Update scipy to 1.16.2

[jan-janssen]

Summary by CodeRabbit

• Chores

  • Updated SciPy to 1.16.2 across environments to improve compatibility, stability, and performance.
  • Updated NumPy to 2.3.3 in the interactive environment for better reliability and alignment with upstream releases.
  • General dependency refresh to ensure smoother setup and fewer environment conflicts.

• Tests

  • No functional changes; existing behavior remains the same, with updates focused on underlying dependencies.

[coderabbitai]

Walkthrough

Dependency versions updated: SciPy from 1.15.2 to 1.16.2 across CI, binder, and project config; NumPy from 2.3.2 to 2.3.3 in binder environment. No other lines changed.

Changes

Cohort / File(s)	Summary of Changes
CI environments \.ci_support/environment-docs.yml, \.ci_support/environment.yml	Bump scipy 1.15.2 → 1.16.2
Binder environment binder/environment.yml	Bump numpy 2.3.2 → 2.3.3; bump scipy 1.15.2 → 1.16.2
Project config pyproject.toml	Bump SciPy dependency 1.15.2 → 1.16.2

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~3 minutes

Possibly related PRs

• Bump scipy from 1.14.0 to 1.14.1 #327 — Updates scipy version in the same files; parallel dependency bump.
• Update scipy to 1.15.1 #389 — Prior scipy bump in identical locations; related dependency maintenance.

Suggested labels

dependencies

Poem

I hop through yml fields with glee,
Nudging SciPy up a minor degree.
Binder packs a NumPy snack,
Envs aligned—no turning back.
Thump-thump goes my QA feet—
Version carrots, crisp and neat. 🥕🐇

Pre-merge checks and finishing touches

✅ 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 “Update scipy to 1.16.2” precisely conveys the core change of this pull request, which is bumping the SciPy dependency version across multiple configuration files. It is concise, specific, and avoids unnecessary details or generic phrasing, enabling reviewers to immediately understand the PR’s focus. This fulfills the requirement that the title clearly summarize the main modification without extraneous information.
Docstring Coverage	✅ Passed	No functions found in the changes. Docstring coverage check skipped.

✨ Finishing touches

🧪 Generate unit tests

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch scipy

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[coderabbitai]

Actionable comments posted: 0

🧹 Nitpick comments (3)

binder/environment.yml (1)

5-6: Align Binder lammps package pins with pyproject optional dependencies

binder/environment.yml currently pins

• pylammpsmpi =0.3.2 (line 14)
• pyiron_lammps =0.4.6 (line 18)

while pyproject.toml optional dependencies use

• pylammpsmpi==0.3.3
• pyiron_lammps==0.4.7

Update these versions in binder/environment.yml to match and avoid drift in tutorials.

.ci_support/environment.yml (1)

12-12: Add CI dry-run to validate SciPy/NumPy pins
Include a mamba env create --name test --file .ci_support/environment.yml --dry-run job to catch unintended downgrades after bumping SciPy to 1.16.2 with NumPy locked at 2.3.3.

pyproject.toml (1)

29-29: Validate SciPy 1.16.2 compatibility and optimize build-system.requires

• SciPy 1.16.2 supports Python 3.11–3.13 and requires NumPy ≥1.25.2; current pins (SciPy==1.16.2, NumPy==2.3.3) are consistent across environments.
• Consider trimming [build-system].requires to only include hatchling and hatch-vcs to prevent pulling runtime dependencies into build isolation.

📜 Review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 218b528 and 720f6ff.

📒 Files selected for processing (4)

• .ci_support/environment-docs.yml (1 hunks)
• .ci_support/environment.yml (1 hunks)
• binder/environment.yml (1 hunks)
• pyproject.toml (1 hunks)

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (13)

• GitHub Check: unittest_old
• GitHub Check: notebooks
• GitHub Check: unittest_siesta
• GitHub Check: unittest_orb
• GitHub Check: unittest_matrix (ubuntu-latest, 3.11)
• GitHub Check: unittest_mace
• GitHub Check: unittest_grace
• GitHub Check: unittest_sphinxdft
• GitHub Check: unittest_qe
• GitHub Check: unittest_matrix (ubuntu-latest, 3.12)
• GitHub Check: unittest_matrix (macos-latest, 3.12)
• GitHub Check: unittest_gpaw
• GitHub Check: coverage

🔇 Additional comments (1)

.ci_support/environment-docs.yml (1)

11-11: Docs env SciPy bump LGTM; no direct SciPy imports in docs.
Run a Sphinx build to catch any deprecation warnings from SciPy.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 85.71%. Comparing base (218b528) to head (720f6ff).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #553   +/-   ##
=======================================
  Coverage   85.71%   85.71%           
=======================================
  Files          43       43           
  Lines        2591     2591           
=======================================
  Hits         2221     2221           
  Misses        370      370           

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