port to f4enix v1

[dodu94]

f4enix package was recently updated to v1 which breaks retrocompatibility. Small fixes are needed in JADE to account for this

Summary by CodeRabbit

• Bug Fixes

  • Updated sphere input generation and material handling for compatibility with the latest supported F4Enix API.
  • Improved OpenMC material conversion, including more reliable nuclide and density handling.
  • Corrected material recovery during benchmark workflows.
  • Fixed a documentation typo and minor formatting issue in OpenMC processing.

• Tests

  • Updated input-generation checks to reflect the current material and output structures.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Advanced

Run ID: 5f5bc333-2850-4102-bd45-d9cf4d6def38

📥 Commits

Reviewing files that changed from the base of the PR and between 85fc7c7 and a791ab6.

📒 Files selected for processing (5)

• pyproject.toml
• src/jade/helper/openmc.py
• src/jade/run/benchmark.py
• src/jade/run/input.py
• tests/run/test_input.py

Included review availability: Your plan provides up to 1 included review per hour; 0 remain after this review.

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Walkthrough

The change updates JADE for F4Enix 1.0.0. Material construction, OpenMC conversion, sphere input generation, benchmark recovery, and tests now use the revised material and parser APIs.

Changes

F4Enix API migration

Layer / File(s)	Summary
Material API contracts pyproject.toml, src/jade/run/input.py	The minimum F4Enix version is 1.0.0. Sphere inputs construct Material and Zaid objects directly.
OpenMC material conversion src/jade/helper/openmc.py, src/jade/run/input.py	OpenMC conversion reads material.zaids, uses explicit density maps, and resolves nuclides from Zaid.fullname.
Sphere integration and validation src/jade/run/input.py, src/jade/run/benchmark.py, tests/run/test_input.py	Sphere inputs and benchmark recovery use mat_section. Tests read NPS and library values from the updated parser structures.

Priority: ⬇️ Low

Estimated code review effort: 3 (Moderate) | ~20 minutes

Merge Risk: ⚪ Minimal · up to a791a

JADE is updated for F4Enix 1.0 material APIs, including sphere generation, OpenMC conversion, and benchmark material recovery. No concrete current-head merge risk remains.

Suggested reviewers: mcampos16

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 33.33% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 18 functions across 4 files. (1 skipped: …	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and concisely describes the main change: porting JADE to f4enix v1.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

Full details: Docstring Coverage

Explanation

Docstring coverage is 33.33% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 18 functions across 4 files. (1 skipped: 1 unsupported.)

• Fix all pre-merge checks with AI

✨ Finishing Touches 💡 1

📝 Generate docstrings 💡

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch update-to-f4enix-v1

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_{A rabbit checks the materials bright
New zaids hop through OpenMC light
Densities follow every trail
Parser paths no longer fail
F4Enix blooms in version one
The migration’s work is done}

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

Files with missing lines	Coverage Δ
src/jade/helper/openmc.py	88.33% <100.00%> (-0.65%)	⬇️
src/jade/run/benchmark.py	86.49% <100.00%> (ø)
src/jade/run/input.py	87.76% <100.00%> (-0.31%)	⬇️

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