def verbosity(self, level: Union[str, int]):
"""
Sets logging configuration for scvi based on chosen level of verbosity.
If "scvi" logger has no StreamHandler, add one.
Else, set its level to `level`.
Parameters
----------
level
Sets "scvi" logging level to `level`
force_terminal
Rich logging option, set to False if piping to file output.
"""
self._verbosity = level
scvi_logger.setLevel(level)
if len(scvi_logger.handlers) == 0:
console = Console(force_terminal=True)
if console.is_jupyter is True:
console.is_jupyter = False
ch = RichHandler(show_path=False, console=console, show_time=False)
formatter = logging.Formatter("%(message)s")
ch.setFormatter(formatter)
scvi_logger.addHandler(ch)
else:
scvi_logger.setLevel(level)
def verbosity(self, level: Union[str, int]):
"""
Sets logging configuration for scvi based on chosen level of verbosity.
Sets "scvi" logging level to `level`
If "scvi" logger has no StreamHandler, add one.
Else, set its level to `level`.
"""
self._verbosity = level
scvi_logger.setLevel(level)
has_streamhandler = False
for handler in scvi_logger.handlers:
if isinstance(handler, RichHandler):
handler.setLevel(level)
logger.info(
"'scvi' logger already has a StreamHandler, set its level to {}."
.format(level))
has_streamhandler = True
if not has_streamhandler:
console = Console(force_terminal=True)
if console.is_jupyter is True:
console.is_jupyter = False
ch = RichHandler(show_path=False, console=console, show_time=False)
formatter = logging.Formatter("%(message)s")
ch.setFormatter(formatter)
scvi_logger.addHandler(ch)
logger.debug(
"Added StreamHandler with custom formatter to 'scvi' logger.")
from rich.console import Console
from rich.logging import RichHandler
# https://github.com/python-poetry/poetry/pull/2366#issuecomment-652418094
# https://github.com/python-poetry/poetry/issues/144#issuecomment-623927302
try:
import importlib.metadata as importlib_metadata
except ModuleNotFoundError:
import importlib_metadata
package_name = "scgen"
__version__ = importlib_metadata.version(package_name)
logger = logging.getLogger(__name__)
# set the logging level
logger.setLevel(logging.INFO)
# nice logging outputs
console = Console(force_terminal=True)
if console.is_jupyter is True:
console.is_jupyter = False
ch = RichHandler(show_path=False, console=console, show_time=False)
formatter = logging.Formatter("scGen: %(message)s")
ch.setFormatter(formatter)
logger.addHandler(ch)
# this prevents double outputs
logger.propagate = False
__all__ = ["setup_anndata", "SCGEN", "SCGENVAE"]
