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This is the crate half of the reverted #1485, on its own, with feedback applied. The alignmentSieve changes are in a separate PR.

What changes

• hp is split into a core rlib (deeptools-core) and an optional Python layer behind the python feature.
• Public API is only normalization (scale_factor, scale_factor_bamcompare) and deseq_scalefactors. covcalc, filehandler, filtering and the other calc helpers are private.
• Normalization and ScaleFactorsMethod are enums with FromStr. A bad method string now returns NormalizationError (thiserror) instead of falling through to a default. The println!s and the unused _fraglen argument are gone from the public functions. bamcoverage and bamcompare parse the strings and turn the error into a ValueError.
• #![warn(missing_docs)], crate level docs, crate metadata. publish = false until we agree on the API.
• default = [], and [tool.maturin] features = ["python"] builds the extension. cargo tree -e normal shows no pyo3 in the core build, and CI now checks that.
• Carried over from chore: Split hp into core rlib + optional python layer #1485: crate rename to deeptools-core, the version sync check against release-please, and the Cargo.lock jsonpath fix.

How it was checked

• cargo test (core only) and cargo test --features python, both without warnings.
• maturin develop --release, then test_bamCoverage_and_bamCompare.py.
• Added tests for the new error paths: unknown method names, RPGC with a zero genome size, and a preset scale factor skipping that check.

What requires further feedback

Two things I decided without being sure:

1. Error scope. Only the public items return proper errors. About 100 panic sites remain in the private modules (55 in filehandler, 29 in covcalc, a few in filtering). They still reach Python as exceptions through pyo3, as before. Converting all of them touches every caller and I'd rather not do it in this PR. Is that acceptable, or do you want it done here?
2. default = []. I made the python feature opt-in so a plain deeptools-core = ... dependency does not pull pyo3, and let maturin switch it on. The other option is to keep default = ["python"] and make consumers write default-features = false. Do you have a preference?

Also, a fair question about what goes public was raised: I kept it to the two pure modules. filtering and filehandler would be the next candidates, but they are where most of the panics are, so I'd expose them in a follow-up with proper errors.

[coderabbitai]

No actionable comments were generated in the recent review.

Walkthrough

The Rust crate is renamed and can build as a core library without Python bindings. Normalization uses typed inputs and explicit errors. Python bindings use the updated API when enabled, and version checks include Cargo files.

Changes: Rust core extraction and normalization

Layer / File(s)	Summary
Typed normalization API and calculations src/normalization.rs, src/lib.rs, src/calc.rs, src/tests/test_normalization.rs, src/tests/test_calc.rs	Normalization methods and sample statistics use typed values. Calculations return errors for invalid inputs. Tests cover parsing, RPGC validation, presets, zero-read cases, and zero-count bins.
Python feature and build integration Cargo.toml, src/lib.rs, src/bamcompare.rs, src/bamcoverage.rs, pyproject.toml, src/tests/mod.rs, .github/workflows/test_rust.yml	Python bindings are gated behind the python feature. Python callers parse typed normalization values and map calculation errors to ValueError. CI builds and tests with and without the feature, and checks the default dependency tree for pyo3.
Cargo version synchronization release-please-config.json, scripts/check_version_sync.py	Release configuration updates the Cargo manifest and lockfile versions. The version-check script compares both with the DeepTools version.

Change: Refactor

Merge Risk: Minimal · up to 024f5

Zero-read normalization and the core dependency check are guarded correctly, leaving no confirmed merge-blocking risk.

Security architecture risk: Low · up to 024f5

The change keeps core calculations separate from Python integration and replaces several silent failures with explicit errors. No expansion of privileged access was identified in the inspected paths. External consumer compatibility and actual build and release outcomes remain unverified.

Retained concerns
No architecture-level concerns identified.

Security review details

Security Blast Radius

• inferred — The demonstrated impact is limited to an in-process Rust API, existing Python normalization callers, and repository build and release metadata. The wider Rust API supplies calculation capabilities rather than additional authority over assets or services; external downstream adoption is not established by repository-local evidence.

Trust Boundaries and Controls

• observed — Caller-supplied method strings cross into typed core calculations through explicit parsing, with errors translated at the Python boundary. Preset scale factors intentionally bypass calculation validation; this behavior is not an authorization bypass and predates the extraction.

Resilience and Maintainability Implications

• inferred — Centralized zero-read checks and explicit error propagation improve containment of invalid calculations at the existing Python boundary. These checks do not establish validation of every numeric input: presets are returned unchanged, and arbitrary finite-value guarantees are outside the demonstrated contract.

Pre-merge checks: 5

Check name	Status	Explanation
Title check		Title names the main change: splitting the hp crate into a deeptools-core crate with a curated public API. Matches the objectives and the Cargo.toml and lib.rs changes. Conventional Commits prefix is …
Description check		Description ties to the changeset. It covers the core/python feature split, the public API limits, the NormalizationError and enum changes, the CI pyo3 check, the version sync carry-over, and the test…
Docstring Coverage		Docstring coverage is inconclusive: files from earlier reviews still need to be rechecked within the check's analysis limits. Not blocking.
Linked Issues check		Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check		Check skipped because no linked issues were found for this pull request.

Full details: Title check

Explanation

Title names the main change: splitting the hp crate into a deeptools-core crate with a curated public API. Matches the objectives and the Cargo.toml and lib.rs changes. Conventional Commits prefix is used.

Full details: Description check

Explanation

Description ties to the changeset. It covers the core/python feature split, the public API limits, the NormalizationError and enum changes, the CI pyo3 check, the version sync carry-over, and the test plan.

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[coderabbitai]

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