Bump mypy and switch from __dict__ to to_dict() method

Author: domdfcoding

.github/workflows/flake8.yml

@@ -35,7 +35,7 @@ jobs:
         if: steps.changes.outputs.code == 'true'
         uses: "actions/setup-python@v5"
         with:
-          python-version: "3.7"
+          python-version: "3.9"
 
       - name: Install dependencies 🔧
         if: steps.changes.outputs.code == 'true'

.github/workflows/mypy.yml

@@ -40,7 +40,7 @@ jobs:
         if: steps.changes.outputs.code == 'true'
         uses: "actions/setup-python@v5"
         with:
-          python-version: "3.7"
+          python-version: "3.9"
 
       - name: Install dependencies 🔧
         run: |

mh_utils/__init__.py

@@ -26,8 +26,66 @@
 #  OR OTHER DEALINGS IN THE SOFTWARE.
 #
 
+# stdlib
+from abc import abstractmethod
+from typing import Dict, Iterable, Iterator, Tuple, TypeVar
+
+# 3rd party
+from domdf_python_tools._is_match import is_match_with
+from domdf_python_tools.doctools import prettify_docstrings
+
+__all__ = ["Dictable"]
+
 __author__: str = "Dominic Davis-Foster"
 __copyright__: str = "2020-2021 Dominic Davis-Foster"
 __license__: str = "MIT License"
 __version__: str = "0.2.2"
 __email__: str = "dominic@davis-foster.co.uk"
+
+_V = TypeVar("_V")
+
+
+@prettify_docstrings
+class Dictable(Iterable[Tuple[str, _V]]):
+	"""
+	The basic structure of a class that can be converted into a dictionary.
+	"""
+
+	@abstractmethod
+	def __init__(self, *args, **kwargs):
+		pass
+
+	def __repr__(self) -> str:
+		return super().__repr__()
+
+	def __str__(self) -> str:
+		return self.__repr__()
+
+	def __iter__(self) -> Iterator[Tuple[str, _V]]:
+		"""
+		Iterate over the attributes of the class.
+		"""
+
+		yield from self.to_dict().items()
+
+	def __getstate__(self) -> Dict[str, _V]:
+		return self.to_dict()
+
+	def __setstate__(self, state):
+		self.__init__(**state)  # type: ignore[misc]
+
+	def __copy__(self):
+		return self.__class__(**self.to_dict())
+
+	def __deepcopy__(self, memodict={}):
+		return self.__copy__()
+
+	@abstractmethod
+	def to_dict(self):
+		return {}  # pragma: no cover (abc)
+
+	def __eq__(self, other) -> bool:
+		if isinstance(other, self.__class__):
+			return is_match_with(other.to_dict(), self.to_dict())
+
+		return NotImplemented

mh_utils/cef_parser/__init__.py

@@ -79,14 +79,15 @@
 from attr_utils.docstrings import add_attrs_doc
 from attr_utils.serialise import serde
 from chemistry_tools.formulae import Formula
-from domdf_python_tools.bases import Dictable, NamedList
+from domdf_python_tools.bases import NamedList
 from domdf_python_tools.doctools import prettify_docstrings
 from domdf_python_tools.pretty_print import FancyPrinter
 from domdf_python_tools.stringlist import DelimitedList
 from domdf_python_tools.typing import PathLike
 from typing_extensions import TypedDict
 
 # this package
+from mh_utils import Dictable
 from mh_utils.utils import make_timedelta
 
 __all__ = [
@@ -125,8 +126,6 @@ def __init__(
 			matches: Optional[Dict[str, "Score"]] = None,
 			):
 
-		super().__init__()
-
 		self.name = str(name)
 		if isinstance(formula, Formula):
 			self.formula = formula
@@ -142,8 +141,7 @@ def __init__(
 		else:
 			raise TypeError(f"'matches' must be a dictionary, not {type(matches)}")
 
-	@property
-	def __dict__(self):
+	def to_dict(self):
 		return dict(
 				name=self.name,
 				formula=self.formula,
@@ -262,7 +260,6 @@ def __init__(
 			peaks: Optional[Sequence[Peak]] = None,
 			rt_ranges: Optional[Sequence["RTRange"]] = None,
 			):
-		super().__init__()
 
 		self.spectrum_type = str(spectrum_type)
 		self.saturation_limit = int(saturation_limit)
@@ -319,8 +316,7 @@ def __init__(
 			"rt_ranges",
 			]
 
-	@property
-	def __dict__(self):
+	def to_dict(self):
 		data = {}
 		for key in self.__slots__:
 			data[key] = getattr(self, key)
@@ -591,7 +587,6 @@ def __init__(
 			results: Optional[Sequence[Molecule]] = None,
 			spectra: Optional[Sequence[Spectrum]] = None,
 			):
-		super().__init__()
 
 		self.algo = str(algo)
 
@@ -615,8 +610,7 @@ def __init__(
 		else:
 			self.spectra = []
 
-	@property
-	def __dict__(self):
+	def to_dict(self):
 		return dict(
 				algo=self.algo,
 				location=self.location,

mh_utils/csv_parser/classes.py

@@ -39,11 +39,13 @@
 import sdjson
 from cawdrey import AlphaDict
 from domdf_python_tools import doctools
-from domdf_python_tools.bases import Dictable
 from domdf_python_tools.doctools import prettify_docstrings
 from domdf_python_tools.paths import PathPlus
 from domdf_python_tools.typing import PathLike
 
+# this package
+from mh_utils import Dictable
+
 __all__ = [
 		"Sample",
 		"Result",
@@ -96,7 +98,6 @@ def __init__(
 			filename,
 			results=None,
 			):
-		super().__init__()
 
 		self.sample_name = sample_name
 		self.sample_type = sample_type
@@ -202,8 +203,7 @@ def from_series(cls: Type[_S], series) -> _S:
 	def __repr__(self):
 		return f"Sample({self.sample_name})"
 
-	@property
-	def __dict__(self):
+	def to_dict(self):
 		return AlphaDict(
 				sample_name=self.sample_name,
 				sample_type=self.sample_type,
@@ -302,7 +302,6 @@ def __init__(
 			flag_severity: str = '',
 			flag_severity_code: int = 0,
 			):
-		super().__init__()
 
 		# Possible also AL (ID Source) and AM (ID Techniques Applied)
 		self._cas = cas
@@ -425,8 +424,7 @@ def from_series(cls: Type[_R], series: pandas.Series) -> _R:
 	def __repr__(self):
 		return f"Result({self.name}; {self.formula}; {self.rt}; {self.score})"
 
-	@property
-	def __dict__(self):
+	def to_dict(self):
 		return AlphaDict(
 				cas=self._cas,
 				name=self.name,

mh_utils/worklist_parser/classes.py

@@ -33,14 +33,14 @@
 
 # 3rd party
 import attr
-import lxml.etree  # type: ignore
+import lxml  # type: ignore
 import pandas  # type: ignore
 from attr_utils.docstrings import add_attrs_doc
 from attr_utils.serialise import serde
-from domdf_python_tools.bases import Dictable
 from domdf_python_tools.doctools import prettify_docstrings
 
 # this package
+from mh_utils import Dictable
 from mh_utils.utils import element_to_bool, strip_string
 from mh_utils.worklist_parser.columns import Column, columns
 from mh_utils.worklist_parser.enums import AttributeType
@@ -70,8 +70,6 @@ def __init__(
 			sample_info: Optional[dict] = None,
 			):
 
-		super().__init__()
-
 		if isinstance(id, UUID):
 			self.id = id
 		else:
@@ -112,8 +110,7 @@ def from_xml(
 				sample_info=parse_sample_info(element.SampleInfo, user_columns),
 				)
 
-	@property
-	def __dict__(self):
+	def to_dict(self):
 		data = {}
 		for key in self.__slots__:
 			if key == "id":
@@ -153,8 +150,6 @@ def __init__(
 			checksum: "Checksum",
 			):
 
-		super().__init__()
-
 		self.version = float(version)
 		self.locked_run_mode = bool(locked_run_mode)
 		self.instrument_name = str(instrument_name)
@@ -165,8 +160,7 @@ def __init__(
 
 	__slots__ = ["version", "user_columns", "jobs", "checksum", "locked_run_mode", "instrument_name", "params"]
 
-	@property
-	def __dict__(self):
+	def to_dict(self):
 		data = {}
 		for key in self.__slots__:
 			data[key] = getattr(self, key)
@@ -332,7 +326,7 @@ def __repr__(self) -> str:
 		if self.undefined:
 			return f"{self.__class__.__name__}(Undefined)"
 		else:
-			slots = self.__slots__  # type: ignore[attr-defined]  # attrs adds __slots__ but mypy doesn't know
+			slots = self.__slots__
 			values = ", ".join(f"{x}={getattr(self, x)!r}" for x in slots if x != "__weakref__")
 			return f"{self.__class__.__name__}({values})"
 

mh_utils/worklist_parser/columns.py

@@ -158,7 +158,7 @@ def from_attribute(cls, attribute: "Attribute") -> "Column":
 				name=attribute.header_name,
 				attribute_id=attribute.attribute_id,
 				attribute_type=attribute.attribute_type,
-				dtype=dtype,  # type: ignore
+				dtype=dtype,
 				default_value=attribute.default_data_value,
 				field_type=attribute.field_type,
 				reorder_id=attribute.reorder_id,

pyproject.toml

@@ -126,7 +126,7 @@ autodoc_exclude_members = [
 ]
 
 [tool.mypy]
-python_version = "3.7"
+python_version = "3.9"
 namespace_packages = true
 check_untyped_defs = true
 warn_unused_ignores = true

repo_helper.yml

@@ -15,7 +15,8 @@ use_whey: true
 min_coverage: 85
 pre_commit_exclude: ^tests/test_xml/.*\.xml$
 preserve_custom_theme: true
-python_deploy_version: 3.7
+mypy_version: 1.16
+python_deploy_version: 3.9
 
 conda_channels:
  - conda-forge

tests/test_worklist_parser/test_columns.py

@@ -85,7 +85,7 @@ def test_cast_value_any(self, value, expects):
 				name="Test Column",
 				attribute_id=1,
 				attribute_type=AttributeType.SystemUsed,
-				dtype=Any,  # type: ignore
+				dtype=Any,
 				default_value="The Default",
 				)