Merge pull request biocommons#729 from davmlaw/issue_178_abc_EDit

biocommons#178 - use abc for Edit class to ensure method definition

src/hgvs/alignmentmapper.py

@@ -57,7 +57,7 @@ def _hgvs_to_zbc(i):
     return i
 
 
-class AlignmentMapper(object):
+class AlignmentMapper:
     """Maps hgvs location objects between genomic (g), non-coding (n) and
     cds (c) coordinates according to a CIGAR string.
 

src/hgvs/config.py

@@ -37,7 +37,7 @@
 logger = logging.getLogger(__name__)
 
 
-class Config(object):
+class Config:
     """provides an attribute-based lookup of configparser sections and
     settings.
 
@@ -75,7 +75,7 @@ def __getattr__(self, k):
     __getitem__ = __getattr__
 
 
-class ConfigGroup(object):
+class ConfigGroup:
     def __init__(self, section):
         self.__dict__["_section"] = section
 

src/hgvs/dataproviders/ncbi.py

@@ -112,7 +112,7 @@ def connect(
     return conn
 
 
-class NCBIBase(object):
+class NCBIBase:
     required_version = "1.1"
 
     _queries = {

src/hgvs/dataproviders/seqfetcher.py

@@ -13,7 +13,7 @@
 _logger = logging.getLogger(__name__)
 
 
-class SeqFetcher(object):
+class SeqFetcher:
     """This class is intended primarily as a mixin for HGVS data providers
     that doen't otherwise have access to sequence data.  It uses the
     fetch_seq() function in this module to fetch sequences from

src/hgvs/decorators/deprecated.py

@@ -8,7 +8,7 @@
 import warnings
 
 
-class deprecated(object):
+class deprecated:
     """Decorator factory class which returns a decorator function that
     marks a function as deprecated. It will result in a warning being
     emitted when the function is used, once per invocation point and

src/hgvs/edit.py

@@ -8,6 +8,7 @@
 location).
 
 """
+import abc
 
 import attr
 import six
@@ -18,7 +19,7 @@
 
 
 @attr.s(slots=True)
-class Edit(object):
+class Edit(abc.ABC):
     def format(self, conf=None):
         return str(self)
 
@@ -46,6 +47,12 @@ def _del_ins_lengths(self, ilen):
             "internal function _del_ins_lengths not implemented for this variant type"
         )
 
+    @property
+    @abc.abstractmethod
+    def type(self):
+        """ return the type of this Edit """
+        pass
+
 
 @attr.s(slots=True)
 class NARefAlt(Edit):

src/hgvs/hgvsposition.py

@@ -7,7 +7,7 @@
 
 
 @attr.s(slots=True, repr=False)
-class HGVSPosition(object):
+class HGVSPosition:
     """
     HGVSPosition -- Represent partial HGVS tags that refer to a position without alleles
 

src/hgvs/intervalmapper.py

@@ -55,7 +55,7 @@
 
 # N.B. This Interval is internal to intervalmapper.py. It is *NOT* the
 # same as the Interval defined in location.py.
-class Interval(object):
+class Interval:
     """Represents a segment of a sequence in interbase
     coordinates (0-based, right-open).
     """
@@ -78,7 +78,7 @@ def __repr__(self):
         )
 
 
-class IntervalPair(object):
+class IntervalPair:
     """Represents a match, insertion, or deletion segment of an
     alignment. If a match, the lengths must be equal; if an insertion or
     deletion, the length of the ref or tgt must be zero respectively."""
@@ -101,7 +101,7 @@ def __repr__(self):
         return "{self.__class__.__name__}(ref={self.ref},tgt={self.tgt})".format(self=self)
 
 
-class IntervalMapper(object):
+class IntervalMapper:
     """Provides mapping between sequence coordinates according to an
     ordered set of IntervalPairs."""
 
@@ -181,7 +181,7 @@ def clip_to_iv(iv, pos):
         return to_start_i, to_end_i
 
 
-class CIGARElement(object):
+class CIGARElement:
     """represents elements of a CIGAR string and provides methods for
     determining the number of ref and tgt bases consumed by the
     operation"""

src/hgvs/location.py

@@ -27,7 +27,7 @@
 
 @attr.s(slots=True, repr=False, cmp=False)
 @total_ordering
-class SimplePosition(object):
+class SimplePosition:
     base = attr.ib(default=None)
     uncertain = attr.ib(default=False)
 
@@ -79,7 +79,7 @@ def __lt__(lhs, rhs):
 
 @attr.s(slots=True, repr=False, cmp=False)
 @total_ordering
-class BaseOffsetPosition(object):
+class BaseOffsetPosition:
     """
     Class for dealing with CDS coordinates in transcript variants.
 
@@ -219,7 +219,7 @@ def __lt__(lhs, rhs):
 
 
 @attr.s(slots=True, repr=False, cmp=False)
-class AAPosition(object):
+class AAPosition:
     base = attr.ib(default=None)
     aa = attr.ib(default=None)
     uncertain = attr.ib(default=False)
@@ -310,7 +310,7 @@ def __ge__(lhs, rhs):
 
 
 @attr.s(slots=True, repr=False)
-class Interval(object):
+class Interval:
     start = attr.ib(default=None)
     end = attr.ib(default=None)
     uncertain = attr.ib(default=False)

src/hgvs/normalizer.py

@@ -21,7 +21,7 @@
 _logger = logging.getLogger(__name__)
 
 
-class Normalizer(object):
+class Normalizer:
     """Perform variant normalization"""
 
     def __init__(

src/hgvs/parser.py

@@ -25,7 +25,7 @@
 from hgvs.generated.hgvs_grammar import createParserClass
 
 
-class Parser(object):
+class Parser:
     """Provides comprehensive parsing of HGVS variant strings (*i.e.*,
     variants represented according to the Human Genome Variation
     Society recommendations) into Python representations.  The class

src/hgvs/posedit.py

@@ -10,7 +10,7 @@
 
 
 @attr.s(slots=True, repr=False)
-class PosEdit(object):
+class PosEdit:
     """
     represents a **simple** variant, consisting of a single position and edit pair
     """

src/hgvs/projector.py

@@ -10,7 +10,7 @@
 import hgvs.alignmentmapper
 
 
-class Projector(object):
+class Projector:
     """
     The Projector class implements liftover between two transcripts via a
     common reference sequence.

src/hgvs/sequencevariant.py

@@ -9,7 +9,7 @@
 
 
 @attr.s(slots=True, repr=False)
-class SequenceVariant(object):
+class SequenceVariant:
     """
     represents a basic HGVS variant.  The only requirement is that each
     component can be stringified; for example, passing pos as either a string

src/hgvs/transcriptmapper.py

@@ -19,7 +19,7 @@
 _logger.warning("This module is deprecated and will be removed in a future release")
 
 
-class TranscriptMapper(object):
+class TranscriptMapper:
     """Provides coordinate (not variant) mapping operations between
     genomic (g), non-coding (n), cds (c), and protein (p) coordinates.
     All coordinates are 1-based inclusive, per the HGVS

src/hgvs/utils/altseq_to_hgvsp.py

@@ -17,7 +17,7 @@
 DBG = False
 
 
-class AltSeqToHgvsp(object):
+class AltSeqToHgvsp:
     def __init__(self, ref_data, alt_data):
         """Constructor
 

src/hgvs/utils/altseqbuilder.py

@@ -20,7 +20,7 @@
 _logger = logging.getLogger(__name__)
 
 
-class AltTranscriptData(object):
+class AltTranscriptData:
     def __init__(
         self,
         seq,
@@ -79,7 +79,7 @@ def __init__(
         self.is_ambiguous = is_ambiguous
 
 
-class AltSeqBuilder(object):
+class AltSeqBuilder:
     EXON = "exon"
     INTRON = "intron"
     F_UTR = "five utr"

src/hgvs/utils/reftranscriptdata.py

@@ -3,7 +3,7 @@
 from hgvs.exceptions import HGVSDataNotAvailableError
 
 
-class RefTranscriptData(object):
+class RefTranscriptData:
     def __init__(self, hdp, tx_ac, pro_ac):
         """helper for generating RefTranscriptData from for c_to_p"""
         tx_info = hdp.get_tx_identity_info(tx_ac)

src/hgvs/validator.py

@@ -25,7 +25,7 @@
 _logger = logging.getLogger(__name__)
 
 
-class Validator(object):
+class Validator:
     """invoke intrinsic and extrinsic validation"""
 
     def __init__(self, hdp, strict=hgvs.global_config.validator.strict):
@@ -39,7 +39,7 @@ def validate(self, var, strict=None):
         return self._ivr.validate(var, strict) and self._evr.validate(var, strict)
 
 
-class IntrinsicValidator(object):
+class IntrinsicValidator:
     """
     Attempts to determine if the HGVS name is internally consistent
 

src/hgvs/variantmapper.py

@@ -26,7 +26,7 @@
 _logger = logging.getLogger(__name__)
 
 
-class VariantMapper(object):
+class VariantMapper:
     r"""Maps SequenceVariant objects between g., n., r., c., and p. representations.
 
     g⟷{c,n,r} projections are similar in that c, n, and r variants

tests/support/crosschecker.py

@@ -10,7 +10,7 @@
 from hgvs.exceptions import HGVSDataNotAvailableError
 
 
-class LineIterator(object):
+class LineIterator:
     """iterate over a stream, keeping last line and # lines read"""
 
     def __init__(self, fh, skip_comments=False):
@@ -29,7 +29,7 @@ def __iter__(self):
             yield line
 
 
-class CrossChecker(object):
+class CrossChecker:
     """base class for testing a group of related variants.  Checks all reasonable combinations of
     g <-> t --> p
 

tests/test_hgvs_dataproviders_uta.py

@@ -19,7 +19,7 @@
 from hgvs.exceptions import HGVSDataNotAvailableError, HGVSError
 
 
-class UTA_Base(object):
+class UTA_Base:
     def test_get_acs_for_protein_seq(self):
         exp = ["NP_001005405.1", "MD5_8fc09b1d9a38a8c55176a0fa922df227"]
         s = """