Replace np.NaN with np.nan for numpy 2.x compatibility#156
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NumPy 2.0 removed `np.NaN` (the deprecated capitalized alias) in
favor of `np.nan` (the canonical lowercase form, which always
existed). This notebook had one usage:
vel_angle[np.abs(vel_angle) > 100] = np.NaN # remove artifacts
This was the only thing keeping the file pinned to `numpy<2` — with
this fix, the notebook works against the current Colab runtime's
`numpy==2.0.2` without needing a kernel restart on install.
(Auto-added cell IDs in the same diff are an nbformat-write
normalization, not a content change.)
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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…i#156) The lock generated by PR dandi#159 pinned `numpy==1.26.4` because the PR-141-era input deps included `numpy>=1.26,<2`. That cap was there because the notebook used `np.NaN` (removed in numpy 2.0). PR dandi#156 already replaced `np.NaN` with `np.nan`, so the cap is now stale and the notebook code is numpy-2.x clean. Re-resolved with `numpy>=1.26` (no upper cap) against the Colab constraints set. The only line that changed is the numpy pin — everything else was already at Colab versions: numpy 1.26.4 -> 2.0.2 (matches Colab — no restart on install) Now the install on Colab is fully no-op for numpy/pandas/scipy/h5py/etc. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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NumPy 2.0 removed the deprecated capitalized alias
np.NaNin favor ofnp.nan(the canonical lowercase form, which has always existed). Searching the repo:np.NaN: 1 notebook —000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure1d.ipynb(one usage)np.NAN,np.Inf,np.product,np.cumproduct,np.sometrue,np.alltrue,np.float_,np.complex_,np.unicode_,np.cast: none in.ipynbfiles outside the (already-excluded) DataJoint subdirs.This PR converts the single occurrence:
That was the only thing keeping this notebook pinned to
numpy<2in #149's lockfile (the resolver dropped numpy from the Colab constraint set for this one becausenp.NaNis gone in numpy 2.x). After this lands, the next regen on #149 will pick upnumpy==2.0.2for this notebook, matching Colab — and Colab users won't need to restart the runtime on install.Notebooks NOT touched (and why)
Two other notebooks were also pinned to
numpy<2in #149's locks, but for unrelated reasons — they don't use any removed numpy APIs:000559/.../reproduce_figure_S1.ipynb— pinned because ofcellpose<4(cellpose 4.x dropped the oldCellposeclass the notebook uses). The numpy<2 is a transitive consequence of cellpose's deps, not a notebook-content issue.000582/Sargolini2006/000582_Sargolini2006_demo.ipynb— pinned viapynapple>=0.6transitive deps. Notebook code is numpy-2.x clean.Those two would need different fixes (cellpose modernization / pynapple version bump) and are out of scope here.
The diff also includes nbformat-added cell
idfields on a few previously-id-less cells — that's an automatic normalization on save, not a content change.🤖 Generated with Claude Code