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run updated pre-commit: black format
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closes Formatting: move to black #220
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slobentanzer committed Jul 31, 2023
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14 changes: 7 additions & 7 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -3,12 +3,12 @@
![Python](https://img.shields.io/badge/python-3.9-blue.svg)
![Python](https://img.shields.io/badge/python-3.10-blue.svg)
[![PyPI version](https://badge.fury.io/py/biocypher.svg)](https://badge.fury.io/py/biocypher)
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[![Powered by the Bioregistry](https://img.shields.io/static/v1?label=Powered%20by&message=Bioregistry&color=BA274A&style=flat&logo=image/png;base64,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)](https://github.com/biopragmatics/bioregistry)

## ❓ Description
Knowledge graphs (KGs) are an [approach to knowledge
Expand Down Expand Up @@ -60,8 +60,8 @@ please join our community at https://biocypher.zulipchat.com!
> This disclaimer was adapted from the [Pooch](https://github.com/fatiando/pooch) project.
## ✍️ Citation
The BioCypher paper has been peer-reviewed in
[Nature Biotechnology](https://www.nature.com/articles/s41587-023-01848-y).
The BioCypher paper has been peer-reviewed in
[Nature Biotechnology](https://www.nature.com/articles/s41587-023-01848-y).
Before, it was available as a preprint at https://arxiv.org/abs/2212.13543.

## Acknowledgements
Expand Down
21 changes: 10 additions & 11 deletions biocypher/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -13,14 +13,14 @@
"""

__all__ = [
'__version__',
'__author__',
'module_data',
'config',
'logfile',
'log',
'Driver',
'BioCypher',
"__version__",
"__author__",
"module_data",
"config",
"logfile",
"log",
"Driver",
"BioCypher",
]

from ._core import BioCypher
Expand All @@ -30,11 +30,10 @@


class Driver(BioCypher):

# initialise parent class but log a warning
def __init__(self, *args, **kwargs):
logger.warning(
'The class `Driver` is deprecated and will be removed in a future '
'release. Please use `BioCypher` instead.'
"The class `Driver` is deprecated and will be removed in a future "
"release. Please use `BioCypher` instead."
)
super().__init__(*args, **kwargs)
52 changes: 25 additions & 27 deletions biocypher/_config/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -23,29 +23,29 @@
import yaml
import appdirs

__all__ = ['module_data', 'module_data_path', 'read_config', 'config', 'reset']
__all__ = ["module_data", "module_data_path", "read_config", "config", "reset"]

_USER_CONFIG_DIR = appdirs.user_config_dir('biocypher', 'saezlab')
_USER_CONFIG_FILE = os.path.join(_USER_CONFIG_DIR, 'conf.yaml')
_USER_CONFIG_DIR = appdirs.user_config_dir("biocypher", "saezlab")
_USER_CONFIG_FILE = os.path.join(_USER_CONFIG_DIR, "conf.yaml")


class MyLoader(yaml.SafeLoader):
def construct_scalar(self, node):
# Check if the scalar contains double quotes and an escape sequence
value = super().construct_scalar(node)
q = bool(node.style == '"')
b = bool('\\' in value.encode('unicode_escape').decode('utf-8'))
b = bool("\\" in value.encode("unicode_escape").decode("utf-8"))
if q and b:
warnings.warn(
(
'Double quotes detected in YAML configuration scalar: '
"Double quotes detected in YAML configuration scalar: "
f"{value.encode('unicode_escape')}. "
'These allow escape sequences and may cause problems, for '
"These allow escape sequences and may cause problems, for "
"instance with the Neo4j admin import files (e.g. '\\t'). "
'Make sure you wanted to do this, and use single quotes '
'whenever possible.'
"Make sure you wanted to do this, and use single quotes "
"whenever possible."
),
category=UserWarning
category=UserWarning,
)
return value

Expand All @@ -57,7 +57,7 @@ def module_data_path(name: str) -> str:

here = os.path.dirname(os.path.abspath(__file__))

return os.path.join(here, f'{name}.yaml')
return os.path.join(here, f"{name}.yaml")


def module_data(name: str) -> Any:
Expand All @@ -71,11 +71,8 @@ def module_data(name: str) -> Any:


def _read_yaml(path: str) -> Optional[dict]:

if os.path.exists(path):

with open(path, 'r') as fp:

with open(path, "r") as fp:
return yaml.load(fp.read(), Loader=MyLoader)


Expand All @@ -89,18 +86,22 @@ def read_config() -> dict:
TODO explain path configuration
"""

defaults = module_data('biocypher_config')
defaults = module_data("biocypher_config")
user = _read_yaml(_USER_CONFIG_FILE) or {}
# TODO account for .yml?
local = _read_yaml('biocypher_config.yaml'
) or _read_yaml('config/biocypher_config.yaml') or {}
local = (
_read_yaml("biocypher_config.yaml")
or _read_yaml("config/biocypher_config.yaml")
or {}
)

for key in defaults:

value = local[key] if key in local else user[key] if key in user else None
value = (
local[key] if key in local else user[key] if key in user else None
)

if value is not None:
if type(defaults[key]) == str: # first level config (like title)
if type(defaults[key]) == str: # first level config (like title)
defaults[key] = value
else:
defaults[key].update(value)
Expand All @@ -114,28 +115,25 @@ def config(*args, **kwargs) -> Optional[Any]:
"""

if args and kwargs:

raise ValueError(
'Setting and getting values in the same call is not allowed.',
"Setting and getting values in the same call is not allowed.",
)

if args:

result = tuple(globals()['_config'].get(key, None) for key in args)
result = tuple(globals()["_config"].get(key, None) for key in args)

return result[0] if len(result) == 1 else result

for key, value in kwargs.items():

globals()['_config'][key].update(value)
globals()["_config"][key].update(value)


def reset():
"""
Reload configuration from the config files.
"""

globals()['_config'] = read_config()
globals()["_config"] = read_config()


reset()
Expand Down
2 changes: 0 additions & 2 deletions biocypher/_config/biocypher_config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -109,5 +109,3 @@ postgresql:
delimiter: '\t'
# import_call_bin_prefix: '' # path to "psql"
# import_call_file_prefix: '/path/to/files'


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