Update pixi and use pyrefly as type checker

[Jens (JensWehner)]

• Replace mypy 2.3.1 with strict Pyrefly 1.3.2 and resolve all resulting diagnostics.
• Add consolidated dev and dev-gpu environments and update Pixi from 0.78 to 0.81.
• Refresh the lockfile, including Python patch releases, NumPy/SciPy/pandas, DFT-D3, and CUDA 13 packages.
• Strengthen typing and validation across PySCF, ASE, model, benchmark, and test code.

pixi env updates

• Python 3.11.15 → 3.11.16 and 3.12.13 → 3.12.14
• NumPy 2.5.2 → 2.5.3, SciPy 1.18.0 → 1.18.1, and pandas 3.0.5 → 3.0.6
• DFT-D3 1.5 → 1.6
• CUDA 13.3 → 13.4, cuDNN 9.25 → 9.26, NCCL 2.30 → 2.31, and cuTensor 2.7 → 2.8
• GCC runtimes 16.1 → 16.2 and LLVM 22 → 23

[Copilot]

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Copilot review overview

Review effort: Lite
Findings: 1

Open (1)

• RunConfig.from_json() treats json.load() output as _RunConfigJson without validating… · New

What changed in this PR

This PR tightens typing across the codebase by migrating from mypy to Pyrefly, adding @override annotations, and strengthening runtime validation/typing in several APIs (PySCF integration, ASE calculator, and benchmark tooling).

Changes:

• Replace mypy configuration/hooks with Pyrefly (pyrefly.toml, pre-commit, pixi tooling, docs).
• Improve type safety via typing_extensions.override, refined type hints, and safer test monkeypatch patterns.
• Update PySCF/ASE integration behavior and add tests around error cases and interface contracts.

File	Description
skala/​tests/​utils.py	Adds @override to a test functional implementation.
skala/​tests/​test_xc_integrator.py	Improves iterator return typing for model feature chunks.
skala/​tests/​test_pyscf_gradients.py	Adds @override annotations for gradient-related test functionals.
skala/​tests/​test_pyscf_classes.py	Adds a regression test for gradients requiring initialized UKS grids.
skala/​tests/​test_model_chunking.py	Replaces lambdas with named functions for monkeypatching; adds @override in test functional.
skala/​tests/​test_gradient_core.py	Adds @override for test functional override clarity.
skala/​tests/​test_gpu4pyscf_gradients.py	Removes type-ignores around torch streams; adds @override in test functionals.
skala/​tests/​test_gpu4pyscf_ao_screening.py	Adds assertions and local vars to satisfy stricter typing for grids.
skala/​tests/​test_evaluation.py	Avoids direct mutation on frozen dataclass by using setattr helper under pytest.raises.
skala/​tests/​test_ase.py	Adds parameter validation tests and reduces type-ignores by asserting calculator shape/types.
skala/​tests/​test_ao_screening.py	Strengthens typing, compilation monkeypatching, and adds NumInt contract/mode tests.
skala/​src/​skala/​pyscf/​xc_integrator.py	Refactors del statements (readability/type tooling).
skala/​src/​skala/​pyscf/​retry.py	Guards callback invocation with a None check.
skala/​src/​skala/​pyscf/​numint.py	Makes SkalaNumInt inherit PySCF NumInt and adds mode validation + libxc shim.
skala/​src/​skala/​pyscf/​memory_estimators.py	Tweaks memory arithmetic types under strict checking.
skala/​src/​skala/​pyscf/​grids.py	Removes type-ignore inheritance, adds overrides, and validates coords/weights before layout prep.
skala/​src/​skala/​pyscf/​gradients.py	Adds @override and explicit runtime error when grids are uninitialized.
skala/​src/​skala/​pyscf/​feature_math.py	Marks forward as an override for feature modules.
skala/​src/​skala/​pyscf/​dft.py	Adds a helper to require SkalaNumInt and adds @override annotations.
skala/​src/​skala/​pyscf/​backend.py	Removes unnecessary type-ignore around torch.from_dlpack.
skala/​src/​skala/​pyscf/​ao_evaluation.py	Adds @override, refactors context fields, and removes apply type-ignores.
skala/​src/​skala/​pyscf/​__init__.py	Refines typing of KS factory functions and generalizes config application with a TypeVar.
skala/​src/​skala/​gpu4pyscf/​grids.py	Removes type-ignore from grids inheritance.
skala/​src/​skala/​gpu4pyscf/​gradients.py	Removes type-ignore from gradient base classes.
skala/​src/​skala/​gpu4pyscf/​dft.py	Removes type-ignore around typing of xc swap for density fitting.
skala/​src/​skala/​functional/​traditional.py	Adds @override annotations to functional methods.
skala/​src/​skala/​functional/​load.py	Adds @override annotations and removes a torch.jit.load type-ignore.
skala/​src/​skala/​dispersion.py	Cleans up type-ignores and adjusts import suppression for Pyrefly.
skala/​src/​skala/​ase/​calculator.py	Introduces validated frozen parameters dataclass and strengthens input/type handling.
pyrefly.toml	Adds strict Pyrefly configuration and missing-import allowlist.
pyproject.toml	Removes mypy tool configuration (migration).
pixi.toml	Updates Pixi requirements, adds pyrefly + typing-extensions, and reshapes environments.
model/​tests/​test_utils.py	Switches tests to use local Irreps wrapper directly.
model/​src/​skala_model/​utils/​symmetric_contraction.py	Migrates to local Irreps type and adds @override on forwards.
model/​src/​skala_model/​utils/​pad_ragged.py	Removes torch.jit tracing type-ignores.
model/​src/​skala_model/​model.py	Adds @override, refines ignores for Pyrefly, and replaces type-ignores with asserts.
model/​src/​skala_model/​layers.py	Adds @override annotations to module forward methods.
model/​pyproject.toml	Pins e3nn version range.
gauxc/​src/​skala_gauxc/​export.py	Removes structured dtype construction type-ignores.
benchmark/​tests/​test_timing.py	Adds unit tests for timeline mark type enforcement.
benchmark/​tests/​test_runner.py	Adds a JSON round-trip test for RunConfig.
benchmark/​tests/​test_orchestrator.py	Replaces lambda monkeypatch with named function for typing.
benchmark/​tests/​test_metrics.py	Adds tests for invalid iteration counts.
benchmark/​tests/​test_docs.py	Replaces generator-throw lambda with explicit failing function for typing.
benchmark/​tests/​test_cli.py	Replaces lambdas with typed fakes for monkeypatch targets.
benchmark/​src/​skala_benchmark/​timing.py	Introduces typed CUDA mark protocol, type checks in timelines, and Generator return types.
benchmark/​src/​skala_benchmark/​runner.py	Adds TypedDicts for JSON config parsing and tightens some types/casts.
benchmark/​src/​skala_benchmark/​report/​prose.py	Normalizes notes with an explicitly typed intermediate list.
benchmark/​src/​skala_benchmark/​metrics.py	Avoids int(None) and improves robustness of iterations metric parsing.
benchmark/​src/​skala_benchmark/​fitting.py	Refactors loops to remove None asserts and improve typing/clarity.
CONTRIBUTING.md	Updates dev instructions to Pixi 0.81 and new dev environment usage.
AGENTS.md	Updates environment/type-checking guidance from mypy to Pyrefly.
.pre-commit-config.yaml	Replaces mypy hook with pyrefly check.
.github/​workflows/​lint.yml	Uses a Pixi environment compatible with updated environment definitions.
.github/​actions/​setup-pixi/​action.yml	Updates Pixi version to v0.81.0.

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[Sebastian Ehlert (awvwgk)]

Thank you, looks good to me.