TODO: Implement reasons
# Prepare inputs
criterion = _as_root_criterion(criterion)
start = as_start_path(start)
# Check start
if start.is_dir() and criterion(start):
return start, "Pass"
# Iterate over all parents
# TODO: Consider adding maximum depth
# TODO: Consider limiting depth to path (e.g. "if p == stop: raise")
for p in start.parents:
if criterion(p):
return p, "Pass"
# Not found
raise RuntimeError("Project root not found.")
def write_csvs(
dirname: PathLike, adata: AnnData, skip_data: bool = True, sep: str = ','
):
"""See :meth:`~anndata.AnnData.write_csvs`.
"""
dirname = Path(dirname)
if dirname.suffix == '.csv':
dirname = dirname.with_suffix('')
logger.info("writing '.csv' files to %s", dirname)
if not dirname.is_dir():
dirname.mkdir(parents=True, exist_ok=True)
dir_uns = dirname / 'uns'
if not dir_uns.is_dir():
dir_uns.mkdir(parents=True, exist_ok=True)
d = dict(
obs=adata._obs,
var=adata._var,
obsm=adata._obsm.to_df(),
varm=adata._varm.to_df(),
)
if not skip_data:
d['X'] = pd.DataFrame(
adata._X.toarray() if issparse(adata._X) else adata._X
)
d_write = {**d, **adata._uns}
not_yet_raised_sparse_warning = True
for key, value in d_write.items():
if issparse(value):
if not_yet_raised_sparse_warning:
warnings.warn(
'Omitting to write sparse annotation.', WriteWarning
)
not_yet_raised_sparse_warning = False
continue
filename = dirname
if key not in {'X', 'var', 'obs', 'obsm', 'varm'}:
filename = dir_uns
filename /= f'{key}.csv'
df = value
if not isinstance(value, pd.DataFrame):
value = np.array(value)
if np.ndim(value) == 0:
value = value[None]
try:
df = pd.DataFrame(value)
except Exception as e:
warnings.warn(
f'Omitting to write {key!r} of type {type(e)}.',
WriteWarning,
)
continue
df.to_csv(
filename,
sep=sep,
header=key in {'obs', 'var', 'obsm', 'varm'},
index=key in {'obs', 'var'},
)
def write_csvs(dirname: PathLike,
adata: AnnData,
skip_data: bool = True,
sep: str = ","):
"""See :meth:`~anndata.AnnData.write_csvs`."""
dirname = Path(dirname)
if dirname.suffix == ".csv":
dirname = dirname.with_suffix("")
logger.info(f"writing .csv files to {dirname}")
if not dirname.is_dir():
dirname.mkdir(parents=True, exist_ok=True)
dir_uns = dirname / "uns"
if not dir_uns.is_dir():
dir_uns.mkdir(parents=True, exist_ok=True)
d = dict(
obs=adata._obs,
var=adata._var,
obsm=adata._obsm.to_df(),
varm=adata._varm.to_df(),
)
if not skip_data:
d["X"] = pd.DataFrame(
adata._X.toarray() if issparse(adata._X) else adata._X)
d_write = {**d, **adata._uns}
not_yet_raised_sparse_warning = True
for key, value in d_write.items():
if issparse(value):
if not_yet_raised_sparse_warning:
warnings.warn("Omitting to write sparse annotation.",
WriteWarning)
not_yet_raised_sparse_warning = False
continue
filename = dirname
if key not in {"X", "var", "obs", "obsm", "varm"}:
filename = dir_uns
filename /= f"{key}.csv"
df = value
if not isinstance(value, pd.DataFrame):
value = np.array(value)
if np.ndim(value) == 0:
value = value[None]
try:
df = pd.DataFrame(value)
except Exception as e:
warnings.warn(
f"Omitting to write {key!r} of type {type(e)}.",
WriteWarning,
)
continue
df.to_csv(
filename,
sep=sep,
header=key in {"obs", "var", "obsm", "varm"},
index=key in {"obs", "var"},
)
def is_excluded(self, path: PathLike) -> bool:
# The exclude pattern is constructed bearing in mind that will
# be called using fullmatch.
if self.exclude is None:
return False
path = Path(path)
if path.is_dir():
return self.exclude["d"].fullmatch(path.name) is not None
return self.exclude["f"].fullmatch(path.name) is not None
def _validate_confd(confd: os.PathLike) -> None:
if not confd.exists():
raise NoConfigDirError(f"{confd} does not exist.")
if not confd.is_dir():
raise ConfigDirNoDirError(f"{confd} is not a directory.")
if stat.S_IMODE(confd.lstat().st_mode) > 0o550:
oct_str = oct(stat.S_IMODE(confd.lstat().st_mode))
raise ConfigDirOwnershipError(
f"{confd} ownership is {oct_str}, max allowed is `0o550`")
for child in confd.iterdir():
if not child.is_file():
_log.warning(
f"Config dir '{confd}' only contains files, not '{child}'!")
continue
if child.suffix != ".json":
_log.warning(
f"Config dir '{confd}' only contains json files, not '{child.name}'!"
)
def write(self,
filename: PathLike,
overwrite: bool = False,
include_version: bool = False) -> Path:
"""
write this configuration to file
:param filename: path to file
:param overwrite: overwrite an existing file
:param include_version: include NEMSpy version information
:returns: path to written file
"""
if not isinstance(filename, Path):
filename = Path(filename)
ensure_directory(filename.parent)
output = f'{self}\n'
if include_version:
output = f'{self.version_header}\n' f'{output}'
if filename.is_dir():
filename = filename / self.name
logging.debug(
f'creating new file "{os.path.relpath(filename.resolve(), Path.cwd())}"'
)
if filename.exists():
logging.debug(
f'{"overwriting" if overwrite else "skipping"} existing file "{os.path.relpath(filename.resolve(), Path.cwd())}"'
)
if not filename.exists() or overwrite:
with open(filename, 'w', newline='\n') as output_file:
output_file.write(output)
return filename
def is_dir(localpath: PathLike) -> bool:
localpath = Path(localpath)
return localpath.is_dir()
