chore: Migrate to numpy 2.x, pydantic 2.13, and target Python 3.12-3.14

.github/workflows/ci.yml

@@ -28,8 +28,15 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.12", "3.13", "3.14"]
         min: [""]
+        exclude:
+          # tensorstore has no clean cp314 Windows wheel: the first one (0.1.79)
+          # and everything >=0.1.77 crash at interpreter shutdown on Windows
+          # (google/tensorstore#275), and there's no earlier cp314 wheel to pin
+          # to. Drop this leg until tensorstore ships a fix.
+          - os: windows-latest
+            python-version: "3.14"
         include:
           - os: ubuntu-latest
             python-version: "3.12"
@@ -51,7 +58,7 @@ jobs:
 
       - run: uv run coverage run -p -m pytest --color=yes -v
 
-      - uses: actions/upload-artifact@v6
+      - uses: actions/upload-artifact@v7
         with:
           name: covreport-${{ matrix.os }}-py${{ matrix.python-version }}-${{ matrix.min }}
           path: ./.coverage*
@@ -82,7 +89,7 @@ jobs:
       contents: write
     steps:
       - name: Download built artifact to dist/
-        uses: actions/download-artifact@v7
+        uses: actions/download-artifact@v8
         with:
           name: Packages
           path: dist

.pre-commit-config.yaml

@@ -5,29 +5,29 @@ ci:
 
 repos:
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.24.1
+    rev: v0.25
     hooks:
       - id: validate-pyproject
 
   - repo: https://github.com/adhtruong/mirrors-typos
-    rev: v1.41.0
+    rev: v1.47.2
     hooks:
       - id: typos
         args: [--force-exclude]  # omitting --write-changes
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.10
+    rev: v0.15.19
     hooks:
       - id: ruff-check
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.19.1
+    rev: v2.1.0
     hooks:
       - id: mypy
         files: "^src/"
         additional_dependencies:
-          - numpy<2.0
+          - numpy
           - pydantic
           - pydantic-settings
           - xarray

pyproject.toml

@@ -17,28 +17,40 @@ name = "microsim"
 dynamic = ["version"]
 description = "Light microscopy simulation in python"
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.12"
 license = { text = "BSD-3-Clause" }
 authors = [{ name = "Talley Lambert", email = "talley.lambert@gmail.com" }]
 classifiers = [
     "Development Status :: 2 - Pre-Alpha",
     "License :: OSI Approved :: BSD License",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Typing :: Typed",
 ]
 dependencies = [
     "annotated-types >=0.7.0",
-    "numpy >=1.26,<2.0",             # something still breaks with 2+
+    # min pins per-python reflect the first release shipping a wheel for that
+    # interpreter (newer pythons need newer compiled deps).
+    "numpy >=2.3.2; python_version >= '3.14'",
+    "numpy >=2.1.0; python_version >= '3.13'",
+    "numpy >=2.0",
     "pint >=0.23",
     "platformdirs >=4.3.6",
+    "pydantic >=2.12; python_version >= '3.14'",
     "pydantic >=2.8",
     "fpbase",
     "pydantic-settings >2.5.0",
+    "scipy >=1.16.1; python_version >= '3.14'",
     "scipy >=1.15.2",
-    "tensorstore >=0.1.70,!=0.1.72",
+    # tensorstore >=0.1.77 crashes at interpreter shutdown on Windows when the
+    # S3/HTTP transport has been used (google/tensorstore#275). Pin below it on
+    # Windows where a clean wheel exists (no cp314 wheel before 0.1.79, so
+    # py3.14 can't be pinned and is unaffected by this cap).
+    "tensorstore <0.1.77; sys_platform == 'win32' and python_version < '3.14'",
+    "tensorstore >=0.1.79; python_version >= '3.14'",
+    "tensorstore >=0.1.76",
     "tqdm >=4.67.1",
     "xarray >=2024.1.0",
     "zarr >=2.17,<3.0",
@@ -50,7 +62,13 @@ repository = "https://github.com/tlambert03/microsim"
 
 # # https://peps.python.org/pep-0621/#dependencies-optional-dependencies
 [project.optional-dependencies]
-view = ["ndv[pyqt,vispy]", "matplotlib>=3.10.1", "pyopengl-accelerate"]
+view = [
+    "ndv[pyqt,vispy]",
+    "matplotlib>=3.10.5; python_version >= '3.14'",
+    "matplotlib>=3.10.1",
+    # optional OpenGL speedup; no cp314 wheel and fails to build from source
+    "pyopengl-accelerate>=3.1.9; python_version < '3.14'",
+]
 io = ["tifffile>=2025.2.18", "imageio[ffmpeg]>=2.22"]
 cosem = [
     "dask>=2024.1.0",
@@ -61,26 +79,22 @@ cosem = [
     "xarray-datatree>=0.0.14",
 ]
 torch = ["torch>=2.6.0", "torchaudio>=2.7.0"]
-jax = [
-    "jax[cpu]>=0.5.2",
-    "dm-tree ==0.1.8; sys_platform == 'darwin'",
-    "dm-tree >=0.1.7",
-]
+jax = ["jax[cpu]>=0.5.2"]
 all = ["microsim[view,io,cosem]", "rich>=13"]
 
 [dependency-groups]
 test = ["pytest>=8.3.5", "pytest-cov>=6.0.0"]
 dev = [
     { include-group = "test" },
     "microsim[all,jax,torch]",
-    "boto3-stubs[s3]",
-    "ipython",
-    "mypy",
     "pdbpp; sys_platform == 'darwin'",
-    "pre-commit-uv",
-    "rich",
-    "ruff",
-    "types-tqdm",
+    "prek>=0.4.5",
+    "rich>=15.0.0",
+    "ruff>=0.15.18",
+    "types-tqdm>=4.68.0.20260608",
+    "mypy>=2.1.0",
+    "ipython>=9.14.1",
+    "boto3-stubs[s3]>=1.43.34",
 ]
 docs = [
     "mkdocs >=1.5.3",
@@ -90,15 +104,20 @@ docs = [
     "mkdocstrings-python ==1.9.2",
     "mkdocs-jupyter==0.24.8",
     "griffe==0.45.3",
-    "griffe-fieldz",
+    "griffe-fieldz==0.1.2",  # 0.5.0 needs a newer griffe than the pin above
 ]
 
+[tool.uv]
+# pillow (transitive via matplotlib/imageio) only ships cp314 wheels from 11.3.0
+constraint-dependencies = ["pillow>=11.3.0; python_version >= '3.14'"]
+
 [tool.uv.sources]
 microsim = { workspace = true }
 
 
 [tool.ruff]
 line-length = 88
+target-version = "py312"
 src = ["src"]
 fix = true
 unsafe-fixes = true
@@ -167,6 +186,14 @@ filterwarnings = [
     "ignore:unclosed transport:ResourceWarning",                     # only on py3.10... not sure why
     "ignore:Clipping negative intensity values:UserWarning",         # when importing FPbase spectra
     "ignore:__array__ implementation doesn't accept a copy keyword",
+    # xarray triggers this numpy>=2.4 deprecation at import time (xarray/core/dtypes.py)
+    "ignore:The 'generic' unit for NumPy timedelta is deprecated:DeprecationWarning",
+    # py3.14's GC surfaces unclosed sockets/responses from third-party network
+    # clients (supabase/s3fs/urllib) as fatal unraisable ResourceWarnings.
+    "ignore::ResourceWarning",
+    "ignore::pytest.PytestUnraisableExceptionWarning",
+    # supabase>=2.31 passes now-deprecated params (timeout/verify/proxy) to postgrest
+    "ignore:The '.*' parameter is deprecated:DeprecationWarning",
 ]
 
 # https://coverage.readthedocs.io/en/6.4/config.html

src/microsim/_data_array.py

@@ -3,14 +3,14 @@
 from collections.abc import Mapping, Sequence
 from typing import TYPE_CHECKING, Any, Protocol, cast, runtime_checkable
 
+import numpy as np
 import xarray
 from pydantic import BaseModel
 
 if TYPE_CHECKING:
     from collections.abc import Hashable, Iterable, Mapping, Sequence
     from pathlib import Path
 
-    import numpy as np
     import numpy.typing as npt
 
     from microsim.schema.backend import NumpyAPI
@@ -82,6 +82,9 @@ def to_cache(da: xrDataArray, path: Path, dtype: npt.DTypeLike | None = None) ->
     da.attrs = _serializable_attrs(da.attrs)
     if hasattr(da.data, "get"):
         da.data = da.data.get()
+    # coerce to a contiguous numpy array: numcodecs calls np.array(..., copy=False),
+    # which raises on numpy>=2 for non-contiguous or non-numpy (e.g. jax) buffers.
+    da.data = np.ascontiguousarray(da.data)
     da.to_zarr(path, mode="w")
 
 

src/microsim/cosem/_client.py

@@ -5,7 +5,7 @@
 import os
 import urllib.response
 from contextlib import suppress
-from urllib.error import URLError
+from urllib.error import HTTPError, URLError
 
 try:
     import boto3
@@ -26,7 +26,7 @@
 from functools import cache
 from pathlib import Path
 from types import MappingProxyType
-from typing import TYPE_CHECKING, Any, TypeVar, get_args
+from typing import TYPE_CHECKING, Any, get_args
 
 import tqdm
 from pydantic import BaseModel
@@ -107,7 +107,12 @@ def _guess_cosem_url_key() -> tuple[str, str]:
                     url = js_text.split("SUPABASE_URL:")[1].split(",")[0].strip("\"'")
                     key = js_text.split("SUPABASE_KEY:")[1].split(",")[0].strip("\"'")
                     return url, key
-            except URLError:
+            except URLError as e:
+                # HTTPError (raised by urlopen on e.g. a 404) is a file-like
+                # object holding an open socket; close it so it isn't reclaimed
+                # later as a ResourceWarning (fatal under filterwarnings=error).
+                if isinstance(e, HTTPError):
+                    e.close()
                 continue
     except Exception as e:
         raise ValueError(f"Failed to fetch Supabase URL and key: {e}") from e
@@ -203,10 +208,7 @@ def _collect_fields(model: type[BaseModel]) -> Iterator[str | tuple]:
             yield field
 
 
-T = TypeVar("T", bound=BaseModel)
-
-
-def fetch_all(type_: type[T]) -> tuple[T, ...]:
+def fetch_all[T: BaseModel](type_: type[T]) -> tuple[T, ...]:
     table_name = type_.__name__.lower().replace("cosem", "")
     query = model_query(type_)
     try:

src/microsim/fft/convolve.py

@@ -7,8 +7,10 @@
 
 
 @no_type_check
-def _apply_conv_mode_no_copy(ret, s1, s2, mode, axes):
-    # same as scipy.signal._signaltools._apply_conv_mode but without the .copy() call
+def _apply_conv_mode_no_copy(ret, s1, s2, mode, axes, xp=None):
+    # same as scipy.signal._signaltools._apply_conv_mode but without the copy.
+    # `xp` is accepted (and ignored) for compatibility with scipy >=1.15, which
+    # added an array-namespace argument and copies via `xp_copy(..., xp=xp)`.
     if mode == "full":
         return ret
     elif mode == "same":

src/microsim/illum/_sim.py

@@ -54,7 +54,7 @@ def axial_sim_plane(
         wvl: float = 0.488,
     ) -> np.ndarray:
         """Return single axial SIM illumination plane."""
-        return structillum_2d(  # type: ignore [no-any-return]
+        return structillum_2d(
             nz=nz + 1,
             nx=nx,
             dz=dz,

src/microsim/schema/_validators.py

@@ -14,7 +14,7 @@
 
 def validate_np_dtype(x: Any) -> np.dtype:
     try:
-        return np.dtype(x)
+        return np.dtype(x)  # type: ignore [no-any-return]
     except Exception as e:
         raise ValueError(f"Cannot cast {x!r} to a numpy dtype: {e}") from e
 

src/microsim/schema/backend.py

@@ -12,16 +12,16 @@
 if TYPE_CHECKING:
     from collections.abc import Sequence
     from types import ModuleType
-    from typing import SupportsIndex, TypeAlias
+    from typing import SupportsIndex
 
     import jax
 
     from microsim._data_array import ArrayProtocol
 
-    _Shape: TypeAlias = tuple[int, ...]
+    type _Shape = tuple[int, ...]
 
     # Anything that can be coerced to a shape tuple
-    _ShapeLike: TypeAlias = SupportsIndex | Sequence[SupportsIndex]
+    type _ShapeLike = SupportsIndex | Sequence[SupportsIndex]
 
 DeviceName = Literal["cpu", "gpu", "auto"]
 BackendName = Literal["numpy", "torch", "jax", "cupy", "auto"]
@@ -93,14 +93,14 @@ def asarray(
         return self.xp.asarray(x, dtype=dtype)
 
     def zeros(
-        self, shape: int | Sequence[int], dtype: npt.DTypeLike = None
+        self, shape: int | Sequence[int], dtype: npt.DTypeLike | None = None
     ) -> npt.NDArray:
         if dtype is None:
             dtype = self.float_dtype
         return self.xp.zeros(shape, dtype=dtype)
 
     def ones(
-        self, shape: int | Sequence[int], dtype: npt.DTypeLike = None
+        self, shape: int | Sequence[int], dtype: npt.DTypeLike | None = None
     ) -> npt.NDArray:
         if dtype is None:
             dtype = self.float_dtype

src/microsim/schema/dimensions.py

@@ -15,7 +15,7 @@
     - here intensity values correspond to gray values (0-255) in the image.
 """
 
-from enum import Enum
+from enum import StrEnum
 from typing import NamedTuple
 
 
@@ -31,7 +31,7 @@ def categorical(self) -> bool:
         return self.category_type is not None
 
 
-class Axis(str, Enum):
+class Axis(StrEnum):
     """Named axes used in microsim."""
 
     X = "x"

src/microsim/schema/modality/_simple_psf.py

@@ -265,7 +265,10 @@ def bin_spectrum(
     # a bin length of at least min_bin_length and at most max_bin_length
     if isinstance(bins, int):
         num_bins = bins
-        w_min, w_max = masked.w.min(), masked.w.max()
+        # cast to float: passing 0-d xarray DataArrays to np.linspace triggers
+        # __array_wrap__ on numpy >=2, which rewraps the result into a Variable
+        # with mismatched dims.
+        w_min, w_max = float(masked.w.min()), float(masked.w.max())
         w_range = w_max - w_min
         bin_length = w_range / num_bins
         if max_bin_length is not None:

src/microsim/schema/simulation.py

@@ -336,6 +336,9 @@ def _write(self, result: xr.DataArray) -> None:
             return
         if hasattr(result.data, "get"):
             result = result.copy(data=result.data.get(), deep=False)
+        # coerce backend arrays (e.g. jax) to a contiguous numpy array; numcodecs
+        # calls np.array(..., copy=False), which raises on numpy>=2 otherwise.
+        result = result.copy(data=np.ascontiguousarray(result.data), deep=False)
         with suppress(Exception):
             try:
                 sim_data = self.model_dump_json()