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Cleanup logger function
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@PicoCentauri
PicoCentauri committed Jul 9, 2024
1 parent fded1ce commit 2a29728
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Showing 6 changed files with 290 additions and 72 deletions.
103 changes: 103 additions & 0 deletions RMSD_rmsd.csv
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# Command line was: mda RMSD -f data/traj.trr -s data/topol.tpr -atomgroup all -v
#
0.0 0.0 2.75841341423869e-07
1.0 0.4000000059604645 4.81326115892731
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4.0 1.600000023841858 6.5917707099361955
5.0 2.0 7.120691623117086
6.0 2.4000000953674316 7.0932971703456404
7.0 2.799999952316284 7.210072442189706
8.0 3.200000047683716 7.350055263419901
9.0 3.5999999046325684 7.844873843255679
10.0 4.0 8.180087119212413
11.0 4.400000095367432 8.227688239882058
12.0 4.800000190734863 8.614257002857027
13.0 5.199999809265137 8.62122036557813
14.0 5.599999904632568 8.67343663635793
15.0 6.0 8.908314639001917
16.0 6.400000095367432 9.22277720732986
17.0 6.800000190734863 9.45809196703627
18.0 7.199999809265137 9.494556715642583
19.0 7.599999904632568 9.851845566465697
20.0 8.0 9.468063262801405
21.0 8.399999618530273 9.72237181955554
22.0 8.800000190734863 9.795817807721628
23.0 9.199999809265137 10.205362972924204
24.0 9.600000381469727 10.27637925301259
25.0 10.0 10.242532811673563
26.0 10.399999618530273 10.475580487935385
27.0 10.800000190734863 10.76729154066856
28.0 11.199999809265137 10.638146968254457
29.0 11.600000381469727 10.637528008136737
30.0 12.0 10.945558487284588
31.0 12.399999618530273 11.119148252661983
32.0 12.800000190734863 11.036844299482748
33.0 13.199999809265137 11.149991488308283
34.0 13.600000381469727 11.490146370071116
35.0 14.0 11.293276708054744
36.0 14.399999618530273 11.465510093595096
37.0 14.800000190734863 11.361783839087757
38.0 15.199999809265137 11.688307451417892
39.0 15.600000381469727 11.677958185946274
40.0 16.0 11.725397471965591
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42.0 16.799999237060547 12.079675543212032
43.0 17.200000762939453 12.017340816368135
44.0 17.600000381469727 11.832623095416574
45.0 18.0 12.078582430542404
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57.0 22.799999237060547 12.758519920522179
58.0 23.200000762939453 12.705814503914063
59.0 23.600000381469727 13.017167838684855
60.0 24.0 12.686333633112097
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62.0 24.799999237060547 12.839709523727292
63.0 25.200000762939453 12.729883878407353
64.0 25.600000381469727 12.653439745733921
65.0 26.0 12.721168883213945
66.0 26.399999618530273 12.995463681469525
67.0 26.799999237060547 13.07793381003199
68.0 27.200000762939453 13.262224704574585
69.0 27.600000381469727 13.300797004390763
70.0 28.0 13.238897757255796
71.0 28.399999618530273 13.087260864183053
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82.0 32.79999923706055 13.53048613632186
83.0 33.20000076293945 13.537338845719567
84.0 33.599998474121094 13.596872138236884
85.0 34.0 13.657265618233158
86.0 34.400001525878906 13.844448099158042
87.0 34.79999923706055 13.82893234282479
88.0 35.20000076293945 13.70458798342047
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90.0 36.0 13.912169269321316
91.0 36.400001525878906 13.901216193796094
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93.0 37.20000076293945 13.65238960999978
94.0 37.599998474121094 13.833306344510708
95.0 38.0 13.756444793478451
96.0 38.400001525878906 13.738460985315902
97.0 38.79999923706055 13.742058599181664
98.0 39.20000076293945 13.921235214646803
99.0 39.599998474121094 13.932457595918546
100.0 40.0 13.879719688365299
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1 change: 1 addition & 0 deletions docs/CHANGELOG.rst
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Expand Up @@ -2,6 +2,7 @@
Changelog
=========

* Cleanup logger function

v0.1.31 (2024-07-08)
------------------------------------------
Expand Down
94 changes: 72 additions & 22 deletions src/mdacli/logger.py
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Expand Up @@ -6,18 +6,55 @@
# Released under the GNU Public Licence, v2 or any higher version
# SPDX-License-Identifier: GPL-2.0-or-later
"""Logging."""

import contextlib
import logging
import sys
import warnings
from pathlib import Path
from typing import List, Optional, Union

from .colors import Emphasise


@contextlib.contextmanager
def setup_logging(logobj, logfile=None, level=logging.WARNING):
def check_suffix(filename: Union[str, Path], suffix: str) -> Union[str, Path]:
"""Check the suffix of a file name and adds if it not existing.
If ``filename`` does not end with ``suffix`` the ``suffix`` is added and a
warning will be issued.
Parameters
----------
filename : Name of the file to be checked.
suffix : Expected filesuffix i.e. ``.txt``.
Returns
-------
Checked and probably extended file name.
"""
Create a logging environment for a given logobj.
path_filename = Path(filename)

if path_filename.suffix != suffix:
warnings.warn(
f"The file name should have a '{suffix}' extension. The user "
f"requested the file with name '{filename}', but it will be saved "
f"as '{filename}{suffix}'.",
stacklevel=1,
)
path_filename = path_filename.parent / (path_filename.name + suffix)

if type(filename) is str:
return str(path_filename)
else:
return path_filename


@contextlib.contextmanager
def setup_logging(
logobj: logging.Logger,
logfile: Optional[Union[str, Path]] = None,
level: int = logging.WARNING,
):
"""Create a logging environment for a given ``log_obj``.
Parameters
----------
Expand All @@ -28,38 +65,51 @@ def setup_logging(logobj, logfile=None, level=logging.WARNING):
level : int
Set the root logger level to the specified level. If for example set
to :py:obj:`logging.DEBUG` detailed debug logs inludcing filename and
function name are displayed. For :py:obj:`logging.INFO only the message
logged from errors, warnings and infos will be displayed.
function name are displayed. For :py:obj:`logging.INFO` only the
message logged from errors, warnings and infos will be displayed.
"""
try:
format = ""
if level == logging.DEBUG:
format = (
"[{levelname}] {filename}:{name}:{funcName}:{lineno}: "
"{message}"
)
else:
format = "{message}"
format += "[{levelname}]:{filename}:{funcName}:{lineno} - "
format += "{message}"

formatter = logging.Formatter(format, style="{")
handlers: List[Union[logging.StreamHandler, logging.FileHandler]] = []

logging.basicConfig(format=format,
handlers=[logging.StreamHandler(sys.stdout)],
level=level,
style='{')
stream_handler = logging.StreamHandler(sys.stdout)
stream_handler.setFormatter(formatter)
handlers.append(stream_handler)

if logfile:
logfile += ".log" * (not logfile.endswith("log"))
handler = logging.FileHandler(filename=logfile, encoding='utf-8')
handler.setFormatter(logging.Formatter(format, style='{'))
logobj.addHandler(handler)
logfile = check_suffix(filename=logfile, suffix=".log")
file_handler = logging.FileHandler(
filename=str(logfile), encoding="utf-8")
file_handler.setFormatter(formatter)
handlers.append(file_handler)
else:
logging.addLevelName(logging.INFO, Emphasise.info("INFO"))
logging.addLevelName(logging.DEBUG, Emphasise.debug("DEBUG"))
logging.addLevelName(logging.WARNING, Emphasise.warning("WARNING"))
logging.addLevelName(logging.ERROR, Emphasise.error("ERROR"))
logobj.info('Logging to file is disabled.')

logging.basicConfig(
format=format, handlers=handlers, level=level, style="{")
logging.captureWarnings(True)

if logfile:
abs_path = str(Path(logfile).absolute().resolve())
logobj.info(f"This log is also available at {abs_path!r}.")
else:
logobj.debug("Logging to file is disabled.")

for handler in handlers:
logobj.addHandler(handler)

yield

finally:
handlers = logobj.handlers[:]
for handler in handlers:
handler.flush()
handler.close()
logobj.removeHandler(handler)
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