chore: Drop support for python 3.9 and add support for 3.13

.github/workflows/formatting.yml

@@ -9,10 +9,10 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.9
+      - name: Set up Python 3.10
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: "3.10"
       - name: Set up Rust
         uses: dtolnay/rust-toolchain@stable
         with:

.github/workflows/linting.yml

@@ -9,10 +9,10 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.9
+      - name: Set up Python 3.10
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: "3.10"
       - name: Set up Rust
         uses: dtolnay/rust-toolchain@stable
         with:

.github/workflows/testing.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
       - uses: actions/checkout@v4

README.md

@@ -10,7 +10,7 @@
   <a href="https://black.readthedocs.io/en/stable/">
     <img alt="Code Style" src="https://img.shields.io/badge/code_style-black-black.svg">
   </a>
-  <img alt="Python Versions" src="https://img.shields.io/badge/python-3.9%20%7C%203.10%20%7C%203.11%20%7C%203.12-blue">
+  <img alt="Python Versions" src="https://img.shields.io/badge/python-3.10%20%7C%203.11%20%7C%203.12%20%7C%203.13-blue">
   <a href="https://github.com/limebit/medmodels/blob/main/LICENSE">
     <img alt="MedModels License" src="https://img.shields.io/github/license/limebit/medmodels.svg">
   </a>

docs/developer_guide/setup.md

@@ -4,7 +4,7 @@ MedModels leverages a combination of Python and Rust code. To contribute effecti
 
 **Requirements:**
 
-- Python (3.9, 3.10, 3.11 or 3.12)
+- Python (3.10, 3.11, 3.12 or 3.13)
 - Rust compiler (follow instructions from [https://www.rust-lang.org/tools/install](https://www.rust-lang.org/tools/install))
 
 **Using the Makefile:**

docs/index.md

@@ -65,7 +65,7 @@ API Reference
 
 ```{only} html
 [![black](https://img.shields.io/badge/code_style-black-black.svg)](https://black.readthedocs.io/en/stable/)
-![python versions](https://img.shields.io/badge/python-3.9%20%7C%203.10%20%7C%203.11%20%7C%203.12-blue)
+![python versions](https://img.shields.io/badge/python-3.10%20%7C%203.11%20%7C%203.12%20%7C%203.13-blue)
 [![license](https://img.shields.io/github/license/limebit/medmodels.svg)](https://github.com/limebit/medmodels/blob/main/LICENSE)
 [![license](https://github.com/limebit/medmodels/actions/workflows/testing.yml/badge.svg?branch=main)](https://github.com/limebit/medmodels/actions/workflows/testing.yml)
 ```

medmodels/_medmodels.pyi

@@ -1,6 +1,5 @@
-import sys
 from enum import Enum
-from typing import Callable, Dict, List, Optional, Sequence, Union
+from typing import Callable, Dict, List, Optional, Sequence, TypeAlias, Union
 
 from medmodels.medrecord.types import (
     Attributes,
@@ -19,11 +18,6 @@ from medmodels.medrecord.types import (
     PolarsNodeDataFrameInput,
 )
 
-if sys.version_info >= (3, 10):
-    from typing import TypeAlias
-else:
-    from typing_extensions import TypeAlias
-
 PyDataType: TypeAlias = Union[
     PyString,
     PyInt,

medmodels/medrecord/_overview.py

@@ -4,15 +4,19 @@
 
 import copy
 from datetime import datetime
-from typing import TYPE_CHECKING, Dict, List, Literal, Optional, Union
+from typing import TYPE_CHECKING, Dict, List, Literal, Optional, TypeAlias, Union
 
 import polars as pl
 
 from medmodels.medrecord.schema import AttributesSchema, AttributeType
-from medmodels.medrecord.types import Attributes, EdgeIndex, NodeIndex
+from medmodels.medrecord.types import (
+    Attributes,
+    EdgeIndex,
+    NodeIndex,
+)
 
 if TYPE_CHECKING:
-    import sys
+    from typing import TypeAlias
 
     from medmodels.medrecord.types import (
         AttributeInfo,
@@ -23,11 +27,6 @@
         TemporalAttributeInfo,
     )
 
-    if sys.version_info >= (3, 10):
-        from typing import TypeAlias
-    else:
-        from typing_extensions import TypeAlias
-
 AttributeDictionary: TypeAlias = Union[
     Dict[EdgeIndex, Attributes], Dict[NodeIndex, Attributes]
 ]

medmodels/medrecord/builder.py

@@ -4,11 +4,6 @@
 
 from typing import TYPE_CHECKING, Dict, List, Optional, Tuple, Union
 
-if TYPE_CHECKING:
-    from typing_extensions import TypeIs
-
-    from medmodels.medrecord.schema import Schema
-
 import medmodels as mm
 from medmodels.medrecord.types import (
     EdgeTuple,
@@ -34,6 +29,11 @@
     is_polars_node_dataframe_input_list,
 )
 
+if TYPE_CHECKING:
+    from typing_extensions import TypeIs
+
+    from medmodels.medrecord.schema import Schema
+
 NodeInputBuilder = Union[
     NodeTuple,
     List[NodeTuple],

medmodels/medrecord/datatype.py

@@ -4,6 +4,7 @@
 
 import typing
 from abc import ABC, abstractmethod
+from typing import TypeAlias
 
 from medmodels._medmodels import (
     PyAny,
@@ -18,14 +19,6 @@
     PyUnion,
 )
 
-if typing.TYPE_CHECKING:
-    import sys
-
-    if sys.version_info >= (3, 10):
-        from typing import TypeAlias
-    else:
-        from typing_extensions import TypeAlias
-
 PyDataType: TypeAlias = typing.Union[
     PyString,
     PyInt,

medmodels/medrecord/querying.py

@@ -3,7 +3,7 @@
 from __future__ import annotations
 
 from enum import Enum
-from typing import TYPE_CHECKING, Callable, List, Union
+from typing import Callable, List, TypeAlias, Union
 
 from medmodels._medmodels import (
     PyAttributesTreeOperand,
@@ -27,14 +27,6 @@
     NodeIndex,
 )
 
-if TYPE_CHECKING:
-    import sys
-
-    if sys.version_info >= (3, 10):
-        from typing import TypeAlias
-    else:
-        from typing_extensions import TypeAlias
-
 NodeQuery: TypeAlias = Callable[["NodeOperand"], None]
 EdgeQuery: TypeAlias = Callable[["EdgeOperand"], None]
 

medmodels/medrecord/types.py

@@ -4,29 +4,20 @@
 
 from datetime import datetime, timedelta
 from typing import (
-    TYPE_CHECKING,
     Dict,
     List,
     Literal,
     Mapping,
     Sequence,
     Tuple,
+    TypeAlias,
     TypedDict,
     Union,
 )
 
 import pandas as pd
 import polars as pl
-
-if TYPE_CHECKING:
-    import sys
-
-    if sys.version_info >= (3, 10):
-        from typing import TypeAlias
-
-        from typing_extensions import TypeIs
-    else:
-        from typing_extensions import TypeAlias, TypeIs
+from typing_extensions import TypeIs
 
 #: A type alias for attributes of a medical record.
 MedRecordAttribute: TypeAlias = Union[str, int]

medmodels/treatment_effect/continuous_estimators.py

@@ -1,21 +1,16 @@
 """Functions to estimate the treatment effect for continuous outcomes."""
 
-from __future__ import annotations
-
 import logging
 from math import sqrt
-from typing import TYPE_CHECKING, Literal, Optional, Set
+from typing import Literal, Optional, Set
 
 import numpy as np
 
+from medmodels.medrecord.medrecord import MedRecord
+from medmodels.medrecord.querying import EdgeOperand
+from medmodels.medrecord.types import Group, MedRecordAttribute, NodeIndex
 from medmodels.treatment_effect.temporal_analysis import find_reference_edge
 
-if TYPE_CHECKING:
-    from medmodels.medrecord.medrecord import MedRecord
-    from medmodels.medrecord.querying import EdgeOperand
-    from medmodels.medrecord.types import Group, MedRecordAttribute, NodeIndex
-
-
 logger = logging.getLogger(__name__)
 
 

medmodels/treatment_effect/estimate.py

@@ -1,22 +1,20 @@
 """Estimators class for calculating treatment effect metrics."""
 
-from __future__ import annotations
-
 from typing import TYPE_CHECKING, Literal, Set, Tuple, TypedDict
 
+from medmodels.medrecord.medrecord import MedRecord
+from medmodels.medrecord.types import MedRecordAttribute, NodeIndex
 from medmodels.treatment_effect.continuous_estimators import (
     average_treatment_effect,
     cohens_d,
     hedges_g,
 )
 from medmodels.treatment_effect.matching.neighbors import NeighborsMatching
 from medmodels.treatment_effect.matching.propensity import PropensityMatching
+from medmodels.treatment_effect.treatment_effect import TreatmentEffect
 
 if TYPE_CHECKING:
-    from medmodels.medrecord.medrecord import MedRecord
-    from medmodels.medrecord.types import MedRecordAttribute, NodeIndex
     from medmodels.treatment_effect.matching.matching import Matching
-    from medmodels.treatment_effect.treatment_effect import TreatmentEffect
 
 
 class SubjectIndices(TypedDict):

medmodels/treatment_effect/matching/algorithms/classic_distance_models.py

@@ -1,17 +1,13 @@
 """Models for matching treated and control units based on distance metrics."""
 
-from __future__ import annotations
-
-from typing import TYPE_CHECKING, Optional, Tuple
+from typing import Optional, Tuple
 
 import numpy as np
 import polars as pl
+from numpy.typing import NDArray
 from scipy.optimize import linear_sum_assignment
 
-if TYPE_CHECKING:
-    from numpy.typing import NDArray
-
-    from medmodels.medrecord.types import MedRecordAttributeInputList
+from medmodels.medrecord.types import MedRecordAttributeInputList
 
 
 def nearest_neighbor(

medmodels/treatment_effect/matching/algorithms/propensity_score.py

@@ -7,33 +7,20 @@
 two groups are comparable.
 """
 
-from __future__ import annotations
-
-from typing import TYPE_CHECKING, Any, Dict, Literal, Optional, Tuple, Union
+from typing import Any, Dict, Literal, Optional, Tuple, TypeAlias, Union
 
 import numpy as np
 import polars as pl
+from numpy.typing import NDArray
 from sklearn.ensemble import RandomForestClassifier
 from sklearn.linear_model import LogisticRegression
 from sklearn.tree import DecisionTreeClassifier
 
+from medmodels.medrecord.types import MedRecordAttributeInputList
 from medmodels.treatment_effect.matching.algorithms.classic_distance_models import (
     nearest_neighbor,
 )
 
-if TYPE_CHECKING:
-    import sys
-
-    from numpy.typing import NDArray
-
-    from medmodels.medrecord.types import MedRecordAttributeInputList
-
-    if sys.version_info >= (3, 10):
-        from typing import TypeAlias
-    else:
-        from typing_extensions import TypeAlias
-
-
 Model: TypeAlias = Literal["logit", "dec_tree", "forest"]
 
 

medmodels/treatment_effect/matching/matching.py

@@ -5,23 +5,13 @@
 score matching and nearest neighbor matching.
 """
 
-from __future__ import annotations
-
 from abc import ABC, abstractmethod
-from typing import TYPE_CHECKING, Literal, Optional, Set, Tuple
+from typing import Literal, Optional, Set, Tuple, TypeAlias
 
 import polars as pl
 
-if TYPE_CHECKING:
-    import sys
-
-    from medmodels.medrecord.medrecord import MedRecord
-    from medmodels.medrecord.types import MedRecordAttributeInputList, NodeIndex
-
-    if sys.version_info >= (3, 10):
-        from typing import TypeAlias
-    else:
-        from typing_extensions import TypeAlias
+from medmodels.medrecord.medrecord import MedRecord
+from medmodels.medrecord.types import MedRecordAttributeInputList, NodeIndex
 
 MatchingMethod: TypeAlias = Literal["propensity", "nearest_neighbors"]
 

medmodels/treatment_effect/matching/neighbors.py

@@ -1,18 +1,14 @@
 """Module for the nearest neighbor matching."""
 
-from __future__ import annotations
-
-from typing import TYPE_CHECKING, Optional, Set
+from typing import Optional, Set
 
+from medmodels import MedRecord
+from medmodels.medrecord.types import MedRecordAttributeInputList, NodeIndex
 from medmodels.treatment_effect.matching.algorithms.classic_distance_models import (
     nearest_neighbor,
 )
 from medmodels.treatment_effect.matching.matching import Matching
 
-if TYPE_CHECKING:
-    from medmodels import MedRecord
-    from medmodels.medrecord.types import MedRecordAttributeInputList, NodeIndex
-
 
 class NeighborsMatching(Matching):
     """Class for the nearest neighbor matching.