Update scipy to 1.17.0 #449

jan-janssen · 2026-01-18T09:45:49Z

Summary by CodeRabbit

Chores
- Updated SciPy to 1.17.0 across project and CI configuration.
- Updated pyscal3 to 3.3.1 in project configuration.

_{✏️ Tip: You can customize this high-level summary in your review settings.}

coderabbitai · 2026-01-18T09:45:59Z

📝 Walkthrough

Walkthrough

SciPy bumped from 1.16.3 to 1.17.0 in .ci_support/environment.yml, .ci_support/environment_mini.yml, and pyproject.toml; pyscal3 bumped from 3.3.0 to 3.3.1 in .ci_support/environment.yml and pyproject.toml. No code or public API changes.

Changes

Cohort / File(s)	Summary
Main environment files `.ci_support/environment.yml`, `pyproject.toml`	Updated `scipy` from `1.16.3` → `1.17.0` and `pyscal3` from `3.3.0` → `3.3.1`.
Minimal environment `.ci_support/environment_mini.yml`	Updated `scipy` from `1.16.3` → `1.17.0`.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~2 minutes

Possibly related PRs

Update scipy to 1.15.1 #306: Updates SciPy dependency version in the same configuration files.
Bump scipy from 1.14.0 to 1.14.1 #243: Performs a similar SciPy version bump across environment and project config files.
Update pyscal to 3.3.0 #371: Modifies pyscal3 version in the same dependency files.

Suggested labels

dependencies, patch

Poem

🐰 A tiny hop, a version nudge,
SciPy and pyscal3 got a gentle judge.
Across three files I danced and spun,
Now builds trot forward—one by one. 🥕

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately reflects the primary change in the PR: updating scipy from 1.16.3 to 1.17.0 across all configuration files.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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coderabbitai

Actionable comments posted: 2

🤖 Fix all issues with AI agents

In @.ci_support/environment_mini.yml:
- Line 7: The Python version constraint mismatch: update the requires-python
field in pyproject.toml to align with SciPy 1.17.0 by changing requires-python =
">=3.10, <3.14" to requires-python = ">=3.11, <3.14" (or alternatively downgrade
SciPy in .ci_support/environment_mini.yml to a 1.16.x release if you must keep
Python 3.10 support); modify the requires-python entry in pyproject.toml
accordingly so it matches the SciPy version declared in
.ci_support/environment_mini.yml.

In `@pyproject.toml`:
- Line 29: The pyproject.toml currently lists "scipy==1.17.0" which requires
Python 3.11–3.14 and therefore conflicts with the project's requires-python =
">=3.10, <3.14"; update the requires-python constraint to match SciPy (e.g.,
">=3.11, <3.14") and adjust the package classifiers (Python :: 3.11, etc.) to
reflect the new supported Python versions; alternatively, if you must keep
supporting 3.10, replace "scipy==1.17.0" with a SciPy release that supports 3.10
and update the lock accordingly.

coderabbitai · 2026-01-18T09:52:06Z

.ci_support/environment_mini.yml

 - coverage
 - numpy =2.3.5
- scipy =1.16.3
+- scipy =1.17.0


⚠️ Potential issue | 🟠 Major

🧩 Analysis chain

🏁 Script executed:

# Check Python version requirement in pyproject.toml rg -n "requires-python" . --type toml -A 1 -B 1 # Check the full environment files cat .ci_support/environment_mini.yml # Search for Python version references in CI rg -n "python" .ci_support/ --type yaml | head -20 # Check for other environment files ls -la .ci_support/

Repository: pyiron/structuretoolkit

Length of output: 837

🌐 Web query:

SciPy 1.17.0 Python version requirement

💡 Result:

SciPy 1.17.0 requires Python 3.11–3.14 (and NumPy >= 1.26.4). [1][2]

Sources:
[1] SciPy 1.17.0 release notes. [2] SciPy 1.17.0 zenodo release metadata.

🏁 Script executed:

# Check other environment files for Python/SciPy versions cat .ci_support/environment.yml cat .ci_support/environment-old.yml # Search for CI workflow files that might define Python versions find . -name "*.yml" -o -name "*.yaml" | grep -E "(github|ci|workflow)" | head -10 fd -e yml -e yaml | grep -E "(github|\.github|workflow)" | head -20

Repository: pyiron/structuretoolkit

Length of output: 1019

🏁 Script executed:

# Check CI workflows for Python versions cat .github/workflows/pipeline.yml | head -80 # Search for Python version matrix in workflows rg -n "python" .github/workflows/ -A 2 -B 2 | head -50

Repository: pyiron/structuretoolkit

Length of output: 5163

Resolve Python version constraint mismatch with SciPy 1.17.0.

SciPy 1.17.0 requires Python 3.11–3.14, but pyproject.toml (line 14) specifies requires-python = ">=3.10, <3.14". Since CI testing only covers Python 3.11+, update the constraint to match:

Change requires-python = ">=3.10, <3.14" to requires-python = ">=3.11, <3.14"

Alternatively, if Python 3.10 support is needed, retain SciPy 1.16.x.

🤖 Prompt for AI Agents

In @.ci_support/environment_mini.yml at line 7, The Python version constraint mismatch: update the requires-python field in pyproject.toml to align with SciPy 1.17.0 by changing requires-python = ">=3.10, <3.14" to requires-python = ">=3.11, <3.14" (or alternatively downgrade SciPy in .ci_support/environment_mini.yml to a 1.16.x release if you must keep Python 3.10 support); modify the requires-python entry in pyproject.toml accordingly so it matches the SciPy version declared in .ci_support/environment_mini.yml.

coderabbitai · 2026-01-18T09:52:06Z

pyproject.toml

    "ase==3.27.0",
    "numpy==2.3.5",
-    "scipy==1.16.3",
+    "scipy==1.17.0",


⚠️ Potential issue | 🟠 Major

Python version constraint requires update.

SciPy 1.17.0 requires Python 3.11-3.14, which conflicts with Line 14's requires-python = ">=3.10, <3.14". Users on Python 3.10 will encounter installation failures when pip attempts to resolve this dependency.

Suggested fix: Update Python version requirement

-requires-python = ">=3.10, <3.14" +requires-python = ">=3.11, <3.14"

Also update the classifiers accordingly:

- "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", "Programming Language :: Python :: 3.13",

🤖 Prompt for AI Agents

In `@pyproject.toml` at line 29, The pyproject.toml currently lists "scipy==1.17.0" which requires Python 3.11–3.14 and therefore conflicts with the project's requires-python = ">=3.10, <3.14"; update the requires-python constraint to match SciPy (e.g., ">=3.11, <3.14") and adjust the package classifiers (Python :: 3.11, etc.) to reflect the new supported Python versions; alternatively, if you must keep supporting 3.10, replace "scipy==1.17.0" with a SciPy release that supports 3.10 and update the lock accordingly.

jan-janssen · 2026-01-18T09:56:26Z

======================================================================
ERROR: test_C15 (test_compound.TestCompound.test_C15)
Tests based on Xie et al., JMR 2021 (DOI:10.1557/s43578-021-00237-y).
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/runner/work/structuretoolkit/structuretoolkit/tests/test_compound.py", line 90, in test_C15
    csa = stk.analyse.get_centro_symmetry_descriptors(structure)[unique_ids]
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
  File "/Users/runner/miniconda3/envs/test/lib/python3.13/site-packages/structuretoolkit/analyse/pyscal.py", line 77, in get_centro_symmetry_descriptors
    sys = ase_to_pyscal(structure)
  File "/Users/runner/miniconda3/envs/test/lib/python3.13/site-packages/structuretoolkit/common/pyscal.py", line 15, in ase_to_pyscal
    import pyscal3 as pc
  File "/Users/runner/miniconda3/envs/test/lib/python3.13/site-packages/pyscal3/__init__.py", line 1, in <module>
    from pyscal3.core import System
  File "/Users/runner/miniconda3/envs/test/lib/python3.13/site-packages/pyscal3/core.py", line 15, in <module>
    from scipy.special import sph_harm
ImportError: cannot import name 'sph_harm' from 'scipy.special' (/Users/runner/miniconda3/envs/test/lib/python3.13/site-packages/scipy/special/__init__.py)

----------------------------------------------------------------------

jan-janssen · 2026-01-18T10:06:23Z

Waiting for pyscal/pyscal3#59

codecov · 2026-01-28T13:27:29Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 82.91%. Comparing base (26ceabe) to head (18570b2).
⚠️ Report is 6 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #449   +/-   ##
=======================================
  Coverage   82.91%   82.91%           
=======================================
  Files          25       25           
  Lines        1820     1820           
=======================================
  Hits         1509     1509           
  Misses        311      311

☔ View full report in Codecov by Sentry.
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jan-janssen added 3 commits January 18, 2026 10:44

Update scipy dependency version to 1.17.0

2986f52

Update scipy version to 1.17.0

bd7b00b

Update scipy version from 1.16.3 to 1.17.0

1549f4e

coderabbitai bot reviewed Jan 18, 2026

View reviewed changes

jan-janssen mentioned this pull request Jan 18, 2026

Bump scipy from 1.16.3 to 1.17.0 pyiron/pyiron_atomistics#1916

Draft

jan-janssen mentioned this pull request Jan 25, 2026

Update scipy to 1.17.0 pyiron/atomistics#618

Draft

jan-janssen added 2 commits January 28, 2026 14:24

Update pyproject.toml

1bec4ba

Update environment.yml

18570b2

jan-janssen merged commit 7850bd2 into main Jan 28, 2026
17 of 18 checks passed

jan-janssen deleted the scipy branch January 28, 2026 13:31

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