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Description
Installing RetroMol without BioCracker raises an error:
(retromol) barbara@MacBookPro raichu % retromol --help
Traceback (most recent call last):
File "/opt/anaconda3/envs/retromol/bin/retromol", line 3, in <module>
from retromol.cli import main
File "/opt/anaconda3/envs/retromol/lib/python3.10/site-packages/retromol/cli.py", line 24, in <module>
from retromol.fingerprint.fingerprint import FingerprintGenerator
File "/opt/anaconda3/envs/retromol/lib/python3.10/site-packages/retromol/fingerprint/fingerprint.py", line 237, in <module>
class FingerprintGenerator:
File "/opt/anaconda3/envs/retromol/lib/python3.10/site-packages/retromol/fingerprint/fingerprint.py", line 409, in FingerprintGenerator
readout: BioCrackerLinearReadout,
NameError: name 'BioCrackerLinearReadout' is not defined
(retromol) barbara@MacBookPro raichu %
The likely culprit is this try-except clause in fingerprint.py:
try:
from biocracker.query.modules import (
LinearReadout as BioCrackerLinearReadout,
Module,
NRPSModule,
PKSModule,
PKSExtenderUnit,
)
_BIOCRACKER = True
except ImportError:
pass
Followed by the following type-hint:
def fingerprint_from_biocracker_readout(
self,
readout: BioCrackerLinearReadout,
by_orf: bool = False,
num_bits: int = 2048,
kmer_sizes: list[int] | None = None,
kmer_weights: dict[int, int] | None = None,
counted: bool = False,
) -> NDArray[np.int8]:
"""
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