Relax Dask, Sphinx and stale dependency pins

.github/workflows/build.yml

@@ -60,9 +60,9 @@ jobs:
       - name: Install dependencies
         run: |
           uv sync --locked --all-extras --group test --no-default-groups --python 3.12
-      - name: Install minimum supported Xarray and SciPy
+      - name: Install minimum supported Xarray, SciPy and Dask
         run: |
-          uv pip install --python .venv 'xarray==2026.9.0' 'scipy==1.16.2'
+          uv pip install --python .venv 'xarray==2026.9.0' 'scipy==1.16.2' 'dask[array,dataframe]==2025.2.0'
       - name: Run tests
         run: |
           uv run --no-sync pytest

.github/workflows/check-docs.yml

@@ -33,9 +33,6 @@ jobs:
         sudo apt update -y
         sudo apt install graphviz  # Needed for documentation
         uv sync --locked --all-extras --group docs --group lint --no-default-groups --python "${{ matrix.python-version }}"
-        # Use newer Dask for task-graph rendering with NumPy 2.
-        uv pip uninstall --python .venv dask-expr
-        uv pip install --python .venv 'dask==2026.8.0'
     - name: Run pre-commit
       run: uv run --no-sync pre-commit run --all-files
     - name: Check for Sphinx doc warnings

.github/workflows/docs.yml

@@ -27,9 +27,6 @@ jobs:
         sudo apt update -y
         sudo apt install graphviz  # Needed for documentation
         uv sync --locked --all-extras --group docs --no-default-groups --python "3.12"
-        # Use newer Dask for task-graph rendering with NumPy 2.
-        uv pip uninstall --python .venv dask-expr
-        uv pip install --python .venv 'dask==2026.8.0'
     - name: Build Sphinx documentation
       run: |
         make -C docs html SPHINXOPTS="-W --keep-going -n"

docs/changelog.rst

@@ -18,6 +18,7 @@ Breaking changes
   Require SciPy >= 1.16.2. (:issue:`1360`)
 - Require Zarr Python >= 3 and Xarray >= 2026.9.0. The default on-disk Zarr
   format remains 2. (:issue:`1355`)
+- Require Dask >= 2025.2.0 and remove the upper bound on Dask. (:issue:`1267`)
 - **Remove BGEN reading and conversion**: ``sgkit.io.bgen.read_bgen``,
   ``sgkit.io.bgen.bgen_to_zarr`` and ``sgkit.io.bgen.rechunk_bgen``, along with
   the ``bgen`` extra and the cbgen and rechunker dependencies.
@@ -67,6 +68,8 @@ Bug fixes
 - Fixed bug causing high memory usage in :func:`pedigree_kinship` when
   evaluating a chunked relationship matrix with the Hamilton-Kerr method.
   (:user:`timothymillar`, :pr:`1335`, :issue:`1333`)
+- :func:`Tajimas_D` now works with newer versions of Dask, and no longer
+  computes allele counts when it is called.
 
 .. Documentation
 .. ~~~~~~~~~~~~~

docs/conf.py

@@ -117,10 +117,12 @@ def filter(self, record: pylogging.LogRecord) -> bool:
 
 autosummary_generate = True
 
+# sphinx-autodoc-typehints refers to Zarr's StoreLike type alias as
+# zarr.core.group.StoreLike, but Zarr documents it as zarr.storage.StoreLike.
+qualname_overrides = {"zarr.core.group.StoreLike": "zarr.storage.StoreLike"}
+
 nitpick_ignore = [
     ("py:class", "sgkit.display.GenotypeDisplay"),
-    # Zarr's StoreLike alias is rendered as an undocumented TypeAliasType.
-    ("py:class", "zarr.storage._common.TypeAliasType"),
 ]
 
 

docs/contributing.rst

@@ -270,21 +270,13 @@ and API documentation.
 Building the documentation requires the Graphviz ``dot`` executable, which you
 can install by following `these instructions <https://graphviz.org/download/#executable-packages>`_.
 
-Documentation builds use the same ``.venv`` as development. Task-graph
-visualization with NumPy 2 needs a newer Dask than the current runtime bound.
-From the repository root, on macOS or Linux, prepare the environment and build
-with ``make``::
+Documentation builds use the same ``.venv`` as development. From the repository
+root, on macOS or Linux, prepare the environment and build with ``make``::
 
    uv sync --locked
-   uv pip uninstall --python .venv dask-expr
-   uv pip install --python .venv 'dask==2026.8.0'
    cd docs
    make html
 
-The old ``dask-expr`` package is removed because it pins the runtime Dask version.
-The Makefile uses ``uv run --no-sync`` to preserve the Dask override during builds.
-Docs CI applies the same override.
-
 The resulting HTML files are in ``_build/html``. After editing documentation,
 run ``make html`` again.
 
@@ -293,10 +285,6 @@ locally with::
 
    make clean html SPHINXOPTS="-W --keep-going -n"
 
-Before running tests, restore the locked development dependencies with
-``uv sync --locked`` from the repository root. Repeat the Dask setup above when
-you next build the documentation.
-
 .. _Sphinx: https://www.sphinx-doc.org/
 
 Review process

pyproject.toml

@@ -24,11 +24,11 @@ dependencies = [
   "numpy >= 2.3.5; sys_platform == \"darwin\"", # Apple ARM chip error
   "numpy >= 2.0; sys_platform != \"darwin\"",
   "xarray >= 2026.9.0",
-  "dask[array,dataframe] >= 2022.01.0, <= 2024.8.0",
+  "dask[array,dataframe] >= 2025.2.0",
   "scipy >= 1.16.2",
   "zarr >= 3",
   "numba",
-  "fsspec != 2021.6.*",
+  "fsspec",
   "scikit-learn",
   "pandas < 3.0",
 ]
@@ -64,14 +64,14 @@ docs = [
   "graphviz",
   "myst_nb",
   "pydata-sphinx-theme",
-  "sphinx < 9.0.0",
+  "sphinx",
   "sphinx_autodoc_typehints",
   "sphinx-copybutton",
   "scanpydoc",
   "ipython",
   "matplotlib",
   "seaborn",
-  "ablog!=0.10.27",
+  "ablog",
   "pickleshare",
 ]
 lint = [

sgkit/stats/popgen.py

@@ -361,6 +361,11 @@ def Fst(
     return conditional_merge_datasets(ds, new_ds, merge)
 
 
+def _harmonic_sum(n: np.ndarray, power: int) -> np.ndarray:
+    # sum of 1 / k**power for k = 1, ..., n - 1
+    return np.asarray((1 / np.arange(1, n) ** power).sum())
+
+
 def Tajimas_D(
     ds: Dataset,
     *,
@@ -470,8 +475,9 @@ def Tajimas_D(
     #       because the computation below requires floats
     n = ac.sum(axis=1, dtype="float").max()
 
-    # (n-1)th harmonic number
-    a1 = (1 / da.arange(1, n)).sum()
+    # (n-1)th harmonic number. n is a lazy scalar, so compute the sum
+    # blockwise rather than passing it to da.arange as a stop value.
+    a1 = da.map_blocks(_harmonic_sum, n, 1, dtype=np.float64)
 
     # calculate Watterson's theta (absolute value)
     theta = S / a1
@@ -484,7 +490,7 @@ def Tajimas_D(
     d = div - theta[:, np.newaxis]
 
     # calculate the denominator (standard deviation)
-    a2 = (1 / (da.arange(1, n) ** 2)).sum()
+    a2 = da.map_blocks(_harmonic_sum, n, 2, dtype=np.float64)
     b1 = (n + 1) / (3 * (n - 1))
     b2 = 2 * (n**2 + n + 3) / (9 * n * (n - 1))
     c1 = b1 - (1 / a1)

sgkit/stats/truncated_svd.py

@@ -159,9 +159,10 @@ def fit_transform(self, X, y=None):
             )
         if self.algorithm == "tsqr":
             if has_keyword(da.linalg.svd, "full_matrices"):
-                u, s, v = da.linalg.svd(X, full_matrices=False)  # pragma: no cover
+                u, s, v = da.linalg.svd(X, full_matrices=False)
             else:
-                u, s, v = da.linalg.svd(X)
+                # Dask versions before 2026.3.0 have no full_matrices argument
+                u, s, v = da.linalg.svd(X)  # pragma: no cover
             u = u[:, : self.n_components]
             s = s[: self.n_components]
             v = v[: self.n_components]