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fix(ci): constrain vtk on Python 3.9 and run dev deps in PR workflow - #137

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fix/vtk-py39-ci
Aug 25, 2026
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fix(ci): constrain vtk on Python 3.9 and run dev deps in PR workflow#137
Hendrik-code merged 1 commit into
mainfrom
fix/vtk-py39-ci

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@Hendrik-code

@Hendrik-code Hendrik-code commented Aug 25, 2026

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Problem

The post-merge tests job fails on ubuntu-latest / Python 3.9:

Installing vtk (9.7.0)
  | Unable to find installation candidates for vtk (9.7.0)
  |   - 27 candidate(s) were identified for the package
  |   - 27 wheel(s) were skipped as your project's environment does not support the identified abi tags

Root cause: vtk 9.7.0 (published 2026-08-15) is the first release with no cp39 wheel — 9.6.2 was the last one. vtk also publishes no requires-python metadata at all, so Poetry cannot auto-exclude it: it picks the newest version, then finds every wheel ABI-incompatible.

Because poetry.lock is gitignored (.gitignore:160), every CI run re-resolves from scratch, so main broke the moment that release landed. No code change was involved.

Why the PR checks were green but main failed

The two workflows installed differently:

Workflow Trigger Install command Dev group?
tests_mr.yml pull_request pip install -e . no
tests.yml push to main python -m poetry install yes

vtk lives only in [tool.poetry.group.dev.dependencies], so the PR job never installed it. Only the post-merge job did.

Changes

1. pyproject.toml — split the vtk constraint by Python version

vtk = [
  { version = ">=9.0,<9.7", python = "<3.10" },
  { version = "*", python = ">=3.10" },
]

2. .github/workflows/tests_mr.yml — install via Poetry, matching tests.yml

Split into Configure python (pip, poetry, flake8, pytest) and Install dependencies (python -m poetry install); tests now run through python -m poetry run pytest so they execute inside the Poetry venv. flake8 still runs from the ambient interpreter, as in tests.yml.

This closes the gap that let the breakage through: PRs now exercise the dev group.

Verification

Run locally against this branch, reproducing the new PR-workflow sequence:

  • Python 3.9 — poetry install exits 0, resolves vtk 9.6.2, installs the root project; poetry run pytest → 462 passed, 6 skipped in 43s.
  • Python 3.10 — still resolves to vtk 9.7.0; no regression for the modern matrix entries.

Follow-ups not included here

  • poetry.lock is gitignored, so CI re-resolves on every run. The new PR job catches this class of break at review time rather than preventing it; committing the lock would prevent it outright — a bigger workflow decision.
  • Python 3.9 is accumulating pins. pyvista is already frozen at ^0.43.2 because 0.44+ requires >=3.10 (current is 0.48.4), and vtk has now followed. 3.9 reached EOL in October 2025; dropping it would remove this category of pin entirely.

🤖 Generated with Claude Code

@Hendrik-code @claude
fix(ci): constrain vtk on Python 3.9 and run dev deps in PR workflow
3a99f16 
vtk 9.7.0 (2026-08-15) is the first release without a cp39 wheel, and vtk
publishes no requires-python metadata, so Poetry cannot exclude it
automatically -- it selects the newest version and then finds all 27 wheels
ABI-incompatible. With no committed lockfile, every CI run re-resolves, so
the post-merge 3.9 job broke the day that release shipped.

Split the vtk constraint by Python version: <9.7 (last cp39 release is
9.6.2) below 3.10, unconstrained from 3.10 on.

The PR workflow installed with `pip install -e .`, which skips the dev
group where vtk lives, while the push-to-main workflow uses `poetry
install`. That is why the PR was green and main failed. Align tests_mr.yml
with tests.yml so PRs exercise the dev group too.

Verified on Python 3.9: `poetry install` succeeds (vtk 9.6.2) and
`poetry run pytest` reports 462 passed, 6 skipped. Python 3.10 still
resolves to vtk 9.7.0.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Copilot AI lite review requested due to automatic review settings August 25, 2026 07:33

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Benchmark comparison

Speed (wall time per call)

baseline 73e7fea vs head 73e7fea · python 3.11.16 · 5 repeats + 1 warmup

Showing the 5 most-changed measurements per case; the rest are collapsed. Rows with a baseline below 3 ms are tagged (noise) — runner jitter on those swamps any real change.

ct_3d — shape (73, 47, 73)

Measurement baseline ms (median ±½·range) head ms (median ±½·range) Δ % p
nii_rescale 41.91 ±0.45 39.71 ±0.11 -5.2% 0.001
nii_resample_from_to 43.64 ±0.08 41.74 ±0.06 -4.3% 0.000
nii_filter_connected_components 4.14 ±0.03 4.31 ±0.14 +4.0% 0.044
nii_fill_holes 4.58 ±0.03 4.68 ±0.05 +2.2% 0.003
nii_dilate_msk 119.29 ±0.41 121.35 ±0.54 +1.7% 0.000
… 31 more measurements
Measurement baseline ms (median ±½·range) head ms (median ±½·range) Δ % p
poi_calc_centroids_nocrop 4.28 ±0.03 4.33 ±0.04 +1.4% 0.028
nii_erode_msk 6.00 ±0.05 6.07 ±0.03 +1.3% 0.034
poi_calc_poi_from_subreg_vert 11.36 ±0.10 11.42 ±0.05 +0.5% 0.504
nii_save 11.48 ±0.16 11.45 ±0.04 -0.3% 0.256
nii_rescale_seg 3.05 ±0.03 3.05 ±0.01 -0.3% 0.829
nii_load_img 11.64 ±0.05 11.62 ±0.11 -0.2% 0.989
metric_voxels 250463.00 ±0.00 250463.00 ±0.00 +0.0% —
metric_labels 3.00 ±0.00 3.00 ±0.00 +0.0% —
metric_foreground_pct 14.51 ±0.00 14.51 ±0.00 +0.0% —
poi_rescale 0.19 ±0.02 0.17 ±0.01 -12.4% (noise) 0.317
poi_map_labels 0.15 ±0.01 0.14 ±0.01 -5.8% (noise) 0.336
nii_set_dtype 0.38 ±0.01 0.36 ±0.01 -5.2% (noise) 0.042
nii_compute_crop 0.29 ±0.02 0.28 ±0.01 -3.5% (noise) 0.166
poi_calc_centroids 2.38 ±0.04 2.45 ±0.09 +2.9% (noise) 0.164
nii_pad_to 0.53 ±0.01 0.54 ±0.03 +2.2% (noise) 0.393
nii_unique 0.57 ±0.01 0.58 ±0.01 +2.1% (noise) 0.016
nii_get_array 0.04 ±0.00 0.04 ±0.00 -1.8% (noise) 0.292
poi_save 0.35 ±0.01 0.36 ±0.01 +1.7% (noise) 0.508
nii_get_connected_components 1.96 ±0.01 1.99 ±0.04 +1.4% (noise) 0.099
poi_reorient 0.32 ±0.01 0.32 ±0.02 +1.4% (noise) 0.373
nii_reorient 0.65 ±0.01 0.66 ±0.04 +1.4% (noise) 0.960
nii_apply_crop 0.51 ±0.02 0.52 ±0.01 +1.2% (noise) 0.842
nii_extract_label 0.33 ±0.02 0.32 ±0.01 -1.1% (noise) 0.984
nii_load_seg 2.60 ±0.05 2.62 ±0.02 +0.8% (noise) 0.845
poi_to_global 0.16 ±0.01 0.15 ±0.01 -0.7% (noise) 0.803
nii_volumes 1.89 ±0.01 1.88 ±0.02 -0.5% (noise) 0.163
poi_load 0.86 ±0.02 0.86 ±0.03 +0.4% (noise) 0.702
nii_center_of_masses 1.80 ±0.02 1.80 ±0.01 -0.4% (noise) 0.619
nii_map_labels 0.79 ±0.03 0.79 ±0.02 -0.3% (noise) 0.795
poi_local_to_global_arr 0.24 ±0.01 0.24 ±0.01 +0.2% (noise) 0.612
poi_resample_from_to 0.54 ±0.01 0.54 ±0.01 +0.1% (noise) 0.849

ct_2d — shape (73, 47, 1)

Measurement baseline ms (median ±½·range) head ms (median ±½·range) Δ % p
nii_rescale 5.43 ±0.13 5.32 ±0.04 -2.2% 0.100
nii_dilate_msk 13.86 ±0.10 13.91 ±0.32 +0.4% 0.390
nii_resample_from_to 7.15 ±0.08 7.17 ±0.09 +0.2% 0.509
metric_voxels 3431.00 ±0.00 3431.00 ±0.00 +0.0% —
metric_labels 3.00 ±0.00 3.00 ±0.00 +0.0% —
… 30 more measurements
Measurement baseline ms (median ±½·range) head ms (median ±½·range) Δ % p
metric_foreground_pct 37.60 ±0.00 37.60 ±0.00 +0.0% —
nii_compute_crop 0.14 ±0.01 0.16 ±0.00 +16.4% (noise) 0.015
nii_set_dtype 0.37 ±0.01 0.42 ±0.04 +12.1% (noise) 0.050
nii_erode_msk 0.90 ±0.02 1.01 ±0.03 +11.4% (noise) 0.001
nii_map_labels 0.45 ±0.02 0.49 ±0.02 +8.6% (noise) 0.023
nii_pad_to 0.52 ±0.01 0.57 ±0.01 +8.4% (noise) 0.000
nii_get_array 0.02 ±0.00 0.02 ±0.00 +7.9% (noise) 0.082
nii_fill_holes 0.78 ±0.01 0.84 ±0.04 +7.6% (noise) 0.010
poi_local_to_global_arr 0.27 ±0.01 0.29 ±0.01 +6.7% (noise) 0.010
nii_apply_crop 0.66 ±0.01 0.70 ±0.02 +6.7% (noise) 0.001
poi_save 0.48 ±0.01 0.51 ±0.02 +6.4% (noise) 0.043
nii_extract_label 0.40 ±0.01 0.43 ±0.01 +6.1% (noise) 0.002
nii_volumes 0.28 ±0.01 0.29 ±0.01 +5.6% (noise) 0.066
nii_rescale_seg 0.72 ±0.03 0.76 ±0.01 +5.2% (noise) 0.021
nii_reorient 0.76 ±0.02 0.79 ±0.02 +5.2% (noise) 0.026
nii_load_seg 1.54 ±0.01 1.60 ±0.02 +4.3% (noise) 0.001
nii_get_connected_components 0.62 ±0.05 0.64 ±0.01 +3.7% (noise) 0.826
poi_reorient 0.46 ±0.01 0.44 ±0.01 -3.6% (noise) 0.020
poi_to_global 0.24 ±0.01 0.23 ±0.01 -3.2% (noise) 0.519
nii_filter_connected_components 0.80 ±0.02 0.82 ±0.03 +2.8% (noise) 0.127
poi_map_labels 0.20 ±0.01 0.21 ±0.01 +2.8% (noise) 0.253
nii_load_img 1.40 ±0.02 1.44 ±0.02 +2.5% (noise) 0.019
nii_save 1.29 ±0.02 1.32 ±0.02 +2.3% (noise) 0.043
poi_load 0.96 ±0.02 0.98 ±0.00 +2.1% (noise) 0.411
poi_calc_centroids_nocrop 1.04 ±0.03 1.07 ±0.01 +2.1% (noise) 0.145
poi_calc_centroids 0.88 ±0.01 0.89 ±0.01 +1.6% (noise) 0.258
poi_rescale 0.26 ±0.01 0.26 ±0.02 -1.4% (noise) 0.866
nii_center_of_masses 0.21 ±0.02 0.21 ±0.01 -1.1% (noise) 0.818
poi_resample_from_to 0.70 ±0.02 0.70 ±0.03 +1.1% (noise) 0.178
nii_unique 0.12 ±0.01 0.12 ±0.01 -0.1% (noise) 0.770

mri_3d — shape (68, 52, 67)

Measurement baseline ms (median ±½·range) head ms (median ±½·range) Δ % p
nii_rescale 39.41 ±0.21 37.13 ±0.07 -5.8% 0.000
nii_resample_from_to 41.07 ±0.19 39.16 ±0.18 -4.6% 0.000
poi_calc_centroids_nocrop 8.97 ±0.05 9.15 ±0.07 +2.1% 0.001
nii_rescale_seg 3.03 ±0.02 3.07 ±0.02 +1.2% 0.014
poi_calc_poi_from_subreg_vert 10.73 ±0.05 10.82 ±0.08 +0.9% 0.132
… 31 more measurements
Measurement baseline ms (median ±½·range) head ms (median ±½·range) Δ % p
nii_filter_connected_components 4.60 ±0.08 4.64 ±0.14 +0.8% 0.192
nii_dilate_msk 153.18 ±0.62 154.20 ±0.87 +0.7% 0.052
nii_erode_msk 7.60 ±0.11 7.56 ±0.07 -0.5% 0.331
nii_fill_holes 5.48 ±0.02 5.51 ±0.02 +0.5% 0.090
nii_load_img 9.43 ±0.03 9.43 ±0.02 +0.0% 0.801
nii_save 9.45 ±0.06 9.45 ±0.05 +0.0% 0.296
metric_voxels 236912.00 ±0.00 236912.00 ±0.00 +0.0% —
metric_labels 8.00 ±0.00 8.00 ±0.00 +0.0% —
metric_foreground_pct 18.21 ±0.00 18.21 ±0.00 +0.0% —
nii_get_array 0.04 ±0.00 0.05 ±0.00 +29.4% (noise) 0.000
poi_save 0.52 ±0.02 0.56 ±0.02 +7.6% (noise) 0.010
nii_apply_crop 0.67 ±0.01 0.71 ±0.02 +5.9% (noise) 0.015
nii_pad_to 0.67 ±0.01 0.71 ±0.02 +5.8% (noise) 0.002
nii_extract_label 0.44 ±0.02 0.46 ±0.01 +4.8% (noise) 0.181
nii_set_dtype 0.50 ±0.01 0.53 ±0.03 +4.7% (noise) 0.030
nii_compute_crop 0.34 ±0.01 0.33 ±0.01 -4.4% (noise) 0.083
poi_map_labels 0.24 ±0.01 0.25 ±0.02 +4.2% (noise) 0.383
poi_to_global 0.27 ±0.01 0.28 ±0.01 +3.7% (noise) 0.025
poi_resample_from_to 0.73 ±0.01 0.75 ±0.02 +3.5% (noise) 0.065
poi_rescale 0.29 ±0.01 0.29 ±0.01 +3.1% (noise) 0.479
nii_reorient 0.82 ±0.03 0.84 ±0.02 +2.7% (noise) 0.442
poi_load 2.06 ±0.02 2.11 ±0.04 +2.6% (noise) 0.066
nii_load_seg 2.70 ±0.02 2.77 ±0.03 +2.5% (noise) 0.004
nii_unique 0.59 ±0.01 0.61 ±0.01 +2.4% (noise) 0.043
poi_reorient 0.48 ±0.03 0.49 ±0.02 +2.3% (noise) 0.124
nii_get_connected_components 2.03 ±0.03 2.07 ±0.25 +1.7% (noise) 0.277
nii_volumes 2.02 ±0.04 2.05 ±0.02 +1.4% (noise) 0.468
nii_center_of_masses 2.06 ±0.01 2.08 ±0.01 +1.1% (noise) 0.000
nii_map_labels 0.97 ±0.02 0.98 ±0.01 +0.5% (noise) 0.312
poi_calc_centroids 2.82 ±0.02 2.83 ±0.04 +0.4% (noise) 0.600
poi_local_to_global_arr 0.29 ±0.01 0.29 ±0.01 -0.1% (noise) 0.432

mri_2d — shape (68, 52, 1)

Measurement baseline ms (median ±½·range) head ms (median ±½·range) Δ % p
nii_rescale 5.46 ±0.07 5.35 ±0.07 -2.1% 0.258
nii_resample_from_to 7.14 ±0.08 7.09 ±0.03 -0.7% 0.067
nii_dilate_msk 18.20 ±0.14 18.22 ±0.07 +0.1% 0.964
metric_voxels 3536.00 ±0.00 3536.00 ±0.00 +0.0% —
metric_labels 7.00 ±0.00 7.00 ±0.00 +0.0% —
… 30 more measurements
Measurement baseline ms (median ±½·range) head ms (median ±½·range) Δ % p
metric_foreground_pct 50.17 ±0.00 50.17 ±0.00 +0.0% —
nii_get_array 0.01 ±0.00 0.02 ±0.00 +27.1% (noise) 0.481
nii_unique 0.12 ±0.02 0.13 ±0.01 +8.9% (noise) 0.386
nii_get_connected_components 0.60 ±0.03 0.64 ±0.08 +7.3% (noise) 0.129
nii_center_of_masses 0.39 ±0.01 0.41 ±0.02 +6.3% (noise) 0.231
nii_set_dtype 0.38 ±0.01 0.40 ±0.01 +5.7% (noise) 0.014
nii_pad_to 0.51 ±0.02 0.54 ±0.02 +5.1% (noise) 0.034
nii_compute_crop 0.14 ±0.01 0.15 ±0.01 +4.9% (noise) 0.174
nii_map_labels 0.47 ±0.01 0.49 ±0.00 +4.8% (noise) 0.004
poi_to_global 0.27 ±0.01 0.26 ±0.01 -4.1% (noise) 0.330
nii_filter_connected_components 0.80 ±0.03 0.84 ±0.02 +4.1% (noise) 0.074
nii_save 1.28 ±0.03 1.33 ±0.02 +4.0% (noise) 0.020
nii_apply_crop 0.63 ±0.01 0.65 ±0.01 +3.5% (noise) 0.003
nii_volumes 0.44 ±0.01 0.46 ±0.01 +3.2% (noise) 0.021
nii_extract_label 0.41 ±0.01 0.42 ±0.01 +2.7% (noise) 0.069
nii_load_img 1.40 ±0.02 1.44 ±0.02 +2.7% (noise) 0.006
poi_calc_centroids_nocrop 1.26 ±0.03 1.30 ±0.02 +2.6% (noise) 0.087
poi_calc_centroids 1.06 ±0.02 1.08 ±0.03 +2.5% (noise) 0.021
nii_rescale_seg 0.73 ±0.02 0.75 ±0.02 +2.5% (noise) 0.189
nii_erode_msk 1.12 ±0.04 1.15 ±0.01 +2.4% (noise) 0.253
nii_load_seg 1.53 ±0.01 1.56 ±0.03 +1.7% (noise) 0.313
poi_local_to_global_arr 0.28 ±0.02 0.29 ±0.01 +1.7% (noise) 0.612
nii_fill_holes 0.98 ±0.01 1.00 ±0.03 +1.6% (noise) 0.122
poi_resample_from_to 0.71 ±0.03 0.72 ±0.01 +1.5% (noise) 0.371
poi_map_labels 0.23 ±0.01 0.23 ±0.01 +1.4% (noise) 0.716
nii_reorient 0.78 ±0.03 0.79 ±0.02 +1.3% (noise) 0.198
poi_load 1.84 ±0.03 1.86 ±0.01 +1.1% (noise) 0.599
poi_save 0.53 ±0.01 0.54 ±0.01 +1.0% (noise) 0.725
poi_reorient 0.47 ±0.02 0.47 ±0.02 +0.3% (noise) 0.578
poi_rescale 0.28 ±0.01 0.28 ±0.01 +0.0% (noise) 0.870

Gate: a measurement fails when the baseline is ≥ 1 ms, the median grows by ≥ 50%, and Welch's t-test gives p < 0.05. metric_* rows are context only.

Memory (peak RSS growth per call)

baseline 73e7fea vs head 73e7fea · python 3.11.16 · 5 repeats + 1 warmup · sampler proc-status, isolation fork · measurement floor ≈ 0.90 MiB

Showing the 5 most-changed measurements per case; the rest are collapsed. Rows with a baseline below 3 MiB are tagged (noise) — runner jitter on those swamps any real change.

ct_3d — shape (73, 47, 73)

Measurement baseline MiB (median ±½·range) head MiB (median ±½·range) Δ % p
nii_set_dtype 5.25 ±0.00 5.21 ±0.00 -0.7% —
poi_resample_from_to 5.28 ±0.00 5.24 ±0.00 -0.7% —
nii_pad_to 5.43 ±0.00 5.39 ±0.00 -0.7% —
nii_extract_label 5.43 ±0.00 5.39 ±0.00 -0.7% —
nii_load_seg 6.02 ±0.00 5.97 ±0.00 -0.7% —
… 31 more measurements
Measurement baseline MiB (median ±½·range) head MiB (median ±½·range) Δ % p
nii_map_labels 5.50 ±0.00 5.46 ±0.00 -0.7% —
nii_apply_crop 5.87 ±0.00 5.83 ±0.00 -0.7% —
nii_reorient 5.91 ±0.00 5.87 ±0.00 -0.7% —
poi_calc_centroids_nocrop 5.93 ±0.00 5.89 ±0.00 -0.7% —
nii_dilate_msk 5.93 ±0.00 5.89 ±0.00 -0.7% —
nii_erode_msk 5.95 ±0.00 5.91 ±0.00 -0.7% —
poi_calc_centroids 6.06 ±0.00 6.02 ±0.00 -0.6% —
nii_fill_holes 6.29 ±0.00 6.25 ±0.00 -0.6% —
nii_get_connected_components 6.62 ±0.00 6.58 ±0.00 -0.6% —
nii_filter_connected_components 6.87 ±0.00 6.83 ±0.00 -0.6% —
poi_calc_poi_from_subreg_vert 7.11 ±0.00 7.07 ±0.00 -0.5% 0.000
nii_load_img 3.57 ±0.00 3.57 ±0.00 -0.1% —
nii_save 3.71 ±0.00 3.71 ±0.00 +0.0% —
nii_rescale 6.18 ±0.00 6.18 ±0.00 +0.0% —
nii_rescale_seg 5.95 ±0.00 5.95 ±0.00 +0.0% —
nii_resample_from_to 6.30 ±0.00 6.30 ±0.00 +0.0% —
nii_volumes 3.53 ±0.00 3.53 ±0.00 +0.0% —
nii_center_of_masses 3.28 ±0.00 3.28 ±0.00 +0.0% —
poi_reorient 3.84 ±0.00 3.84 ±0.00 +0.0% —
poi_to_global 3.09 ±0.00 3.09 ±0.00 +0.0% —
metric_voxels 250463.00 ±0.00 250463.00 ±0.00 +0.0% —
metric_labels 3.00 ±0.00 3.00 ±0.00 +0.0% —
metric_foreground_pct 14.51 ±0.00 14.51 ±0.00 +0.0% —
nii_get_array 1.65 ±0.00 1.65 ±0.00 +0.0% (noise) —
nii_compute_crop 2.90 ±0.00 2.90 ±0.00 +0.0% (noise) —
nii_unique 2.96 ±0.00 2.96 ±0.00 +0.0% (noise) —
poi_rescale 2.61 ±0.00 2.61 ±0.00 +0.0% (noise) —
poi_local_to_global_arr 2.96 ±0.00 2.96 ±0.00 +0.0% (noise) —
poi_save 1.41 ±0.00 1.41 ±0.00 +0.0% (noise) —
poi_map_labels 1.78 ±0.00 1.78 ±0.00 +0.0% (noise) —
poi_load 1.62 ±0.00 1.62 ±0.00 +0.0% (noise) —

ct_2d — shape (73, 47, 1)

Measurement baseline MiB (median ±½·range) head MiB (median ±½·range) Δ % p
nii_set_dtype 5.18 ±0.00 5.14 ±0.00 -0.8% —
poi_resample_from_to 5.21 ±0.00 5.18 ±0.00 -0.7% —
nii_pad_to 5.36 ±0.00 5.32 ±0.00 -0.7% —
nii_extract_label 5.37 ±0.00 5.33 ±0.00 -0.7% —
nii_map_labels 5.43 ±0.00 5.39 ±0.00 -0.7% —
… 30 more measurements
Measurement baseline MiB (median ±½·range) head MiB (median ±½·range) Δ % p
nii_apply_crop 5.80 ±0.00 5.77 ±0.00 -0.7% —
nii_reorient 5.84 ±0.00 5.80 ±0.00 -0.7% —
nii_dilate_msk 5.87 ±0.00 5.83 ±0.00 -0.7% —
nii_erode_msk 5.88 ±0.00 5.84 ±0.00 -0.7% —
poi_calc_centroids_nocrop 5.93 ±0.00 5.89 ±0.00 -0.7% —
nii_load_seg 5.95 ±0.00 5.91 ±0.00 -0.7% —
poi_calc_centroids 5.99 ±0.00 5.95 ±0.00 -0.7% —
nii_fill_holes 6.22 ±0.00 6.18 ±0.00 -0.6% —
nii_get_connected_components 6.55 ±0.00 6.52 ±0.00 -0.6% —
nii_filter_connected_components 6.80 ±0.00 6.77 ±0.00 -0.6% —
nii_load_img 3.50 ±0.00 3.50 ±0.00 +0.0% —
nii_save 3.65 ±0.00 3.65 ±0.00 +0.0% —
nii_rescale 6.11 ±0.00 6.11 ±0.00 +0.0% —
nii_rescale_seg 5.88 ±0.00 5.88 ±0.00 +0.0% —
nii_resample_from_to 6.23 ±0.00 6.23 ±0.00 +0.0% —
nii_volumes 3.46 ±0.00 3.46 ±0.00 +0.0% —
nii_center_of_masses 3.21 ±0.00 3.21 ±0.00 +0.0% —
poi_reorient 3.77 ±0.00 3.77 ±0.00 +0.0% —
poi_to_global 3.02 ±0.00 3.02 ±0.00 +0.0% —
metric_voxels 3431.00 ±0.00 3431.00 ±0.00 +0.0% —
metric_labels 3.00 ±0.00 3.00 ±0.00 +0.0% —
metric_foreground_pct 37.60 ±0.00 37.60 ±0.00 +0.0% —
nii_get_array 1.59 ±0.00 1.59 ±0.00 +0.0% (noise) —
nii_compute_crop 2.84 ±0.00 2.84 ±0.00 +0.0% (noise) —
nii_unique 2.90 ±0.00 2.90 ±0.00 +0.0% (noise) —
poi_rescale 2.54 ±0.00 2.54 ±0.00 +0.0% (noise) —
poi_local_to_global_arr 2.89 ±0.00 2.89 ±0.00 +0.0% (noise) —
poi_save 1.34 ±0.00 1.34 ±0.00 +0.0% (noise) —
poi_map_labels 1.71 ±0.00 1.71 ±0.00 +0.0% (noise) —
poi_load 1.55 ±0.00 1.55 ±0.00 +0.0% (noise) —

mri_3d — shape (68, 52, 67)

Measurement baseline MiB (median ±½·range) head MiB (median ±½·range) Δ % p
poi_resample_from_to 5.21 ±0.00 5.18 ±0.00 -0.7% —
nii_set_dtype 5.24 ±0.00 5.20 ±0.00 -0.7% —
nii_pad_to 5.36 ±0.00 5.32 ±0.00 -0.7% —
nii_extract_label 5.37 ±0.00 5.33 ±0.00 -0.7% —
nii_map_labels 5.43 ±0.00 5.39 ±0.00 -0.7% —
… 31 more measurements
Measurement baseline MiB (median ±½·range) head MiB (median ±½·range) Δ % p
nii_apply_crop 5.80 ±0.00 5.77 ±0.00 -0.7% —
nii_reorient 5.84 ±0.00 5.80 ±0.00 -0.7% —
poi_calc_centroids_nocrop 5.86 ±0.00 5.82 ±0.00 -0.7% —
nii_dilate_msk 5.87 ±0.00 5.83 ±0.00 -0.7% —
nii_erode_msk 5.88 ±0.00 5.84 ±0.00 -0.7% —
nii_load_seg 5.95 ±0.00 5.91 ±0.00 -0.7% —
poi_calc_centroids 5.99 ±0.00 5.95 ±0.00 -0.7% —
nii_fill_holes 6.22 ±0.00 6.18 ±0.00 -0.6% —
nii_get_connected_components 6.55 ±0.00 6.52 ±0.00 -0.6% —
nii_filter_connected_components 6.80 ±0.00 6.77 ±0.00 -0.6% —
poi_calc_poi_from_subreg_vert 7.11 ±0.00 7.07 ±0.00 -0.5% —
nii_load_img 3.56 ±0.00 3.56 ±0.00 +0.0% —
nii_save 3.65 ±0.00 3.65 ±0.00 +0.0% —
nii_rescale 6.11 ±0.00 6.11 ±0.00 +0.0% —
nii_rescale_seg 5.88 ±0.00 5.88 ±0.00 +0.0% —
nii_resample_from_to 6.23 ±0.00 6.23 ±0.00 +0.0% —
nii_volumes 3.46 ±0.00 3.46 ±0.00 +0.0% —
nii_center_of_masses 3.21 ±0.00 3.21 ±0.00 +0.0% —
poi_reorient 3.77 ±0.00 3.77 ±0.00 +0.0% —
poi_to_global 3.02 ±0.00 3.02 ±0.00 +0.0% —
metric_voxels 236912.00 ±0.00 236912.00 ±0.00 +0.0% —
metric_labels 8.00 ±0.00 8.00 ±0.00 +0.0% —
metric_foreground_pct 18.21 ±0.00 18.21 ±0.00 +0.0% —
nii_get_array 1.59 ±0.00 1.59 ±0.00 +0.0% (noise) —
nii_compute_crop 2.84 ±0.00 2.84 ±0.00 +0.0% (noise) —
nii_unique 2.90 ±0.00 2.90 ±0.00 +0.0% (noise) —
poi_rescale 2.54 ±0.00 2.54 ±0.00 +0.0% (noise) —
poi_local_to_global_arr 2.89 ±0.00 2.89 ±0.00 +0.0% (noise) —
poi_save 1.40 ±0.00 1.40 ±0.00 +0.0% (noise) —
poi_map_labels 1.71 ±0.00 1.71 ±0.00 +0.0% (noise) —
poi_load 1.55 ±0.00 1.55 ±0.00 +0.0% (noise) —

mri_2d — shape (68, 52, 1)

Measurement baseline MiB (median ±½·range) head MiB (median ±½·range) Δ % p
poi_resample_from_to 5.21 ±0.00 5.18 ±0.00 -0.7% —
nii_set_dtype 5.24 ±0.00 5.20 ±0.00 -0.7% —
nii_pad_to 5.36 ±0.00 5.32 ±0.00 -0.7% —
nii_extract_label 5.37 ±0.00 5.33 ±0.00 -0.7% —
nii_map_labels 5.43 ±0.00 5.39 ±0.00 -0.7% —
… 30 more measurements
Measurement baseline MiB (median ±½·range) head MiB (median ±½·range) Δ % p
nii_apply_crop 5.80 ±0.00 5.77 ±0.00 -0.7% —
nii_reorient 5.84 ±0.00 5.80 ±0.00 -0.7% —
nii_dilate_msk 5.87 ±0.00 5.83 ±0.00 -0.7% —
nii_erode_msk 5.88 ±0.00 5.84 ±0.00 -0.7% —
poi_calc_centroids_nocrop 5.93 ±0.00 5.89 ±0.00 -0.7% —
nii_load_seg 5.95 ±0.00 5.91 ±0.00 -0.7% —
poi_calc_centroids 5.99 ±0.00 5.95 ±0.00 -0.7% —
nii_fill_holes 6.22 ±0.00 6.18 ±0.00 -0.6% —
nii_get_connected_components 6.55 ±0.00 6.52 ±0.00 -0.6% —
nii_filter_connected_components 6.80 ±0.00 6.77 ±0.00 -0.6% —
nii_load_img 3.56 ±0.00 3.56 ±0.00 +0.0% —
nii_save 3.65 ±0.00 3.65 ±0.00 +0.0% —
nii_rescale 6.11 ±0.00 6.11 ±0.00 +0.0% —
nii_rescale_seg 5.88 ±0.00 5.88 ±0.00 +0.0% —
nii_resample_from_to 6.23 ±0.00 6.23 ±0.00 +0.0% —
nii_volumes 3.46 ±0.00 3.46 ±0.00 +0.0% —
nii_center_of_masses 3.21 ±0.00 3.21 ±0.00 +0.0% —
poi_reorient 3.77 ±0.00 3.77 ±0.00 +0.0% —
poi_to_global 3.02 ±0.00 3.02 ±0.00 +0.0% —
metric_voxels 3536.00 ±0.00 3536.00 ±0.00 +0.0% —
metric_labels 7.00 ±0.00 7.00 ±0.00 +0.0% —
metric_foreground_pct 50.17 ±0.00 50.17 ±0.00 +0.0% —
nii_get_array 1.59 ±0.00 1.59 ±0.00 +0.0% (noise) —
nii_compute_crop 2.84 ±0.00 2.84 ±0.00 +0.0% (noise) —
nii_unique 2.90 ±0.00 2.90 ±0.00 +0.0% (noise) —
poi_rescale 2.54 ±0.00 2.54 ±0.00 +0.0% (noise) —
poi_local_to_global_arr 2.89 ±0.00 2.89 ±0.00 +0.0% (noise) —
poi_save 1.40 ±0.00 1.40 ±0.00 +0.0% (noise) —
poi_map_labels 1.71 ±0.00 1.71 ±0.00 +0.0% (noise) —
poi_load 1.55 ±0.00 1.55 ±0.00 +0.0% (noise) —

Gate: a measurement fails when the baseline is ≥ 1 MiB, the median grows by ≥ 50%, and Welch's t-test gives p < 0.05. metric_* rows are context only.

@Hendrik-code
Hendrik-code merged commit e71e3e2 into main Aug 25, 2026
6 checks passed
@Hendrik-code
Hendrik-code deleted the fix/vtk-py39-ci branch August 25, 2026 07:37
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