Merge pull request #72 from aCLImatise/attrs

Replace dataclasses with attrs throughout

Author: multimeric

.isort.cfg

@@ -1,2 +1,2 @@
 [settings]
-known_third_party = WDL,click,cwl_utils,cwltool,dataclasses,inflection,pkg_resources,pyhash,pyparsing,pytest,ruamel,setuptools,spacy,wdlgen,wordsegment,regex,num2words,word2number,psutil,packaging,docker,attr
+known_third_party = WDL,click,cwl_utils,cwltool,inflection,pkg_resources,pyhash,pyparsing,pytest,ruamel,setuptools,spacy,wdlgen,wordsegment,regex,num2words,word2number,psutil,packaging,docker,attr

.pre-commit-config.yaml

@@ -10,8 +10,6 @@ repos:
           - "--force-grid-wrap=0"
           - "--use-parentheses"
           - "--line-width=88"
-          - "--thirdparty"
-          - "dataclasses"
 
   - repo: https://github.com/psf/black
     rev: 20.8b1

aclimatise/cli_types.py

@@ -4,11 +4,13 @@
 import typing
 from enum import Enum
 
-from dataclasses import dataclass
+import attr
 
+from aclimatise.yaml import AttrYamlMixin
 
-@dataclass(unsafe_hash=True)
-class CliType:
+
+@attr.s(auto_attribs=True, frozen=True)
+class CliType(AttrYamlMixin):
     """
     A data type used in the command-line
     """
@@ -55,7 +57,7 @@ def representable(self) -> set:
     _representable = set()
 
 
-@dataclass(unsafe_hash=True)
+@attr.s(auto_attribs=True, frozen=True)
 class CliEnum(CliType):
     """
     One of a list of possible options
@@ -67,7 +69,7 @@ class CliEnum(CliType):
     """
 
 
-@dataclass(unsafe_hash=True)
+@attr.s(auto_attribs=True, frozen=True)
 class CliFloat(CliType):
     """
     Takes a floating-point value
@@ -76,7 +78,7 @@ class CliFloat(CliType):
     pass
 
 
-@dataclass(unsafe_hash=True)
+@attr.s(auto_attribs=True, frozen=True)
 class CliInteger(CliType):
     """
     Takes an integer value
@@ -85,7 +87,7 @@ class CliInteger(CliType):
     _representable = {CliFloat}
 
 
-@dataclass(unsafe_hash=True)
+@attr.s(auto_attribs=True, frozen=True)
 class CliString(CliType):
     """
     Takes a string value
@@ -94,7 +96,7 @@ class CliString(CliType):
     pass
 
 
-@dataclass(unsafe_hash=True)
+@attr.s(auto_attribs=True, frozen=True)
 class CliBoolean(CliType):
     """
     Takes a boolean value
@@ -103,7 +105,7 @@ class CliBoolean(CliType):
     pass
 
 
-@dataclass(unsafe_hash=True)
+@attr.s(auto_attribs=True, frozen=True)
 class CliFileSystemType(CliType):
     """
     Takes a directory / file path
@@ -115,7 +117,7 @@ class CliFileSystemType(CliType):
     """
 
 
-@dataclass(unsafe_hash=True)
+@attr.s(auto_attribs=True, frozen=True)
 class CliDir(CliFileSystemType):
     """
     Takes a directory path
@@ -124,7 +126,7 @@ class CliDir(CliFileSystemType):
     pass
 
 
-@dataclass(unsafe_hash=True)
+@attr.s(auto_attribs=True, frozen=True)
 class CliFile(CliFileSystemType):
     """
     Takes a file path
@@ -133,7 +135,7 @@ class CliFile(CliFileSystemType):
     pass
 
 
-@dataclass(unsafe_hash=True)
+@attr.s(auto_attribs=True, frozen=True)
 class CliDict(CliType):
     """
     Takes a dictionary value
@@ -150,7 +152,7 @@ class CliDict(CliType):
     """
 
 
-@dataclass(unsafe_hash=True)
+@attr.s(auto_attribs=True, frozen=True)
 class CliList(CliType):
     """
     Takes a list value
@@ -162,7 +164,7 @@ class CliList(CliType):
     """
 
 
-@dataclass(unsafe_hash=True)
+@attr.s(auto_attribs=True, frozen=True)
 class CliTuple(CliType):
     """
     Takes a list of values with a fixed length, possibly each with different types

aclimatise/converter/__init__.py

@@ -4,7 +4,7 @@
 from pathlib import Path
 from typing import Generator, Iterable, List, Set, TextIO, Tuple, Type
 
-from dataclasses import dataclass
+import attr
 
 from aclimatise.model import CliArgument, Command, Flag
 from aclimatise.name_generation import (
@@ -16,16 +16,21 @@
     name_to_camel,
     name_to_snake,
 )
+from aclimatise.yaml import AttrYamlMixin
 
 
-@dataclass
-class NamedArgument:
+@attr.s(
+    auto_attribs=True,
+)
+class NamedArgument(AttrYamlMixin):
     arg: CliArgument
     name: str
 
 
-@dataclass
-class WrapperGenerator:
+@attr.s(
+    auto_attribs=True,
+)
+class WrapperGenerator(AttrYamlMixin):
     """
     Abstract base class for a class that converts a Command object into a string that defines a tool
     wrapper in a certain workflow language

aclimatise/converter/cwl.py

@@ -2,6 +2,7 @@
 from pathlib import Path
 from typing import List
 
+import attr
 from cwl_utils.parser_v1_1 import (
     CommandInputParameter,
     CommandLineBinding,
@@ -10,7 +11,6 @@
     CommandOutputParameter,
     DockerRequirement,
 )
-from dataclasses import dataclass
 
 from aclimatise import cli_types
 from aclimatise.cli_types import CliType
@@ -19,7 +19,7 @@
 from aclimatise.yaml import yaml
 
 
-@dataclass
+@attr.s(auto_attribs=True)
 class CwlGenerator(WrapperGenerator):
     case = "snake"
 

aclimatise/converter/yml.py

@@ -3,14 +3,14 @@
 from pathlib import Path
 from typing import Generator, List
 
-from dataclasses import dataclass
+import attr
 
 from aclimatise.converter import WrapperGenerator
 from aclimatise.model import Command
 from aclimatise.yaml import yaml
 
 
-@dataclass
+@attr.s(auto_attribs=True)
 class YmlGenerator(WrapperGenerator):
     """
     Internal YML format

aclimatise/integration.py

@@ -1,6 +1,6 @@
 import typing
 
-import dataclasses
+import attr
 
 from aclimatise.flag_parser.parser import CliParser
 from aclimatise.model import Command, Flag
@@ -32,7 +32,7 @@ def parse_help(cmd: typing.Collection[str], text: str, max_length=1000) -> Comma
         # Combine the flags from both help and usage
         named=list(Flag.combine([help_command.named, usage_command.named])),
     )
-    for field in dataclasses.fields(Command):
+    for field in attr.fields(Command):
         fields[field.name] = (
             fields.get(field.name)
             or getattr(help_command, field.name)

aclimatise/model.py

@@ -11,7 +11,6 @@
 from operator import attrgetter
 
 import attr
-from dataclasses import dataclass, field
 from ruamel.yaml import yaml_object
 from word2number import w2n
 
@@ -21,7 +20,7 @@
 from aclimatise.name_generation import segment_string
 from aclimatise.nlp import wordsegment
 from aclimatise.usage_parser.model import UsageInstance
-from aclimatise.yaml import yaml
+from aclimatise.yaml import AttrYamlMixin, yaml
 
 
 def first(lst: typing.List, default):
@@ -50,13 +49,15 @@ def useless_name(name: typing.List[str]):
 
 
 @yaml_object(yaml)
-@dataclass
-class Command:
+@attr.s(
+    auto_attribs=True,
+)
+class Command(AttrYamlMixin):
     """
     Class representing an entire command or subcommand, e.g. `bwa mem` or `grep`
     """
 
-    def __post_init__(self):
+    def __attrs_post_init__(self):
         # Store certain special flags in their own fields
         if self.help_flag is None:
             for flag in self.named:
@@ -235,12 +236,12 @@ def command_tree(self) -> typing.Generator["Command", None, None]:
     The command line used to invoke this command, e.g. ["bwa", "mem"]
     """
 
-    positional: typing.List["Positional"] = field(default_factory=list)
+    positional: typing.List["Positional"] = attr.ib(factory=list)
     """
     All positional arguments supported by this command
     """
 
-    named: typing.List["Flag"] = field(default_factory=list)
+    named: typing.List["Flag"] = attr.ib(factory=list)
     """
     All named arguments (flags) supported by this command
     """
@@ -250,12 +251,12 @@ def command_tree(self) -> typing.Generator["Command", None, None]:
     The parent command, if this is a subcommand
     """
 
-    subcommands: typing.List["Command"] = field(default_factory=list)
+    subcommands: typing.List["Command"] = attr.ib(factory=list)
     """
     A list of subcommands of this command, e.g. "bwa" has the subcommand "bwa mem"
     """
 
-    usage: typing.List["UsageInstance"] = field(default_factory=list)
+    usage: typing.List["UsageInstance"] = attr.ib(factory=list)
     """
     Different usage examples provided by the help
     """
@@ -293,7 +294,7 @@ def command_tree(self) -> typing.Generator["Command", None, None]:
 
 @yaml_object(yaml)
 @attr.s(auto_attribs=True)
-class CliArgument:
+class CliArgument(AttrYamlMixin):
     """
     A generic parent class for both named and positional CLI arguments
     """
@@ -428,11 +429,10 @@ class Flag(CliArgument):
     Describes the arguments to this flag, e.g. ``-n 1`` has a single numeric argument
     """
 
-    def __post_init__(self):
+    def __attrs_post_init__(self):
         if self.optional is None:
             # Flags are optional by default
             self.optional = True
-        super().__post_init__()
 
     @staticmethod
     def deduplicate(flags: typing.Collection["Flag"]) -> typing.List["Flag"]:
@@ -595,8 +595,8 @@ def shortest_synonym(self) -> str:
 
 
 @yaml_object(yaml)
-@dataclass
-class FlagSynonym:
+@attr.s(auto_attribs=True)
+class FlagSynonym(AttrYamlMixin):
     """
     Internal class for storing the arguments for a single synonym
     """
@@ -679,8 +679,8 @@ def infer_type(string) -> typing.Optional[cli_types.CliType]:
 
 
 @yaml_object(yaml)
-@dataclass
-class FlagArg(abc.ABC):
+@attr.s(auto_attribs=True)
+class FlagArg(abc.ABC, AttrYamlMixin):
     """
     The data model for the argument or arguments for a flag, for example a flag might have no arguments, it might have
     one argument, it might accept one option from a list of options, or it might accept an arbitrary number of inputs
@@ -709,7 +709,7 @@ def num_args(self) -> int:
 
 
 @yaml_object(yaml)
-@dataclass
+@attr.s(auto_attribs=True)
 class EmptyFlagArg(FlagArg):
     """
     A flag that has no arguments, e.g. `--quiet` that is either present or not present
@@ -723,7 +723,7 @@ def get_type(self):
 
 
 @yaml_object(yaml)
-@dataclass
+@attr.s(auto_attribs=True)
 class OptionalFlagArg(FlagArg):
     """
     When the flag has multiple arguments, some of which are optional, e.g.
@@ -757,7 +757,7 @@ def get_type(self):
 
 
 @yaml_object(yaml)
-@dataclass
+@attr.s(auto_attribs=True)
 class SimpleFlagArg(FlagArg):
     """
     When a flag has one single argument, e.g. `-e PATTERN`, where PATTERN is the argument
@@ -779,7 +779,7 @@ def get_type(self):
 
 
 @yaml_object(yaml)
-@dataclass
+@attr.s(auto_attribs=True)
 class RepeatFlagArg(FlagArg):
     """
     When a flag accepts 1 or more arguments, e.g. `--samout SAMOUTS [SAMOUTS ...]`
@@ -805,7 +805,7 @@ def get_type(self):
 
 
 @yaml_object(yaml)
-@dataclass
+@attr.s(auto_attribs=True)
 class ChoiceFlagArg(FlagArg):
     """
     When a flag accepts one option from a list of options, e.g. `-s {yes,no,reverse}`