build: update requirements and build system (#555)

.github/workflows/checks.yaml

@@ -7,7 +7,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
 

pyproject.toml

@@ -16,13 +16,11 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 description = "VICC normalization routine for variations"
 license = {file = "LICENSE"}
 dependencies = [
@@ -50,18 +48,10 @@ Source = "https://github.com/cancervariants/variation-normalization"
 "Bug Tracker" = "https://github.com/cancervariants/variation-normalization/issues"
 
 [build-system]
-requires = ["setuptools>=64"]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
 build-backend = "setuptools.build_meta"
 
-[tool.setuptools.dynamic]
-version = {attr = "variation.version.__version__"}
-
-# Scanning for namespace packages in the ``src`` directory is true by
-# default in pyproject.toml, so you do NOT need to include the
-# `tool.setuptools.packages.find` if it looks like the following:
-# [tool.setuptools.packages.find]
-# namespaces = true
-# where = ["src"]
+[tool.setuptools_scm]
 
 [tool.pytest.ini_options]
 addopts = "--cov=src --cov-report term-missing"

src/variation/__init__.py

@@ -1 +1,10 @@
 """The Variation Normalization package."""
+
+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("variation-normalizer")
+except PackageNotFoundError:
+    __version__ = "unknown"
+finally:
+    del version, PackageNotFoundError

src/variation/classifiers/amplification_classifier.py

@@ -1,7 +1,5 @@
 """A module for the Amplification Classifier"""
 
-from typing import List
-
 from variation.classifiers.classifier import Classifier
 from variation.schemas.classification_response_schema import (
     AmplificationClassification,
@@ -13,15 +11,15 @@
 class AmplificationClassifier(Classifier):
     """The Amplification Classifier class"""
 
-    def exact_match_candidates(self) -> List[List[TokenType]]:
+    def exact_match_candidates(self) -> list[list[TokenType]]:
         """Return the token match candidates for the amplification classification.
 
         :return: List of list of tokens, where order matters, that represent an
         amplification classification.
         """
         return [[TokenType.GENE, TokenType.AMPLIFICATION]]
 
-    def match(self, tokens: List[Token]) -> AmplificationClassification:
+    def match(self, tokens: list[Token]) -> AmplificationClassification:
         """Return the amplification classification from a list of token matches.
 
         :param tokens: List of ordered tokens that are exact match candidates for an

src/variation/classifiers/cdna_deletion_classifier.py

@@ -1,7 +1,5 @@
 """A module for the Cdna Deletion Classifier."""
 
-from typing import List
-
 from variation.classifiers.classifier import Classifier
 from variation.schemas.classification_response_schema import (
     CdnaDeletionClassification,
@@ -13,15 +11,15 @@
 class CdnaDeletionClassifier(Classifier):
     """The Cdna Deletion Classifier class."""
 
-    def exact_match_candidates(self) -> List[List[TokenType]]:
+    def exact_match_candidates(self) -> list[list[TokenType]]:
         """Return the token match candidates for the cdna deletion classification.
 
         :return: List of list of tokens, where order matters, that represent a cdna
         deletion classification.
         """
         return [[TokenType.GENE, TokenType.CDNA_DELETION]]
 
-    def match(self, tokens: List[Token]) -> CdnaDeletionClassification:
+    def match(self, tokens: list[Token]) -> CdnaDeletionClassification:
         """Return the cdna deletion classification from a list of token matches.
 
         :param tokens: List of ordered tokens that are exact match candidates for a

src/variation/classifiers/cdna_delins_classifier.py

@@ -1,7 +1,5 @@
 """A module for the Cdna DelIns Classifier."""
 
-from typing import List
-
 from variation.classifiers.classifier import Classifier
 from variation.schemas.classification_response_schema import (
     CdnaDelInsClassification,
@@ -13,15 +11,15 @@
 class CdnaDelInsClassifier(Classifier):
     """The Cdna DelIns Classifier class."""
 
-    def exact_match_candidates(self) -> List[List[TokenType]]:
+    def exact_match_candidates(self) -> list[list[TokenType]]:
         """Return the token match candidates for the cdna delins classification.
 
         :return: List of list of tokens, where order matters, that represent a cdna
         delins classification.
         """
         return [[TokenType.GENE, TokenType.CDNA_DELINS]]
 
-    def match(self, tokens: List[Token]) -> CdnaDelInsClassification:
+    def match(self, tokens: list[Token]) -> CdnaDelInsClassification:
         """Return the cdna delins classification from a list of token matches.
 
         :param tokens: List of ordered tokens that are exact match candidates for a

src/variation/classifiers/cdna_insertion_classifier.py

@@ -1,7 +1,5 @@
 """A module for the Cdna insertion Classifier."""
 
-from typing import List
-
 from variation.classifiers.classifier import Classifier
 from variation.schemas.classification_response_schema import (
     CdnaInsertionClassification,
@@ -13,15 +11,15 @@
 class CdnaInsertionClassifier(Classifier):
     """The Cdna insertion Classifier class."""
 
-    def exact_match_candidates(self) -> List[List[TokenType]]:
+    def exact_match_candidates(self) -> list[list[TokenType]]:
         """Return the token match candidates for the cdna insertion classification.
 
         :return: List of list of tokens, where order matters, that represent a cdna
         insertion classification.
         """
         return [[TokenType.GENE, TokenType.CDNA_INSERTION]]
 
-    def match(self, tokens: List[Token]) -> CdnaInsertionClassification:
+    def match(self, tokens: list[Token]) -> CdnaInsertionClassification:
         """Return the cdna insertion classification from a list of token matches.
 
         :param tokens: List of ordered tokens that are exact match candidates for a

src/variation/classifiers/cdna_reference_agree_classifier.py

@@ -1,7 +1,5 @@
 """A module for the cDNA Reference Agree Classifier."""
 
-from typing import List
-
 from variation.classifiers.classifier import Classifier
 from variation.schemas.classification_response_schema import (
     CdnaReferenceAgreeClassification,
@@ -13,7 +11,7 @@
 class CdnaReferenceAgreeClassifier(Classifier):
     """The Cdna Reference Agree Classifier class."""
 
-    def exact_match_candidates(self) -> List[List[TokenType]]:
+    def exact_match_candidates(self) -> list[list[TokenType]]:
         """Return the token match candidates for the cdna reference agree
         classification.
 
@@ -29,7 +27,7 @@ def exact_match_candidates(self) -> List[List[TokenType]]:
             ],
         ]
 
-    def match(self, tokens: List[Token]) -> CdnaReferenceAgreeClassification:
+    def match(self, tokens: list[Token]) -> CdnaReferenceAgreeClassification:
         """Return the cdna reference agree classification from a list of token matches.
 
         :param tokens: List of ordered tokens that are exact match candidates for a

src/variation/classifiers/cdna_substitution_classifier.py

@@ -1,7 +1,5 @@
 """A module for the Cdna Substitution Classifier."""
 
-from typing import List, Optional
-
 from variation.classifiers.classifier import Classifier
 from variation.schemas.classification_response_schema import (
     CdnaSubstitutionClassification,
@@ -13,7 +11,7 @@
 class CdnaSubstitutionClassifier(Classifier):
     """The Cdna Substitution Classifier class."""
 
-    def exact_match_candidates(self) -> List[List[TokenType]]:
+    def exact_match_candidates(self) -> list[list[TokenType]]:
         """Return the token match candidates for the cdna substitution classification.
 
         :return: List of list of tokens, where order matters, that represent a cdna
@@ -28,7 +26,7 @@ def exact_match_candidates(self) -> List[List[TokenType]]:
             ],
         ]
 
-    def match(self, tokens: List[Token]) -> Optional[CdnaSubstitutionClassification]:
+    def match(self, tokens: list[Token]) -> CdnaSubstitutionClassification | None:
         """Return the cdna substitution classification from a list of token matches.
 
         :param tokens: List of ordered tokens that are exact match candidates for a

src/variation/classifiers/classifier.py

@@ -1,7 +1,6 @@
 """Module for Classification methods."""
 
 from abc import ABC, abstractmethod
-from typing import List, Optional
 
 from variation.schemas.classification_response_schema import Classification
 from variation.schemas.token_response_schema import Token, TokenType
@@ -11,7 +10,7 @@ class Classifier(ABC):
     """The Classifier class."""
 
     @abstractmethod
-    def match(self, tokens: List[Token]) -> Optional[Classification]:
+    def match(self, tokens: list[Token]) -> Classification | None:
         """Return the classification from a list of token matches.
 
         :param tokens: List of ordered tokens that are exact match candidates for a
@@ -20,14 +19,14 @@ def match(self, tokens: List[Token]) -> Optional[Classification]:
         """
 
     @abstractmethod
-    def exact_match_candidates(self) -> List[List[TokenType]]:
+    def exact_match_candidates(self) -> list[list[TokenType]]:
         """Return the token match candidates for a given classification.
 
         :return: List of list of tokens, where order matters, that represent a given
             classification.
         """
 
-    def can_classify(self, tokens: List[Token]) -> bool:
+    def can_classify(self, tokens: list[Token]) -> bool:
         """Return whether or not a list of tokens can be classified by a given
         classification
 
@@ -36,7 +35,7 @@ def can_classify(self, tokens: List[Token]) -> bool:
             matters, to represent a given classification. `False`, otherwise.
         """
         token_types = [t.token_type for t in tokens]
-        exact_matches: List[List[TokenType]] = [
+        exact_matches: list[list[TokenType]] = [
             c for c in self.exact_match_candidates() if token_types == c
         ]
 

src/variation/classifiers/genomic_deletion_ambiguous.py

@@ -1,7 +1,5 @@
 """A module for the Genomic Deletion Ambiguous Classifier."""
 
-from typing import List
-
 from variation.classifiers.classifier import Classifier
 from variation.schemas.classification_response_schema import (
     GenomicDeletionAmbiguousClassification,
@@ -14,7 +12,7 @@
 class GenomicDeletionAmbiguousClassifier(Classifier):
     """The Genomic Deletion Ambiguous Classifier class."""
 
-    def exact_match_candidates(self) -> List[List[TokenType]]:
+    def exact_match_candidates(self) -> list[list[TokenType]]:
         """Return the token match candidates for the genomic ambiguous deletion
         classification.
 
@@ -23,7 +21,7 @@ def exact_match_candidates(self) -> List[List[TokenType]]:
         """
         return [[TokenType.GENE, TokenType.GENOMIC_DELETION_AMBIGUOUS]]
 
-    def match(self, tokens: List[Token]) -> GenomicDeletionAmbiguousClassification:
+    def match(self, tokens: list[Token]) -> GenomicDeletionAmbiguousClassification:
         """Return the genomic ambiguous deletion classification from a list of token
         matches.
 

src/variation/classifiers/genomic_deletion_classifier.py

@@ -1,7 +1,5 @@
 """A module for the Genomic Deletion Classifier."""
 
-from typing import List
-
 from variation.classifiers.classifier import Classifier
 from variation.schemas.classification_response_schema import (
     GenomicDeletionClassification,
@@ -13,15 +11,15 @@
 class GenomicDeletionClassifier(Classifier):
     """The Genomic Deletion Classifier class."""
 
-    def exact_match_candidates(self) -> List[List[TokenType]]:
+    def exact_match_candidates(self) -> list[list[TokenType]]:
         """Return the token match candidates for the genomic deletion classification.
 
         :return: List of list of tokens, where order matters, that represent a genomic
         deletion classification.
         """
         return [[TokenType.GENE, TokenType.GENOMIC_DELETION]]
 
-    def match(self, tokens: List[Token]) -> GenomicDeletionClassification:
+    def match(self, tokens: list[Token]) -> GenomicDeletionClassification:
         """Return the genomic deletion classification from a list of token matches.
 
         :param tokens: List of ordered tokens that are exact match candidates for a

src/variation/classifiers/genomic_delins_classifier.py

@@ -1,7 +1,5 @@
 """A module for the Genomic DelIns Classifier."""
 
-from typing import List
-
 from variation.classifiers.classifier import Classifier
 from variation.schemas.classification_response_schema import (
     GenomicDelInsClassification,
@@ -13,15 +11,15 @@
 class GenomicDelInsClassifier(Classifier):
     """The Genomic DelIns Classifier class."""
 
-    def exact_match_candidates(self) -> List[List[TokenType]]:
+    def exact_match_candidates(self) -> list[list[TokenType]]:
         """Return the token match candidates for the genomic delins classification.
 
         :return: List of list of tokens, where order matters, that represent a genomic
         delins classification.
         """
         return [[TokenType.GENE, TokenType.GENOMIC_DELINS]]
 
-    def match(self, tokens: List[Token]) -> GenomicDelInsClassification:
+    def match(self, tokens: list[Token]) -> GenomicDelInsClassification:
         """Return the genomic delins classification from a list of token matches.
 
         :param tokens: List of ordered tokens that are exact match candidates for a

src/variation/classifiers/genomic_duplication_ambiguous.py

@@ -1,7 +1,5 @@
 """A module for the Genomic Duplication Ambiguous Classifier."""
 
-from typing import List
-
 from variation.classifiers.classifier import Classifier
 from variation.schemas.classification_response_schema import (
     GenomicDuplicationAmbiguousClassification,
@@ -14,7 +12,7 @@
 class GenomicDuplicationAmbiguousClassifier(Classifier):
     """The Genomic Duplication Ambiguous Classifier class."""
 
-    def exact_match_candidates(self) -> List[List[TokenType]]:
+    def exact_match_candidates(self) -> list[list[TokenType]]:
         """Return the token match candidates for the genomic ambiguous duplication
         classification.
 
@@ -23,7 +21,7 @@ def exact_match_candidates(self) -> List[List[TokenType]]:
         """
         return [[TokenType.GENE, TokenType.GENOMIC_DUPLICATION_AMBIGUOUS]]
 
-    def match(self, tokens: List[Token]) -> GenomicDuplicationAmbiguousClassification:
+    def match(self, tokens: list[Token]) -> GenomicDuplicationAmbiguousClassification:
         """Return the genomic ambiguous duplication classification from a list of token
         matches.
 

src/variation/classifiers/genomic_duplication_classifier.py

@@ -1,7 +1,5 @@
 """A module for the Genomic Duplication Classifier."""
 
-from typing import List
-
 from variation.classifiers.classifier import Classifier
 from variation.schemas.classification_response_schema import (
     GenomicDuplicationClassification,
@@ -13,15 +11,15 @@
 class GenomicDuplicationClassifier(Classifier):
     """The Genomic Duplication Classifier class."""
 
-    def exact_match_candidates(self) -> List[List[TokenType]]:
+    def exact_match_candidates(self) -> list[list[TokenType]]:
         """Return the token match candidates for the genomic duplication classification.
 
         :return: List of list of tokens, where order matters, that represent a genomic
         duplication classification.
         """
         return [[TokenType.GENE, TokenType.GENOMIC_DUPLICATION]]
 
-    def match(self, tokens: List[Token]) -> GenomicDuplicationClassification:
+    def match(self, tokens: list[Token]) -> GenomicDuplicationClassification:
         """Return the genomic duplication classification from a list of token matches.
 
         :param tokens: List of ordered tokens that are exact match candidates for a