Standardize class init docstrings (#3529)

Standardize class initialization comment throughout project

Bio/Affy/CelFile.py

@@ -61,7 +61,7 @@ class Record:
     """
 
     def __init__(self):
-        """Initialize class."""
+        """Initialize the class."""
         self.version = None
         self.GridCornerUL = None
         self.GridCornerUR = None

Bio/AlignIO/MauveIO.py

@@ -107,7 +107,7 @@ class MauveWriter(SequentialAlignmentWriter):
     """Mauve/XMFA alignment writer."""
 
     def __init__(self, *args, **kwargs):
-        """Initialize."""
+        """Initialize the class."""
         super().__init__(*args, **kwargs)
         self._wrote_header = False
         self._wrote_first = False

Bio/Application/__init__.py

@@ -100,7 +100,7 @@ class ApplicationError(subprocess.CalledProcessError):
     """
 
     def __init__(self, returncode, cmd, stdout="", stderr=""):
-        """Initialize."""
+        """Initialize the class."""
         self.returncode = returncode
         self.cmd = cmd
         self.stdout = stdout

Bio/Entrez/Parser.py

@@ -260,7 +260,7 @@ class DataHandlerMeta(type):
     """A metaclass is needed until Python supports @classproperty."""
 
     def __init__(cls, *args, **kwargs):
-        """Initialize."""
+        """Initialize the class."""
         cls._directory = None
 
     @property

Bio/GenBank/Record.py

@@ -168,7 +168,7 @@ class Record:
     SEQUENCE_FORMAT = "%" + str(GB_SEQUENCE_INDENT) + "s"
 
     def __init__(self):
-        """Initialize."""
+        """Initialize the class."""
         self.accession = []
         self.base_counts = ""
         self.comment = ""
@@ -512,7 +512,7 @@ class Reference:
     """
 
     def __init__(self):
-        """Initialize."""
+        """Initialize the class."""
         self.number = ""
         self.bases = ""
         self.authors = ""
@@ -617,7 +617,7 @@ class Feature:
     """
 
     def __init__(self, key="", location=""):
-        """Initialize."""
+        """Initialize the class."""
         self.key = key
         self.location = location
         self.qualifiers = []
@@ -647,7 +647,7 @@ class Qualifier:
     """
 
     def __init__(self, key="", value=""):
-        """Initialize."""
+        """Initialize the class."""
         self.key = key
         self.value = value
 

Bio/GenBank/Scanner.py

@@ -60,7 +60,7 @@ class InsdcScanner:
     SEQUENCE_HEADERS = ["XXX"]  # with right hand side spaces removed
 
     def __init__(self, debug=0):
-        """Initialize."""
+        """Initialize the class."""
         assert len(self.RECORD_START) == self.HEADER_WIDTH
         for marker in self.SEQUENCE_HEADERS:
             assert marker == marker.rstrip()

Bio/Graphics/BasicChromosome.py

@@ -106,7 +106,7 @@ class Organism(_ChromosomeComponent):
     """
 
     def __init__(self, output_format="pdf"):
-        """Initialize."""
+        """Initialize the class."""
         _ChromosomeComponent.__init__(self)
 
         # customizable attributes

Bio/Graphics/Comparative.py

@@ -44,7 +44,7 @@ class ComparativeScatterPlot:
     """
 
     def __init__(self, output_format="pdf"):
-        """Initialize."""
+        """Initialize the class."""
         # customizable attributes
         self.number_of_columns = 1
         self.page_size = letter

Bio/Graphics/Distribution.py

@@ -37,7 +37,7 @@ class DistributionPage:
     """
 
     def __init__(self, output_format="pdf"):
-        """Initialize."""
+        """Initialize the class."""
         self.distributions = []
 
         # customizable attributes
@@ -250,7 +250,7 @@ class LineDistribution:
     """
 
     def __init__(self):
-        """Initialize."""
+        """Initialize the class."""
         pass
 
     def draw(self, cur_drawing, start_x, start_y, end_x, end_y):

Bio/Graphics/KGML_vis.py

@@ -120,7 +120,7 @@ class KGMLCanvas:
         show_reaction_entries=True,
         margins=(0.02, 0.02),
     ):
-        """Initialize."""
+        """Initialize the class."""
         self.pathway = pathway
         self.show_maps = show_maps
         self.show_orthologs = show_orthologs

Bio/HMM/DynamicProgramming.py

@@ -322,5 +322,5 @@ class LogDPAlgorithms(AbstractDPAlgorithms):
     """
 
     def __init__(self, markov_model, sequence):
-        """Initialize."""
+        """Initialize the class."""
         raise NotImplementedError("Haven't coded this yet...")

Bio/HMM/Trainer.py

@@ -50,7 +50,7 @@ class AbstractTrainer:
     """Provide generic functionality needed in all trainers."""
 
     def __init__(self, markov_model):
-        """Initialize."""
+        """Initialize the class."""
         self._markov_model = markov_model
 
     def log_likelihood(self, probabilities):
@@ -355,7 +355,7 @@ class KnownStateTrainer(AbstractTrainer):
     """
 
     def __init__(self, markov_model):
-        """Initialize."""
+        """Initialize the class."""
         AbstractTrainer.__init__(self, markov_model)
 
     def train(self, training_seqs):

Bio/LogisticRegression.py

@@ -30,7 +30,7 @@ class LogisticRegression:
     """
 
     def __init__(self):
-        """Initialize."""
+        """Initialize the class."""
         self.beta = []
 
 

Bio/PDB/HSExposure.py

@@ -25,7 +25,7 @@ class _AbstractHSExposure(AbstractPropertyMap):
     """
 
     def __init__(self, model, radius, offset, hse_up_key, hse_down_key, angle_key=None):
-        """Initialize.
+        """Initialize class.
 
         :param model: model
         :type model: L{Model}
@@ -140,7 +140,7 @@ class HSExposureCA(_AbstractHSExposure):
     """
 
     def __init__(self, model, radius=12, offset=0):
-        """Initialse class.
+        """Initialize class.
 
         :param model: the model that contains the residues
         :type model: L{Model}
@@ -275,7 +275,7 @@ class ExposureCN(AbstractPropertyMap):
     """Residue exposure as number of CA atoms around its CA atom."""
 
     def __init__(self, model, radius=12.0, offset=0):
-        """Initialize.
+        """Initialize class.
 
         A residue's exposure is defined as the number of CA atoms around
         that residue's CA atom. A dictionary is returned that uses a L{Residue}

Bio/SearchIO/_legacy/NCBIStandalone.py

@@ -850,7 +850,7 @@ class BlastParser(AbstractParser):
     """Parses BLAST data into a Record.Blast object."""
 
     def __init__(self):
-        """Initialize."""
+        """Initialize the class."""
         self._scanner = _Scanner()
         self._consumer = _BlastConsumer()
 
@@ -864,7 +864,7 @@ class PSIBlastParser(AbstractParser):
     """Parses BLAST data into a Record.PSIBlast object."""
 
     def __init__(self):
-        """Initialize."""
+        """Initialize the class."""
         self._scanner = _Scanner()
         self._consumer = _PSIBlastConsumer()
 

Bio/kNN.py

@@ -42,7 +42,7 @@ class kNN:
     """
 
     def __init__(self):
-        """Initialize."""
+        """Initialize the class."""
         self.classes = set()
         self.xs = []
         self.ys = []

Bio/motifs/alignace.py

@@ -15,7 +15,7 @@ class Record(list):
     """AlignACE record (subclass of Python list)."""
 
     def __init__(self):
-        """Initialize."""
+        """Initialize the class."""
         self.parameters = None
 
 

Bio/motifs/meme.py

@@ -109,7 +109,7 @@ class Record(list):
     """
 
     def __init__(self):
-        """Initialize."""
+        """Initialize the class."""
         self.version = ""
         self.datafile = ""
         self.command = ""

Bio/motifs/transfac.py

@@ -81,7 +81,7 @@ class Record(list):
     """
 
     def __init__(self):
-        """Initialize."""
+        """Initialize the class."""
         self.version = None
 
     def __str__(self):

Scripts/xbbtools/xbb_translations.py

@@ -22,7 +22,7 @@ class xbb_translations:
     """A class for doing translations."""
 
     def __init__(self):
-        """Initialize."""
+        """Initialize the class."""
         pass
 
     def frame1(self, seq, translation_table=1):

Tests/test_KGML_graphics.py

@@ -57,7 +57,7 @@ class PathwayData:
     """Convenience structure for testing pathway data."""
 
     def __init__(self, name, element_counts, show_pathway_image=False):
-        """Initialize."""
+        """Initialize the class."""
         self.infilename = os.path.join("KEGG", "ko%s.xml" % name)
         self.outfilename = os.path.join("KEGG", "ko%s.kgml" % name)
         self.element_counts = element_counts

Tests/test_KGML_nographics.py

@@ -26,7 +26,7 @@ class PathwayData:
         pathway_image,
         show_pathway_image=False,
     ):
-        """Initialize."""
+        """Initialize the class."""
         self.infilename = infilename
         self.outfilename = outfilename
         self.element_counts = element_counts

Tests/test_SeqIO.py

@@ -163,7 +163,7 @@ class ForwardOnlyHandle:
     """Mimic a network handle without seek and tell methods etc."""
 
     def __init__(self, handle):
-        """Initialize."""
+        """Initialize the class."""
         self._handle = handle
 
     def __iter__(self):