More dependency pins

.github/workflows/ci.yml

@@ -22,14 +22,14 @@ jobs:
       - run: pipx run check-manifest
 
   test:
-    name: Test ${{ matrix.os }} py${{ matrix.python-version }} ${{ matrix.min }}
+    name: Test ${{ matrix.os }} py${{ matrix.python-version }} ${{ matrix.min }} ${{ matrix.resolution }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
         python-version: ["3.12", "3.13", "3.14"]
-        min: [""]
+        resolution: ["highest"]
         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
@@ -41,6 +41,16 @@ jobs:
           - os: ubuntu-latest
             python-version: "3.12"
             min: "minimal"
+          # test the lowest dependency versions we claim to support
+          - os: ubuntu-latest
+            python-version: "3.12"
+            resolution: "lowest-direct"
+          - os: ubuntu-latest
+            python-version: "3.13"
+            resolution: "lowest-direct"
+          - os: ubuntu-latest
+            python-version: "3.14"
+            resolution: "lowest-direct"
 
     env:
       UV_PYTHON: ${{ matrix.python-version }}
@@ -54,13 +64,13 @@ jobs:
       - if: ${{ matrix.min == 'minimal' }}
         run: uv sync --no-dev --group test
       - if: ${{ matrix.min != 'minimal' }}
-        run: uv sync --no-dev --group test --all-extras
+        run: uv sync --no-dev --group test --all-extras --resolution ${{ matrix.resolution }}
 
       - run: uv run coverage run -p -m pytest --color=yes -v
 
       - uses: actions/upload-artifact@v7
         with:
-          name: covreport-${{ matrix.os }}-py${{ matrix.python-version }}-${{ matrix.min }}
+          name: covreport-${{ matrix.os }}-py${{ matrix.python-version }}-${{ matrix.min }}-${{ matrix.resolution }}
           path: ./.coverage*
           include-hidden-files: true
 

pyproject.toml

@@ -31,16 +31,16 @@ classifiers = [
 ]
 dependencies = [
     "annotated-types >=0.7.0",
-    # min pins per-python reflect the first release shipping a wheel for that
-    # interpreter (newer pythons need newer compiled deps).
+    # min pins per-python reflect the first release shipping a wheel
     "numpy >=2.3.2; python_version >= '3.14'",
     "numpy >=2.1.0; python_version >= '3.13'",
     "numpy >=2.0",
-    "pint >=0.23",
+    "pint >=0.24.4",
     "platformdirs >=4.3.6",
-    "pydantic >=2.12; python_version >= '3.14'",
+    # pydantic 2.12.0/.1 mis-build some models under py3.14 (deferred annotations).
+    "pydantic >=2.12.2; python_version >= '3.14'",
     "pydantic >=2.8",
-    "fpbase",
+    "fpbase >=0.1.2",
     "pydantic-settings >2.5.0",
     "scipy >=1.16.1; python_version >= '3.14'",
     "scipy >=1.15.2",
@@ -52,8 +52,9 @@ dependencies = [
     "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",
+    "xarray >=2025.7.0; python_version >= '3.14'",
+    "xarray >=2025.1.1",
+    "zarr >=3",
 ]
 
 [project.urls]
@@ -64,22 +65,30 @@ repository = "https://github.com/tlambert03/microsim"
 [project.optional-dependencies]
 view = [
     "ndv[pyqt,vispy]",
-    "matplotlib>=3.10.5; python_version >= '3.14'",
-    "matplotlib>=3.10.1",
+    # matplotlib <3.10.7 calls pyparsing's deprecated `oneOf` (warns with
+    # pyparsing >=3.3).
+    "matplotlib>=3.10.7",
     # 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",
     "imageio>=2.22",
     "boto3>=1.32",
-    "supabase>=2.13.0",
+    # supabase <2.17 bundles the deprecated `gotrue` (warns at import; renamed
+    # to supabase_auth in 2.17).
+    "supabase>=2.17.0",
     "s3fs>=0.4.2",
-    "xarray-datatree>=0.0.14",
 ]
-torch = ["torch>=2.6.0", "torchaudio>=2.7.0"]
-jax = ["jax[cpu]>=0.5.2"]
+torch = [
+    # torch/torchaudio only ship cp314 wheels from 2.9.0.
+    "torch>=2.9.0; python_version >= '3.14'",
+    "torchaudio>=2.9.0; python_version >= '3.14'",
+    "torch>=2.6.0",
+    "torchaudio>=2.7.0",
+]
+# jaxlib only ships cp314 wheels from 0.7.1 (jax/jaxlib versions are coupled).
+jax = ["jax[cpu]>=0.7.1; python_version >= '3.14'", "jax[cpu]>=0.5.2"]
 all = ["microsim[view,io,cosem]", "rich>=13"]
 
 [dependency-groups]
@@ -194,6 +203,13 @@ filterwarnings = [
     "ignore::pytest.PytestUnraisableExceptionWarning",
     # supabase>=2.31 passes now-deprecated params (timeout/verify/proxy) to postgrest
     "ignore:The '.*' parameter is deprecated:DeprecationWarning",
+    # zarr v3 (esp. 3.0.x) warns that the string-coord dtype / vlen-utf8 codec
+    # used for channel names isn't in the v3 spec yet; intentional and benign.
+    "ignore:The data type .* does not have a Zarr V3 specification:FutureWarning",
+    "ignore:The \\w+ .* is currently not part in the Zarr format 3 specification:UserWarning",
+    # numcodecs >=0.16.4 (pulled in with older zarr 3.x) deprecates its bundled
+    # crc32c at import time; harmless and outside our control.
+    "ignore:crc32c usage is deprecated:DeprecationWarning",
 ]
 
 # https://coverage.readthedocs.io/en/6.4/config.html

src/microsim/_data_array.py

@@ -62,7 +62,7 @@ def __mul__(self, other: Any) -> ArrayProtocol: ...
 
 
 def from_cache(path: Path, xp: NumpyAPI | None = None) -> xrDataArray:
-    data_set = xarray.open_zarr(path)
+    data_set = xarray.open_zarr(path, consolidated=False)
     # get the first data variable
     first_da = next(iter(data_set.data_vars))
     # xarray.open_zarr uses dask by default.  we may want that eventually
@@ -85,7 +85,9 @@ def to_cache(da: xrDataArray, path: Path, dtype: npt.DTypeLike | None = None) ->
     # 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")
+    # consolidated metadata is not part of the zarr v3 spec (zarr emits a warning);
+    # skip it so reads/writes stay spec-compliant across zarr 2 and 3.
+    da.to_zarr(path, mode="w", consolidated=False)
 
 
 def _serializable_attrs(attrs: Any) -> Any:

src/microsim/cosem/models.py

@@ -24,8 +24,6 @@
 
 if TYPE_CHECKING:
     import numpy as np
-    import xarray as xr
-    from datatree import DataTree
     from tensorstore import TensorStore
 
 # ------------------------ MODELS ------------------------
@@ -172,15 +170,6 @@ def read(
             bin_mode=_bin_mode,
         )
 
-    def read_xarray(self) -> "xr.DataArray | DataTree":
-        """Read image as xarray or DataTree.
-
-        This is less tested and used than `read`.  Let me know if you need it.
-        """
-        from microsim.cosem._xarray import read_xarray
-
-        return read_xarray(self.url)
-
     @property
     def attrs(self) -> dict[str, Any]:
         if not getattr(self, "_attrs", None):

src/microsim/schema/simulation.py

@@ -347,7 +347,9 @@ def _write(self, result: xr.DataArray) -> None:
             result.attrs = {"microsim.Simulation": sim_data}
         result.coords[Axis.C] = [c.name for c in result.coords[Axis.C].values]
         if self.output_path.suffix == ".zarr":
-            result.to_zarr(self.output_path, mode="w")
+            # consolidated metadata is not part of the zarr v3 spec (zarr warns);
+            # skip it so reads/writes stay spec-compliant across zarr 2 and 3.
+            result.to_zarr(self.output_path, mode="w", consolidated=False)
         elif self.output_path.suffix in (".nc",):
             result.to_netcdf(self.output_path)
         elif self.output_path.suffix in (".tif", ".tiff"):