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Misc improvements #390

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merged 4 commits into from
Dec 5, 2024
Merged

Misc improvements #390

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913b6a0
log whole environment
mschwoer Nov 27, 2024
527fc84
remove obsolete property and setter for raw_path_list
mschwoer Nov 27, 2024
0c970a9
docstrings
mschwoer Nov 27, 2024
c0d7a8d
make speclib file removal safe
mschwoer Nov 27, 2024
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48 changes: 29 additions & 19 deletions alphadia/planning.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
import os
import socket
from datetime import datetime
from importlib import metadata
from pathlib import Path

import alphabase
Expand Down Expand Up @@ -48,16 +49,23 @@ def __init__(

Parameters
----------
raw_data : list

output_folder : str
output folder to save the results

raw_path_list : list
list of input file locations

config_path : str, optional
yaml file containing the default config.
library_path : str, optional
path to the spectral library file. If not provided, the library is built from fasta files

config_update_path : str, optional
yaml file to update the default config.
fasta_path_list : list, optional
list of fasta file locations to build the library from

config_update : dict, optional
config_base_path : str, optional
yaml file containing the default config.

config : dict, optional
dict to update the default config. Can be used for debugging purposes etc.

quant_path : str, optional
Expand Down Expand Up @@ -96,7 +104,7 @@ def __init__(
# print environment
self.log_environment()

# 1. default config path is not defined in the function definition to account for for different path separators on different OS
# 1. default config path is not defined in the function definition to account for different path separators on different OS
if config_base_path is None:
# default yaml config location under /misc/config/config.yaml
config_base_path = os.path.join(
Expand All @@ -113,7 +121,7 @@ def __init__(
update_config = Config("user defined")
update_config.from_dict(config)
else:
update_config = config
update_config = config # TODO what is it in this case?

self.config.update([update_config], print_modifications=True)

Expand All @@ -130,15 +138,6 @@ def __init__(

torch.set_num_threads(self.config["general"]["thread_count"])

@property
def raw_path_list(self) -> list[str]:
"""List of input files locations."""
return self._raw_path_list

@raw_path_list.setter
def raw_path_list(self, raw_path_list: list[str]):
self._raw_path_list = raw_path_list

@property
def config(self) -> Config:
"""Dict with all configuration parameters for the extraction."""
Expand All @@ -158,14 +157,22 @@ def spectral_library(self, spectral_library: SpecLibFlat) -> None:
self._spectral_library = spectral_library

def log_environment(self):
logger.progress("=================== Environment ===================")
logger.progress("================ AlphaX Environment ===============")
logger.progress(f"{'alphatims':<15} : {alphatims.__version__:}")
logger.progress(f"{'alpharaw':<15} : {alpharaw.__version__}")
logger.progress(f"{'alphabase':<15} : {alphabase.__version__}")
logger.progress(f"{'alphapeptdeep':<15} : {peptdeep.__version__}")
logger.progress(f"{'directlfq':<15} : {directlfq.__version__}")
logger.progress("===================================================")

logger.progress("================= Pip Environment =================")
pip_env = [
f"{dist.metadata['Name']}=={dist.version}"
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I thought about using debug Level logging. Bit I guess it doesnt hurt to have this by default.

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you will never need this until you need it, so I would leave it on by default

what about the progress level anyway? could this not be INFO?

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The idea is that progress has the important stuff and is colored green so you can find it faster when checking output

for dist in metadata.distributions()
]
logger.progress(" ".join(pip_env))
logger.progress("===================================================")

def init_alphabase(self):
"""Init alphabase by registering custom modifications."""

Expand Down Expand Up @@ -393,7 +400,10 @@ def run(

def clean(self):
if not self.config["general"]["save_library"]:
os.remove(os.path.join(self.output_folder, "speclib.hdf"))
try:
os.remove(os.path.join(self.output_folder, "speclib.hdf"))
except Exception as e:
logger.exception(f"Error deleting library: {e}")


def _log_exception_event(
Expand Down
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