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Hd codes/issue4655 #4702

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Hd codes/issue4655 #4702

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49b712b
Fix E402: Module level import not at top of file
HD-Codes Sep 5, 2024
e3c932c
Fix F401 unused imports and F821 undefined logger
HD-Codes Sep 5, 2024
171503b
Fix PEP 8 issues in package/MDAnalysis/__init__.py
HD-Codes Sep 5, 2024
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55 changes: 28 additions & 27 deletions package/MDAnalysis/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -150,23 +150,45 @@

"""

__all__ = ['Universe', 'Writer',
'AtomGroup', 'ResidueGroup', 'SegmentGroup']

import logging
import warnings
from typing import Dict


logger = logging.getLogger("MDAnalysis.__init__")

from .version import __version__

try:
from .authors import __authors__
except ImportError:
logger = logging.getLogger("MDAnalysis.__init__")
logger.info('Could not find authors.py, __authors__ will be empty.')
__authors__ = []

__all__ = ['Universe', 'Writer', 'AtomGroup', 'ResidueGroup', 'SegmentGroup', '__version__',
'SelectionError', 'NoDataError', 'ApplicationError', 'SelectionWarning',
'MissingDataWarning', 'ConversionWarning', 'FileFormatWarning', 'StreamWarning',
'start_logging', 'stop_logging', 'units', 'Merge', 'converters']

# custom exceptions and warnings
from .exceptions import (
SelectionError, NoDataError, ApplicationError, SelectionWarning,
MissingDataWarning, ConversionWarning, FileFormatWarning,
StreamWarning
)

from .lib import log
from .lib.log import start_logging, stop_logging
from . import units

# Bring some often used objects into the current namespace
from .core.universe import Universe, Merge
from .core.groups import AtomGroup, ResidueGroup, SegmentGroup
from .coordinates.core import writer as Writer

# After Universe import
from . import converters

from .due import due, Doi, BibTeX

# Registry of Readers, Parsers and Writers known to MDAnalysis
# Metaclass magic fills these as classes are declared.
_READERS: Dict = {}
Expand All @@ -183,15 +205,6 @@
_TOPOLOGY_ATTRNAMES: Dict = {} # {lower case name w/o _ : name}


# custom exceptions and warnings
from .exceptions import (
SelectionError, NoDataError, ApplicationError, SelectionWarning,
MissingDataWarning, ConversionWarning, FileFormatWarning,
StreamWarning
)

from .lib import log
from .lib.log import start_logging, stop_logging

logging.getLogger("MDAnalysis").addHandler(log.NullHandler())
del logging
Expand All @@ -201,18 +214,6 @@
module='MDAnalysis')


from . import units

# Bring some often used objects into the current namespace
from .core.universe import Universe, Merge
from .core.groups import AtomGroup, ResidueGroup, SegmentGroup
from .coordinates.core import writer as Writer

# After Universe import
from . import converters

from .due import due, Doi, BibTeX

due.cite(Doi("10.25080/majora-629e541a-00e"),
description="Molecular simulation analysis library",
path="MDAnalysis", cite_module=True)
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