Allow Metric to use dataclasses or attr

* Update util.metric and related util.inspect modules to work with
  dataclasses or attr
* Update test_metric to test both dataclasses and attr classes
* Remove attr from non-test requirements

Closes Issue #45

docs/api.rst

@@ -34,6 +34,9 @@ Metric files
 
 .. seealso::
 
+   https://docs.python.org/3/library/dataclasses.html
+       Documentation for the dataclasses standard module
+
    https://www.attrs.org/en/stable/examples.html
 
        The attrs website for bringing back the joy to writing classes.

fgpyo/read_structure.py

@@ -61,15 +61,14 @@
     - :class:`~fgpyo.read_structure.SubReadWithQuals` -- Contains the bases and qualities that
         correspond to the given read segment
 """
+import dataclasses
 import enum
 from typing import Iterable
 from typing import Iterator
 from typing import List
 from typing import Optional
 from typing import Tuple
 
-import attr
-
 # A character that can be put in place of a number in a read structure to mean "0 or more bases".
 ANY_LENGTH_CHAR: str = "+"
 
@@ -87,7 +86,7 @@ def __str__(self) -> str:
         return self.value
 
 
-@attr.s(frozen=True, auto_attribs=True, kw_only=True)
+@dataclasses.dataclass(frozen=True, kw_only=True)
 class SubReadWithoutQuals:
     """Contains the bases that correspond to the given read segment"""
 
@@ -99,7 +98,7 @@ def kind(self) -> SegmentType:
         return self.segment.kind
 
 
-@attr.s(frozen=True, auto_attribs=True, kw_only=True)
+@dataclasses.dataclass(frozen=True, kw_only=True)
 class SubReadWithQuals:
     """Contains the bases and qualities that correspond to the given read segment"""
 
@@ -112,7 +111,7 @@ def kind(self) -> SegmentType:
         return self.segment.kind
 
 
-@attr.s(frozen=True, auto_attribs=True, kw_only=True)
+@dataclasses.dataclass(frozen=True, kw_only=True)
 class ReadSegment:
     """Encapsulates all the information about a segment within a read structure. A segment can
     either have a definite length, in which case length must be Some(Int), or an indefinite length
@@ -178,7 +177,7 @@ def _resized(self, end: int) -> "ReadSegment":
         if self.has_fixed_length and self.fixed_length == new_length:
             return self
         else:
-            return attr.evolve(self, length=new_length)
+            return dataclasses.replace(self, length=new_length)
 
     def __str__(self) -> str:
         if self.has_fixed_length:
@@ -187,7 +186,7 @@ def __str__(self) -> str:
             return f"{ANY_LENGTH_CHAR}{self.kind.value}"
 
 
-@attr.s(frozen=True, auto_attribs=True, kw_only=True)
+@dataclasses.dataclass(frozen=True, kw_only=True)
 class ReadStructure(Iterable[ReadSegment]):
     """Describes the structure of a give read.  A read contains one or more read segments. A read
     segment describes a contiguous stretch of bases of the same type (ex. template bases) of some
@@ -231,7 +230,7 @@ def with_variable_last_segment(self) -> "ReadStructure":
         if not last_segment.has_fixed_length:
             return self
         else:
-            last_segment = attr.evolve(last_segment, length=None)
+            last_segment = dataclasses.replace(last_segment, length=None)
             return ReadStructure(segments=self.segments[:-1] + (last_segment,))
 
     def extract(self, bases: str) -> Tuple[SubReadWithoutQuals, ...]:
@@ -285,7 +284,7 @@ def from_segments(
             off = 0
             segs = []
             for seg in segments:
-                seg = attr.evolve(seg, offset=off)
+                seg = dataclasses.replace(seg, offset=off)
                 off += seg.length if seg.has_fixed_length else 0
                 segs.append(seg)
             segments = tuple(segs)

fgpyo/sam/__init__.py

@@ -151,6 +151,7 @@
     - :func:`~fgpyo.sam.calc_edit_info` -- calculates how a read differs from the reference
 """
 
+import dataclasses
 import enum
 import io
 from pathlib import Path
@@ -164,7 +165,6 @@
 from typing import Tuple
 from typing import Union
 
-import attr
 import pysam
 from pysam import AlignedSegment
 from pysam import AlignmentFile as SamFile
@@ -385,7 +385,7 @@ def is_clipping(self) -> bool:
         return self == CigarOp.S or self == CigarOp.H
 
 
-@attr.s(frozen=True, slots=True)
+@dataclasses.dataclass(frozen=True, slots=True)
 class CigarElement:
     """Represents an element in a Cigar
 
@@ -394,14 +394,13 @@ class CigarElement:
         - operator (CigarOp): the operator of the element
     """
 
-    length: int = attr.ib()
-    operator: CigarOp = attr.ib()
+    length: int
+    operator: CigarOp
 
-    @length.validator
-    def _validate_length(self, attribute: Any, value: int) -> None:
+    def __post_init__(self) -> None:
         """Validates the length attribute is greater than zero."""
-        if value <= 0:
-            raise ValueError(f"Cigar element must have a length > 0, found {value}")
+        if self.length <= 0:
+            raise ValueError(f"Cigar element must have a length > 0, found {self.length}")
 
     @property
     def length_on_query(self) -> int:
@@ -423,15 +422,15 @@ class CigarParsingException(Exception):
     pass
 
 
-@attr.s(frozen=True, slots=True)
+@dataclasses.dataclass(frozen=True, slots=True)
 class Cigar:
     """Class representing a cigar string.
 
     Attributes:
         - elements (Tuple[CigarElement, ...]): zero or more cigar elements
     """
 
-    elements: Tuple[CigarElement, ...] = attr.ib(default=())
+    elements: Tuple[CigarElement, ...] = ()
 
     @classmethod
     def from_cigartuples(cls, cigartuples: Optional[List[Tuple[int, int]]]) -> "Cigar":
@@ -518,7 +517,7 @@ def length_on_target(self) -> int:
         return sum([elem.length_on_target for elem in self.elements])
 
 
-@attr.s(auto_attribs=True, frozen=True)
+@dataclasses.dataclass(frozen=True)
 class SupplementaryAlignment:
     """Stores a supplementary alignment record produced by BWA and stored in the SA SAM tag.
 
@@ -531,12 +530,12 @@ class SupplementaryAlignment:
         nm: the number of edits
     """
 
-    reference_name: str = attr.ib()
-    start: int = attr.ib()
-    is_forward: bool = attr.ib()
-    cigar: Cigar = attr.ib()
-    mapq: int = attr.ib()
-    nm: int = attr.ib()
+    reference_name: str
+    start: int
+    is_forward: bool
+    cigar: Cigar
+    mapq: int
+    nm: int
 
     def __str__(self) -> str:
         return ",".join(
@@ -620,7 +619,7 @@ def set_pair_info(r1: AlignedSegment, r2: AlignedSegment, proper_pair: bool = Tr
     r2.template_length = -insert_size
 
 
-@attr.s(auto_attribs=True, frozen=True)
+@dataclasses.dataclass(frozen=True)
 class ReadEditInfo:
     """
     Counts various stats about how a read compares to a reference sequence.
@@ -709,7 +708,7 @@ def calculate_edit_info(
     )
 
 
-@attr.s(auto_attribs=True, frozen=True)
+@dataclasses.dataclass(frozen=True)
 class Template:
     """A container for alignment records corresponding to a single sequenced template
     or insert.

fgpyo/util/inspect.py

@@ -3,6 +3,7 @@
 from typing import Dict
 from typing import Iterable
 from typing import List
+from typing import Protocol
 from typing import Tuple
 from typing import Type
 from typing import Union
@@ -16,17 +17,76 @@
 else:
     from typing_extensions import TypeAlias
 
+import dataclasses
 import functools
+from dataclasses import MISSING as DATACLASSES_MISSING
+from dataclasses import fields as get_dataclasses_fields
+from dataclasses import is_dataclass as is_dataclasses_class
 from enum import Enum
 from functools import partial
 from pathlib import PurePath
+from typing import TYPE_CHECKING
 from typing import Callable
 from typing import Optional
-
-import attr
+from typing import TypeVar
 
 import fgpyo.util.types as types
 
+try:
+    import attr
+
+    _use_attr = True
+    from attr import NOTHING as ATTR_NOTHING
+    from attr import fields as get_attr_fields
+    from attr import fields_dict as get_attr_fields_dict
+
+    Attribute = attr.Attribute
+
+    MISSING = {DATACLASSES_MISSING, ATTR_NOTHING}
+except ImportError:
+    _use_attr = False
+    attr = None
+    ATTR_NOTHING = None
+    Attribute = TypeVar("Attribute", bound=object)  # type: ignore
+
+    def get_attr_fields(cls: type) -> Tuple[dataclasses.Field, ...]:  # type: ignore
+        return ()
+
+    def get_attr_fields_dict(cls: type) -> Dict[str, dataclasses.Field]:  # type: ignore
+        return {}
+
+    MISSING = {DATACLASSES_MISSING}
+
+if TYPE_CHECKING:
+    from _typeshed import DataclassInstance as DataclassesProtocol
+else:
+
+    class DataclassesProtocol(Protocol):
+        __dataclasses_fields__: Dict[str, dataclasses.Field]
+
+
+if TYPE_CHECKING and _use_attr:
+    from attr import AttrsInstance
+else:
+
+    class AttrsInstance(Protocol):  # type: ignore
+        __attrs_attrs__: Dict[str, Any]
+
+
+def is_attr_class(cls: type) -> bool:  # type: ignore
+    return hasattr(cls, "__attrs_attrs__")
+
+
+MISSING_OR_NONE = {*MISSING, None}
+DataclassesOrAttrClass = Union[DataclassesProtocol, AttrsInstance]
+FieldType: TypeAlias = Union[dataclasses.Field, attr.Attribute]
+
+
+def get_dataclasses_fields_dict(
+    class_or_instance: Union[DataclassesProtocol, Type[DataclassesProtocol]],
+) -> Dict[str, dataclasses.Field]:
+    return {field.name: field for field in get_dataclasses_fields(class_or_instance)}
+
 
 class ParserNotFoundException(Exception):
     pass
@@ -254,9 +314,36 @@ def dict_parse(dict_string: str) -> Dict[Any, Any]:
     return parser
 
 
+def get_fields_dict(cls: Type[DataclassesOrAttrClass]) -> Dict[str, FieldType]:
+    """
+    Get the fields dict from either a dataclasses or attr dataclass.
+
+    Combine results in case someone chooses to mix them through inheritance.
+    """
+    if not (is_dataclasses_class(cls) or is_attr_class(cls)):
+        raise ValueError("cls must a dataclasses or attr class")
+    return {
+        **(get_dataclasses_fields_dict(cls) if is_dataclasses_class(cls) else {}),
+        **(get_attr_fields_dict(cls) if is_attr_class(cls) else {}),  # type: ignore
+    }
+
+
+def get_fields(cls: Type[DataclassesOrAttrClass]) -> Tuple[FieldType, ...]:
+    if not (is_dataclasses_class(cls) or is_attr_class(cls)):
+        raise ValueError("cls must a dataclasses or attr class")
+    return (get_dataclasses_fields(cls) if is_dataclasses_class(cls) else ()) + (
+        get_attr_fields(cls) if is_attr_class(cls) else ()  # type: ignore
+    )
+
+
+AttrFromType = TypeVar("AttrFromType")
+
+
 def attr_from(
-    cls: Type, kwargs: Dict[str, str], parsers: Optional[Dict[type, Callable[[str], Any]]] = None
-) -> Any:
+    cls: Type[AttrFromType],
+    kwargs: Dict[str, str],
+    parsers: Optional[Dict[type, Callable[[str], Any]]] = None,
+) -> AttrFromType:
     """Builds an attr class from key-word arguments
 
     Args:
@@ -265,15 +352,16 @@ def attr_from(
         parsers: a dictionary of parser functions to apply to specific types
     """
     return_values: Dict[str, Any] = {}
-    for attribute in attr.fields(cls):
+    for attribute in get_fields(cls):  # type: ignore
         return_value: Any
         if attribute.name in kwargs:
             str_value: str = kwargs[attribute.name]
             set_value: bool = False
 
             # Use the converter if provided
-            if attribute.converter is not None:
-                return_value = attribute.converter(str_value)
+            converter = getattr(attribute, "converter", None)
+            if converter is not None:
+                return_value = converter(str_value)
                 set_value = True
 
             # try getting a known parser
@@ -305,21 +393,21 @@ def attr_from(
             ), f"No value given and no default for attribute `{attribute.name}`"
             return_value = attribute.default
             # when the default is attr.NOTHING, just use None
-            if return_value is attr.NOTHING:
+            if return_value in MISSING:
                 return_value = None
 
         return_values[attribute.name] = return_value
 
     return cls(**return_values)
 
 
-def attribute_is_optional(attribute: attr.Attribute) -> bool:
+def attribute_is_optional(attribute: FieldType) -> bool:
     """Returns True if the attribute is optional, False otherwise"""
     return types.get_origin_type(attribute.type) is Union and isinstance(
         None, types.get_arg_types(attribute.type)
     )
 
 
-def attribute_has_default(attribute: attr.Attribute) -> bool:
+def attribute_has_default(attribute: FieldType) -> bool:
     """Returns True if the attribute has a default value, False otherwise"""
-    return attribute.default != attr.NOTHING or attribute_is_optional(attribute)
+    return attribute.default not in MISSING_OR_NONE or attribute_is_optional(attribute)