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Update numpy to 2.4.3 and pint to 0.25.3#63

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jan-janssen merged 7 commits intomainfrom
numpy
Apr 20, 2026
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Update numpy to 2.4.3 and pint to 0.25.3#63
jan-janssen merged 7 commits intomainfrom
numpy

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github-actions Bot commented Jan 3, 2026

Binder 👈 Launch a binder notebook on branch pyiron/sphinx_parser/numpy

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waiting for pyiron/semantikon#341

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stale Bot commented Feb 12, 2026

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

@stale stale Bot added the stale label Feb 12, 2026
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@samwaseda Is there any chance we can get this merged soon? I see that semantikon is still in beta but at the same time this restriction blocks the numpy update here for sphinx_parser and based on this the update for atomistics.

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Not sure if I understand what you are suggesting... Simply ignore the tests and merge it?

@stale stale Bot removed the stale label Mar 27, 2026
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Not sure if I understand what you are suggesting... Simply ignore the tests and merge it?

I guess I would just release another 0.X Version of semantikon with numpy 2.4 support.

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But is it so urgently important?

Copilot AI review requested due to automatic review settings April 20, 2026 07:10
@jan-janssen jan-janssen changed the title Update numpy to 2.4.0 Update numpy to 2.4.3 and pint to 0.25.3 Apr 20, 2026
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Up to standards ✅

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Pull request overview

Updates dependency pins to newer NumPy (and Pint) versions across the Python package metadata and multiple conda environments used for CI/docs/Binder.

Changes:

  • Bump NumPy pin in pyproject.toml and conda environment files.
  • Bump Pint pin in pyproject.toml and CI conda environment.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 7 comments.

File Description
pyproject.toml Updates pinned runtime dependencies (NumPy, Pint).
docs/environment.yml Updates NumPy pin for the docs build environment.
.ci_support/environment.yml Updates pinned dependencies for the CI conda environment (NumPy, Pint).
.binder/environment.yml Updates NumPy pin for the Binder environment.

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Comment thread docs/environment.yml
Comment on lines +13 to 15
- numpy =2.4.3
- black =25.1.0
- h5py =3.16.0
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NumPy is pinned here to 2.4.0, but pyproject.toml pins NumPy to 2.4.3. Please keep the pins consistent across packaging and documentation environments (or explicitly call out that docs build uses a different NumPy) to prevent hard-to-reproduce doc build issues.

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Comment thread docs/environment.yml
- coverage
- setuptools
- numpy =2.3.5
- numpy =2.4.3
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Along with the NumPy bump, this environment remains on Pint 0.25.2 while pyproject.toml has Pint 0.25.3. If docs builds are intended to match the packaged dependency set, consider bumping Pint here too (or documenting why it must remain older).

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Comment thread .binder/environment.yml
Comment on lines +7 to 9
- numpy =2.4.3
- black =25.1.0
- h5py =3.16.0
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NumPy is pinned here to 2.4.0, but pyproject.toml pins 2.4.3 (and CI may use a different pin). Please keep the Binder environment aligned with the version used for packaging/CI to reduce "works in one env but not another" issues.

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- coverage
- setuptools
- numpy =2.3.5
- numpy =2.4.3
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This updates NumPy to 2.4.3, but other env definitions (e.g., docs and Binder) pin NumPy to 2.4.0. Please standardize on a single NumPy patch version across all environment files and pyproject.toml (or document why they intentionally differ), otherwise debugging CI vs docs/Binder failures becomes harder.

Suggested change
- numpy =2.4.3
- numpy =2.4.0

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- sphinxdft-data =0.0.1
- semantikon =1.0.0
- pint =0.25.2
- pint =0.25.3
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Pint is bumped here to 0.25.3, but some other conda env files still pin Pint to 0.25.2. Please align Pint pins across environments (or add an explicit reason for the divergence) to avoid subtle unit-handling differences between CI and docs/Binder.

Suggested change
- pint =0.25.3
- pint =0.25.2

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Comment thread pyproject.toml
]
dependencies = [
"numpy==2.3.5",
"numpy==2.4.3",
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PR title says updating NumPy to 2.4.0, but this file pins NumPy to 2.4.3. Please align the intended NumPy version across the repo (and update the PR title/description if 2.4.3 is intended) to avoid confusing or divergent dependency resolution between packaging and conda envs.

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Comment thread pyproject.toml
Comment on lines 29 to 31
"semantikon==1.0.0",
"pint==0.25.2",
"pint==0.25.3",
"pyyaml==6.0.3",
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This bumps Pint to 0.25.3 for the package, but some conda environment files still pin Pint to 0.25.2. That can lead to behavior differences between pip installs and docs/CI/Binder environments; consider updating all environment.yml pins to the same Pint version (or documenting why they must differ).

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codecov Bot commented Apr 20, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 88.54%. Comparing base (da02fd1) to head (0de6a47).
⚠️ Report is 8 commits behind head on main.

Additional details and impacted files
@@           Coverage Diff           @@
##             main      #63   +/-   ##
=======================================
  Coverage   88.54%   88.54%           
=======================================
  Files           8        8           
  Lines         812      812           
=======================================
  Hits          719      719           
  Misses         93       93           

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@jan-janssen jan-janssen merged commit fe9c658 into main Apr 20, 2026
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@jan-janssen jan-janssen deleted the numpy branch April 20, 2026 07:16
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4 participants