build(deps): Bump the python group across 1 directory with 16 updates - #296
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#296 (dependabot, 16 packages) fails `quality` and all four `tests-and-type-check` legs. The runtime stack is fine — every leg reports 1111 passed before dying on `uv run ty check`. One package is responsible: ty 0.0.18 -> 0.0.65, which emits 16 diagnostics. Reproduced by running `uvx --from ty==0.0.65 ty check` against main. Fifteen were tooling artifacts. One was a real bug. `SVDynamics` declared `name: str` and `has_explicit_level: bool` as mutable protocol members. Mutable members are invariant, so `RandomWalk.name: Literal["random_walk"]` never actually satisfied the protocol, and `SV_DYNAMICS_REGISTRY: dict[str, type[SVDynamics]]` was unassignable. Declaring them read-only properties makes the members covariant and the narrowing legal. `@runtime_checkable` is unaffected: `isinstance` checks attribute presence, which pydantic fields still provide. Note `Mapping[str, type[SVDynamics]]` does *not* fix this — measured, still 16 diagnostics. Container covariance does not change the element check. The remaining 14 were `invalid-assignment` on lines like with pytest.raises(ValidationError): data.endog = np.zeros((100, 3)) where the assignment *is* the assertion. ty >= 0.0.65 models pydantic frozen semantics and rejects them statically. The rule is now ignored for `tests/**` only; `src/` keeps it, which is what surfaced the protocol bug. Four inline `# ty: ignore[invalid-assignment]` comments in test_sv_spec.py and test_volatility.py are now redundant and removed — they were earlier patches for this same pattern. `_check_finite` used `zip(frame.columns, finite, strict=True)`, which ty could not unpack. Rewritten as a boolean mask over the index: shorter, no suppression needed. Dependabot now groups ty/ruff/prek separately from runtime dependencies. Bundled together, one new lint rule blocks everything else in the PR — #296 stalled numpy 2.4.6's fix for `np.linalg.svd(hermitian=True)` returning non-unitary `vh`, which matters for a library factorising covariances. Verified on both halves of the pinned matrix — ty 0.0.18, 0.0.65 and 0.0.67 all clean, `make check` passes, and the suite passes on py3.11/PyMC 5/ArviZ 0 (1111 passed) and py3.12/PyMC 6/ArviZ 1 (1112 passed).
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Diagnosed: 15 of the 16 Only I verified the fix directly against this branch's @dependabot rebase |
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Correction on my own Sequence is: merge #299 → rebase this again → green. Verified in advance by overlaying this branch's |
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…299) #296 (dependabot, 16 packages) fails `quality` and all four `tests-and-type-check` legs. The runtime stack is fine — every leg reports 1111 passed before dying on `uv run ty check`. One package is responsible: ty 0.0.18 -> 0.0.65, which emits 16 diagnostics. Reproduced by running `uvx --from ty==0.0.65 ty check` against main. Fifteen were tooling artifacts. One was a real bug. `SVDynamics` declared `name: str` and `has_explicit_level: bool` as mutable protocol members. Mutable members are invariant, so `RandomWalk.name: Literal["random_walk"]` never actually satisfied the protocol, and `SV_DYNAMICS_REGISTRY: dict[str, type[SVDynamics]]` was unassignable. Declaring them read-only properties makes the members covariant and the narrowing legal. `@runtime_checkable` is unaffected: `isinstance` checks attribute presence, which pydantic fields still provide. Note `Mapping[str, type[SVDynamics]]` does *not* fix this — measured, still 16 diagnostics. Container covariance does not change the element check. The remaining 14 were `invalid-assignment` on lines like with pytest.raises(ValidationError): data.endog = np.zeros((100, 3)) where the assignment *is* the assertion. ty >= 0.0.65 models pydantic frozen semantics and rejects them statically. The rule is now ignored for `tests/**` only; `src/` keeps it, which is what surfaced the protocol bug. Four inline `# ty: ignore[invalid-assignment]` comments in test_sv_spec.py and test_volatility.py are now redundant and removed — they were earlier patches for this same pattern. `_check_finite` used `zip(frame.columns, finite, strict=True)`, which ty could not unpack. Rewritten as a boolean mask over the index: shorter, no suppression needed. Dependabot now groups ty/ruff/prek separately from runtime dependencies. Bundled together, one new lint rule blocks everything else in the PR — #296 stalled numpy 2.4.6's fix for `np.linalg.svd(hermitian=True)` returning non-unitary `vh`, which matters for a library factorising covariances. Verified on both halves of the pinned matrix — ty 0.0.18, 0.0.65 and 0.0.67 all clean, `make check` passes, and the suite passes on py3.11/PyMC 5/ArviZ 0 (1111 passed) and py3.12/PyMC 6/ArviZ 1 (1112 passed).
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@dependabot rebase |
Bumps the python group with 16 updates in the / directory: | Package | From | To | | --- | --- | --- | | [numpy](https://github.com/numpy/numpy) | `2.4.2` | `2.4.6` | | [pandas](https://github.com/pandas-dev/pandas) | `3.0.1` | `3.0.5` | | [pydantic](https://github.com/pydantic/pydantic) | `2.12.5` | `2.13.4` | | [xarray](https://github.com/pydata/xarray) | `2026.2.0` | `2026.7.0` | | [scipy](https://github.com/scipy/scipy) | `1.17.0` | `1.17.1` | | [pytest](https://github.com/pytest-dev/pytest) | `9.0.2` | `9.1.1` | | [prek](https://github.com/j178/prek) | `0.3.4` | `0.4.12` | | [ty](https://github.com/astral-sh/ty) | `0.0.18` | `0.0.66` | | [pytest-cov](https://github.com/pytest-dev/pytest-cov) | `7.0.0` | `7.1.0` | | [ruff](https://github.com/astral-sh/ruff) | `0.15.2` | `0.16.1` | | [typing-extensions](https://github.com/python/typing_extensions) | `4.15.0` | `4.16.0` | | [ipython](https://github.com/ipython/ipython) | `9.10.0` | `9.16.1` | | [shibuya](https://github.com/lepture/shibuya) | `2026.7.11` | `2026.7.12` | | [ipykernel](https://github.com/ipython/ipykernel) | `7.2.0` | `7.3.0` | | [jupytext](https://github.com/jupytext/jupytext) | `1.19.4` | `1.19.5` | | [sphinx-codeautolink](https://github.com/felix-hilden/sphinx-codeautolink) | `0.18.1` | `0.19.0` | Updates `numpy` from 2.4.2 to 2.4.6 - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](numpy/numpy@v2.4.2...v2.4.6) Updates `pandas` from 3.0.1 to 3.0.5 - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Commits](pandas-dev/pandas@v3.0.1...v3.0.5) Updates `pydantic` from 2.12.5 to 2.13.4 - [Release notes](https://github.com/pydantic/pydantic/releases) - [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md) - [Commits](pydantic/pydantic@v2.12.5...v2.13.4) Updates `xarray` from 2026.2.0 to 2026.7.0 - [Release notes](https://github.com/pydata/xarray/releases) - [Commits](pydata/xarray@v2026.02.0...v2026.07.0) Updates `scipy` from 1.17.0 to 1.17.1 - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](scipy/scipy@v1.17.0...v1.17.1) Updates `pytest` from 9.0.2 to 9.1.1 - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest@9.0.2...9.1.1) Updates `prek` from 0.3.4 to 0.4.12 - [Release notes](https://github.com/j178/prek/releases) - [Changelog](https://github.com/j178/prek/blob/master/CHANGELOG.md) - [Commits](j178/prek@v0.3.4...v0.4.12) Updates `ty` from 0.0.18 to 0.0.66 - [Release notes](https://github.com/astral-sh/ty/releases) - [Changelog](https://github.com/astral-sh/ty/blob/main/CHANGELOG.md) - [Commits](astral-sh/ty@0.0.18...0.0.66) Updates `pytest-cov` from 7.0.0 to 7.1.0 - [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst) - [Commits](pytest-dev/pytest-cov@v7.0.0...v7.1.0) Updates `ruff` from 0.15.2 to 0.16.1 - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](astral-sh/ruff@0.15.2...0.16.1) Updates `typing-extensions` from 4.15.0 to 4.16.0 - [Release notes](https://github.com/python/typing_extensions/releases) - [Changelog](https://github.com/python/typing_extensions/blob/main/CHANGELOG.md) - [Commits](python/typing_extensions@4.15.0...4.16.0) Updates `ipython` from 9.10.0 to 9.16.1 - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@9.10.0...9.16.1) Updates `shibuya` from 2026.7.11 to 2026.7.12 - [Release notes](https://github.com/lepture/shibuya/releases) - [Changelog](https://github.com/lepture/shibuya/blob/main/docs/changelog.rst) - [Commits](lepture/shibuya@2026.7.11...2026.7.12) Updates `ipykernel` from 7.2.0 to 7.3.0 - [Release notes](https://github.com/ipython/ipykernel/releases) - [Changelog](https://github.com/ipython/ipykernel/blob/main/CHANGELOG.md) - [Commits](ipython/ipykernel@v7.2.0...v7.3.0) Updates `jupytext` from 1.19.4 to 1.19.5 - [Release notes](https://github.com/jupytext/jupytext/releases) - [Changelog](https://github.com/jupytext/jupytext/blob/main/CHANGELOG.md) - [Commits](jupytext/jupytext@v1.19.4...v1.19.5) Updates `sphinx-codeautolink` from 0.18.1 to 0.19.0 - [Release notes](https://github.com/felix-hilden/sphinx-codeautolink/releases) - [Commits](felix-hilden/sphinx-codeautolink@v0.18.1...v0.19.0) --- updated-dependencies: - dependency-name: ipykernel dependency-version: 7.3.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python - dependency-name: ipython dependency-version: 9.16.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python - dependency-name: jupytext dependency-version: 1.19.5 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python - dependency-name: numpy dependency-version: 2.4.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python - dependency-name: pandas dependency-version: 3.0.5 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python - dependency-name: prek dependency-version: 0.4.11 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python - dependency-name: pydantic dependency-version: 2.13.4 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python - dependency-name: pytest dependency-version: 9.1.1 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python - dependency-name: pytest-cov dependency-version: 7.1.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python - dependency-name: ruff dependency-version: 0.16.1 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python - dependency-name: scipy dependency-version: 1.17.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python - dependency-name: shibuya dependency-version: 2026.7.12 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python - dependency-name: sphinx-codeautolink dependency-version: 0.19.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python - dependency-name: ty dependency-version: 0.0.65 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python - dependency-name: typing-extensions dependency-version: 4.16.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python - dependency-name: xarray dependency-version: 2026.7.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python ... 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Looks like these dependencies are updatable in another way, so this is no longer needed. |
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #296 +/- ##
=====================================
Coverage 96.1% 96.1%
=====================================
Files 55 55
Lines 3548 3548
Branches 441 441
=====================================
Hits 3410 3410
Misses 102 102
Partials 36 36 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Bumps the python group with 16 updates in the / directory:
2.4.22.4.63.0.13.0.52.12.52.13.42026.2.02026.7.01.17.01.17.19.0.29.1.10.3.40.4.120.0.180.0.667.0.07.1.00.15.20.16.14.15.04.16.09.10.09.16.12026.7.112026.7.127.2.07.3.01.19.41.19.50.18.10.19.0Updates
numpyfrom 2.4.2 to 2.4.6Release notes
Sourced from numpy's releases.
... (truncated)
Commits
b832a09Merge pull request #31462 from charris/prepare-2.4.657cc147REL: Prepare for the NumPy 2.4.6 release0c72b0bMerge pull request #31459 from charris/backport-313479778d26BUG: core: Don't call INCREF/DECREF on descr in NpyStringAcquireAllocator. (#...e0e3876BUG: core: Don't call INCREF/DECREF on descr in NpyStringAcquireAllocator. (#...d1bffebBUG:np.linalg.svd(..., hermitian=True)returns non-unitaryvh(#31347)8d8d7e5Merge pull request #31453 from seberg/issue-31452bddaab7BUG: Fix regression inarr.conj()37a1eccMerge pull request #31444 from charris/begin-2.4.63c0e043MAINT: Prepare 2.4.x for further developmentUpdates
pandasfrom 3.0.1 to 3.0.5Release notes
Sourced from pandas's releases.
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Commits
e68db09RLS: 3.0.50697623Backport PR #66428: DOC: update whatsnew for 3.0.5 (#66430)5d846d0Backport PR #66090 on branch 3.0.x (BLD: exclude numpy 2.5.0 when building wh...bef7a2bBackport PR #66169 on branch 3.0.x (CI: Fix pyarrow-nightly job (stale nightl...8188eb1RLS: 3.0.4 (#66079)bd35f15[3.0.x] BUG: fix CoW issue in eval() (#66072)6195872[backport 3.0.x] BUG: anchor whole alternation in Series.str.match for PyArro...70313beBackport PR #66051 on branch 3.0.x (BUG: fix regression in DataFrame setitem ...57ed3e2[backport 3.0.x] Bump pypa/cibuildwheel from 3.4.1 to 4.1.0 (#65934) (#66026)f9693fc[backport 3.0.x] BUG(pandas 3.0 regression): drop(index=...) doesn't accept N...Updates
pydanticfrom 2.12.5 to 2.13.4Release notes
Sourced from pydantic's releases.
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Changelog
Sourced from pydantic's changelog.
... (truncated)
Commits
cf67d4bFix lintingf0d8a21Prepare release v2.13.45e3fe1dCheck for pydantic tag pattern in CI7f9edccDocument tagging conventionsb46a0c9Adaptpydantic-corelinker flags on macOS50629c8Update to PyPy 7.3.228522ebbPreserveRootModelcore metadataa37f3afAdaptMISSINGsentinel test to work with unreleasedtyping_extensionsver...909259aRemove Logfire example in documentation2c4174cBump libc from 0.2.155 to 0.2.185Updates
xarrayfrom 2026.2.0 to 2026.7.0Release notes
Sourced from xarray's releases.
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Commits
0238035Release notes for v2026.07.0 (#11445)02cd481resolve the sparse errors (#11439)be61a82zarr deprecation: enums becoming string literals (#11438)1e1973bopen an issue even with a missing log file (#11436)718ee3dDOC fix parameter name in CoordinateTransform.reverse docstring (#11433)030c929Adapt test_dataset_math_errors for coming NumPy changes (#11435)b8141f6Address coming pd.infer_freq behavior change (#11434)66e7d83MAINT: remove pandas 2.2 compat (incl. infer_freq) (#11430)1cecceeBump the actions group with 5 updates (#11428)71138a7Fix incorrect parameter name in cumulative() docstrings (#11425)Updates
scipyfrom 1.17.0 to 1.17.1Release notes
Sourced from scipy's releases.
Commits
527eb7fREL: 1.17.1 release commit [wheel build]f11663bMerge pull request #24584 from tylerjereddy/treddy_prep_1.17.12c49e68DOC: PR 24584 revisions400fa15safely convert index dtypes to intc for csgraph and superLU8c70404MAINT: PR 24584 revisions [wheel build]6dda8c1BUG: PR 24584 revisions4a187e5DOC: PR 24584 revisions463ee9fENH: linalg/inv: re-enable overwrite_a for 2D inputs (#24442)df746eeBUG: linalg: restore dtypes in inv, solve, det246bfeeMAINT:optimize: Enable multi-phase init to DIRECTUpdates
pytestfrom 9.0.2 to 9.1.1Release notes
Sourced from pytest's releases.
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Commits
cf470ecPrepare release version 9.1.1e0c8ce6Merge pull request #14625 from pytest-dev/patchback/backports/9.1.x/a07c31a97...1b82d16Merge pull request #14624 from pytest-dev/patchback/backports/9.1.x/b375b79ec...501c4bcMerge pull request #14596 from bluetech/doc-classmethodb61f588Merge pull request #14622 from chrisburr/fix-14608-initial-conftest-test-subdir9a567e0[automated] Update plugin list (#14617) (#14618)ef8b299Merge pull request #14620 from pytest-dev/patchback/backports/9.1.x/680f9f3ed...66abd07Merge pull request #14220 from bysiber/fix-stale-iexp-raisesgroup79fbf93Merge pull request #14612 from pytest-dev/patchback/backports/9.1.x/974ed48b6...0d312ebMerge pull request #14611 from bluetech/parametrize-argvalues-typingUpdates
prekfrom 0.3.4 to 0.4.12Release notes
Sourced from prek's releases.
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Changelog
Sourced from prek's changelog.
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Commits
728238cBump version to 0.4.12 (#2473)e5403caAdd--require-groupfor hook group intersections (#2472)370fc41Use ssl-certs to load custom certificates (#2470)7cc64caRewrite benchmark documentation (#2469)6a81c10Update ubuntu Docker tag to v26 (#2466)500a9d4Run Conda tests sequentially (#2468)ebc1c38Run .NET tests sequentially on Unix (#2467)88fec17Update Rust crate tokio-util to v0.7.19 (#2463)9d9c9f5Use full object IDs in diff snapshots (#2448)0c7fc84Update Rust crate tokio to v1.53.1 (#2462)Updates
tyfrom 0.0.18 to 0.0.66Release notes
Sourced from ty's releases.
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Changelog
Sourced from ty's changelog.
... (truncated)
Commits
3e28e58Bump version to 0.0.66 (#4166)87de836Bump version to 0.0.65 (#4113)d784badREADME: Add link to Stable milestone (#4112)b4c1978Update actions/setup-python action to v7 (#4110)8d216a3Update actions/checkout action to v7.0.1 (#4107)06f44e9Update dependency prek to v0.4.10 (#4108)b3665fdUpdate prek dependencies (#4109)5e64a13Bump version to 0.0.64 (#4097)46f4915Bump version to 0.0.63 (#4071)df75992Bump version to 0.0.62 (#4057)Updates
pytest-covfrom 7.0.0 to 7.1.0Changelog
Sourced from pytest-cov's changelog.
Commits
66c8a52Bump version: 7.0.0 → 7.1.0f707662Make the examples use pypy 3.11.6049a78Make context test use the old ctracer (seems the new sysmon tracer behaves di...8ebf20bUpdate changelog.861d30eRemove the backup context manager - shouldn't be needed since coverage 5.0, ...fd4c956Pass the precision on the nulled total (seems that there's some caching goion...78c9c4eOnly run the 3.9 on older deps.4849a92Punctuation.197c35eUpdate changelog and hopefully I don't forget to publish release again :))14dc1c9Update examples to use 3.11 and make the adhoc layout example look a bit more...Updates
rufffrom 0.15.2 to 0.16.1Release notes
Sourced from ruff's releases.