renamed "mark" module with "hook"

extras/fileformats/extras/application/archive.py

@@ -10,7 +10,7 @@
 import pydra.engine.specs
 from fileformats.generic import FsObject
 from fileformats.core.utils import set_cwd
-from fileformats.core import mark, FileSet
+from fileformats.core import hook, FileSet
 from fileformats.application import Zip, Tar, TarGzip
 
 
@@ -47,10 +47,10 @@
 Compressed = FileSet.type_var("Compressed")
 
 
-@mark.converter(source_format=FsObject, target_format=Tar)
-@mark.converter(source_format=FsObject, target_format=TarGzip, compression="gz")
-@mark.converter(source_format=Compressed, target_format=Tar[Compressed])
-@mark.converter(
+@hook.converter(source_format=FsObject, target_format=Tar)
+@hook.converter(source_format=FsObject, target_format=TarGzip, compression="gz")
+@hook.converter(source_format=Compressed, target_format=Tar[Compressed])
+@hook.converter(
     source_format=Compressed, target_format=TarGzip[Compressed], compression="gz"
 )
 @pydra.mark.task
@@ -102,10 +102,10 @@ def create_tar(
     return Path(out_file)
 
 
-@mark.converter(source_format=Tar, target_format=FsObject)
-@mark.converter(source_format=TarGzip, target_format=FsObject)
-@mark.converter(source_format=Tar[Compressed], target_format=Compressed)
-@mark.converter(source_format=TarGzip[Compressed], target_format=Compressed)
+@hook.converter(source_format=Tar, target_format=FsObject)
+@hook.converter(source_format=TarGzip, target_format=FsObject)
+@hook.converter(source_format=Tar[Compressed], target_format=Compressed)
+@hook.converter(source_format=TarGzip[Compressed], target_format=Compressed)
 @pydra.mark.task
 @pydra.mark.annotate({"return": {"out_file": Path}})
 def extract_tar(
@@ -136,8 +136,8 @@ def extract_tar(
     return extracted[0]
 
 
-@mark.converter(source_format=FsObject, target_format=Zip)
-@mark.converter(source_format=Compressed, target_format=Zip[Compressed])
+@hook.converter(source_format=FsObject, target_format=Zip)
+@hook.converter(source_format=Compressed, target_format=Zip[Compressed])
 @pydra.mark.task
 @pydra.mark.annotate(
     {
@@ -198,8 +198,8 @@ def create_zip(
     return Path(out_file)
 
 
-@mark.converter(source_format=Zip, target_format=FsObject)
-@mark.converter(source_format=Zip[Compressed], target_format=Compressed)
+@hook.converter(source_format=Zip, target_format=FsObject)
+@hook.converter(source_format=Zip[Compressed], target_format=Compressed)
 @pydra.mark.task
 @pydra.mark.annotate({"return": {"out_file": Path}})
 def extract_zip(in_file: Zip, extract_dir: Path) -> Path:

extras/fileformats/extras/application/serialization.py

@@ -4,12 +4,12 @@
 import yaml
 import pydra.mark
 import pydra.engine.specs
-from fileformats.core import mark
+from fileformats.core import hook
 from fileformats.application import DataSerialization, Json, Yaml
 
 
-@mark.converter(target_format=Json, output_format=Json)
-@mark.converter(target_format=Yaml, output_format=Yaml)
+@hook.converter(target_format=Json, output_format=Json)
+@hook.converter(target_format=Yaml, output_format=Yaml)
 @pydra.mark.task
 @pydra.mark.annotate({"return": {"out_file": DataSerialization}})
 def convert_data_serialization(

extras/fileformats/extras/image/converters.py

@@ -3,15 +3,15 @@
 import tempfile
 import pydra.mark
 import pydra.engine.specs
-from fileformats.core import mark
+from fileformats.core import hook
 from fileformats.image.raster import RasterImage, Bitmap, Gif, Jpeg, Png, Tiff
 
 
-@mark.converter(target_format=Bitmap, output_format=Bitmap)
-@mark.converter(target_format=Gif, output_format=Gif)
-@mark.converter(target_format=Jpeg, output_format=Jpeg)
-@mark.converter(target_format=Png, output_format=Png)
-@mark.converter(target_format=Tiff, output_format=Tiff)
+@hook.converter(target_format=Bitmap, output_format=Bitmap)
+@hook.converter(target_format=Gif, output_format=Gif)
+@hook.converter(target_format=Jpeg, output_format=Jpeg)
+@hook.converter(target_format=Png, output_format=Png)
+@hook.converter(target_format=Tiff, output_format=Tiff)
 @pydra.mark.task
 @pydra.mark.annotate({"return": {"out_file": RasterImage}})
 def convert_image(

fileformats/application/serialization.py

@@ -2,7 +2,7 @@
 import typing as ty
 from random import Random
 from pathlib import Path
-from ..core import mark, DataType
+from ..core import hook, DataType
 from ..core.mixin import WithClassifiers
 from ..generic import File
 from ..core.exceptions import FormatMismatchError
@@ -41,12 +41,12 @@ class DataSerialization(WithClassifiers, File):
 
     iana_mime = None
 
-    @mark.extra
+    @hook.extra
     def load(self):
         """Load the contents of the file into a dictionary"""
         raise NotImplementedError
 
-    @mark.extra
+    @hook.extra
     def save(data):
         """Serialise a dictionary to a new file"""
         raise NotImplementedError
@@ -68,7 +68,7 @@ class Json(DataSerialization):
     ext = ".json"
     allowed_classifiers = (JsonSchema, InformalSchema)
 
-    @mark.check
+    @hook.check
     def load(self):
         try:
             with open(self.fspath) as f:

fileformats/core/converter.py

@@ -99,7 +99,7 @@ def register_converter(
         source_format: type,
         converter_tuple: ty.Tuple[ty.Callable, ty.Dict[str, ty.Any]],
     ):
-        """Registers a converter task within a class attribute. Called by the @fileformats.mark.converter
+        """Registers a converter task within a class attribute. Called by the @fileformats.hook.converter
         decorator.
 
         Parameters

fileformats/core/fileset.py

@@ -35,7 +35,7 @@
     FileFormatsExtrasPkgNotCheckedError,
 )
 from .datatype import DataType
-from . import mark
+from . import hook
 
 try:
     from typing import Self
@@ -188,7 +188,7 @@ def metadata(self) -> ty.Dict[str, ty.Any]:
             metadata = None
         return metadata
 
-    @mark.extra
+    @hook.extra
     def read_metadata(self) -> ty.Dict[str, ty.Any]:
         """Reads any metadata associated with the fileset and returns it as a dict"""
         raise NotImplementedError
@@ -518,7 +518,7 @@ def register_converter(
         converter_tuple: ty.Tuple[ty.Callable, ty.Dict[str, ty.Any]],
     ):
         """Registers a converter task within a class attribute. Called by the
-        @fileformats.mark.converter decorator.
+        @fileformats.hook.converter decorator.
 
         Parameters
         ----------
@@ -844,7 +844,7 @@ def sample(
         if not dest_dir:
             dest_dir = Path(tempfile.mkdtemp())
         # Need to use mock to get an instance in order to use the singledispatch-based
-        # mark.extra decorator
+        # hook.extra decorator
         mock = cls.mock()
         fspaths = mock.generate_sample_data(dest_dir, seed, stem)
         try:
@@ -857,7 +857,7 @@ def sample(
             )
         return obj
 
-    @mark.extra
+    @hook.extra
     def generate_sample_data(
         self, dest_dir: Path, seed: int = 0, stem: str = None
     ) -> ty.Iterable[Path]:

fileformats/core/mark.py → fileformats/core/hook.py

@@ -39,7 +39,7 @@ def check(method):
     Parameters
     ----------
     method : Function
-        the method to mark as a check
+        the method to hook as a check
     """
     method.__annotations__[DataType.CHECK_ANNOTATION] = None
     return method

fileformats/core/mixin.py

@@ -2,7 +2,7 @@
 import re
 import typing as ty
 from collections import defaultdict
-from . import mark
+from . import hook
 from .fileset import FileSet
 from .utils import classproperty, describe_task, to_mime_format_name
 from .converter import SubtypeVar
@@ -30,7 +30,7 @@ class WithMagicNumber:
     binary: bool
     magic_number: ty.Union[str, bytes]
 
-    @mark.check
+    @hook.check
     def check_magic_number(self):
         if self.binary and isinstance(self.magic_number, str):
             magic_bytes = bytes.fromhex(self.magic_number)
@@ -74,7 +74,7 @@ class WithMagicVersion:
     magic_pattern_offset = 0
     magic_pattern_maxlength = None
 
-    @mark.required
+    @hook.required
     @property
     def version(self) -> ty.Union[str, ty.Tuple[str]]:
         read_length = (
@@ -169,7 +169,7 @@ class MyFileFormatWithSeparateHeader(WithSeparateHeader, MyFileFormat):
     def nested_types(cls):
         return (cls.header_type,)
 
-    @mark.required
+    @hook.required
     @property
     def header(self):
         return self.header_type(self.select_by_ext(self.header_type))
@@ -200,7 +200,7 @@ class MyFileFormatWithSideCars(WithSideCars, MyFileFormat):
         the file-formats of the expected side-car files
     """
 
-    @mark.required
+    @hook.required
     @property
     def side_cars(self):
         return [tp(self.select_by_ext(tp)) for tp in self.side_car_types]
@@ -555,7 +555,7 @@ def register_converter(
         source_format: type,
         converter_tuple: ty.Tuple[ty.Callable, ty.Dict[str, ty.Any]],
     ):
-        """Registers a converter task within a class attribute. Called by the @fileformats.mark.converter
+        """Registers a converter task within a class attribute. Called by the @fileformats.hook.converter
         decorator.
 
         Parameters

fileformats/core/tests/test_classifiers.py

@@ -3,7 +3,7 @@
 import pytest
 import pydra.mark
 from fileformats.core import from_mime, DataType, FileSet
-from fileformats.core.mark import converter
+from fileformats.core.hook import converter
 from fileformats.application import Zip
 from fileformats.generic import DirectoryContaining
 from fileformats.field import Array, Integer, Decimal, Text, Boolean

fileformats/core/tests/test_converter.py

@@ -4,7 +4,7 @@
 import pytest
 from pydra.engine.specs import File
 from fileformats.testing import Foo, Bar, Baz, Qux
-from fileformats.core import mark
+from fileformats.core import hook
 from fileformats.core.exceptions import FormatConversionError
 from conftest import write_test_file
 
@@ -18,7 +18,7 @@
 def foo_bar_converter():
     work_dir = Path(tempfile.mkdtemp())
 
-    @mark.converter
+    @hook.converter
     @pydra.mark.task
     @pydra.mark.annotate({"return": {"out_file": Bar}})
     def foo_bar_converter_(in_file: Foo):
@@ -31,7 +31,7 @@ def foo_bar_converter_(in_file: Foo):
 def baz_bar_converter():
     work_dir = Path(tempfile.mkdtemp())
 
-    @mark.converter(out_file="out")
+    @hook.converter(out_file="out")
     @pydra.mark.task
     @pydra.mark.annotate({"return": {"out": Bar}})
     def baz_bar_converter_(in_file: Baz):
@@ -84,7 +84,7 @@ def FooQuxConverter():
         name="Output", fields=output_fields, bases=(specs.ShellOutSpec,)
     )
 
-    @mark.converter(source_format=Foo, target_format=Qux)
+    @hook.converter(source_format=Foo, target_format=Qux)
     class FooQuxConverter_(ShellCommandTask):
 
         input_spec = FooQux_input_spec

fileformats/core/tests/test_detection.py

@@ -167,7 +167,7 @@ def test_nested_directories_fail2(work_dir):
 
 #     ext = ".foo"
 
-#     @mark.required
+#     @hook.required
 #     @property
 #     def bar(self):
 #         return self.select_by_ext(".bar")

fileformats/core/tests/test_general.py

@@ -5,7 +5,7 @@
 from fileformats.field import Integer, Boolean, Decimal, Array, Text
 from fileformats.testing import Foo
 from fileformats.core.exceptions import FileFormatsError, FormatMismatchError
-from fileformats.core import mark
+from fileformats.core import hook
 from conftest import write_test_file
 
 
@@ -162,12 +162,12 @@ def test_header_overwrite(work_dir):
 
 
 class YFile(ImageWithInlineHeader):
-    @mark.required
+    @hook.required
     @property
     def y(self):
         return self.metadata["y"]
 
-    @mark.check
+    @hook.check
     def y_value(self):
         if self.y <= 10:
             raise FormatMismatchError(f"'y' property is not > 10 ({self.y})")

fileformats/core/tests/test_mixin.py

@@ -1,6 +1,6 @@
 from conftest import write_test_file
 from fileformats.generic import File
-from fileformats.core import mark
+from fileformats.core import hook
 from fileformats.core.mixin import WithMagicNumber, WithSeparateHeader, WithSideCars
 from fileformats.core.exceptions import FormatMismatchError
 
@@ -48,7 +48,7 @@ class FileWithSeparateHeader(WithSeparateHeader, File):
     image_type = "sample-image-type"
     binary = False
 
-    @mark.check
+    @hook.check
     def check_image_type(self):
         if self.metadata[self.image_type_key] != self.image_type:
             raise FormatMismatchError(
@@ -121,7 +121,7 @@ class FileWithSideCars(WithSideCars, ImageWithInlineHeader):
     experiment_type_key = "experiment-type"
     experiment_type = "sample-experiment-type"
 
-    @mark.check
+    @hook.check
     def check_image_type(self):
         """Loaded from inline-header"""
         if self.metadata[self.image_type_key] != self.image_type:
@@ -130,7 +130,7 @@ def check_image_type(self):
                 f"found {self.metadata[self.image_type_key]}"
             )
 
-    @mark.check
+    @hook.check
     def check_experiment_type(self):
         """Loaded from side-car"""
         if self.metadata["header"][self.experiment_type_key] != self.experiment_type:

fileformats/core/tests/test_utils.py

@@ -7,7 +7,7 @@
 import typing as ty
 import time
 import pytest
-from fileformats.core import FileSet, mark
+from fileformats.core import FileSet, hook
 from fileformats.generic import File, Directory, FsObject
 from fileformats.core.mixin import WithSeparateHeader
 from fileformats.core.utils import find_matching, to_mime, from_mime, from_paths
@@ -260,12 +260,12 @@ class LuigiMario(File):
         ext = ".luigi.mario"
 
     class DoubleMario(FileSet):
-        @mark.required
+        @hook.required
         @property
         def bar(self):
             return Mario(self.select_by_ext(Mario))
 
-        @mark.required
+        @hook.required
         @property
         def luigi_bar(self):
             return LuigiMario(self.select_by_ext(LuigiMario))