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.

.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

src/gbd_mapping_generator/cause_builder.py

@@ -3,7 +3,8 @@
 from .data import get_cause_data, get_cause_list
 from .globals import ID_TYPES
 from .util import (
-    SPACING,
+    DOUBLE_SPACING,
+    SINGLE_SPACING,
     TAB,
     TEXTWIDTH,
     make_import,
@@ -21,16 +22,16 @@ def get_base_types():
         ("name", "str"),
         ("kind", "str"),
         ("gbd_id", ID_TYPES.C_ID),
-        ("me_id", f"Union[{ID_TYPES.ME_ID}, Unknown]"),
+        ("me_id", f"{ID_TYPES.ME_ID} | Unknown"),
         ("most_detailed", "bool"),
         ("level", "int"),
         ("restrictions", "Restrictions"),
     ]
     cause_attrs += [
-        ("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"),
     ]
 
     return {
@@ -140,24 +141,24 @@ def make_causes(causes_list):
 
 def build_mapping_template():
     out = make_module_docstring("Mapping templates for GBD causes.", __file__)
-    out += make_import("typing", ("Union", "Tuple")) + "\n"
-    out += make_import(".id", (ID_TYPES.C_ID, ID_TYPES.ME_ID, "Unknown"))
-    out += make_import(".base_template", ("Restrictions", "ModelableEntity", "GbdRecord"))
-    out += make_import(".sequela_template", ("Sequela",))
+    out += make_import("__future__", ("annotations",)) + "\n"
+    out += make_import(".base_template", ("GbdRecord", "ModelableEntity", "Restrictions"))
     out += make_import(".etiology_template", ("Etiology",))
+    out += make_import(".id", ("Unknown", ID_TYPES.C_ID, ID_TYPES.ME_ID))
+    out += make_import(".sequela_template", ("Sequela",))
 
     for entity, info in get_base_types().items():
-        out += SPACING
+        out += DOUBLE_SPACING
         out += make_record(entity, **info)
     return out
 
 
 def build_mapping():
     out = make_module_docstring("Mapping of GBD causes.", __file__)
-    out += make_import(".id", (ID_TYPES.C_ID, ID_TYPES.ME_ID, "UNKNOWN"))
     out += make_import(".base_template", ("Restrictions",))
     out += make_import(".cause_template", ("Cause", "Causes"))
-    out += make_import(".sequela", ("sequelae",))
-    out += make_import(".etiology", ("etiologies",)) + SPACING
+    out += make_import(".etiology", ("etiologies",))
+    out += make_import(".id", ("UNKNOWN", ID_TYPES.C_ID, ID_TYPES.ME_ID))
+    out += make_import(".sequela", ("sequelae",)) + SINGLE_SPACING
     out += make_causes(get_cause_data())
     return out

src/gbd_mapping_generator/covariate_builder.py

@@ -1,7 +1,14 @@
 from .base_template_builder import gbd_record_attrs, modelable_entity_attrs
 from .data import get_covariate_data, get_covariate_list
 from .globals import ID_TYPES, CovariateDataSeq
-from .util import SPACING, TAB, make_import, make_module_docstring, make_record
+from .util import (
+    DOUBLE_SPACING,
+    SINGLE_SPACING,
+    TAB,
+    make_import,
+    make_module_docstring,
+    make_record,
+)
 
 IMPORTABLES_DEFINED = ("Covariate", "covariates")
 
@@ -10,7 +17,7 @@ def get_base_types():
     cov_attrs = [
         ("name", "str"),
         ("kind", "str"),
-        ("gbd_id", f"Union[{ID_TYPES.COV_ID}, None]"),
+        ("gbd_id", f"{ID_TYPES.COV_ID} | None"),
         ("by_age", "bool"),
         ("by_sex", "bool"),
         ("dichotomous", "bool"),
@@ -90,19 +97,18 @@ def make_covariates(covariate_list: CovariateDataSeq) -> str:
 
 def build_mapping_template():
     out = make_module_docstring("Mapping templates for GBD covariates.", __file__)
-    out += make_import("typing", ("Union",)) + "\n"
+    out += make_import(".base_template", ("GbdRecord", "ModelableEntity"))
     out += make_import(".id", (ID_TYPES.COV_ID,))
-    out += make_import(".base_template", ("ModelableEntity", "GbdRecord"))
 
     for entity, info in get_base_types().items():
-        out += SPACING
+        out += DOUBLE_SPACING
         out += make_record(entity, **info)
     return out
 
 
 def build_mapping():
     out = make_module_docstring("Mapping of GBD covariates.", __file__)
-    out += make_import(".id", (ID_TYPES.COV_ID,))
-    out += make_import(".covariate_template", ("Covariate", "Covariates")) + SPACING
+    out += make_import(".covariate_template", ("Covariate", "Covariates"))
+    out += make_import(".id", (ID_TYPES.COV_ID,)) + SINGLE_SPACING
     out += make_covariates(get_covariate_data())
     return out

src/gbd_mapping_generator/data.py

@@ -1,5 +1,3 @@
-from typing import List
-
 import numpy as np
 import pandas as pd
 
@@ -120,7 +118,7 @@ def get_covariate_list(with_survey=False):
 #####################################################
 
 
-def get_sequela_data() -> List:
+def get_sequela_data() -> list:
     sequelae = gbd.get_sequela_id_mapping()
 
     return list(
@@ -134,7 +132,7 @@ def get_sequela_data() -> List:
     )
 
 
-def get_etiology_data() -> List:
+def get_etiology_data() -> list:
     etiologies = gbd.get_rei_metadata(rei_set_id=ETIOLOGY_SET_ID)
     etiologies = etiologies[etiologies["most_detailed"] == 1]
 
@@ -325,7 +323,7 @@ def get_all_risk_metadata():
     return risks
 
 
-def get_risk_data() -> List:
+def get_risk_data() -> list:
     risks = get_all_risk_metadata()
     causes = get_causes().set_index("cause_id")
 
@@ -490,7 +488,7 @@ def get_risk_data() -> List:
     return out
 
 
-def get_duplicate_indices(names: List[str]) -> List[int]:
+def get_duplicate_indices(names: list[str]) -> list[int]:
     dup_indices = []
     check = set()
     for i, v in enumerate(names):