Prepare for NumPy 2 forward compatibility by natsukium · Pull Request #3420 · DeepLabCut/DeepLabCut

natsukium · 2026-07-20T14:29:28Z

Much of the scientific-Python ecosystem has moved to NumPy 2, so the numpy<2 cap in the core dependencies increasingly conflicts with other packages sharing an environment. This PR does the groundwork for eventually lifting that cap while leaving the cap itself in place: following the review, it is a preparatory step for forward compatibility rather than a switch to NumPy 2.

Each fix is a separate commit, with the details and rationale in its message.

What changes

Replace APIs NumPy 2 removed: np.trapz → np.trapezoid (keeping an np.trapz fallback while NumPy 1 is supported), np.product → np.prod, and np.percentile(interpolation=) → np.percentile(method=). All three raise AttributeError/TypeError on NumPy 2.
Estimate tracklet rank with a dense SVD instead of scipy.linalg.interpolative.svd, which raises "array must not contain infs or NaNs" on finite input under NumPy 2, breaking any stitching that computes tracklet affinities. The replacement is exact and deterministic where the interpolative routine was randomized, and it makes the all-zero guard added in Pins numpy<2, fix svd for scipy>=1.11.0 #2827 redundant.
Compare montblanc assemblies order-independently in the assembler test. The order of equally-scored assemblies within a frame is arbitrary and not fixed by NumPy's sorts; NumPy 2 emits two of them swapped, so the comparison failed although every coordinate matched.
Raise the numpy lower bound to >=1.22.4. method= only exists from NumPy 1.22, and pandas>=2.2 already requires >=1.22.4 on Python 3.10, so nothing that could previously be installed is affected.

The numpy<2 upper bound is unchanged.

Why the cap stays

The imgaug concern raised in review is the blocker, and a hard one: imgaug 0.4.0 fails at import under NumPy 2.

imgaug/imgaug.py:45:  NP_FLOAT_TYPES = set(np.sctypes["float"])
AttributeError: `np.sctypes` was removed in the NumPy 2.0 release.

There has been no imgaug release since 0.4.0 (June 2020), so this will not be fixed upstream, and imgaug is currently a core dependency rather than a TF extra.

Moving imgaug to the TF extras (#3240) is necessary but not sufficient. imgaug declares no numpy upper bound of its own, and neither do all the pinned TensorFlow versions — only TF 2.15–2.17 constrain numpy to <2:

extra	resolved TensorFlow	caps numpy to `<2`?
`tf`	2.15.1 (py≤3.11) / 2.17.1 (py3.12)	yes
`tf-cu11`	2.14	no
`tf-cu12`	2.18	no
`tf-latest`	≥2.18	no
`apple_mchips`	2.14 (py<3.12) / 2.17.1 (py≥3.12)	no / yes

So when the core cap is eventually lifted, numpy<2 should move to the TF extras alongside imgaug. Otherwise [tf-cu11], [tf-cu12] and [tf-latest] installs would pair imgaug with NumPy 2 and fail at import.

The other dependencies raised in review did not reproduce as blockers (checked on NumPy 2.4.6 / Python 3.11):

albumentations 1.4.3 installs and runs under NumPy 2. Every transform used in pose_estimation_pytorch/data/transforms.py works with keypoint and bbox targets, except CoarseDropout (no bbox support) and ElasticTransform (no keypoint support) — albumentations' own limitations, which behave identically on NumPy 1.
filterpy 1.4.5's KalmanFilter, as used by the SORT tracker in core/trackingutils.py, works under NumPy 2.
scipy resolves to a NumPy 2 compatible build. Its >=1.9 floor would need revisiting only if minimum-version installs are targeted, since NumPy 2 support starts at scipy 1.13.

Testing

The core test suite passes identically on NumPy 1.22.4 and NumPy 2.

Running the test suite against NumPy 2 in CI as a non-blocking job would keep this from regressing while the remaining blockers are resolved. Happy to add that here or in a follow-up.

deruyter92

@natsukium, thanks a lot for your recent valuable contributions. These are definitely improving the codebase!

Regarding this PR:
I wouldn't be in favor of removing the upper bound just yet. Instead of directly jumping to full numpy 2 support I would prefer to accept all the improvements in this PR as a preparatory step for forward compatibility.

The reason I foresee issues:

albumentations is currently still pinned at <=1.4.3
Most TF code still depends on imgaug (we could move the upperbound to TF extras to solve this)
compatiblity with other packages like filterpy, scipy need to be verified and bounds adjusted accordingly

If we can leave the upperbound as is for the current PR, I strongly approve of your changes!

deruyter92 · 2026-07-22T10:00:28Z

By the way, would you mind if I push directly to this branch? I might add one or two commits if I spot any remaining cases.
So far, it seems quite complete!

Copilot

Pull request overview

This PR updates DeepLabCut to support NumPy 2.x by lifting the core dependency cap to <3 and applying targeted compatibility fixes for APIs/behaviors that changed or were removed in NumPy 2.

Changes:

Relax numpy dependency from <2 to <3 and raise the lower bound to >=1.22.4.
Update code paths affected by NumPy 2 API changes (e.g., np.percentile(..., method=...), np.prod, np.trapezoid/np.trapz compatibility).
Stabilize a multi-animal assembly test by comparing outputs in an order-independent canonical ordering.

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
`tests/test_inferenceutils.py`	Makes the multi-animal assembly test order-independent to accommodate NumPy 2 sort tie-breaking changes.
`pyproject.toml`	Lifts NumPy upper cap to `<3` and raises lower bound to `>=1.22.4`.
`deeplabcut/refine_training_dataset/stitch.py`	Replaces SciPy interpolative SVD usage with NumPy SVD for rank estimation (compatibility-related).
`deeplabcut/pose_estimation_tensorflow/core/predict_multianimal.py`	Uses `np.trapezoid` when available to avoid NumPy 2 deprecations, with fallback to `np.trapz`.
`deeplabcut/pose_estimation_pytorch/apis/prune_paf_graph.py`	Same `np.trapezoid`/`np.trapz` compatibility adjustment for AUC/separability computation.
`deeplabcut/core/trackingutils.py`	Switches `np.product` to `np.prod` for NumPy 2 compatibility.
`deeplabcut/core/inferenceutils.py`	Updates `np.percentile` call to use `method=` (NumPy 2 compatible).
`deeplabcut/core/crossvalutils.py`	Same `np.trapezoid`/`np.trapz` compatibility adjustment for AUC/separability computation.

Comments suppressed due to low confidence (1)

deeplabcut/refine_training_dataset/stitch.py:394

estimate_rank can hit a divide-by-zero when the Hankel matrix is all zeros (or when the leading singular value is 0), because eigen[0] becomes 0 and is used as a divisor. This yields runtime warnings and can propagate NaNs/inf into diff. Adding an early-return guard keeps behavior well-defined (rank 0) and avoids unnecessary work on degenerate inputs.

        eigen = s**2
        diff = np.abs(np.diff(eigen / eigen[0]))
        return np.argmin(diff > tol)

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deruyter92 · 2026-07-22T10:08:04Z

Linking related issue #3240 here (dropping albumentations)

np.percentile's interpolation= keyword is removed in NumPy 2, and its replacement, method=, only exists from NumPy 1.22. Expressing that call with a single spelling that works across the whole supported range therefore requires a floor of at least 1.22. Raising the declared floor changes nothing that could previously be installed: pandas>=2.2, a core dependency, already requires numpy>=1.22.4 on Python 3.10, the lowest supported interpreter, so numpy 1.18.5 was never selectable.

np.trapz, np.product, and np.percentile's interpolation keyword raise AttributeError or TypeError on recent NumPy 2.x, where the core pipeline already runs. Switch to np.trapezoid (np.trapz fallback for NumPy 1), np.prod, and np.percentile(method=); all behave identically from NumPy 1.22, the lower bound, up. https://numpy.org/doc/stable/numpy_2_0_migration_guide.html#main-namespace https://numpy.org/doc/stable/reference/generated/numpy.percentile.html

Tracklet stitching estimated a Hankelet's rank from its singular values via scipy.linalg.interpolative.svd. On NumPy 2 that randomized routine raises "array must not contain infs or NaNs" on finite input, so any stitching that computes tracklet affinities fails at runtime. Only the singular values matter, so use np.linalg.svd(compute_uv=False): exact, deterministic, identical on NumPy 1.22.4 and 2. It also returns zeros for an all-zero matrix instead of raising, making the DeepLabCut#2827 guard against scipy>=1.11's all-zero ValueError redundant; it is removed. scipy is removing the backend's noncompliant randomization: scipy/scipy#18367

The test checked assembled keypoints against a stored ground truth with np.testing.assert_equal. The order of equally-scored assemblies within a frame is arbitrary and not fixed by NumPy's sorts, and NumPy 2 emits two of them swapped, so the comparison failed though every coordinate matched. Sort both point sets into a canonical order first, pinning the coordinates without constraining the ordering.

natsukium · 2026-07-25T07:52:29Z

Thanks for the careful review! I couldn't reproduce numpy 2 problems with albumentations, filterpy or scipy.
That's only at the unit test level though, so it doesn't rule out issues in real training runs.

Also, would it be worth adding a non-blocking CI job that runs the suite against numpy 2?
It would give us a signal for when the pin can be dropped.

Feel free to push directly to this branch. Note that I force-pushed just now, so please pull first.

This commit partly reverts 4b977b4 where a divide by zero guard was removed. An all-zeros array is not a realistic scenario, but we are not winning anything by removing the guard.

The function existed identically (verbatim) in crossvalutils.py`and `prune_paf_graph.py`. Now deduplicated and imported.

Replace inline `(np.trapezoid if hasattr(...) else np.trapz)` runtime checks with a `_trapz = getattr(np, "trapezoid", np.trapz)` constant in both `crossvalutils.py` and `predict_multianimal.py`. The attribute test now runs once at import time instead of on every hot-path call.

deruyter92 · 2026-07-27T15:24:18Z

Regarding your recommendation: I agree that it will be worthwhile adding a non-blocking CI test for this, good suggestion! This holds also for other dependencies as well. I'm opening a separate PR for this.

deruyter92

@natsukium, thanks again! I've pushed just a few minor additions. (moving the hassatr check out of the hot path; removing a duplicate function). Let me know if you agree.

The PR looks great and I think it would be useful to merge soon!

deruyter92 reviewed Jul 22, 2026

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deruyter92 requested a review from Copilot July 22, 2026 10:03

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Comment thread deeplabcut/refine_training_dataset/stitch.py Outdated

natsukium added 4 commits July 25, 2026 16:31

natsukium force-pushed the support-numpy-2 branch from 79d6903 to 0cd0291 Compare July 25, 2026 07:36

natsukium changed the title ~~support numpy 2~~ Prepare for NumPy 2 forward compatibility Jul 25, 2026

deruyter92 added 4 commits July 27, 2026 16:22

Tracklet: restore divsion-by-zero guard

8477582

This commit partly reverts 4b977b4 where a divide by zero guard was removed. An all-zeros array is not a realistic scenario, but we are not winning anything by removing the guard.

add basic test for Tracklet.estimate_rank

92ea5e6

deduplicate crossvalutils._calc_separability into a shared utility

0bcb30a

The function existed identically (verbatim) in crossvalutils.py`and `prune_paf_graph.py`. Now deduplicated and imported.

deruyter92 approved these changes Jul 27, 2026

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deruyter92 assigned MMathisLab and deruyter92 Jul 28, 2026

deruyter92 requested review from AlexEMG and MMathisLab July 28, 2026 18:07

deruyter92 added the dependencies Pull requests that update a dependency file label Jul 28, 2026

deruyter92 mentioned this pull request Jul 30, 2026

Add CI workflow lane for dependency testing (canary lane) #3430

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deruyter92 added this to the Refresh/bump core dependencies milestone Jul 30, 2026

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Prepare for NumPy 2 forward compatibility - #3420

Prepare for NumPy 2 forward compatibility#3420
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natsukium:support-numpy-2

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natsukium commented Jul 20, 2026 •

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