Merge pull request #143 from khaeru/python-3.13

Confirm support for Python 3.13 and drop 3.8

.github/workflows/pytest.yaml

@@ -27,18 +27,19 @@ jobs:
         # release. Only test SparseDataArray where possible.
         # Earliest version supported by genno = earliest Python that has not
         # reached EOL
-        - {version: "3.9", extras: ",sparse"}
-        - {version: "3.10", extras: ",sparse"}
-        - {version: "3.11", extras: ",sparse"}
+        - {version: "3.9", extras: ".[sparse]"}
+        - {version: "3.10", extras: ".[sparse]"}
+        - {version: "3.11", extras: ".[sparse]"}
+        - {version: "3.12", extras: ".[sparse]"}
         # Latest release / latest supported by genno / testable on GHA
-        - {version: "3.12", extras: ",sparse"}
+        - {version: "3.13", extras: '"Pint > 0.24"'}
 
         # For fresh releases and development versions of Python, compiled binary
         # wheels are not available for some dependencies, e.g. numpy, pandas.
         # Compiling these on the job runner requires a more elaborate build
         # environment, currently out of scope for genno. Exclude these versions
         # from CI.
-        # - {version: "3.13.0-rc.1", extras: ""}  # Development version
+        # - {version: "3.14.0-beta.1", extras: ""}  # Development version
 
       fail-fast: false
 
@@ -61,7 +62,7 @@ jobs:
         macos-skip-brew-update: true
 
     - name: Install the Python package and dependencies
-      run: pip install --upgrade --upgrade-strategy=eager .[tests${{ matrix.python.extras }}]
+      run: pip install --upgrade --upgrade-strategy=eager .[tests] ${{ matrix.python.extras }}
 
     - name: Run test suite using pytest
       run: |

doc/conf.py

@@ -77,6 +77,7 @@
     "dask$": ":std:doc:`dask:index`",
     "pint$": ":std:doc:`pint <pint:index>`",
     "plotnine$": ":class:`plotnine.ggplot`",
+    "pyarrow$": ":std:doc:`pyarrow <pyarrow:python/index>`",
     "pyam$": ":std:doc:`pyam:index`",
     "sphinx$": ":std:doc:`sphinx <sphinx:index>`",
 }
@@ -108,6 +109,7 @@
     "platformdirs": ("https://platformdirs.readthedocs.io/en/latest", None),
     "plotnine": ("https://plotnine.org", None),
     "pyam": ("https://pyam-iamc.readthedocs.io/en/stable", None),
+    "pyarrow": ("https://arrow.apache.org/docs", None),
     "python": ("https://docs.python.org/3", None),
     "pytest": ("https://docs.pytest.org/en/stable", None),
     "sdmx1": ("https://sdmx1.readthedocs.io/en/stable", None),

doc/whatsnew.rst

@@ -4,7 +4,14 @@ What's new
 Next release
 ============
 
-- genno is compatible and tested with `NumPy 2.0 <https://numpy.org/doc/stable/release/2.0.0-notes.html>`_, released 2024-06-16 (:issue:`140`, :pull:`141`).
+- :mod:`genno` supports and is tested on:
+
+  - `Python 3.13 <https://www.python.org/downloads/release/python-3130/>`_, released 2024-10-07 (:pull:`143`).
+    As of release time, support for :class:`.SparseDataArray` awaits :mod:`sparse`, thus `numba <https://github.com/numba/numba/issues/9413>`__ and `llvmlite <https://github.com/numba/llvmlite/issues/1084>`__.
+    :class:`.SparseDataArray` should be usable once these dependencies are updated.
+  - `NumPy 2.0 <https://numpy.org/doc/stable/release/2.0.0-notes.html>`_, released 2024-06-16 (:issue:`140`, :pull:`141`).
+
+- Support for Python 3.8 is dropped (:pull:`143`), as it has reached end-of-life.
 
 v1.26.0 (2024-03-27)
 ====================

genno/caching.py

@@ -5,7 +5,7 @@
 from hashlib import blake2b
 from inspect import getmembers, iscode
 from pathlib import Path
-from typing import TYPE_CHECKING, Callable, Optional, Set, Union
+from typing import TYPE_CHECKING, Callable, Optional, Union
 
 import pandas as pd
 
@@ -19,7 +19,7 @@
 log = logging.getLogger(__name__)
 
 # Types to ignore in Encoder.default()
-IGNORE: Set[type] = set()
+IGNORE: set[type] = set()
 
 
 @singledispatch

genno/compat/graphviz.py

@@ -1,6 +1,6 @@
 import re
 from os import PathLike
-from typing import Literal, Mapping, Optional, Set, Union
+from typing import Literal, Mapping, Optional, Union
 
 from genno.core.describe import is_list_of_keys, label
 
@@ -55,9 +55,9 @@ def __init__(
         self.graph = Digraph(graph_attr=self.ga, node_attr=na, edge_attr=edge_attr)
 
         # Nodes or edges already seen
-        self.seen: Set[str] = set()
+        self.seen: set[str] = set()
         # Nodes already connected to the graph
-        self.connected: Set[str] = set()
+        self.connected: set[str] = set()
 
     def get_attrs(self, kind: Literal["data", "func"], name: str, **defaults) -> dict:
         """Prepare attributes for a node of `kind`.

genno/compat/pint.py

@@ -11,13 +11,12 @@
 """
 
 from importlib.metadata import version
-from typing import Tuple, Type
 
 import pint
 
 try:
-    PintError: Tuple[Type[Exception], ...] = (pint.PintError,)
-    ApplicationRegistry: Type = pint.ApplicationRegistry
+    PintError: tuple[type[Exception], ...] = (pint.PintError,)
+    ApplicationRegistry: type = pint.ApplicationRegistry
 except AttributeError:  # pragma: no cover
     # Older versions of pint, e.g. 0.17
     PintError = (type("PintError", (Exception,), {}), pint.DefinitionSyntaxError)

genno/compat/plotnine/plot.py

@@ -1,7 +1,7 @@
 import logging
 from abc import ABC, abstractmethod
 from pathlib import Path
-from typing import Any, Dict, Hashable, Optional, Sequence
+from typing import Any, Hashable, Optional, Sequence
 from warnings import warn
 
 import plotnine as p9
@@ -31,7 +31,7 @@ class Plot(ABC):
     #: accepted by :meth:`generate`.
     inputs: Sequence[Hashable] = []
     #: Keyword arguments for :any:`plotnine.ggplot.save`.
-    save_args: Dict[str, Any] = dict(verbose=False)
+    save_args: dict[str, Any] = dict(verbose=False)
 
     # TODO add static geoms automatically in generate()
     __static: Sequence = []

genno/compat/pyam/__init__.py

@@ -1,7 +1,6 @@
 import logging
 from functools import partial
 from importlib.util import find_spec
-from typing import List
 
 from genno import Computer, Key
 from genno.config import handles
@@ -31,7 +30,7 @@ def iamc(c: Computer, info):
     name = info.pop("variable")
 
     # Chain of keys produced: first entry is the key for the base quantity
-    keys: List[Key] = [Key(info.pop("base"))]
+    keys: list[Key] = [Key(info.pop("base"))]
 
     # Second entry is a simple rename
     keys.append(single_key(c.add_single(Key(name, keys[0].dims, keys[0].tag), keys[0])))

genno/compat/sdmx/operator.py

@@ -1,4 +1,4 @@
-from typing import Dict, Hashable, Iterable, List, Mapping, Optional, Tuple, Union
+from typing import Hashable, Iterable, Mapping, Optional, Union
 
 import genno
 from genno import Quantity
@@ -23,7 +23,7 @@
 def codelist_to_groups(
     codes: Union["sdmx.model.common.Codelist", Iterable["sdmx.model.common.Code"]],
     dim: Optional[str] = None,
-) -> Mapping[str, Mapping[str, List[str]]]:
+) -> Mapping[str, Mapping[str, list[str]]]:
     """Convert `codes` into a mapping from parent items to their children.
 
     The returned value is suitable for use with :func:`~.operator.aggregate`.
@@ -74,7 +74,7 @@ def dataset_to_quantity(ds: "sdmx.model.common.BaseDataSet") -> Quantity:
           of `ds`, if any.
     """
     # Assemble attributes
-    attrs: Dict[str, str] = {}
+    attrs: dict[str, str] = {}
     if ds.described_by:  # pragma: no cover
         attrs.update(dataflow_urn=util.urn(ds.described_by))
     if ds.structured_by:
@@ -139,7 +139,7 @@ def quantity_to_dataset(
         series_dims = list(dims[:od_index] + dims[od_index + 1 :])
         grouped: Iterable = qty.to_series().groupby(series_dims)
         # For as_obs()
-        obs_dims: Tuple[Hashable, ...] = (od.id,)
+        obs_dims: tuple[Hashable, ...] = (od.id,)
         key_slice = slice(od_index, od_index + 1)
     else:
         # Pseudo-groupby object

genno/compat/sdmx/util.py

@@ -1,4 +1,4 @@
-from typing import Optional, Tuple, Type, Union
+from typing import Optional, Union
 
 import sdmx
 
@@ -29,10 +29,10 @@ def urn(obj: "sdmx.model.common.MaintainableArtefact") -> str:
 
 def handle_version(
     version: Union["sdmx.format.Version", str, None],
-) -> Tuple[
+) -> tuple[
     "sdmx.format.Version",
-    Type["sdmx.model.common.BaseDataSet"],
-    Type["sdmx.model.common.BaseObservation"],
+    type["sdmx.model.common.BaseDataSet"],
+    type["sdmx.model.common.BaseObservation"],
 ]:
     """Handle `version` arguments for :mod:`.sdmx.operator`.
 

genno/compat/xarray.py

@@ -11,7 +11,6 @@
     Optional,
     Protocol,
     Sequence,
-    Tuple,
     TypeVar,
     Union,
 )
@@ -74,11 +73,11 @@ def coords(self) -> xarray.core.coordinates.DataArrayCoordinates: ...
 
     @property
     @abstractmethod
-    def dims(self) -> Tuple[Hashable, ...]: ...
+    def dims(self) -> tuple[Hashable, ...]: ...
 
     @property
     @abstractmethod
-    def shape(self) -> Tuple[int, ...]: ...
+    def shape(self) -> tuple[int, ...]: ...
 
     @property
     @abstractmethod
@@ -204,7 +203,7 @@ def min(
     @abstractmethod
     def pipe(
         self,
-        func: Union[Callable[..., T], Tuple[Callable[..., T], str]],
+        func: Union[Callable[..., T], tuple[Callable[..., T], str]],
         *args: Any,
         **kwargs: Any,
     ): ...

genno/config.py

@@ -6,16 +6,11 @@
 from typing import (
     Any,
     Callable,
-    Dict,
     Iterable,
-    List,
     Mapping,
     MutableMapping,
     Optional,
     Sequence,
-    Set,
-    Tuple,
-    Type,
     Union,
 )
 from warnings import warn
@@ -29,7 +24,7 @@
 log = logging.getLogger(__name__)
 
 #: Registry of configuration section handlers.
-HANDLERS: Dict[str, "ConfigHandler"] = {}
+HANDLERS: dict[str, "ConfigHandler"] = {}
 
 #: .. deprecated:: 1.25.0
 #:    Instead, use:
@@ -41,7 +36,7 @@
 #:       handles("section_name", False, False)(store)
 #:
 #: Configuration sections/keys to be stored with no action.
-STORE: Set[str] = set()
+STORE: set[str] = set()
 
 
 def configure(path: Optional[Union[Path, str]] = None, **config):
@@ -182,7 +177,7 @@ def parse_config(
     data = PathHandler().handle(data, c)
 
     # Assemble a queue of (args, kwargs) for Computer.add_queue()
-    queue: List[Tuple[Tuple, Dict]] = []
+    queue: list[tuple[tuple, dict]] = []
 
     # Sections to discard, e.g. with handler._store = False
     discard = set()
@@ -341,7 +336,7 @@ def general(c: Computer, info):
             # log.debug(f"Inferred dimensions ({', '.join(key.dims)}) for '*'")
 
         # If info["comp"] is None, the task is a list that collects other keys
-        _seq: Type = list
+        _seq: type = list
         task = []
 
         if info["comp"] is not None:

genno/core/attrseries.py

@@ -10,7 +10,6 @@
     Mapping,
     Optional,
     Sequence,
-    Tuple,
     Union,
     cast,
 )
@@ -249,13 +248,13 @@ def data(self):
         return self.values
 
     @property
-    def dims(self) -> Tuple[Hashable, ...]:
+    def dims(self) -> tuple[Hashable, ...]:
         """Like :attr:`xarray.DataArray.dims`."""
         # If 0-D, the single dimension has name `None` → discard
         return tuple(filter(None, self.index.names))
 
     @property
-    def shape(self) -> Tuple[int, ...]:
+    def shape(self) -> tuple[int, ...]:
         """Like :attr:`xarray.DataArray.shape`."""
         idx = self.index.remove_unused_levels()
         return tuple(len(idx.levels[i]) for i in map(idx.names.index, self.dims))
@@ -294,7 +293,10 @@ def drop_vars(
         return self.droplevel(names)
 
     def expand_dims(self, dim=None, axis=None, **dim_kwargs: Any) -> "AttrSeries":
-        """Like :meth:`xarray.DataArray.expand_dims`."""
+        """Like :meth:`xarray.DataArray.expand_dims`.
+
+        .. todo:: Support passing a mapping of length > 1 to `dim`.
+        """
         if isinstance(dim, list):
             dim = dict.fromkeys(dim, [])
         dim = either_dict_or_kwargs(dim, dim_kwargs, "expand_dims")
@@ -620,7 +622,7 @@ def xindexes(self):  # pragma: no cover
     # Internal methods
     def align_levels(
         self, other: "AttrSeries"
-    ) -> Tuple[Sequence[Hashable], "AttrSeries"]:
+    ) -> tuple[Sequence[Hashable], "AttrSeries"]:
         """Return a copy of `self` with ≥1 dimension(s) in the same order as `other`.
 
         Work-around for https://github.com/pandas-dev/pandas/issues/25760 and other