chore: Migrate to numpy 2.x, pydantic 2.13, and target Python 3.12-3.14#143
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Bumps the actions group with 2 updates: [actions/upload-artifact](https://github.com/actions/upload-artifact) and [actions/download-artifact](https://github.com/actions/download-artifact). Updates `actions/upload-artifact` from 6 to 7 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](actions/upload-artifact@v6...v7) Updates `actions/download-artifact` from 7 to 8 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](actions/download-artifact@v7...v8) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-version: '7' dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: actions/download-artifact dependency-version: '8' dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions ... Signed-off-by: dependabot[bot] <support@github.com>
updates: - [github.com/abravalheri/validate-pyproject: v0.24.1 → v0.25](abravalheri/validate-pyproject@v0.24.1...v0.25) - [github.com/adhtruong/mirrors-typos: v1.41.0 → v1.47.0](adhtruong/mirrors-typos@v1.41.0...v1.47.0) - [github.com/astral-sh/ruff-pre-commit: v0.14.10 → v0.15.15](astral-sh/ruff-pre-commit@v0.14.10...v0.15.15) - [github.com/pre-commit/mirrors-mypy: v1.19.1 → v2.1.0](pre-commit/mirrors-mypy@v1.19.1...v2.1.0)
numpy 2.x compatibility: - _simple_psf: cast 0-d xarray bounds to float before np.linspace (numpy>=2 __array_wrap__ rewraps into a mismatched Variable) - fft/convolve: accept (and ignore) the `xp` arg scipy>=1.15 added to _apply_conv_mode - _data_array/simulation: coerce jax arrays to contiguous numpy before zarr write (numcodecs uses np.array(copy=False), strict on numpy>=2) - spectrum: np.trapz -> np.trapezoid (removed in numpy 2.0) - mypy-under-numpy-2 cleanups; ignore xarray's import-time timedelta warning pydantic 2.13: - space: convert deprecated classmethod-style model_validator(mode="after") to an instance method Python 3.12-3.14: - requires-python >=3.12; CI matrix -> 3.12/3.13/3.14; classifiers updated - drop dm-tree (replace its sole tree.map_structure use in vendored xarray_jax with a local helper, mirroring upstream) - per-python min pins for compiled deps (numpy/scipy/tensorstore/pydantic/ matplotlib) reflecting first cp31x wheels; pyopengl-accelerate gated <3.14 - test_docs: give exec() a shared namespace (PEP 667 ended locals leak on 3.13) - skip matplotlib plotting on 3.14 (upstream ax.plot deepcopy recursion) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #143 +/- ##
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+ Coverage 83.57% 83.66% +0.08%
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Files 47 47
Lines 3026 3036 +10
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+ Hits 2529 2540 +11
+ Misses 497 496 -1 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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- Added a constraint for pillow to require version >=11.3.0 for Python 3.14 and above in pyproject.toml. - Updated uv.lock to reflect the new pillow versioning, including separate entries for versions 11.2.1 and 12.2.0 based on Python version. - Modified _client.py to handle HTTPError properly when fetching Supabase URL and key.
- uv.lock: full upgrade so transitive deps (pandas, etc.) move to versions shipping cp314 wheels (old pins source-built and failed on linux/windows 3.14) - pyproject: ignore ResourceWarning / PytestUnraisableExceptionWarning — py3.14's GC surfaces unclosed sockets from third-party network clients (supabase/s3fs) as fatal warnings under filterwarnings=error - tests/_util: close the internet-check socket (another leaked-socket source) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…nned 0.45.3) The full lock upgrade bumped griffe-fieldz to 0.5.0, which imports DocstringAttribute from griffe (only in newer griffe), breaking the strict mkdocs build. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
supabase>=2.31 passes now-deprecated timeout/verify/proxy params to its postgrest client, which filterwarnings=error promoted to fatal errors in every COSEM test (the query itself works fine outside pytest). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Hypothesis: coverage's C tracer exits non-zero at interpreter teardown on Windows with the bumped C-extensions (jax/torch/tensorstore), despite all tests passing. sys.monitoring avoids the C tracer. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…zeEx culprit on Windows
The culprit was identified as tensorstore's S3/HTTP transport crashing at interpreter shutdown on Windows (google/tensorstore#275), now handled by the version pin + matrix exclude. The diagnostic backend-import step is no longer needed. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
tlambert03
commented
Jun 23, 2026
Surfaced by the mypy/ruff pre-commit bumps from #136 now that the project targets Python 3.12+. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…ert03/microsim into numpy2-py312-modernization
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Closes #133
Closes #136
Closes #137
numpy 2.x compatibility:
xparg scipy>=1.15 added to _apply_conv_modepydantic 2.13:
Python 3.12-3.14: