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chore(deps): bump numpy from 1.26.4 to 2.0.2 [BLOCKED]#463

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chore(deps): bump numpy from 1.26.4 to 2.0.2 [BLOCKED]#463
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Bumps numpy from 1.26.4 to 2.0.2.

Release notes

Sourced from numpy's releases.

NumPy 2.0.2 release (Aug 26, 2024)

NumPy 2.0.2 Release Notes

NumPy 2.0.2 is a maintenance release that fixes bugs and regressions discovered after the 2.0.1 release.

The Python versions supported by this release are 3.9-3.12.

Contributors

A total of 13 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

  • Bruno Oliveira +
  • Charles Harris
  • Chris Sidebottom
  • Christian Heimes +
  • Christopher Sidebottom
  • Mateusz Sokół
  • Matti Picus
  • Nathan Goldbaum
  • Pieter Eendebak
  • Raghuveer Devulapalli
  • Ralf Gommers
  • Sebastian Berg
  • Yair Chuchem +

Pull requests merged

A total of 19 pull requests were merged for this release.

  • #27000: REL: Prepare for the NumPy 2.0.1 release [wheel build]
  • #27001: MAINT: prepare 2.0.x for further development
  • #27021: BUG: cfuncs.py: fix crash when sys.stderr is not available
  • #27022: DOC: Fix migration note for alltrue and sometrue
  • #27061: BUG: use proper input and output descriptor in array_assign_subscript...
  • #27073: BUG: Mirror VQSORT_ENABLED logic in Quicksort
  • #27074: BUG: Bump Highway to latest master
  • #27077: BUG: Off by one in memory overlap check
  • #27122: BUG: Use the new npyv_loadable_stride_ functions for ldexp and...
  • #27126: BUG: Bump Highway to latest
  • #27128: BUG: add missing error handling in public_dtype_api.c
  • #27129: BUG: fix another cast setup in array_assign_subscript
  • #27130: BUG: Fix building NumPy in FIPS mode
  • #27131: BLD: update vendored Meson for cross-compilation patches
  • #27146: MAINT: Scipy openblas 0.3.27.44.4
  • #27151: BUG: Do not accidentally store dtype metadata in np.save
  • #27195: REV: Revert undef I and document it
  • #27213: BUG: Fix NPY_RAVEL_AXIS on backwards compatible NumPy 2 builds
  • #27279: BUG: Fix array_equal for numeric and non-numeric scalar types

... (truncated)

Commits
  • 854252d Merge pull request #27280 from charris/prepare-2.0.2
  • cffa071 REL: Prepare for the NumPy 2.0.2 release [wheel build]
  • 1693029 Merge pull request #27279 from charris/backport-27275
  • da9f9c3 BUG: Fix array_equal for numeric and non-numeric scalar types
  • ee1cf96 Merge pull request #27213 from charris/backport-27202
  • 49dec35 BUG: Fix NPY_RAVEL_AXIS on backwards compatible NumPy 2 builds
  • be56ae2 Merge pull request #27195 from charris/backport-27182
  • 75b039c REV: Revert undef I and document it
  • 428e2ba Merge pull request #27151 from charris/backport-27143
  • 451516d BUG: Do not accidentally store dtype metadata in np.save
  • Additional commits viewable in compare view

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Bumps [numpy](https://github.com/numpy/numpy) from 1.26.4 to 2.0.2.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v1.26.4...v2.0.2)

---
updated-dependencies:
- dependency-name: numpy
  dependency-version: 2.0.2
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot Bot added dependencies Pull requests that update a dependency file python Pull requests that update python code labels Jan 7, 2026
@greptile-apps

greptile-apps Bot commented Jan 7, 2026

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Greptile Summary

Updated numpy from 1.26.4 to 2.0.2, a major version upgrade with breaking changes.

Critical Issues Found:

  • Breaking change: NumPy 2.0 removed deprecated type aliases like np.int_, np.float_, etc. The codebase uses dtype=np.int_ in at least 35+ locations across test files (tests/all_in_one.py, tests/outputhandling/test_output_config.py). These will cause AttributeError at runtime and need to be replaced with np.intp or built-in int.
  • Dependency compatibility: The comment in pyproject.toml:21 states "Pinned < 2.0 by cellmlmanip dependency" but the version is now 2.0.2. This suggests cellmlmanip compatibility should be verified, especially since it's a direct dependency.
  • Numba compatibility: The project heavily uses numba and numba-cuda with numpy arrays. NumPy 2.0 support in Numba was only added in Numba 0.60+. The current pyproject.toml doesn't pin a minimum numba version, which could cause issues.

Testing Required:

  • Verify all tests pass with numpy 2.0.2
  • Check cellmlmanip works with numpy 2.0
  • Ensure numba and numba-cuda versions are compatible with numpy 2.0

Confidence Score: 1/5

  • This PR will likely break the codebase due to numpy 2.0 incompatibilities
  • NumPy 2.0 is a major release with breaking changes. The codebase uses deprecated type aliases (np.int_) in 35+ locations that will cause AttributeError failures. Additionally, the comment about cellmlmanip dependency requiring numpy < 2.0 suggests potential compatibility issues that haven't been addressed. Without evidence of successful test runs or compatibility verification, this upgrade poses significant risk.
  • All files using numpy need attention, particularly tests/all_in_one.py and tests/outputhandling/test_output_config.py which use deprecated np.int_ extensively

Important Files Changed

Filename Overview
pyproject.toml Updated numpy to 2.0.2, but comment still says "Pinned < 2.0 by cellmlmanip dependency" - comment is now inaccurate
ci/requirements.ci.txt Updated numpy to 2.0.2 in CI requirements

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2 files reviewed, 1 comment

Edit Code Review Agent Settings | Greptile

Comment thread pyproject.toml
license-files = ["src/LICEN[CS]E*"]
dependencies = [
"numpy==1.26.4", # Pinned < 2.0 by cellmlmanip dependency
"numpy==2.0.2", # Pinned < 2.0 by cellmlmanip dependency

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style: comment says "Pinned < 2.0 by cellmlmanip dependency" but version is now 2.0.2

Suggested change
"numpy==2.0.2", # Pinned < 2.0 by cellmlmanip dependency
"numpy==2.0.2",
Prompt To Fix With AI
This is a comment left during a code review.
Path: pyproject.toml
Line: 21:21

Comment:
**style:** comment says "Pinned &lt; 2.0 by `cellmlmanip` dependency" but version is now 2.0.2

```suggestion
    "numpy==2.0.2",
```

How can I resolve this? If you propose a fix, please make it concise.

@ccam80 ccam80 changed the title chore(deps): bump numpy from 1.26.4 to 2.0.2 chore(deps): bump numpy from 1.26.4 to 2.0.2 [BLOCKED] Jan 7, 2026
@ccam80

ccam80 commented Jan 7, 2026

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Blocked by #416

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