From 0219ac0334e52cef6d6052a8fb81a37ce3c20e19 Mon Sep 17 00:00:00 2001 From: jdidion Date: Thu, 22 Feb 2024 09:11:48 -0800 Subject: [PATCH 01/17] drop py37 support, remove dependencies related to typing backward-compatibility --- .github/workflows/pythonpackage.yml | 2 +- fgpyo/fasta/builder.py | 2 +- fgpyo/fastx/__init__.py | 1 + fgpyo/io/__init__.py | 1 + fgpyo/read_structure.py | 1 + fgpyo/sam/builder.py | 1 + fgpyo/util/inspect.py | 91 ++- fgpyo/util/logging.py | 8 +- fgpyo/util/types.py | 56 +- fgpyo/vcf/__init__.py | 1 + fgpyo/vcf/tests/test_builder.py | 8 +- poetry.lock | 985 ++++++++++++---------------- pyproject.toml | 42 +- 13 files changed, 523 insertions(+), 676 deletions(-) diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml index 3101ca59..670e4396 100644 --- a/.github/workflows/pythonpackage.yml +++ b/.github/workflows/pythonpackage.yml @@ -9,7 +9,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - PYTHON_VERSION: ["3.7", "3.8", "3.9", "3.10"] + PYTHON_VERSION: ["3.8", "3.9", "3.10", "3.11", "3.12"] steps: - uses: actions/checkout@v2 diff --git a/fgpyo/fasta/builder.py b/fgpyo/fasta/builder.py index bf4eeac8..ea60b244 100755 --- a/fgpyo/fasta/builder.py +++ b/fgpyo/fasta/builder.py @@ -32,6 +32,7 @@ 'AAAAAAAAAANNN' """ + import textwrap from pathlib import Path from typing import TYPE_CHECKING @@ -48,7 +49,6 @@ def samtools_dict(*args: Any) -> None: def samtools_faidx(*args: Any) -> None: pass - else: from pysam import dict as samtools_dict from pysam import faidx as samtools_faidx diff --git a/fgpyo/fastx/__init__.py b/fgpyo/fastx/__init__.py index b256c183..360f9198 100644 --- a/fgpyo/fastx/__init__.py +++ b/fgpyo/fastx/__init__.py @@ -24,6 +24,7 @@ seq2: GGGG, seq2: TTTT """ + from contextlib import AbstractContextManager from pathlib import Path from types import TracebackType diff --git a/fgpyo/io/__init__.py b/fgpyo/io/__init__.py index 3457c7d1..e9e59f5f 100644 --- a/fgpyo/io/__init__.py +++ b/fgpyo/io/__init__.py @@ -42,6 +42,7 @@ "10" """ + import gzip import io import os diff --git a/fgpyo/read_structure.py b/fgpyo/read_structure.py index a1f61a8d..e9555d58 100644 --- a/fgpyo/read_structure.py +++ b/fgpyo/read_structure.py @@ -61,6 +61,7 @@ correspond to the given read segment """ + import enum from typing import Iterable from typing import Iterator diff --git a/fgpyo/sam/builder.py b/fgpyo/sam/builder.py index f2e716b3..122a3067 100755 --- a/fgpyo/sam/builder.py +++ b/fgpyo/sam/builder.py @@ -10,6 +10,7 @@ - :class:`~fgpyo.sam.builder.SamBuilder` -- A builder class that allows the accumulation of alignment records and access as a list and writing to file. """ + from array import array from pathlib import Path from random import Random diff --git a/fgpyo/util/inspect.py b/fgpyo/util/inspect.py index b35f307e..206aee57 100644 --- a/fgpyo/util/inspect.py +++ b/fgpyo/util/inspect.py @@ -1,28 +1,25 @@ +import functools import sys +import typing +from enum import Enum +from functools import partial +from pathlib import PurePath from typing import Any +from typing import Callable from typing import Dict from typing import Iterable from typing import List +from typing import Literal +from typing import Optional from typing import Tuple from typing import Type from typing import Union -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal if sys.version_info >= (3, 12): from typing import TypeAlias else: from typing_extensions import TypeAlias -import functools -from enum import Enum -from functools import partial -from pathlib import PurePath -from typing import Callable -from typing import Optional - import attr import fgpyo.util.types as types @@ -60,13 +57,17 @@ def split_at_given_level( decrease_in_depth += high_level_split.count(char) outer_depth_of_split += increase_in_depth - decrease_in_depth - assert outer_depth_of_split >= 0, "Unpaired depth character! Likely incorrect output" + assert ( + outer_depth_of_split >= 0 + ), "Unpaired depth character! Likely incorrect output" current_outer_splits.append(high_level_split) if outer_depth_of_split == 0: out_vals.append(split_delim.join(current_outer_splits)) current_outer_splits = [] - assert outer_depth_of_split == 0, "Unpaired depth character! Likely incorrect output!" + assert ( + outer_depth_of_split == 0 + ), "Unpaired depth character! Likely incorrect output!" return out_vals @@ -74,7 +75,9 @@ def split_at_given_level( def _get_parser( - cls: Type, type_: TypeAlias, parsers: Optional[Dict[type, Callable[[str], Any]]] = None + cls: Type, + type_: TypeAlias, + parsers: Optional[Dict[type, Callable[[str], Any]]] = None, ) -> partial: """Attempts to find a parser for a provided type. @@ -112,8 +115,8 @@ def get_parser() -> partial: raise ValueError("Unable to parse set (try typing.Set[type])") elif type_ == dict: raise ValueError("Unable to parse dict (try typing.Mapping[type])") - elif types.get_origin_type(type_) == list: - subtypes = types.get_arg_types(type_) + elif typing.get_origin(type_) == list: + subtypes = typing.get_args(type_) assert ( len(subtypes) == 1 @@ -133,8 +136,8 @@ def get_parser() -> partial: ] ) ) - elif types.get_origin_type(type_) == set: - subtypes = types.get_arg_types(type_) + elif typing.get_origin(type_) == set: + subtypes = typing.get_args(type_) assert ( len(subtypes) == 1 ), "Sets are allowed only one subtype per PEP specification!" @@ -149,18 +152,20 @@ def get_parser() -> partial: if s == "{}" else [ subtype_parser(item) - for item in set(split_at_given_level(s[1:-1], split_delim=",")) + for item in set( + split_at_given_level(s[1:-1], split_delim=",") + ) ] ) ) - elif types.get_origin_type(type_) == tuple: + elif typing.get_origin(type_) == tuple: subtype_parsers = [ _get_parser( cls, subtype, parsers, ) - for subtype in types.get_arg_types(type_) + for subtype in typing.get_args(type_) ] def tuple_parse(tuple_string: str) -> Tuple[Any, ...]: @@ -175,7 +180,9 @@ def tuple_parse(tuple_string: str) -> Tuple[Any, ...]: if len(tuple_string) == 0: return () else: - val_strings = split_at_given_level(tuple_string, split_delim=",") + val_strings = split_at_given_level( + tuple_string, split_delim="," + ) return tuple( parser(val_str) for parser, val_str in zip(subtype_parsers, val_strings) @@ -183,8 +190,8 @@ def tuple_parse(tuple_string: str) -> Tuple[Any, ...]: return functools.partial(tuple_parse) - elif types.get_origin_type(type_) == dict: - subtypes = types.get_arg_types(type_) + elif typing.get_origin(type_) == dict: + subtypes = typing.get_args(type_) assert ( len(subtypes) == 2 ), "Dict object must have exactly 2 subtypes per PEP specification!" @@ -211,10 +218,14 @@ def dict_parse(dict_string: str) -> Dict[Any, Any]: if len(dict_string) == 0: return {} else: - outer_splits = split_at_given_level(dict_string, split_delim=",") + outer_splits = split_at_given_level( + dict_string, split_delim="," + ) out_dict = {} for outer_split in outer_splits: - inner_splits = split_at_given_level(outer_split, split_delim=";") + inner_splits = split_at_given_level( + outer_split, split_delim=";" + ) assert ( len(inner_splits) % 2 == 0 ), "Inner splits of dict didn't have matched key val pairs" @@ -231,15 +242,21 @@ def dict_parse(dict_string: str) -> Dict[Any, Any]: return functools.partial(type_) elif type_ == NoneType: return functools.partial(types.none_parser) - elif types.get_origin_type(type_) is Union: + elif typing.get_origin(type_) is Union: return types.make_union_parser( union=type_, - parsers=[_get_parser(cls, arg, parsers) for arg in types.get_arg_types(type_)], + parsers=[ + _get_parser(cls, arg, parsers) + for arg in typing.get_args(type_) + ], ) - elif types.get_origin_type(type_) is Literal: # Py>=3.7. + elif typing.get_origin(type_) is Literal: # Py>=3.7. return types.make_literal_parser( type_, - [_get_parser(cls, type(arg), parsers) for arg in types.get_arg_types(type_)], + [ + _get_parser(cls, type(arg), parsers) + for arg in typing.get_args(type_) + ], ) else: raise ParserNotFoundException( @@ -258,7 +275,9 @@ def dict_parse(dict_string: str) -> Dict[Any, Any]: def attr_from( - cls: Type, kwargs: Dict[str, str], parsers: Optional[Dict[type, Callable[[str], Any]]] = None + cls: Type, + kwargs: Dict[str, str], + parsers: Optional[Dict[type, Callable[[str], Any]]] = None, ) -> Any: """Builds an attr class from key-word arguments @@ -292,7 +311,11 @@ def attr_from( # try setting by casting # Note that while bools *can* be cast from string, all non-empty strings evaluate to # True, because python, so we need to check for that explicitly - if not set_value and attribute.type is not None and not attribute.type == bool: + if ( + not set_value + and attribute.type is not None + and not attribute.type == bool + ): try: return_value = attribute.type(str_value) set_value = True @@ -319,8 +342,8 @@ def attr_from( def attribute_is_optional(attribute: attr.Attribute) -> 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) + return typing.get_origin(attribute.type) is Union and isinstance( + None, typing.get_args(attribute.type) ) diff --git a/fgpyo/util/logging.py b/fgpyo/util/logging.py index 97174fe6..5c1210b5 100644 --- a/fgpyo/util/logging.py +++ b/fgpyo/util/logging.py @@ -34,19 +34,13 @@ """ import logging -import sys - -if sys.version_info >= (3, 8): - from typing import Literal -else: - from typing_extensions import Literal - import socket from contextlib import AbstractContextManager from logging import Logger from threading import RLock from typing import Any from typing import Callable +from typing import Literal from typing import Optional from typing import Union diff --git a/fgpyo/util/types.py b/fgpyo/util/types.py index 822c4dc2..74cc566e 100644 --- a/fgpyo/util/types.py +++ b/fgpyo/util/types.py @@ -1,49 +1,15 @@ import collections import inspect -import sys import typing from enum import Enum from functools import partial from typing import Callable from typing import Iterable +from typing import Literal from typing import Type from typing import TypeVar from typing import Union -# `get_origin_type` is a method that gets the outer type (ex list in a List[str]) -# `get_arg_types` is a method that gets the inner type (ex str in a List[str]) -if sys.version_info >= (3, 8): - from typing import Literal - - get_origin_type = typing.get_origin - get_arg_types = typing.get_args -else: - import typing_inspect - from typing_extensions import Literal - - def get_origin_type(tp: Type) -> Type: - """Returns the outer type of a Typing object (ex list in a List[T])""" - - if type(tp) is type(Literal): # Py<=3.6. - return Literal - origin = typing_inspect.get_origin(tp) - return { - typing.List: list, - typing.Iterable: collections.abc.Iterable, - typing.Sequence: collections.abc.Sequence, - typing.Tuple: tuple, - typing.Set: set, - typing.Mapping: dict, - typing.Dict: dict, - }.get(origin, origin) - - def get_arg_types(tp: Type) -> Type: - """Gets the inner types of a Typing object (ex T in a List[T])""" - - if type(tp) is type(Literal): # Py<=3.6. - return tp.__values__ - return typing_inspect.get_args(tp, evaluate=True) # evaluate=True default on Py>=3.7. - UnionType = TypeVar("UnionType", bound="Union") EnumType = TypeVar("EnumType", bound="Enum") @@ -109,7 +75,7 @@ def is_constructible_from_str(type_: type) -> bool: def _is_optional(type_: type) -> bool: """Returns true if type_ is optional""" - return get_origin_type(type_) is Union and type(None) in get_arg_types(type_) + return typing.get_origin(type_) is Union and type(None) in typing.get_args(type_) def _make_union_parser_worker( @@ -137,7 +103,9 @@ def _make_union_parser_worker( raise ValueError(f"{value} could not be parsed as any of {union}") -def make_union_parser(union: Type[UnionType], parsers: Iterable[Callable[[str], type]]) -> partial: +def make_union_parser( + union: Type[UnionType], parsers: Iterable[Callable[[str], type]] +) -> partial: """Generates a parser function for a union type object and set of parsers for the possible parsers to that union type object """ @@ -145,12 +113,14 @@ def make_union_parser(union: Type[UnionType], parsers: Iterable[Callable[[str], def _make_literal_parser_worker( - literal: Type[LiteralType], parsers: Iterable[Callable[[str], LiteralType]], value: str + literal: Type[LiteralType], + parsers: Iterable[Callable[[str], LiteralType]], + value: str, ) -> LiteralType: """Worker function behind literal parsing. Iterates through possible literals and returns the value produced by the first literal that matches expectation. Otherwise raises an error if none work""" - for arg, p in zip(get_arg_types(literal), parsers): + for arg, p in zip(typing.get_args(literal), parsers): try: if p(value) == arg: return arg @@ -158,7 +128,7 @@ def _make_literal_parser_worker( pass raise InspectException( "invalid choice: {!r} (choose from {})".format( - value, ", ".join(map(repr, map(str, get_arg_types(literal)))) + value, ", ".join(map(repr, map(str, typing.get_args(literal)))) ) ) @@ -174,7 +144,11 @@ def make_literal_parser( def is_list_like(type_: type) -> bool: """Returns true if the value is a list or list like object""" - return get_origin_type(type_) in [list, collections.abc.Iterable, collections.abc.Sequence] + return typing.get_origin(type_) in [ + list, + collections.abc.Iterable, + collections.abc.Sequence, + ] def none_parser(value: str) -> Literal[None]: diff --git a/fgpyo/vcf/__init__.py b/fgpyo/vcf/__init__.py index f6f837a0..d364e704 100644 --- a/fgpyo/vcf/__init__.py +++ b/fgpyo/vcf/__init__.py @@ -48,6 +48,7 @@ order via the :func:`~fgpyo.vcf.builder.VariantBuilder.to_sorted_list()` method. """ + from contextlib import contextmanager from pathlib import Path from typing import Generator diff --git a/fgpyo/vcf/tests/test_builder.py b/fgpyo/vcf/tests/test_builder.py index 58f39752..2a16d797 100644 --- a/fgpyo/vcf/tests/test_builder.py +++ b/fgpyo/vcf/tests/test_builder.py @@ -81,9 +81,11 @@ def _get_random_variant_inputs( key: ( random_generator.randint(0, 100) if value_type == VcfFieldType.INTEGER - else random_generator.uniform(0, 1) - if value_type == VcfFieldType.FLOAT - else random_generator.choice(["Up", "Down"]) + else ( + random_generator.uniform(0, 1) + if value_type == VcfFieldType.FLOAT + else random_generator.choice(["Up", "Down"]) + ) ) for key, value_type in _INFO_FIELD_TYPES.items() } diff --git a/poetry.lock b/poetry.lock index b4360a92..720e205d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,191 +1,296 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. 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:: Libraries :: Python Modules", -] -include = [ - "LICENSE", + "Topic :: Software Development :: Documentation", + "Topic :: Software Development :: Libraries :: Python Modules", ] +include = ["LICENSE"] [tool.poetry.dependencies] -python = ">=3.7.0,<4.0" +python = ">=3.8.0,<4.0" attrs = ">=19.3.0" -typing_extensions = { version = ">=3.7.4", python = "<3.8" } # Literal support -typing_inspect = { version = ">=0.3.1", python = "<3.8" } # inspecting types -sphinx = {version = "4.3.1", optional = true} -sphinx_rtd_theme = {version = "^1.3.0", optional = true} pysam = ">=0.22.0" pytest = ">=7.4.0" +sphinx = { version = "4.3.1", optional = true } +sphinx_rtd_theme = { version = "^1.3.0", optional = true } +typing_extensions = { version = ">=3.7.4", python = "<3.12" } [tool.poetry.extras] docs = ["sphinx", "sphinx_rtd_theme"] [tool.poetry.dev-dependencies] -setuptools = ">=68.0.0" -pytest = ">=5.4.2" -mypy = [ - { version = ">=0.770", python = "<3.8" }, - { version = ">=1.7.0", python = ">=3.8"} -] +black = ">=23.3.0" flake8 = [ - { version = ">=3.8.1", python = "<3.12.0" }, + { version = ">=5.0.0", python = "<3.12.0" }, { version = ">=6.1.0", python = ">=3.12.0" }, ] -black = ">=19.10b0" -pytest-cov = ">=2.8.1" isort = ">=5.10.1" +mypy = ">=1.7.0" +pytest = ">=5.4.2" +pytest-cov = ">=2.8.1" +setuptools = ">=68.0.0" [build-system] -requires = ["poetry>=1.5"] -build-backend = "poetry.masonry.api" +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" From acf946f126abae98a6bf1e1e570d231f116deda4 Mon Sep 17 00:00:00 2001 From: jdidion Date: Thu, 22 Feb 2024 09:12:35 -0800 Subject: [PATCH 02/17] reformat --- fgpyo/util/inspect.py | 40 +++++++++------------------------------- fgpyo/util/types.py | 5 +---- 2 files changed, 10 insertions(+), 35 deletions(-) diff --git a/fgpyo/util/inspect.py b/fgpyo/util/inspect.py index 206aee57..9d05b791 100644 --- a/fgpyo/util/inspect.py +++ b/fgpyo/util/inspect.py @@ -57,17 +57,13 @@ def split_at_given_level( decrease_in_depth += high_level_split.count(char) outer_depth_of_split += increase_in_depth - decrease_in_depth - assert ( - outer_depth_of_split >= 0 - ), "Unpaired depth character! Likely incorrect output" + assert outer_depth_of_split >= 0, "Unpaired depth character! Likely incorrect output" current_outer_splits.append(high_level_split) if outer_depth_of_split == 0: out_vals.append(split_delim.join(current_outer_splits)) current_outer_splits = [] - assert ( - outer_depth_of_split == 0 - ), "Unpaired depth character! Likely incorrect output!" + assert outer_depth_of_split == 0, "Unpaired depth character! Likely incorrect output!" return out_vals @@ -152,9 +148,7 @@ def get_parser() -> partial: if s == "{}" else [ subtype_parser(item) - for item in set( - split_at_given_level(s[1:-1], split_delim=",") - ) + for item in set(split_at_given_level(s[1:-1], split_delim=",")) ] ) ) @@ -180,9 +174,7 @@ def tuple_parse(tuple_string: str) -> Tuple[Any, ...]: if len(tuple_string) == 0: return () else: - val_strings = split_at_given_level( - tuple_string, split_delim="," - ) + val_strings = split_at_given_level(tuple_string, split_delim=",") return tuple( parser(val_str) for parser, val_str in zip(subtype_parsers, val_strings) @@ -218,14 +210,10 @@ def dict_parse(dict_string: str) -> Dict[Any, Any]: if len(dict_string) == 0: return {} else: - outer_splits = split_at_given_level( - dict_string, split_delim="," - ) + outer_splits = split_at_given_level(dict_string, split_delim=",") out_dict = {} for outer_split in outer_splits: - inner_splits = split_at_given_level( - outer_split, split_delim=";" - ) + inner_splits = split_at_given_level(outer_split, split_delim=";") assert ( len(inner_splits) % 2 == 0 ), "Inner splits of dict didn't have matched key val pairs" @@ -245,18 +233,12 @@ def dict_parse(dict_string: str) -> Dict[Any, Any]: elif typing.get_origin(type_) is Union: return types.make_union_parser( union=type_, - parsers=[ - _get_parser(cls, arg, parsers) - for arg in typing.get_args(type_) - ], + parsers=[_get_parser(cls, arg, parsers) for arg in typing.get_args(type_)], ) elif typing.get_origin(type_) is Literal: # Py>=3.7. return types.make_literal_parser( type_, - [ - _get_parser(cls, type(arg), parsers) - for arg in typing.get_args(type_) - ], + [_get_parser(cls, type(arg), parsers) for arg in typing.get_args(type_)], ) else: raise ParserNotFoundException( @@ -311,11 +293,7 @@ def attr_from( # try setting by casting # Note that while bools *can* be cast from string, all non-empty strings evaluate to # True, because python, so we need to check for that explicitly - if ( - not set_value - and attribute.type is not None - and not attribute.type == bool - ): + if not set_value and attribute.type is not None and not attribute.type == bool: try: return_value = attribute.type(str_value) set_value = True diff --git a/fgpyo/util/types.py b/fgpyo/util/types.py index 74cc566e..9bcee785 100644 --- a/fgpyo/util/types.py +++ b/fgpyo/util/types.py @@ -10,7 +10,6 @@ from typing import TypeVar from typing import Union - UnionType = TypeVar("UnionType", bound="Union") EnumType = TypeVar("EnumType", bound="Enum") # conceptually bound to "Literal" but that's not valid in the spec @@ -103,9 +102,7 @@ def _make_union_parser_worker( raise ValueError(f"{value} could not be parsed as any of {union}") -def make_union_parser( - union: Type[UnionType], parsers: Iterable[Callable[[str], type]] -) -> partial: +def make_union_parser(union: Type[UnionType], parsers: Iterable[Callable[[str], type]]) -> partial: """Generates a parser function for a union type object and set of parsers for the possible parsers to that union type object """ From 9d8ccf79c301770dda13b938cbaf3e4e38b15472 Mon Sep 17 00:00:00 2001 From: jdidion Date: Thu, 22 Feb 2024 09:22:35 -0800 Subject: [PATCH 03/17] rever reformatting --- fgpyo/fasta/builder.py | 21 +- fgpyo/fasta/tests/test_builder.py | 22 +- fgpyo/io/tests/test_io.py | 27 +-- fgpyo/sam/__init__.py | 12 +- fgpyo/sam/tests/test_sam.py | 4 +- fgpyo/sam/tests/test_template_iterator.py | 4 +- fgpyo/tests/test_read_structure.py | 42 +--- fgpyo/util/inspect.py | 39 +--- fgpyo/util/logging.py | 19 +- fgpyo/util/tests/test_logging.py | 7 +- fgpyo/util/tests/test_metric.py | 17 +- fgpyo/util/types.py | 8 +- fgpyo/vcf/builder.py | 6 +- fgpyo/vcf/tests/test_builder.py | 22 +- poetry.lock | 246 +++++++++++++++++----- pyproject.toml | 3 +- 16 files changed, 238 insertions(+), 261 deletions(-) diff --git a/fgpyo/fasta/builder.py b/fgpyo/fasta/builder.py index ea60b244..5a7a90f6 100755 --- a/fgpyo/fasta/builder.py +++ b/fgpyo/fasta/builder.py @@ -49,6 +49,7 @@ def samtools_dict(*args: Any) -> None: def samtools_faidx(*args: Any) -> None: pass + else: from pysam import dict as samtools_dict from pysam import faidx as samtools_faidx @@ -91,10 +92,7 @@ class ContigBuilder: """ def __init__( - self, - name: str, - assembly: str, - species: str, + self, name: str, assembly: str, species: str, ): self.name = name self.assembly = assembly @@ -146,10 +144,7 @@ class FastaBuilder: """ def __init__( - self, - assembly: str = "testassembly", - species: str = "testspecies", - line_length: int = 80, + self, assembly: str = "testassembly", species: str = "testspecies", line_length: int = 80, ): self.assembly: str = assembly self.species: str = species @@ -161,10 +156,7 @@ def __getitem__(self, key: str) -> ContigBuilder: return self.__contig_builders[key] def add( - self, - name: str, - assembly: Optional[str] = None, - species: Optional[str] = None, + self, name: str, assembly: Optional[str] = None, species: Optional[str] = None, ) -> ContigBuilder: """ Creates and returns a new ContigBuilder for a contig with the provided name. @@ -189,10 +181,7 @@ def add( self.__contig_builders[name] = builder return builder - def to_file( - self, - path: Path, - ) -> None: + def to_file(self, path: Path,) -> None: """ Writes out the set of accumulated contigs to a FASTA file at the `path` given. Also generates the accompanying fasta index file (`.fa.fai`) and sequence diff --git a/fgpyo/fasta/tests/test_builder.py b/fgpyo/fasta/tests/test_builder.py index b3dbb438..a1db172a 100644 --- a/fgpyo/fasta/tests/test_builder.py +++ b/fgpyo/fasta/tests/test_builder.py @@ -25,17 +25,10 @@ def test_bases_length_from_ContigBuilder_add_default() -> None: @pytest.mark.parametrize( - "name, bases, times, length_bases", - [ - ("chr1", "AAA", 3, 9), - ("chr2", "TTT", 10, 30), - ], + "name, bases, times, length_bases", [("chr1", "AAA", 3, 9), ("chr2", "TTT", 10, 30),], ) def test_bases_length_from_ContigBuilder_add( - name: str, - bases: str, - times: int, - length_bases: int, + name: str, bases: str, times: int, length_bases: int, ) -> None: """Checks that the number of bases in each contig is correct""" builder = FastaBuilder() @@ -60,17 +53,10 @@ def test_contig_dict_is_not_accessable() -> None: @pytest.mark.parametrize( "name, bases, times, expected", - [ - ("chr3", "AAA a", 3, ("AAAA" * 3)), - ("chr2", "TT T gT", 10, ("TTTGT" * 10)), - ], + [("chr3", "AAA a", 3, ("AAAA" * 3)), ("chr2", "TT T gT", 10, ("TTTGT" * 10)),], ) def test_bases_string_from_ContigBuilder_add( - name: str, - bases: str, - times: int, - expected: str, - tmp_path: Path, + name: str, bases: str, times: int, expected: str, tmp_path: Path, ) -> None: """ Reads bases back from fasta and checks that extra spaces are removed and bases are uppercase diff --git a/fgpyo/io/tests/test_io.py b/fgpyo/io/tests/test_io.py index d4cf286d..aa785aa1 100644 --- a/fgpyo/io/tests/test_io.py +++ b/fgpyo/io/tests/test_io.py @@ -84,16 +84,9 @@ def test_assert_path_is_writeable_pass() -> None: @pytest.mark.parametrize( - "suffix, expected", - [ - (".gz", io.TextIOWrapper), - (".fa", io.TextIOWrapper), - ], + "suffix, expected", [(".gz", io.TextIOWrapper), (".fa", io.TextIOWrapper),], ) -def test_reader( - suffix: str, - expected: Any, -) -> None: +def test_reader(suffix: str, expected: Any,) -> None: """Tests fgpyo.io.to_reader""" with NamedTemp(suffix=suffix, mode="r", delete=True) as read_file: with fio.to_reader(path=Path(read_file.name)) as reader: @@ -101,16 +94,9 @@ def test_reader( @pytest.mark.parametrize( - "suffix, expected", - [ - (".gz", io.TextIOWrapper), - (".fa", io.TextIOWrapper), - ], + "suffix, expected", [(".gz", io.TextIOWrapper), (".fa", io.TextIOWrapper),], ) -def test_writer( - suffix: str, - expected: Any, -) -> None: +def test_writer(suffix: str, expected: Any,) -> None: """Tests fgpyo.io.to_writer()""" with NamedTemp(suffix=suffix, mode="w", delete=True) as write_file: with fio.to_writer(path=Path(write_file.name)) as writer: @@ -121,10 +107,7 @@ def test_writer( "suffix, list_to_write", [(".txt", ["Test with a flat file", 10]), (".gz", ["Test with a gzip file", 10])], ) -def test_read_and_write_lines( - suffix: str, - list_to_write: List[Any], -) -> None: +def test_read_and_write_lines(suffix: str, list_to_write: List[Any],) -> None: """Test fgpyo.fio.read_lines and write_lines""" with NamedTemp(suffix=suffix, mode="w", delete=True) as read_file: fio.write_lines(path=Path(read_file.name), lines_to_write=list_to_write) diff --git a/fgpyo/sam/__init__.py b/fgpyo/sam/__init__.py index bb9fa6a3..11b61344 100644 --- a/fgpyo/sam/__init__.py +++ b/fgpyo/sam/__init__.py @@ -863,11 +863,7 @@ def all_recs(self) -> Iterator[AlignedSegment]: for rec in recs: yield rec - def write_to( - self, - writer: SamFile, - primary_only: bool = False, - ) -> None: + def write_to(self, writer: SamFile, primary_only: bool = False,) -> None: """Write the records associated with the template to file. Args: @@ -883,11 +879,7 @@ def write_to( for rec in rec_iter: writer.write(rec) - def set_tag( - self, - tag: str, - value: Union[str, int, float, None], - ) -> None: + def set_tag(self, tag: str, value: Union[str, int, float, None],) -> None: """Add a tag to all records associated with the template. Setting a tag to `None` will remove the tag. diff --git a/fgpyo/sam/tests/test_sam.py b/fgpyo/sam/tests/test_sam.py index 29a013f7..94fc944a 100755 --- a/fgpyo/sam/tests/test_sam.py +++ b/fgpyo/sam/tests/test_sam.py @@ -154,9 +154,7 @@ def test_sam_file_open_writing( def test_sam_file_open_writing_header_keyword( - expected_records: List[pysam.AlignedSegment], - header_dict: AlignmentHeader, - tmp_path: Path, + expected_records: List[pysam.AlignedSegment], header_dict: AlignmentHeader, tmp_path: Path, ) -> None: # Use SamWriter # use header as a keyword argument diff --git a/fgpyo/sam/tests/test_template_iterator.py b/fgpyo/sam/tests/test_template_iterator.py index 79ab9283..397603d0 100644 --- a/fgpyo/sam/tests/test_template_iterator.py +++ b/fgpyo/sam/tests/test_template_iterator.py @@ -73,9 +73,7 @@ def test_to_templates() -> None: assert len(list(template2.all_recs())) == 2 -def test_write_template( - tmp_path: Path, -) -> None: +def test_write_template(tmp_path: Path,) -> None: builder = SamBuilder() template = Template.build( [ diff --git a/fgpyo/tests/test_read_structure.py b/fgpyo/tests/test_read_structure.py index f317f60a..64b230f8 100644 --- a/fgpyo/tests/test_read_structure.py +++ b/fgpyo/tests/test_read_structure.py @@ -31,24 +31,9 @@ def _S(off: int, len: int) -> ReadSegment: ("1M", (_M(0, 1),)), ("1S", (_S(0, 1),)), ("101T", (_T(0, 101),)), - ( - "5B101T", - ( - _B(0, 5), - _T(5, 101), - ), - ), + ("5B101T", (_B(0, 5), _T(5, 101),),), ("123456789T", (_T(0, 123456789),)), - ( - "10T10B10B10S10M", - ( - _T(0, 10), - _B(10, 10), - _B(20, 10), - _S(30, 10), - _M(40, 10), - ), - ), + ("10T10B10B10S10M", (_T(0, 10), _B(10, 10), _B(20, 10), _S(30, 10), _M(40, 10),),), ], ) def test_read_structure_from_string(string: str, segments: Tuple[ReadSegment, ...]) -> None: @@ -58,24 +43,8 @@ def test_read_structure_from_string(string: str, segments: Tuple[ReadSegment, .. @pytest.mark.parametrize( "string,segments", [ - ( - "75T 8B 8B 75T", - ( - _T(0, 75), - _B(75, 8), - _B(83, 8), - _T(91, 75), - ), - ), - ( - " 75T 8B 8B 75T ", - ( - _T(0, 75), - _B(75, 8), - _B(83, 8), - _T(91, 75), - ), - ), + ("75T 8B 8B 75T", (_T(0, 75), _B(75, 8), _B(83, 8), _T(91, 75),),), + (" 75T 8B 8B 75T ", (_T(0, 75), _B(75, 8), _B(83, 8), _T(91, 75),),), ], ) def test_read_structure_from_string_with_whitespace( @@ -98,8 +67,7 @@ def test_read_structure_variable_once_and_only_once_last_segment_ok( @pytest.mark.parametrize( - "string", - ["++M", "5M++T", "5M70+T", "+M+T", "+M70T"], + "string", ["++M", "5M++T", "5M70+T", "+M+T", "+M70T"], ) def test_read_structure_variable_once_and_only_once_last_segment_exception(string: str) -> None: with pytest.raises(Exception): diff --git a/fgpyo/util/inspect.py b/fgpyo/util/inspect.py index 9d05b791..3d2d5b3e 100644 --- a/fgpyo/util/inspect.py +++ b/fgpyo/util/inspect.py @@ -71,9 +71,7 @@ def split_at_given_level( def _get_parser( - cls: Type, - type_: TypeAlias, - parsers: Optional[Dict[type, Callable[[str], Any]]] = None, + cls: Type, type_: TypeAlias, parsers: Optional[Dict[type, Callable[[str], Any]]] = None, ) -> partial: """Attempts to find a parser for a provided type. @@ -117,11 +115,7 @@ def get_parser() -> partial: assert ( len(subtypes) == 1 ), "Lists are allowed only one subtype per PEP specification!" - subtype_parser = _get_parser( - cls, - subtypes[0], - parsers, - ) + subtype_parser = _get_parser(cls, subtypes[0], parsers,) return functools.partial( lambda s: list( [] @@ -137,11 +131,7 @@ def get_parser() -> partial: assert ( len(subtypes) == 1 ), "Sets are allowed only one subtype per PEP specification!" - subtype_parser = _get_parser( - cls, - subtypes[0], - parsers, - ) + subtype_parser = _get_parser(cls, subtypes[0], parsers,) return functools.partial( lambda s: set( set({}) @@ -154,12 +144,7 @@ def get_parser() -> partial: ) elif typing.get_origin(type_) == tuple: subtype_parsers = [ - _get_parser( - cls, - subtype, - parsers, - ) - for subtype in typing.get_args(type_) + _get_parser(cls, subtype, parsers,) for subtype in typing.get_args(type_) ] def tuple_parse(tuple_string: str) -> Tuple[Any, ...]: @@ -188,16 +173,8 @@ def tuple_parse(tuple_string: str) -> Tuple[Any, ...]: len(subtypes) == 2 ), "Dict object must have exactly 2 subtypes per PEP specification!" (key_parser, val_parser) = ( - _get_parser( - cls, - subtypes[0], - parsers, - ), - _get_parser( - cls, - subtypes[1], - parsers, - ), + _get_parser(cls, subtypes[0], parsers,), + _get_parser(cls, subtypes[1], parsers,), ) def dict_parse(dict_string: str) -> Dict[Any, Any]: @@ -257,9 +234,7 @@ def dict_parse(dict_string: str) -> Dict[Any, Any]: def attr_from( - cls: Type, - kwargs: Dict[str, str], - parsers: Optional[Dict[type, Callable[[str], Any]]] = None, + cls: Type, kwargs: Dict[str, str], parsers: Optional[Dict[type, Callable[[str], Any]]] = None, ) -> Any: """Builds an attr class from key-word arguments diff --git a/fgpyo/util/logging.py b/fgpyo/util/logging.py index 5c1210b5..d30c9dab 100644 --- a/fgpyo/util/logging.py +++ b/fgpyo/util/logging.py @@ -125,9 +125,7 @@ def __exit__( return False def record( - self, - reference_name: Optional[str] = None, - position: Optional[int] = None, + self, reference_name: Optional[str] = None, position: Optional[int] = None, ) -> bool: """Record an item at a given genomic coordinate. Args: @@ -147,10 +145,7 @@ def record( else: return False - def record_alignment( - self, - rec: AlignedSegment, - ) -> bool: + def record_alignment(self, rec: AlignedSegment,) -> bool: """Correctly record pysam.AlignedSegments (zero-based coordinates). Args: @@ -164,11 +159,7 @@ def record_alignment( else: return self.record(rec.reference_name, rec.reference_start + 1) - def _log( - self, - refname: Optional[str] = None, - position: Optional[int] = None, - ) -> None: + def _log(self, refname: Optional[str] = None, position: Optional[int] = None,) -> None: """Helper method to print the log message. Args: @@ -187,9 +178,7 @@ def _log( self.printer(f"{self.verb} {self.count:,d} {self.noun}: {coordinate}") - def log_last( - self, - ) -> bool: + def log_last(self,) -> bool: """Force logging the last record, for example when progress has completed.""" if self._count_mod_unit != 0: self._log(refname=self._last_reference_name, position=self._last_position) diff --git a/fgpyo/util/tests/test_logging.py b/fgpyo/util/tests/test_logging.py index 09f21235..358baa04 100644 --- a/fgpyo/util/tests/test_logging.py +++ b/fgpyo/util/tests/test_logging.py @@ -43,12 +43,7 @@ def test_progress_logger_as_context_manager() -> None: @pytest.mark.parametrize( - "record", - [ - (r1_mapped_named), - (r2_unmapped_named), - (r2_unmapped_un_named), - ], + "record", [(r1_mapped_named), (r2_unmapped_named), (r2_unmapped_un_named),], ) def test_record_alignment_mapped_record(record: pysam.AlignedSegment) -> None: # Define instance of ProgressLogger diff --git a/fgpyo/util/tests/test_metric.py b/fgpyo/util/tests/test_metric.py index d84ed4b1..8da5cc49 100644 --- a/fgpyo/util/tests/test_metric.py +++ b/fgpyo/util/tests/test_metric.py @@ -34,13 +34,7 @@ class DummyMetric(Metric["DummyMetric"]): dict_value: Dict[int, str] = attr.ib() tuple_value: Tuple[int, str] = attr.ib() list_value: List[str] = attr.ib() - complex_value: Dict[ - int, - Dict[ - Tuple[int, int], - Set[str], - ], - ] = attr.ib() + complex_value: Dict[int, Dict[Tuple[int, int], Set[str],],] = attr.ib() DUMMY_METRICS: List[DummyMetric] = [ @@ -53,9 +47,7 @@ class DummyMetric(Metric["DummyMetric"]): optional_int_value=-5, optional_bool_value=True, optional_enum_value=EnumTest.EnumVal3, - dict_value={ - 1: "test1", - }, + dict_value={1: "test1",}, tuple_value=(0, "test1"), list_value=[], complex_value={1: {(5, 1): set({"mapped_test_val1", "setval2"})}}, @@ -138,10 +130,7 @@ class PersonDefault(Metric["PersonDefault"]): @pytest.mark.parametrize("metric", DUMMY_METRICS) -def test_metric_roundtrip( - tmp_path: Path, - metric: DummyMetric, -) -> None: +def test_metric_roundtrip(tmp_path: Path, metric: DummyMetric,) -> None: path: Path = tmp_path / "metrics.txt" DummyMetric.write(path, metric) diff --git a/fgpyo/util/types.py b/fgpyo/util/types.py index 9bcee785..fa630495 100644 --- a/fgpyo/util/types.py +++ b/fgpyo/util/types.py @@ -78,9 +78,7 @@ def _is_optional(type_: type) -> bool: def _make_union_parser_worker( - union: Type[UnionType], - parsers: Iterable[Callable[[str], UnionType]], - value: str, + union: Type[UnionType], parsers: Iterable[Callable[[str], UnionType]], value: str, ) -> UnionType: """Worker function behind union parsing. Iterates through possible parsers for the union and returns the value produced by the first parser that works. Otherwise raises an error if none @@ -110,9 +108,7 @@ def make_union_parser(union: Type[UnionType], parsers: Iterable[Callable[[str], def _make_literal_parser_worker( - literal: Type[LiteralType], - parsers: Iterable[Callable[[str], LiteralType]], - value: str, + literal: Type[LiteralType], parsers: Iterable[Callable[[str], LiteralType]], value: str, ) -> LiteralType: """Worker function behind literal parsing. Iterates through possible literals and returns the value produced by the first literal that matches expectation. diff --git a/fgpyo/vcf/builder.py b/fgpyo/vcf/builder.py index a1307096..c2018838 100644 --- a/fgpyo/vcf/builder.py +++ b/fgpyo/vcf/builder.py @@ -363,11 +363,7 @@ def add_format_header( header_line += ">" self.add_header_line(header_line) - def add_filter_header( - self, - name: str, - description: Optional[str] = None, - ) -> None: + def add_filter_header(self, name: str, description: Optional[str] = None,) -> None: """ Add a FILTER header field to the VCF header. diff --git a/fgpyo/vcf/tests/test_builder.py b/fgpyo/vcf/tests/test_builder.py index 2a16d797..7697e564 100644 --- a/fgpyo/vcf/tests/test_builder.py +++ b/fgpyo/vcf/tests/test_builder.py @@ -51,8 +51,7 @@ def _get_random_contig( def _get_random_variant_inputs( - random_generator: random.Random, - sequence_dict: Dict[str, Dict[str, Any]], + random_generator: random.Random, sequence_dict: Dict[str, Dict[str, Any]], ) -> Mapping[str, Any]: """ Randomly generate inputs that should produce a valid Variant. Don't include format fields. @@ -227,9 +226,7 @@ def _get_is_compressed(input_file: Path) -> bool: @pytest.mark.parametrize("compress", (True, False)) def test_zero_sample_vcf_round_trip( - temp_path: Path, - zero_sample_record_inputs: Tuple[Mapping[str, Any], ...], - compress: bool, + temp_path: Path, zero_sample_record_inputs: Tuple[Mapping[str, Any], ...], compress: bool, ) -> None: """ Test if zero-sample VCF (no genotypes) output records match the records read in from the @@ -252,24 +249,13 @@ def test_zero_sample_vcf_round_trip( def _add_random_genotypes( - random_generator: random.Random, - record_input: Mapping[str, Any], - sample_ids: Iterable[str], + random_generator: random.Random, record_input: Mapping[str, Any], sample_ids: Iterable[str], ) -> Mapping[str, Any]: """Add random genotypes to the record input.""" genotypes = { sample_id: { "GT": random_generator.choice( - [ - (None,), - (0, 0), - (0, 1), - (1, 0), - (1, 1), - (None, 0), - (0, None), - (1, None), - ] + 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+++ b/fgpyo/fasta/builder.py @@ -92,7 +92,10 @@ class ContigBuilder: """ def __init__( - self, name: str, assembly: str, species: str, + self, + name: str, + assembly: str, + species: str, ): self.name = name self.assembly = assembly @@ -144,7 +147,10 @@ class FastaBuilder: """ def __init__( - self, assembly: str = "testassembly", species: str = "testspecies", line_length: int = 80, + self, + assembly: str = "testassembly", + species: str = "testspecies", + line_length: int = 80, ): self.assembly: str = assembly self.species: str = species @@ -156,7 +162,10 @@ def __getitem__(self, key: str) -> ContigBuilder: return self.__contig_builders[key] def add( - self, name: str, assembly: Optional[str] = None, species: Optional[str] = None, + self, + name: str, + assembly: Optional[str] = None, + species: Optional[str] = None, ) -> ContigBuilder: """ Creates and returns a new ContigBuilder for a contig with the provided name. @@ -181,7 +190,10 @@ def add( self.__contig_builders[name] = builder return builder - def to_file(self, path: Path,) -> None: + def to_file( + self, + path: Path, + ) -> None: """ Writes out the set of accumulated contigs to a FASTA file at the `path` given. Also generates the accompanying fasta index file (`.fa.fai`) and sequence diff --git a/fgpyo/fasta/tests/test_builder.py b/fgpyo/fasta/tests/test_builder.py index a1db172a..b3dbb438 100644 --- a/fgpyo/fasta/tests/test_builder.py +++ b/fgpyo/fasta/tests/test_builder.py @@ -25,10 +25,17 @@ def test_bases_length_from_ContigBuilder_add_default() -> None: @pytest.mark.parametrize( - "name, bases, times, length_bases", [("chr1", "AAA", 3, 9), ("chr2", "TTT", 10, 30),], + "name, bases, times, length_bases", + [ + ("chr1", "AAA", 3, 9), + ("chr2", "TTT", 10, 30), + ], ) def test_bases_length_from_ContigBuilder_add( - name: str, bases: str, times: int, length_bases: int, + name: str, + bases: str, + times: int, + length_bases: int, ) -> None: """Checks that the number of bases in each contig is correct""" builder = FastaBuilder() @@ -53,10 +60,17 @@ def test_contig_dict_is_not_accessable() -> None: @pytest.mark.parametrize( "name, bases, times, expected", - [("chr3", "AAA a", 3, ("AAAA" * 3)), ("chr2", "TT T gT", 10, ("TTTGT" * 10)),], + [ + ("chr3", "AAA a", 3, ("AAAA" * 3)), + ("chr2", "TT T gT", 10, ("TTTGT" * 10)), + ], ) def test_bases_string_from_ContigBuilder_add( - name: str, bases: str, times: int, expected: str, tmp_path: Path, + name: str, + bases: str, + times: int, + expected: str, + tmp_path: Path, ) -> None: """ Reads bases back from fasta and checks that extra spaces are removed and bases are uppercase diff --git a/fgpyo/io/tests/test_io.py b/fgpyo/io/tests/test_io.py index aa785aa1..d4cf286d 100644 --- a/fgpyo/io/tests/test_io.py +++ b/fgpyo/io/tests/test_io.py @@ -84,9 +84,16 @@ def test_assert_path_is_writeable_pass() -> None: @pytest.mark.parametrize( - "suffix, expected", [(".gz", io.TextIOWrapper), (".fa", io.TextIOWrapper),], + "suffix, expected", + [ + (".gz", io.TextIOWrapper), + (".fa", io.TextIOWrapper), + ], ) -def test_reader(suffix: str, expected: Any,) -> None: +def test_reader( + suffix: str, + expected: Any, +) -> None: """Tests fgpyo.io.to_reader""" with NamedTemp(suffix=suffix, mode="r", delete=True) as read_file: with fio.to_reader(path=Path(read_file.name)) as reader: @@ -94,9 +101,16 @@ def test_reader(suffix: str, expected: Any,) -> None: @pytest.mark.parametrize( - "suffix, expected", [(".gz", io.TextIOWrapper), (".fa", io.TextIOWrapper),], + "suffix, expected", + [ + (".gz", io.TextIOWrapper), + (".fa", io.TextIOWrapper), + ], ) -def test_writer(suffix: str, expected: Any,) -> None: +def test_writer( + suffix: str, + expected: Any, +) -> None: """Tests fgpyo.io.to_writer()""" with NamedTemp(suffix=suffix, mode="w", delete=True) as write_file: with fio.to_writer(path=Path(write_file.name)) as writer: @@ -107,7 +121,10 @@ def test_writer(suffix: str, expected: Any,) -> None: "suffix, list_to_write", [(".txt", ["Test with a flat file", 10]), (".gz", ["Test with a gzip file", 10])], ) -def test_read_and_write_lines(suffix: str, list_to_write: List[Any],) -> None: +def test_read_and_write_lines( + suffix: str, + list_to_write: List[Any], +) -> None: """Test fgpyo.fio.read_lines and write_lines""" with NamedTemp(suffix=suffix, mode="w", delete=True) as read_file: fio.write_lines(path=Path(read_file.name), lines_to_write=list_to_write) diff --git a/fgpyo/sam/__init__.py b/fgpyo/sam/__init__.py index 11b61344..bb9fa6a3 100644 --- a/fgpyo/sam/__init__.py +++ b/fgpyo/sam/__init__.py @@ -863,7 +863,11 @@ def all_recs(self) -> Iterator[AlignedSegment]: for rec in recs: yield rec - def write_to(self, writer: SamFile, primary_only: bool = False,) -> None: + def write_to( + self, + writer: SamFile, + primary_only: bool = False, + ) -> None: """Write the records associated with the template to file. Args: @@ -879,7 +883,11 @@ def write_to(self, writer: SamFile, primary_only: bool = False,) -> None: for rec in rec_iter: writer.write(rec) - def set_tag(self, tag: str, value: Union[str, int, float, None],) -> None: + def set_tag( + self, + tag: str, + value: Union[str, int, float, None], + ) -> None: """Add a tag to all records associated with the template. Setting a tag to `None` will remove the tag. diff --git a/fgpyo/sam/tests/test_sam.py b/fgpyo/sam/tests/test_sam.py index 94fc944a..29a013f7 100755 --- a/fgpyo/sam/tests/test_sam.py +++ b/fgpyo/sam/tests/test_sam.py @@ -154,7 +154,9 @@ def test_sam_file_open_writing( def test_sam_file_open_writing_header_keyword( - expected_records: List[pysam.AlignedSegment], header_dict: AlignmentHeader, tmp_path: Path, + expected_records: List[pysam.AlignedSegment], + header_dict: AlignmentHeader, + tmp_path: Path, ) -> None: # Use SamWriter # use header as a keyword argument diff --git a/fgpyo/sam/tests/test_template_iterator.py b/fgpyo/sam/tests/test_template_iterator.py index 397603d0..79ab9283 100644 --- a/fgpyo/sam/tests/test_template_iterator.py +++ b/fgpyo/sam/tests/test_template_iterator.py @@ -73,7 +73,9 @@ def test_to_templates() -> None: assert len(list(template2.all_recs())) == 2 -def test_write_template(tmp_path: Path,) -> None: +def test_write_template( + tmp_path: Path, +) -> None: builder = SamBuilder() template = Template.build( [ diff --git a/fgpyo/tests/test_read_structure.py b/fgpyo/tests/test_read_structure.py index 64b230f8..f317f60a 100644 --- a/fgpyo/tests/test_read_structure.py +++ b/fgpyo/tests/test_read_structure.py @@ -31,9 +31,24 @@ def _S(off: int, len: int) -> ReadSegment: ("1M", (_M(0, 1),)), ("1S", (_S(0, 1),)), ("101T", (_T(0, 101),)), - ("5B101T", (_B(0, 5), _T(5, 101),),), + ( + "5B101T", + ( + _B(0, 5), + _T(5, 101), + ), + ), ("123456789T", (_T(0, 123456789),)), - ("10T10B10B10S10M", (_T(0, 10), _B(10, 10), _B(20, 10), _S(30, 10), _M(40, 10),),), + ( + "10T10B10B10S10M", + ( + _T(0, 10), + _B(10, 10), + _B(20, 10), + _S(30, 10), + _M(40, 10), + ), + ), ], ) def test_read_structure_from_string(string: str, segments: Tuple[ReadSegment, ...]) -> None: @@ -43,8 +58,24 @@ def test_read_structure_from_string(string: str, segments: Tuple[ReadSegment, .. @pytest.mark.parametrize( "string,segments", [ - ("75T 8B 8B 75T", (_T(0, 75), _B(75, 8), _B(83, 8), _T(91, 75),),), - (" 75T 8B 8B 75T ", (_T(0, 75), _B(75, 8), _B(83, 8), _T(91, 75),),), + ( + "75T 8B 8B 75T", + ( + _T(0, 75), + _B(75, 8), + _B(83, 8), + _T(91, 75), + ), + ), + ( + " 75T 8B 8B 75T ", + ( + _T(0, 75), + _B(75, 8), + _B(83, 8), + _T(91, 75), + ), + ), ], ) def test_read_structure_from_string_with_whitespace( @@ -67,7 +98,8 @@ def test_read_structure_variable_once_and_only_once_last_segment_ok( @pytest.mark.parametrize( - "string", ["++M", "5M++T", "5M70+T", "+M+T", "+M70T"], + "string", + ["++M", "5M++T", "5M70+T", "+M+T", "+M70T"], ) def test_read_structure_variable_once_and_only_once_last_segment_exception(string: str) -> None: with pytest.raises(Exception): diff --git a/fgpyo/util/inspect.py b/fgpyo/util/inspect.py index 3d2d5b3e..9d05b791 100644 --- a/fgpyo/util/inspect.py +++ b/fgpyo/util/inspect.py @@ -71,7 +71,9 @@ def split_at_given_level( def _get_parser( - cls: Type, type_: TypeAlias, parsers: Optional[Dict[type, Callable[[str], Any]]] = None, + cls: Type, + type_: TypeAlias, + parsers: Optional[Dict[type, Callable[[str], Any]]] = None, ) -> partial: """Attempts to find a parser for a provided type. @@ -115,7 +117,11 @@ def get_parser() -> partial: assert ( len(subtypes) == 1 ), "Lists are allowed only one subtype per PEP specification!" - subtype_parser = _get_parser(cls, subtypes[0], parsers,) + subtype_parser = _get_parser( + cls, + subtypes[0], + parsers, + ) return functools.partial( lambda s: list( [] @@ -131,7 +137,11 @@ def get_parser() -> partial: assert ( len(subtypes) == 1 ), "Sets are allowed only one subtype per PEP specification!" - subtype_parser = _get_parser(cls, subtypes[0], parsers,) + subtype_parser = _get_parser( + cls, + subtypes[0], + parsers, + ) return functools.partial( lambda s: set( set({}) @@ -144,7 +154,12 @@ def get_parser() -> partial: ) elif typing.get_origin(type_) == tuple: subtype_parsers = [ - _get_parser(cls, subtype, parsers,) for subtype in typing.get_args(type_) + _get_parser( + cls, + subtype, + parsers, + ) + for subtype in typing.get_args(type_) ] def tuple_parse(tuple_string: str) -> Tuple[Any, ...]: @@ -173,8 +188,16 @@ def tuple_parse(tuple_string: str) -> Tuple[Any, ...]: len(subtypes) == 2 ), "Dict object must have exactly 2 subtypes per PEP specification!" (key_parser, val_parser) = ( - _get_parser(cls, subtypes[0], parsers,), - _get_parser(cls, subtypes[1], parsers,), + _get_parser( + cls, + subtypes[0], + parsers, + ), + _get_parser( + cls, + subtypes[1], + parsers, + ), ) def dict_parse(dict_string: str) -> Dict[Any, Any]: @@ -234,7 +257,9 @@ def dict_parse(dict_string: str) -> Dict[Any, Any]: def attr_from( - cls: Type, kwargs: Dict[str, str], parsers: Optional[Dict[type, Callable[[str], Any]]] = None, + cls: Type, + kwargs: Dict[str, str], + parsers: Optional[Dict[type, Callable[[str], Any]]] = None, ) -> Any: """Builds an attr class from key-word arguments diff --git a/fgpyo/util/logging.py b/fgpyo/util/logging.py index d30c9dab..5c1210b5 100644 --- a/fgpyo/util/logging.py +++ b/fgpyo/util/logging.py @@ -125,7 +125,9 @@ def __exit__( return False def record( - self, reference_name: Optional[str] = None, position: Optional[int] = None, + self, + reference_name: Optional[str] = None, + position: Optional[int] = None, ) -> bool: """Record an item at a given genomic coordinate. Args: @@ -145,7 +147,10 @@ def record( else: return False - def record_alignment(self, rec: AlignedSegment,) -> bool: + def record_alignment( + self, + rec: AlignedSegment, + ) -> bool: """Correctly record pysam.AlignedSegments (zero-based coordinates). Args: @@ -159,7 +164,11 @@ def record_alignment(self, rec: AlignedSegment,) -> bool: else: return self.record(rec.reference_name, rec.reference_start + 1) - def _log(self, refname: Optional[str] = None, position: Optional[int] = None,) -> None: + def _log( + self, + refname: Optional[str] = None, + position: Optional[int] = None, + ) -> None: """Helper method to print the log message. Args: @@ -178,7 +187,9 @@ def _log(self, refname: Optional[str] = None, position: Optional[int] = None,) - self.printer(f"{self.verb} {self.count:,d} {self.noun}: {coordinate}") - def log_last(self,) -> bool: + def log_last( + self, + ) -> bool: """Force logging the last record, for example when progress has completed.""" if self._count_mod_unit != 0: self._log(refname=self._last_reference_name, position=self._last_position) diff --git a/fgpyo/util/tests/test_logging.py b/fgpyo/util/tests/test_logging.py index 358baa04..09f21235 100644 --- a/fgpyo/util/tests/test_logging.py +++ b/fgpyo/util/tests/test_logging.py @@ -43,7 +43,12 @@ def test_progress_logger_as_context_manager() -> None: @pytest.mark.parametrize( - "record", [(r1_mapped_named), (r2_unmapped_named), (r2_unmapped_un_named),], + "record", + [ + (r1_mapped_named), + (r2_unmapped_named), + (r2_unmapped_un_named), + ], ) def test_record_alignment_mapped_record(record: pysam.AlignedSegment) -> None: # Define instance of ProgressLogger diff --git a/fgpyo/util/tests/test_metric.py b/fgpyo/util/tests/test_metric.py index 8da5cc49..d84ed4b1 100644 --- a/fgpyo/util/tests/test_metric.py +++ b/fgpyo/util/tests/test_metric.py @@ -34,7 +34,13 @@ class DummyMetric(Metric["DummyMetric"]): dict_value: Dict[int, str] = attr.ib() tuple_value: Tuple[int, str] = attr.ib() list_value: List[str] = attr.ib() - complex_value: Dict[int, Dict[Tuple[int, int], Set[str],],] = attr.ib() + complex_value: Dict[ + int, + Dict[ + Tuple[int, int], + Set[str], + ], + ] = attr.ib() DUMMY_METRICS: List[DummyMetric] = [ @@ -47,7 +53,9 @@ class DummyMetric(Metric["DummyMetric"]): optional_int_value=-5, optional_bool_value=True, optional_enum_value=EnumTest.EnumVal3, - dict_value={1: "test1",}, + dict_value={ + 1: "test1", + }, tuple_value=(0, "test1"), list_value=[], complex_value={1: {(5, 1): set({"mapped_test_val1", "setval2"})}}, @@ -130,7 +138,10 @@ class PersonDefault(Metric["PersonDefault"]): @pytest.mark.parametrize("metric", DUMMY_METRICS) -def test_metric_roundtrip(tmp_path: Path, metric: DummyMetric,) -> None: +def test_metric_roundtrip( + tmp_path: Path, + metric: DummyMetric, +) -> None: path: Path = tmp_path / "metrics.txt" DummyMetric.write(path, metric) diff --git a/fgpyo/util/types.py b/fgpyo/util/types.py index fa630495..9bcee785 100644 --- a/fgpyo/util/types.py +++ b/fgpyo/util/types.py @@ -78,7 +78,9 @@ def _is_optional(type_: type) -> bool: def _make_union_parser_worker( - union: Type[UnionType], parsers: Iterable[Callable[[str], UnionType]], value: str, + union: Type[UnionType], + parsers: Iterable[Callable[[str], UnionType]], + value: str, ) -> UnionType: """Worker function behind union parsing. Iterates through possible parsers for the union and returns the value produced by the first parser that works. Otherwise raises an error if none @@ -108,7 +110,9 @@ def make_union_parser(union: Type[UnionType], parsers: Iterable[Callable[[str], def _make_literal_parser_worker( - literal: Type[LiteralType], parsers: Iterable[Callable[[str], LiteralType]], value: str, + literal: Type[LiteralType], + parsers: Iterable[Callable[[str], LiteralType]], + value: str, ) -> LiteralType: """Worker function behind literal parsing. Iterates through possible literals and returns the value produced by the first literal that matches expectation. diff --git a/fgpyo/vcf/builder.py b/fgpyo/vcf/builder.py index c2018838..a1307096 100644 --- a/fgpyo/vcf/builder.py +++ b/fgpyo/vcf/builder.py @@ -363,7 +363,11 @@ def add_format_header( header_line += ">" self.add_header_line(header_line) - def add_filter_header(self, name: str, description: Optional[str] = None,) -> None: + def add_filter_header( + self, + name: str, + description: Optional[str] = None, + ) -> None: """ Add a FILTER header field to the VCF header. diff --git a/fgpyo/vcf/tests/test_builder.py b/fgpyo/vcf/tests/test_builder.py index 7697e564..2a16d797 100644 --- a/fgpyo/vcf/tests/test_builder.py +++ b/fgpyo/vcf/tests/test_builder.py @@ -51,7 +51,8 @@ def _get_random_contig( def _get_random_variant_inputs( - random_generator: random.Random, sequence_dict: Dict[str, Dict[str, Any]], + random_generator: random.Random, + sequence_dict: Dict[str, Dict[str, Any]], ) -> Mapping[str, Any]: """ Randomly generate inputs that should produce a valid Variant. Don't include format fields. @@ -226,7 +227,9 @@ def _get_is_compressed(input_file: Path) -> bool: @pytest.mark.parametrize("compress", (True, False)) def test_zero_sample_vcf_round_trip( - temp_path: Path, zero_sample_record_inputs: Tuple[Mapping[str, Any], ...], compress: bool, + temp_path: Path, + zero_sample_record_inputs: Tuple[Mapping[str, Any], ...], + compress: bool, ) -> None: """ Test if zero-sample VCF (no genotypes) output records match the records read in from the @@ -249,13 +252,24 @@ def test_zero_sample_vcf_round_trip( def _add_random_genotypes( - random_generator: random.Random, record_input: Mapping[str, Any], sample_ids: Iterable[str], + random_generator: random.Random, + record_input: Mapping[str, Any], + sample_ids: Iterable[str], ) -> Mapping[str, Any]: """Add random genotypes to the record input.""" genotypes = { sample_id: { "GT": random_generator.choice( - [(None,), (0, 0), (0, 1), (1, 0), (1, 1), (None, 0), (0, None), (1, None),] + [ + (None,), + (0, 0), + (0, 1), + (1, 0), + (1, 1), + (None, 0), + (0, None), + (1, None), + ] ) } for sample_id in sample_ids diff --git a/poetry.lock b/poetry.lock index 5b3a6853..4ff27323 100644 --- a/poetry.lock +++ b/poetry.lock @@ -60,25 +60,26 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] [[package]] name = "black" -version = "19.10b0" +version = "20.8b1" description = "The uncompromising code formatter." optional = false python-versions = ">=3.6" files = [ - {file = "black-19.10b0-py36-none-any.whl", hash = "sha256:1b30e59be925fafc1ee4565e5e08abef6b03fe455102883820fe5ee2e4734e0b"}, - {file = "black-19.10b0.tar.gz", hash = "sha256:c2edb73a08e9e0e6f65a0e6af18b059b8b1cdd5bef997d7a0b181df93dc81539"}, + {file = "black-20.8b1.tar.gz", hash = "sha256:1c02557aa099101b9d21496f8a914e9ed2222ef70336404eeeac8edba836fbea"}, ] [package.dependencies] appdirs = "*" -attrs = ">=18.1.0" -click = ">=6.5" +click = ">=7.1.2" +mypy-extensions = ">=0.4.3" pathspec = ">=0.6,<1" -regex = "*" -toml = ">=0.9.4" +regex = ">=2020.1.8" +toml = ">=0.10.1" typed-ast = ">=1.4.0" +typing-extensions = ">=3.7.4" [package.extras] +colorama = ["colorama (>=0.4.3)"] d = ["aiohttp (>=3.3.2)", "aiohttp-cors"] [[package]] @@ -1138,4 +1139,4 @@ docs = ["sphinx", "sphinx_rtd_theme"] [metadata] lock-version = "2.0" python-versions = ">=3.8.0,<4.0" -content-hash = "943145eda74584c2dc95239fc3cf4d6985d44faf7d726cd910736946e90a0edc" +content-hash = "56a85341c1f01de8f4f1ad1e5e280449c4328bbd6790e1a3c7023e79f7ce8078" diff --git a/pyproject.toml b/pyproject.toml index dc305d24..c4b82224 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -35,7 +35,7 @@ typing_extensions = { version = ">=3.7.4", python = "<3.12" } docs = ["sphinx", "sphinx_rtd_theme"] [tool.poetry.dev-dependencies] -black = "19.10b0" +black = "20.8b1" click = "<8.1.0" flake8 = [ { version = ">=5.0.0", python = "<3.12.0" }, From fd51f01a5fd274ad6832018d56d16b11eed6693b Mon Sep 17 00:00:00 2001 From: jdidion Date: Thu, 22 Feb 2024 09:29:20 -0800 Subject: [PATCH 05/17] revert reformatting --- fgpyo/fasta/builder.py | 1 - fgpyo/fastx/__init__.py | 1 - fgpyo/io/__init__.py | 1 - fgpyo/read_structure.py | 1 - fgpyo/sam/builder.py | 1 - fgpyo/util/inspect.py | 8 ++------ fgpyo/util/types.py | 4 +--- fgpyo/vcf/__init__.py | 1 - 8 files changed, 3 insertions(+), 15 deletions(-) diff --git a/fgpyo/fasta/builder.py b/fgpyo/fasta/builder.py index 59d1cca9..bf4eeac8 100755 --- a/fgpyo/fasta/builder.py +++ b/fgpyo/fasta/builder.py @@ -32,7 +32,6 @@ 'AAAAAAAAAANNN' """ - import textwrap from pathlib import Path from typing import TYPE_CHECKING diff --git a/fgpyo/fastx/__init__.py b/fgpyo/fastx/__init__.py index 360f9198..b256c183 100644 --- a/fgpyo/fastx/__init__.py +++ b/fgpyo/fastx/__init__.py @@ -24,7 +24,6 @@ seq2: GGGG, seq2: TTTT """ - from contextlib import AbstractContextManager from pathlib import Path from types import TracebackType diff --git a/fgpyo/io/__init__.py b/fgpyo/io/__init__.py index e9e59f5f..3457c7d1 100644 --- a/fgpyo/io/__init__.py +++ b/fgpyo/io/__init__.py @@ -42,7 +42,6 @@ "10" """ - import gzip import io import os diff --git a/fgpyo/read_structure.py b/fgpyo/read_structure.py index e9555d58..a1f61a8d 100644 --- a/fgpyo/read_structure.py +++ b/fgpyo/read_structure.py @@ -61,7 +61,6 @@ correspond to the given read segment """ - import enum from typing import Iterable from typing import Iterator diff --git a/fgpyo/sam/builder.py b/fgpyo/sam/builder.py index 122a3067..f2e716b3 100755 --- a/fgpyo/sam/builder.py +++ b/fgpyo/sam/builder.py @@ -10,7 +10,6 @@ - :class:`~fgpyo.sam.builder.SamBuilder` -- A builder class that allows the accumulation of alignment records and access as a list and writing to file. """ - from array import array from pathlib import Path from random import Random diff --git a/fgpyo/util/inspect.py b/fgpyo/util/inspect.py index 9d05b791..e5c085c7 100644 --- a/fgpyo/util/inspect.py +++ b/fgpyo/util/inspect.py @@ -71,9 +71,7 @@ def split_at_given_level( def _get_parser( - cls: Type, - type_: TypeAlias, - parsers: Optional[Dict[type, Callable[[str], Any]]] = None, + cls: Type, type_: TypeAlias, parsers: Optional[Dict[type, Callable[[str], Any]]] = None, ) -> partial: """Attempts to find a parser for a provided type. @@ -257,9 +255,7 @@ def dict_parse(dict_string: str) -> Dict[Any, Any]: def attr_from( - cls: Type, - kwargs: Dict[str, str], - parsers: Optional[Dict[type, Callable[[str], Any]]] = None, + cls: Type, kwargs: Dict[str, str], parsers: Optional[Dict[type, Callable[[str], Any]]] = None, ) -> Any: """Builds an attr class from key-word arguments diff --git a/fgpyo/util/types.py b/fgpyo/util/types.py index 9bcee785..7dafe0b1 100644 --- a/fgpyo/util/types.py +++ b/fgpyo/util/types.py @@ -110,9 +110,7 @@ def make_union_parser(union: Type[UnionType], parsers: Iterable[Callable[[str], def _make_literal_parser_worker( - literal: Type[LiteralType], - parsers: Iterable[Callable[[str], LiteralType]], - value: str, + literal: Type[LiteralType], parsers: Iterable[Callable[[str], LiteralType]], value: str, ) -> LiteralType: """Worker function behind literal parsing. Iterates through possible literals and returns the value produced by the first literal that matches expectation. diff --git a/fgpyo/vcf/__init__.py b/fgpyo/vcf/__init__.py index d364e704..f6f837a0 100644 --- a/fgpyo/vcf/__init__.py +++ b/fgpyo/vcf/__init__.py @@ -48,7 +48,6 @@ order via the :func:`~fgpyo.vcf.builder.VariantBuilder.to_sorted_list()` method. """ - from contextlib import contextmanager from pathlib import Path from typing import Generator From faefc196ec0ccf5c08694d643d6906f6721dda25 Mon Sep 17 00:00:00 2001 From: jdidion Date: Thu, 22 Feb 2024 09:32:02 -0800 Subject: [PATCH 06/17] revert reformatting --- fgpyo/util/inspect.py | 4 ++-- fgpyo/util/types.py | 2 +- pyproject.toml | 3 +-- 3 files changed, 4 insertions(+), 5 deletions(-) diff --git a/fgpyo/util/inspect.py b/fgpyo/util/inspect.py index e5c085c7..f38f898a 100644 --- a/fgpyo/util/inspect.py +++ b/fgpyo/util/inspect.py @@ -71,7 +71,7 @@ def split_at_given_level( def _get_parser( - cls: Type, type_: TypeAlias, parsers: Optional[Dict[type, Callable[[str], Any]]] = None, + cls: Type, type_: TypeAlias, parsers: Optional[Dict[type, Callable[[str], Any]]] = None ) -> partial: """Attempts to find a parser for a provided type. @@ -255,7 +255,7 @@ def dict_parse(dict_string: str) -> Dict[Any, Any]: def attr_from( - cls: Type, kwargs: Dict[str, str], parsers: Optional[Dict[type, Callable[[str], Any]]] = None, + cls: Type, kwargs: Dict[str, str], parsers: Optional[Dict[type, Callable[[str], Any]]] = None ) -> Any: """Builds an attr class from key-word arguments diff --git a/fgpyo/util/types.py b/fgpyo/util/types.py index 7dafe0b1..5af7e08a 100644 --- a/fgpyo/util/types.py +++ b/fgpyo/util/types.py @@ -110,7 +110,7 @@ def make_union_parser(union: Type[UnionType], parsers: Iterable[Callable[[str], def _make_literal_parser_worker( - literal: Type[LiteralType], parsers: Iterable[Callable[[str], LiteralType]], value: str, + literal: Type[LiteralType], parsers: Iterable[Callable[[str], LiteralType]], value: str ) -> LiteralType: """Worker function behind literal parsing. Iterates through possible literals and returns the value produced by the first literal that matches expectation. diff --git a/pyproject.toml b/pyproject.toml index c4b82224..9ccf16c4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -35,8 +35,7 @@ typing_extensions = { version = ">=3.7.4", python = "<3.12" } docs = ["sphinx", "sphinx_rtd_theme"] [tool.poetry.dev-dependencies] -black = "20.8b1" -click = "<8.1.0" +black = ">=19.10b" flake8 = [ { version = ">=5.0.0", python = "<3.12.0" }, { version = ">=6.1.0", python = ">=3.12.0" }, From e6f0d86e5f6553dd10c8a0f5fd709d4f2177022a Mon Sep 17 00:00:00 2001 From: jdidion Date: Thu, 22 Feb 2024 09:32:54 -0800 Subject: [PATCH 07/17] update lockfile --- poetry.lock | 243 ++++++++++++---------------------------------------- 1 file changed, 53 insertions(+), 190 deletions(-) diff --git a/poetry.lock b/poetry.lock index 4ff27323..87d5f5c9 100644 --- a/poetry.lock +++ b/poetry.lock @@ -11,17 +11,6 @@ files = [ {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"}, ] -[[package]] -name = "appdirs" -version = "1.4.4" -description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -optional = false -python-versions = "*" -files = [ - 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python: "3.7" + python: "3.8" sphinx: configuration: docs/conf.py python: From 296066e50ad5554d35afc2083f48808773fb15e1 Mon Sep 17 00:00:00 2001 From: jdidion Date: Thu, 22 Feb 2024 09:42:24 -0800 Subject: [PATCH 11/17] revert additional python versions in build matrix --- .github/workflows/pythonpackage.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml index 670e4396..9f813d65 100644 --- a/.github/workflows/pythonpackage.yml +++ b/.github/workflows/pythonpackage.yml @@ -9,7 +9,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - PYTHON_VERSION: ["3.8", "3.9", "3.10", "3.11", "3.12"] + PYTHON_VERSION: ["3.8", "3.9", "3.10"] steps: - uses: actions/checkout@v2 From cdffe8aca27d71ea5d097b59779420d8e3ca84ea Mon Sep 17 00:00:00 2001 From: jdidion Date: Thu, 22 Feb 2024 09:45:46 -0800 Subject: [PATCH 12/17] revert reformatting --- fgpyo/util/types.py | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/fgpyo/util/types.py b/fgpyo/util/types.py index 5af7e08a..e378574d 100644 --- a/fgpyo/util/types.py +++ b/fgpyo/util/types.py @@ -139,11 +139,7 @@ def make_literal_parser( def is_list_like(type_: type) -> bool: """Returns true if the value is a list or list like object""" - return typing.get_origin(type_) in [ - list, - collections.abc.Iterable, - collections.abc.Sequence, - ] + return typing.get_origin(type_) in [list, collections.abc.Iterable, collections.abc.Sequence] def none_parser(value: str) -> Literal[None]: From 4cbefc0d3027e7935b6e091eb49823cf59c387af Mon Sep 17 00:00:00 2001 From: jdidion Date: Thu, 22 Feb 2024 09:57:11 -0800 Subject: [PATCH 13/17] add test --- fgpyo/util/tests/test_types.py | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 fgpyo/util/tests/test_types.py diff --git a/fgpyo/util/tests/test_types.py b/fgpyo/util/tests/test_types.py new file mode 100644 index 00000000..c9c8eaac --- /dev/null +++ b/fgpyo/util/tests/test_types.py @@ -0,0 +1,10 @@ +from typing import Iterable +from typing import List +from typing import Sequence + +from fgpyo.util import types + +def test_is_listlike() -> None: + assert types.is_list_like(List[str]) + assert types.is_list_like(Iterable[str]) + assert types.is_list_like(Sequence[str]) \ No newline at end of file From 7239e272acc574b19d0ec9ba7ba9277e3c58a80a Mon Sep 17 00:00:00 2001 From: jdidion Date: Thu, 22 Feb 2024 10:00:19 -0800 Subject: [PATCH 14/17] reformat --- fgpyo/util/tests/test_types.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/fgpyo/util/tests/test_types.py b/fgpyo/util/tests/test_types.py index c9c8eaac..c49d2d78 100644 --- a/fgpyo/util/tests/test_types.py +++ b/fgpyo/util/tests/test_types.py @@ -4,7 +4,8 @@ from fgpyo.util import types + def test_is_listlike() -> None: assert types.is_list_like(List[str]) assert types.is_list_like(Iterable[str]) - assert types.is_list_like(Sequence[str]) \ No newline at end of file + assert types.is_list_like(Sequence[str]) From c5ab8e5efe58c605a7d424c6916449a191c8ce67 Mon Sep 17 00:00:00 2001 From: jdidion Date: Thu, 22 Feb 2024 10:21:34 -0800 Subject: [PATCH 15/17] update version in readme --- README.md | 2 +- fgpyo/util/inspect.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 18806561..92ada0de 100644 --- a/README.md +++ b/README.md @@ -37,7 +37,7 @@ `pip install fgpyo` -**Requires python 3.7+** +**Requires python 3.8+** See documentation on [fgpyo.readthedocs.org][rtd-link]. diff --git a/fgpyo/util/inspect.py b/fgpyo/util/inspect.py index f38f898a..700d8bb2 100644 --- a/fgpyo/util/inspect.py +++ b/fgpyo/util/inspect.py @@ -233,7 +233,7 @@ def dict_parse(dict_string: str) -> Dict[Any, Any]: union=type_, parsers=[_get_parser(cls, arg, parsers) for arg in typing.get_args(type_)], ) - elif typing.get_origin(type_) is Literal: # Py>=3.7. + elif typing.get_origin(type_) is Literal: return types.make_literal_parser( type_, [_get_parser(cls, type(arg), parsers) for arg in typing.get_args(type_)], From 03a9788132a47623815069b081caf4c2649d3f88 Mon Sep 17 00:00:00 2001 From: jdidion Date: Thu, 22 Feb 2024 10:22:35 -0800 Subject: [PATCH 16/17] update version in readme --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 92ada0de..87eaf420 100644 --- a/README.md +++ b/README.md @@ -48,7 +48,7 @@ See documentation on [fgpyo.readthedocs.org][rtd-link]. A simple way to create an environment with the desired version of python and poetry is to use [conda][conda-link]. E.g.: ```bash -conda create -n fgpyo -c conda-forge "python>=3.6" poetry +conda create -n fgpyo -c conda-forge "python>=3.8" poetry conda activate fgpyo poetry install ``` From 7d3f84651bad02a456c36d6a13ea583f56fa7ff5 Mon Sep 17 00:00:00 2001 From: jdidion Date: Thu, 22 Feb 2024 15:57:28 -0800 Subject: [PATCH 17/17] revert formatting --- fgpyo/vcf/tests/test_builder.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/fgpyo/vcf/tests/test_builder.py b/fgpyo/vcf/tests/test_builder.py index 2a16d797..58f39752 100644 --- a/fgpyo/vcf/tests/test_builder.py +++ b/fgpyo/vcf/tests/test_builder.py @@ -81,11 +81,9 @@ def _get_random_variant_inputs( key: ( random_generator.randint(0, 100) if value_type == VcfFieldType.INTEGER - else ( - random_generator.uniform(0, 1) - if value_type == VcfFieldType.FLOAT - else random_generator.choice(["Up", "Down"]) - ) + else random_generator.uniform(0, 1) + if value_type == VcfFieldType.FLOAT + else random_generator.choice(["Up", "Down"]) ) for key, value_type in _INFO_FIELD_TYPES.items() }