standardize logging.getLogger() to use __name__ (Issue #5369)

package/CHANGELOG

@@ -17,11 +17,16 @@ The rules for this file:
 ??/??/?? IAlibay, orbeckst, marinegor, tylerjereddy, ljwoods2, marinegor,
          spyke7, talagayev, tanii1125, BradyAJohnston, hejamu, jeremyleung521,
          harshitgajjela-droid, kunjsinha, aygarwal, jauy123, Dreamstick9,
-         ollyfutur, Amarendra22, charity-g, ParthUppal523
+         ollyfutur, Amarendra22, charity-g, ParthUppal523,Jatin-Khiyani
 
  * 2.11.0
 
 Fixes
+  * Standardized logging.getLogger() calls to use \_\_name__ instead of
+   hardcoded strings across analysis, coordinates, topology,
+   converters, core, and guesser modules. Some modules had
+   mismatched or misspelled logger names (e.g. coordinates/PDB.py
+   used "PBD") which are now also corrected (Issue #5369)
  * `MDAnalysis.analysis.nucleicacids.WatsonCrickDist`, `MinorPairDist`,
    and `MajorPairDist` now match residue names against the full resname
    instead of only the first character, fixing incorrect behaviour with

package/MDAnalysis/__init__.py

@@ -157,7 +157,7 @@
 from typing import Dict
 
 
-logger = logging.getLogger("MDAnalysis.__init__")
+logger = logging.getLogger(__name__)
 
 from .version import __version__
 

package/MDAnalysis/analysis/align.py

@@ -218,7 +218,7 @@
 
 from .base import AnalysisBase
 
-logger = logging.getLogger("MDAnalysis.analysis.align")
+logger = logging.getLogger(__name__)
 
 
 def rotation_matrix(a, b, weights=None):

package/MDAnalysis/analysis/atomicdistances.py

@@ -116,7 +116,7 @@
 import logging
 from .base import AnalysisBase, ResultsGroup
 
-logger = logging.getLogger("MDAnalysis.analysis.atomicdistances")
+logger = logging.getLogger(__name__)
 
 
 class AtomicDistances(AnalysisBase):

package/MDAnalysis/analysis/contacts.py

@@ -225,7 +225,7 @@ def is_any_closer(r, r0, dist=2.5):
 from MDAnalysis.core.groups import AtomGroup, UpdatingAtomGroup
 from .base import AnalysisBase, ResultsGroup
 
-logger = logging.getLogger("MDAnalysis.analysis.contacts")
+logger = logging.getLogger(__name__)
 
 
 def soft_cut_q(r, r0, beta=5.0, lambda_constant=1.8):

package/MDAnalysis/analysis/density.py

@@ -177,7 +177,7 @@
 
 import logging
 
-logger = logging.getLogger("MDAnalysis.analysis.density")
+logger = logging.getLogger(__name__)
 
 
 class DensityAnalysis(AnalysisBase):

package/MDAnalysis/analysis/diffusionmap.py

@@ -145,7 +145,7 @@
 from .rms import rmsd
 from .base import AnalysisBase, ResultsGroup
 
-logger = logging.getLogger("MDAnalysis.analysis.diffusionmap")
+logger = logging.getLogger(__name__)
 
 
 class DistanceMatrix(AnalysisBase):

package/MDAnalysis/analysis/distances.py

@@ -65,7 +65,7 @@
 import warnings
 import logging
 
-logger = logging.getLogger("MDAnalysis.analysis.distances")
+logger = logging.getLogger(__name__)
 
 
 def contact_matrix(coord, cutoff=15.0, returntype="numpy", box=None):

package/MDAnalysis/analysis/gnm.py

@@ -97,7 +97,7 @@
 
 from MDAnalysis.analysis.base import Results
 
-logger = logging.getLogger("MDAnalysis.analysis.GNM")
+logger = logging.getLogger(__name__)
 
 
 def _dsq(a, b):

package/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py

@@ -718,7 +718,7 @@ def analysis(current, output, u, **kwargs):
 
 from ..base import AnalysisBase
 
-logger = logging.getLogger("MDAnalysis.analysis.WaterBridgeAnalysis")
+logger = logging.getLogger(__name__)
 
 
 class WaterBridgeAnalysis(AnalysisBase):

package/MDAnalysis/analysis/legacy/x3dna.py

@@ -135,7 +135,7 @@
 from MDAnalysis import ApplicationError
 from MDAnalysis.lib.util import asiterable, deprecate, realpath, which
 
-logger = logging.getLogger("MDAnalysis.analysis.x3dna")
+logger = logging.getLogger(__name__)
 
 
 @deprecate(

package/MDAnalysis/analysis/msd.py

@@ -278,7 +278,7 @@
 from ..core import groups
 import collections
 
-logger = logging.getLogger("MDAnalysis.analysis.msd")
+logger = logging.getLogger(__name__)
 
 due.cite(
     Doi("10.21105/joss.00877"),

package/MDAnalysis/analysis/rms.py

@@ -172,7 +172,7 @@
 from ..lib.util import asiterable, iterable, get_weights
 
 
-logger = logging.getLogger("MDAnalysis.analysis.rmsd")
+logger = logging.getLogger(__name__)
 
 
 def rmsd(a, b, weights=None, center=False, superposition=False):

package/MDAnalysis/converters/ParmEdParser.py

@@ -122,7 +122,7 @@
 )
 from ..core.topology import Topology
 
-logger = logging.getLogger("MDAnalysis.converters.ParmEdParser")
+logger = logging.getLogger(__name__)
 
 
 def squash_identical(values):

package/MDAnalysis/converters/RDKitParser.py

@@ -70,7 +70,7 @@
 )
 from ..topology.base import TopologyReaderBase, change_squash
 
-logger = logging.getLogger("MDAnalysis.converters.RDKitParser")
+logger = logging.getLogger(__name__)
 
 
 def _rdkit_atom_to_RS(atom):

package/MDAnalysis/coordinates/IMD.py

@@ -175,7 +175,7 @@ class MockIMDClient:
         )
         HAS_IMDCLIENT = False
 
-logger = logging.getLogger("MDAnalysis.coordinates.IMDReader")
+logger = logging.getLogger(__name__)
 
 
 class IMDReader(StreamReaderBase):

package/MDAnalysis/coordinates/PDB.py

@@ -158,7 +158,7 @@
 from ..exceptions import NoDataError
 
 
-logger = logging.getLogger("MDAnalysis.coordinates.PBD")
+logger = logging.getLogger(__name__)
 
 # Pairs of residue name / atom name in use to deduce PDB formatted atom names
 Pair = collections.namedtuple("Atom", "resname name")

package/MDAnalysis/coordinates/TPR.py

@@ -59,7 +59,7 @@
 
 import logging
 
-logger = logging.getLogger("MDAnalysis.coordinates.TPR")
+logger = logging.getLogger(__name__)
 
 import numpy as np
 

package/MDAnalysis/coordinates/TRC.py

@@ -77,7 +77,7 @@
 
 import logging
 
-logger = logging.getLogger("MDAnalysis.coordinates.GROMOS11")
+logger = logging.getLogger(__name__)
 
 
 class TRCReader(base.ReaderBase):

package/MDAnalysis/coordinates/TRJ.py

@@ -141,7 +141,8 @@
 from . import base
 from ..lib import util
 from ..lib.util import store_init_arguments
-logger = logging.getLogger("MDAnalysis.coordinates.AMBER")
+
+logger = logging.getLogger(__name__)
 
 
 try:

package/MDAnalysis/coordinates/XYZ.py

@@ -88,7 +88,7 @@
 import warnings
 import logging
 
-logger = logging.getLogger("MDAnalysis.coordinates.XYZ")
+logger = logging.getLogger(__name__)
 
 from . import base
 from .timestep import Timestep

package/MDAnalysis/core/universe.py

@@ -107,7 +107,7 @@
 from .topologyobjects import TopologyObject
 from ..guesser.base import get_guesser
 
-logger = logging.getLogger("MDAnalysis.core.universe")
+logger = logging.getLogger(__name__)
 
 
 def _update_topology_by_ids(universe, atomwise_resids, atomwise_segids):

package/MDAnalysis/guesser/base.py

@@ -43,7 +43,7 @@
 from typing import Dict
 import copy
 
-logger = logging.getLogger("MDAnalysis.guesser.base")
+logger = logging.getLogger(__name__)
 
 
 class _GuesserMeta(type):

package/MDAnalysis/topology/LAMMPSParser.py

@@ -108,7 +108,7 @@
 from ..guesser.tables import SYMB2Z
 from ..guesser.tables import masses as mass_table
 
-logger = logging.getLogger("MDAnalysis.topology.LAMMPS")
+logger = logging.getLogger(__name__)
 
 
 # Sections will all start with one of these words

package/MDAnalysis/topology/PDBParser.py

@@ -93,7 +93,7 @@
 )
 
 # Set up a logger for the PDBParser
-logger = logging.getLogger("MDAnalysis.topology.PDBParser")
+logger = logging.getLogger(__name__)
 
 
 def float_or_default(val, default):

package/MDAnalysis/topology/PSFParser.py

@@ -68,7 +68,7 @@
 )
 from ..core.topology import Topology
 
-logger = logging.getLogger("MDAnalysis.topology.PSF")
+logger = logging.getLogger(__name__)
 
 
 class PSFParser(TopologyReaderBase):

package/MDAnalysis/topology/TOPParser.py

@@ -117,7 +117,7 @@
 import warnings
 import logging
 
-logger = logging.getLogger("MDAnalysis.topology.TOPParser")
+logger = logging.getLogger(__name__)
 
 
 class TypeIndices(AtomAttr):

package/MDAnalysis/topology/TPRParser.py

@@ -177,7 +177,7 @@
 
 import logging
 
-logger = logging.getLogger("MDAnalysis.topology.TPRparser")
+logger = logging.getLogger(__name__)
 
 
 class TPRParser(TopologyReaderBase):