Add support for numpy 2+

[gtrevisan]

• unpin numpy to allow v2+,
• lock deps to use latest numpy 2.4.3,
• replace numpy.trapz with scipy.integrate.trapezoid,
• check for numpy issues when importing MDSplus to avoid insecure fallback.

Note

trapz was deprecated in v2.0 and renamed to trapezoid, and eventually dropped in v2.4.

Caution

this will definitely break DIII-D workflows due to their old MDSplus version (7.139.59).
I'll push a fix -- i.e. a newer MDSplus version -- upon merge for my "public installation"...

[Copilot]

Pull request overview

This PR updates the project to be compatible with NumPy 2.x by loosening the NumPy upper bound, refreshing lockfiles to a NumPy 2.4.3 resolution, replacing deprecated numpy.trapz usage, and attempting to prevent an insecure mdsthin fallback when MDSplus fails due to NumPy-related import problems.

Changes:

• Unpin NumPy (numpy>=1.26.0) and update lockfiles to resolve to NumPy 2.4.3.
• Replace numpy.trapz with scipy.integrate.trapezoid in code paths that integrate signals.
• Add logic intended to detect NumPy-related MDSplus import failures and raise instead of falling back to mdsthin.

Reviewed changes

Copilot reviewed 4 out of 6 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
pyproject.toml	Removes NumPy <2.0.0 upper bound to allow NumPy 2+.
poetry.lock	Updates locked packages to a NumPy 2.4.3 environment (incl. netcdf4 metadata changes).
uv.lock	Updates uv lock resolution to NumPy 2.4.3 and removes NumPy <2.0.0 pin.
disruption_py/settings/time_setting.py	Replaces np.trapz with scipy.integrate.trapezoid.
disruption_py/machine/cmod/thomson.py	Replaces np.trapz and updates SciPy import usage accordingly.
disruption_py/inout/mds.py	Adds NumPy-related import failure detection to avoid mdsthin fallback.

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[ZanderKeith]

Confirmed results for the physics methods are unchanged between numpy 1.26.4, 2.0.2, and 2.4.4.

[yumouwei]

I also got the error with MDSplus on omega so I'll wait for your fix.

[gtrevisan]

what did you get? maybe this new error while testing out the branch?

disruption-py/disruption_py/inout/mds.py

Line 28 in dadb1df

raise ImportError("MDSplus vs numpy incompatibility") from e

I've just updated the "public installations", please retry and LMK!

[gtrevisan]

I reran all tests on all machines for several numpy versions, and updated MDSplus APIs:

	numpy<2	numpy>2,<2.4	numpy>2.4
C-MOD	🟩 🟢	🟩 🟢	🟩 🟢
DIII-D	🟩 🟢	🟩 🟢	🟩 🟢
HBT-EP	🟩 🟢	🟩 🟢	🟩 🟢

where: 🟩 = fast tests, 🟢 = full tests.

[yumouwei]

Yes I got the "MDSplus vs numpy incompatibility" error while running pytest and scripts/default.py in my private installation. I'll figure out how to point to your MDSplus installation later.

Can confirm the public installation works without running into the error.

[gtrevisan]

it's now based on the $DISPY_DIR as provided in the public snippets. then simply:

export PYTHONPATH="$DISPY_DIR/mdsplus/stable/python:$PYTHONPATH"

please try and test as I've carried out all tests from my part and would probably merge later today.

[yumouwei]

I tested using your MDSplus installation with my private dis-py installation and it worked.