Refactor: replace np.ndarray with npt.NDArray in type hints

.gitignore

@@ -109,3 +109,4 @@ doc/source/quickstart/.ipynb_checkpoints/
 dist
 .python-version
 answer_nosetests.xml
+.venv/

yt/_typing.py

@@ -1,6 +1,7 @@
 from typing import Any, Optional, TypeAlias
 
 import numpy as np
+import numpy.typing as npt
 import unyt as un
 
 FieldDescT = tuple[str, tuple[str, list[str], str | None]]
@@ -12,12 +13,12 @@
 FieldKey = tuple[FieldType, FieldName]
 ImplicitFieldKey = FieldName
 AnyFieldKey = FieldKey | ImplicitFieldKey
-DomainDimensions = tuple[int, ...] | list[int] | np.ndarray
+DomainDimensions = tuple[int, ...] | list[int] | npt.NDArray
 
 ParticleCoordinateTuple = tuple[
     str,  # particle type
-    tuple[np.ndarray, np.ndarray, np.ndarray],  # xyz
-    float | np.ndarray,  # hsml
+    tuple[npt.NDArray, npt.NDArray, npt.NDArray],  # xyz
+    float | npt.NDArray,  # hsml
 ]
 
 # Geometry specific types
@@ -33,5 +34,5 @@
 # np.ndarray[...] syntax is runtime-valid from numpy 1.22, we quote it until our minimal
 # runtime requirement is bumped to, or beyond this version
 
-MaskT = Optional["np.ndarray[Any, np.dtype[np.bool_]]"]
-AlphaT = Optional["np.ndarray[Any, np.dtype[np.float64]]"]
+MaskT = Optional["npt.NDArray[np.bool_]"]
+AlphaT = Optional["npt.NDArray[np.float64]"]

yt/frontends/artio/data_structures.py

@@ -3,6 +3,7 @@
 from collections import defaultdict
 
 import numpy as np
+import numpy.typing as npt
 
 from yt.data_objects.field_data import YTFieldData
 from yt.data_objects.index_subobjects.octree_subset import OctreeSubset
@@ -339,10 +340,10 @@ def _read_fluid_fields(self, fields, dobj, chunk=None):
 
     def _icoords_to_fcoords(
         self,
-        icoords: np.ndarray,
-        ires: np.ndarray,
+        icoords: npt.NDArray,
+        ires: npt.NDArray,
         axes: tuple[int, ...] | None = None,
-    ) -> tuple[np.ndarray, np.ndarray]:
+    ) -> tuple[npt.NDArray, npt.NDArray]:
         """
         Accepts icoords and ires and returns appropriate fcoords and fwidth.
         Mostly useful for cases where we have irregularly spaced or structured

yt/frontends/ramses/hilbert.py

@@ -1,6 +1,7 @@
 from typing import Any, Optional
 
 import numpy as np
+import numpy.typing as npt
 
 from yt.data_objects.selection_objects.region import YTRegion
 from yt.geometry.selection_routines import (
@@ -49,8 +50,8 @@
 
 
 def hilbert3d(
-    ijk: "np.ndarray[Any, np.dtype[np.int64]]", bit_length: int
-) -> "np.ndarray[Any, np.dtype[np.float64]]":
+    ijk: "npt.NDArray[np.int64]", bit_length: int
+) -> "npt.NDArray[np.int64]":
     """Compute the order using Hilbert indexing.
 
     Arguments
@@ -70,11 +71,11 @@ def hilbert3d(
 def get_intersecting_cpus(
     ds,
     region: YTRegion,
-    LE: Optional["np.ndarray[Any, np.dtype[np.float64]]"] = None,
+    LE: Optional["npt.NDArray[np.float64]"] = None,
     dx: float = 1.0,
     dx_cond: float | None = None,
     factor: float = 4.0,
-    bound_keys: Optional["np.ndarray[Any, np.dtype[np.float64]]"] = None,
+    bound_keys: Optional["npt.NDArray[np.float64]"] = None,
 ) -> set[int]:
     """
     Find the subset of CPUs that intersect the bbox in a recursive fashion.
@@ -119,8 +120,8 @@ def get_intersecting_cpus(
 
 def get_cpu_list_cuboid(
     ds,
-    X: "np.ndarray[Any, np.dtype[np.float64]]",
-    bound_keys: "np.ndarray[Any, np.dtype[np.float64]]",
+    X: "npt.NDArray[np.float64]",
+    bound_keys: "npt.NDArray[np.float64]",
 ) -> set[int]:
     """
     Return the list of the CPU intersecting with the cuboid containing the positions.

yt/frontends/ramses/io.py

@@ -3,6 +3,7 @@
 from typing import TYPE_CHECKING, Union
 
 import numpy as np
+import numpy.typing as npt
 from unyt import unyt_array
 
 from yt._maintenance.deprecation import issue_deprecation_warning
@@ -37,7 +38,7 @@ def convert_ramses_ages(ds, conformal_ages):
 
 
 def convert_ramses_conformal_time_to_physical_time(
-    ds, conformal_time: np.ndarray
+    ds, conformal_time: npt.NDArray
 ) -> unyt_array:
     """
     Convert conformal times (as defined in RAMSES) to physical times.
@@ -82,7 +83,7 @@ def _ramses_particle_binary_file_handler(
     subset: "RAMSESDomainSubset",
     fields: list[FieldKey],
     count: int,
-) -> dict[FieldKey, np.ndarray]:
+) -> dict[FieldKey, npt.NDArray]:
     """General file handler for binary file, called by _read_particle_subset
 
     Parameters
@@ -96,7 +97,7 @@ def _ramses_particle_binary_file_handler(
     count: integer
         The number of elements to count
     """
-    tr = {}
+    tr: dict[FieldKey, npt.NDArray] = {}
     ds = subset.domain.ds
     foffsets = particle_handler.field_offsets
     fname = particle_handler.fname
@@ -130,7 +131,7 @@ def _ramses_particle_csv_file_handler(
     subset: "RAMSESDomainSubset",
     fields: list[FieldKey],
     count: int,
-) -> dict[FieldKey, np.ndarray]:
+) -> dict[FieldKey, npt.NDArray]:
     """General file handler for csv file, called by _read_particle_subset
 
     Parameters
@@ -146,7 +147,7 @@ def _ramses_particle_csv_file_handler(
     """
     from yt.utilities.on_demand_imports import _pandas as pd
 
-    tr = {}
+    tr: dict[FieldKey, npt.NDArray] = {}
     ds = subset.domain.ds
     foffsets = particle_handler.field_offsets
     fname = particle_handler.fname

yt/frontends/ramses/particle_handlers.py

@@ -7,6 +7,7 @@
 from typing import TYPE_CHECKING, Any
 
 import numpy as np
+import numpy.typing as npt
 
 from yt._typing import FieldKey
 from yt.config import ytcfg
@@ -71,7 +72,7 @@ class ParticleFileHandler(abc.ABC, HandlerMixin):
     #       assumed to be `self`).
     reader: Callable[
         ["RAMSESDomainSubset", list[FieldKey], int],
-        dict[FieldKey, np.ndarray],
+        dict[FieldKey, npt.NDArray],
     ]
 
     # Name of the config section (if any)
@@ -162,7 +163,7 @@ def header(self) -> dict[str, Any]:
         self.read_header()
         return self._header
 
-    def handle_field(self, field: FieldKey, data_dict: dict[FieldKey, np.ndarray]):
+    def handle_field(self, field: FieldKey, data_dict: dict[FieldKey, npt.NDArray]):
         """
         This function allows custom code to be called to handle special cases,
         such as the particle birth time.
@@ -173,7 +174,7 @@ def handle_field(self, field: FieldKey, data_dict: dict[FieldKey, np.ndarray]):
         ----------
         field : FieldKey
             The field name.
-        data_dict : dict[FieldKey, np.ndarray]
+        data_dict : dict[FieldKey, npt.NDArray]
             A dictionary containing the data.
 
         By default, this function does nothing.
@@ -346,7 +347,7 @@ def birth_file_fname(self):
     def has_birth_file(self):
         return os.path.exists(self.birth_file_fname)
 
-    def handle_field(self, field: FieldKey, data_dict: dict[FieldKey, np.ndarray]):
+    def handle_field(self, field: FieldKey, data_dict: dict[FieldKey, npt.NDArray]):
         _ptype, fname = field
         if not (fname == "particle_birth_time" and self.ds.cosmological_simulation):
             return
@@ -492,7 +493,7 @@ def read_header(self):
         self._field_offsets = field_offsets
         self._field_types = _pfields
 
-    def handle_field(self, field: FieldKey, data_dict: dict[FieldKey, np.ndarray]):
+    def handle_field(self, field: FieldKey, data_dict: dict[FieldKey, npt.NDArray]):
         _ptype, fname = field
         if not (fname == "particle_birth_time" and self.ds.cosmological_simulation):
             return

yt/frontends/rockstar/data_structures.py

@@ -4,6 +4,7 @@
 from typing import Any, Optional
 
 import numpy as np
+import numpy.typing as npt
 
 from yt.data_objects.static_output import ParticleDataset
 from yt.frontends.halo_catalog.data_structures import HaloCatalogFile
@@ -21,7 +22,7 @@ class RockstarBinaryFile(HaloCatalogFile):
     header: dict
     _position_offset: int
     _member_offset: int
-    _Npart: "np.ndarray[Any, np.dtype[np.int64]]"
+    _Npart: "npt.NDArray[np.int64]"
     _ids_halos: list[int]
     _file_size: int
 
@@ -49,7 +50,7 @@ def __init__(self, ds, io, filename, file_id, range):
 
     def _read_member(
         self, ihalo: int
-    ) -> Optional["np.ndarray[Any, np.dtype[np.int64]]"]:
+    ) -> Optional["npt.NDArray[np.int64]"]:
         if ihalo not in self._ids_halos:
             return None
 

yt/frontends/stream/misc.py

@@ -1,12 +1,13 @@
 import numpy as np
+import numpy.typing as npt
 
 from yt._typing import DomainDimensions
 
 
 def _validate_cell_widths(
-    cell_widths: list[np.ndarray],
+    cell_widths: list[npt.NDArray],
     domain_dimensions: DomainDimensions,
-) -> list[np.ndarray]:
+) -> list[npt.NDArray]:
     # check dimensionality
     if (nwids := len(cell_widths)) != (ndims := len(domain_dimensions)):
         raise ValueError(

yt/geometry/coordinates/coordinate_handler.py

@@ -10,6 +10,7 @@
 from yt.funcs import fix_unitary, is_sequence, parse_center_array, validate_width_tuple
 from yt.units.yt_array import YTArray, YTQuantity
 from yt.utilities.exceptions import YTCoordinateNotImplemented, YTInvalidWidthError
+import numpy.typing as npt
 
 
 def _unknown_coord(data):
@@ -158,7 +159,7 @@ def pixelize(
         periodic=True,
         *,
         return_mask: Literal[False],
-    ) -> "np.ndarray[Any, np.dtype[np.float64]]": ...
+    ) -> "npt.NDArray[np.float64]": ...
 
     @overload
     def pixelize(
@@ -173,7 +174,7 @@ def pixelize(
         *,
         return_mask: Literal[True],
     ) -> tuple[
-        "np.ndarray[Any, np.dtype[np.float64]]", "np.ndarray[Any, np.dtype[np.bool_]]"
+        "npt.NDArray[np.float64]", "npt.NDArray[np.bool_]"
     ]: ...
 
     @abc.abstractmethod

yt/geometry/geometry_handler.py

@@ -3,6 +3,7 @@
 import weakref
 
 import numpy as np
+import numpy.typing as npt
 
 from yt._maintenance.deprecation import issue_deprecation_warning
 from yt.config import ytcfg
@@ -51,10 +52,10 @@ def _detect_output_fields(self):
 
     def _icoords_to_fcoords(
         self,
-        icoords: np.ndarray,
-        ires: np.ndarray,
+        icoords: npt.NDArray,
+        ires: npt.NDArray,
         axes: tuple[int, ...] | None = None,
-    ) -> tuple[np.ndarray, np.ndarray]:
+    ) -> tuple[npt.NDArray, npt.NDArray]:
         # What's the use of raising NotImplementedError for this, when it's an
         # abstract base class?  Well, only *some* of the subclasses have it --
         # and for those that *don't*, we should not be calling it -- and since

yt/geometry/grid_geometry_handler.py

@@ -3,6 +3,7 @@
 from collections import defaultdict
 
 import numpy as np
+import numpy.typing as npt
 
 from yt.arraytypes import blankRecordArray
 from yt.config import ytcfg
@@ -447,10 +448,10 @@ def _chunk_io(
 
     def _icoords_to_fcoords(
         self,
-        icoords: np.ndarray,
-        ires: np.ndarray,
+        icoords: npt.NDArray,
+        ires: npt.NDArray,
         axes: tuple[int, ...] | None = None,
-    ) -> tuple[np.ndarray, np.ndarray]:
+    ) -> tuple[npt.NDArray, npt.NDArray]:
         """
         Accepts icoords and ires and returns appropriate fcoords and fwidth.
         Mostly useful for cases where we have irregularly spaced or structured

yt/geometry/oct_geometry_handler.py

@@ -1,4 +1,5 @@
 import numpy as np
+import numpy.typing as npt
 
 from yt.fields.field_detector import FieldDetector
 from yt.geometry.geometry_handler import Index
@@ -119,10 +120,10 @@ def _mesh_sampling_particle_field(data):
 
     def _icoords_to_fcoords(
         self,
-        icoords: np.ndarray,
-        ires: np.ndarray,
+        icoords: npt.NDArray,
+        ires: npt.NDArray,
         axes: tuple[int, ...] | None = None,
-    ) -> tuple[np.ndarray, np.ndarray]:
+    ) -> tuple[npt.NDArray, npt.NDArray]:
         """
         Accepts icoords and ires and returns appropriate fcoords and fwidth.
         Mostly useful for cases where we have irregularly spaced or structured

yt/loaders.py

@@ -15,6 +15,7 @@
 from urllib.parse import urlsplit
 
 import numpy as np
+import numpy.typing as npt
 from more_itertools import always_iterable
 
 from yt._maintenance.deprecation import (
@@ -687,7 +688,7 @@ def load_amr_grids(
 
 
 def load_particles(
-    data: Mapping[AnyFieldKey, np.ndarray | tuple[np.ndarray, str]],
+    data: Mapping[AnyFieldKey, npt.NDArray | tuple[npt.NDArray, str]],
     length_unit=None,
     bbox=None,
     sim_time=None,
@@ -826,7 +827,7 @@ def parse_unit(unit, dimension):
     field_units, data, _ = process_data(data)
     sfh = StreamDictFieldHandler()
 
-    pdata: dict[AnyFieldKey, np.ndarray | tuple[np.ndarray, str]] = {}
+    pdata: dict[AnyFieldKey, npt.NDArray | tuple[npt.NDArray, str]] = {}
     for key in data.keys():
         field: FieldKey
         if not isinstance(key, tuple):
@@ -1816,7 +1817,7 @@ def load_hdf5_file(
     fn: Union[str, "os.PathLike[str]"],
     root_node: str | None = "/",
     fields: list[str] | None = None,
-    bbox: np.ndarray | None = None,
+    bbox: npt.NDArray | None = None,
     nchunks: int = 0,
     dataset_arguments: dict | None = None,
 ):