drop python 3.9 support (#119)

Category: other
JIRA issue: MIC-5489

Changes and notes
Drop Python 3.9 support.
Use built in list, dicts, and tuples
Use pipe syntax instead of Union or Optional.

Testing
Built templates and compared to current templates.

Author: hussain-jafari

.github/workflows/build.yml

@@ -14,7 +14,7 @@ jobs:
   build:
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
     uses: 
       ihmeuw/vivarium_build_utils/.github/workflows/build.yml@main
     with:

CHANGELOG.rst

@@ -1,3 +1,9 @@
+**4.1.0 - 11/06/24**
+
+ - Drop support for Python 3.9
+ - Modernize type hints
+ - Update imports written by builders to be isort compliant
+
 **4.0.0 - 05/20/24**
 
  - Rebuild with GBD 2021 data

docs/source/conf.py

@@ -60,6 +60,7 @@
     "sphinx.ext.mathjax",
     "sphinx.ext.napoleon",
     "sphinx.ext.viewcode",
+    "sphinx_autodoc_typehints",
 ]
 
 # Add any paths that contain templates here, relative to this directory.

setup.py

@@ -36,6 +36,7 @@
     doc_requirements = [
         "sphinx>=6.2.1, <7.0",
         "sphinx-rtd-theme",
+        "sphinx-autodoc-typehints",
     ]
 
     lint_requirements = [

src/gbd_mapping/base_template.py

@@ -4,8 +4,6 @@
 
 Any manual changes will be lost.
 """
-from typing import Tuple, Union
-
 from .id import c_id, cov_id, hs_id, me_id, rei_id, s_id, scalar
 
 
@@ -19,7 +17,7 @@ def to_dict(self):
             attr = getattr(self, item)
             if isinstance(attr, GbdRecord):
                 out[item] = attr.to_dict()
-            elif isinstance(attr, Tuple) and attr:
+            elif isinstance(attr, tuple) and attr:
                 if isinstance(attr[0], GbdRecord):
                     out[item] = tuple(r.to_dict() for r in attr)
             elif attr is not None:
@@ -70,7 +68,8 @@ class ModelableEntity(GbdRecord):
     def __init__(self,
                  name: str,
                  kind: str,
-                 gbd_id: Union[c_id, s_id, hs_id, me_id, cov_id, rei_id, None], ):
+                 gbd_id: c_id | s_id | hs_id | me_id | cov_id | rei_id | None,
+    ):
         super().__init__()
         self.name = name
         self.kind = kind

src/gbd_mapping/cause_template.py

@@ -4,7 +4,7 @@
 
 Any manual changes will be lost.
 """
-from typing import Tuple, Union
+from __future__ import annotations
 
 from .base_template import GbdRecord, ModelableEntity, Restrictions
 from .etiology_template import Etiology
@@ -21,14 +21,14 @@ def __init__(self,
                  name: str,
                  kind: str,
                  gbd_id: c_id,
-                 me_id: Union[me_id, Unknown],
+                 me_id: me_id | Unknown,
                  most_detailed: bool,
                  level: int,
                  restrictions: Restrictions,
-                 parent: "Cause" = None,
-                 sub_causes: Tuple["Cause", ...] = None,
-                 sequelae: Tuple[Sequela, ...] = None,
-                 etiologies: Tuple[Etiology, ...] = None, ):
+                 parent: Cause | None = None,
+                 sub_causes: tuple[Cause, ...] | None = None,
+                 sequelae: tuple[Sequela, ...] | None = None,
+                 etiologies: tuple[Etiology, ...] | None = None, ):
         super().__init__(name=name,
                          kind=kind,
                          gbd_id=gbd_id)

src/gbd_mapping/covariate_template.py

@@ -4,8 +4,6 @@
 
 Any manual changes will be lost.
 """
-from typing import Union
-
 from .base_template import GbdRecord, ModelableEntity
 from .id import cov_id
 
@@ -17,7 +15,7 @@ class Covariate(ModelableEntity):
     def __init__(self,
                  name: str,
                  kind: str,
-                 gbd_id: Union[cov_id, None],
+                 gbd_id: cov_id | None,
                  by_age: bool,
                  by_sex: bool,
                  dichotomous: bool, ):

src/gbd_mapping/etiology_template.py

@@ -4,8 +4,6 @@
 
 Any manual changes will be lost.
 """
-from typing import Union
-
 from .base_template import GbdRecord, ModelableEntity
 from .id import rei_id
 
@@ -17,7 +15,7 @@ class Etiology(ModelableEntity):
     def __init__(self,
                  name: str,
                  kind: str,
-                 gbd_id: Union[rei_id, None], ):
+                 gbd_id: rei_id | None, ):
         super().__init__(name=name,
                          kind=kind,
                          gbd_id=gbd_id)

src/gbd_mapping/risk_factor_template.py

@@ -4,7 +4,7 @@
 
 Any manual changes will be lost.
 """
-from typing import Tuple, Union
+from __future__ import annotations
 
 from .base_template import Categories, GbdRecord, ModelableEntity, Restrictions, Tmred
 from .cause_template import Cause
@@ -24,14 +24,14 @@ def __init__(self,
                  gbd_id: rei_id,
                  level: int,
                  most_detailed: bool,
-                 distribution: Union[str, None],
+                 distribution: str | None,
                  population_attributable_fraction_calculation_type: str,
                  restrictions: Restrictions,
-                 affected_causes: Tuple[Cause, ...],
-                 population_attributable_fraction_of_one_causes: Tuple[Cause, ...],
-                 parent: Union["RiskFactor", None] = None,
-                 sub_risk_factors: Tuple["RiskFactor", ...] = None,
-                 affected_risk_factors: Tuple["RiskFactor", ...] = None,
+                 affected_causes: tuple[Cause, ...],
+                 population_attributable_fraction_of_one_causes: tuple[Cause, ...],
+                 parent: RiskFactor | None = None,
+                 sub_risk_factors: tuple[RiskFactor, ...] = None,
+                 affected_risk_factors: tuple[RiskFactor, ...] = None,
                  categories: Categories = None,
                  tmred: Tmred = None,
                  relative_risk_scalar: scalar = None, ):

src/gbd_mapping_generator/base_template_builder.py

@@ -1,4 +1,4 @@
-from .util import SPACING, make_import, make_module_docstring, make_record
+from .util import DOUBLE_SPACING, make_import, make_module_docstring, make_record
 
 IMPORTABLES_DEFINED = ("GbdRecord", "ModelableEntity", "Restrictions", "Tmred", "Categories")
 
@@ -7,7 +7,7 @@
 modelable_entity_attrs = (
     ("name", "str"),
     ("kind", "str"),
-    ("gbd_id", "Union[c_id, s_id, hs_id, me_id, cov_id, rei_id, None]"),
+    ("gbd_id", "c_id | s_id | hs_id | me_id | cov_id | rei_id | None"),
 )
 restrictions_attrs = (
     ("male_only", "bool"),
@@ -64,7 +64,7 @@ def to_dict(self):
             attr = getattr(self, item)
             if isinstance(attr, GbdRecord):
                 out[item] = attr.to_dict()
-            elif isinstance(attr, Tuple) and attr:
+            elif isinstance(attr, tuple) and attr:
                 if isinstance(attr[0], GbdRecord):
                     out[item] = tuple(r.to_dict() for r in attr)
             elif attr is not None:
@@ -121,7 +121,6 @@ def build_mapping() -> str:
 
     """
     templates = make_module_docstring("Template classes for GBD entities", __file__)
-    templates += make_import("typing", ["Union", "Tuple"])
     templates += (
         make_import(
             ".id",
@@ -135,12 +134,12 @@ def build_mapping() -> str:
                 "scalar",
             ],
         )
-        + SPACING
+        + DOUBLE_SPACING
     )
     templates += make_gbd_record()
 
     for entity, info in get_base_types().items():
-        templates += SPACING
+        templates += DOUBLE_SPACING
         templates += make_record(entity, **info)
 
     return templates