Split up ext::secondary file

[JoeyBF]

As the comments say, this integrates the secondary machinery by having the primary and secondary variants of structs (Resolution, ResolutionHomomorphism, etc.) in the same file.

Summary by CodeRabbit

• New Features

  • Added secondary-lift support across chain complexes, resolutions, and maps.
  • Exposed new secondary resolution, homotopy, and homomorphism capabilities for deeper spectral-sequence calculations.
  • Added new secondary-page computation and nullhomotopy helpers.

• Refactor

  • Moved secondary-related implementations into dedicated internal modules.
  • Updated module visibility and re-exports so the new secondary types remain available through the public API.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: ASSERTIVE

Plan: Pro

Run ID: 30ccba7e-3e29-476b-b4ea-b228fb1c1a13

📥 Commits

Reviewing files that changed from the base of the PR and between 468f658 and d731aa3.

📒 Files selected for processing (5)

• ext/src/chain_complex/chain_homotopy.rs
• ext/src/chain_complex/mod.rs
• ext/src/resolution.rs
• ext/src/resolution_homomorphism.rs
• ext/src/secondary.rs

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📝 Walkthrough

Walkthrough

Refactors the "secondary" lift machinery in the ext crate by extracting concrete implementations of SecondaryResolution, SecondaryResolutionHomomorphism, and SecondaryChainHomotopy from secondary.rs into dedicated pub(crate) mod secondary submodules within resolution.rs, resolution_homomorphism.rs, and chain_homotopy.rs, which are then re-exported from secondary.rs.

Changes

Secondary Lift Module Reorganization

Layer / File(s)	Summary
Module visibility and re-exports ext/src/chain_complex/mod.rs, ext/src/secondary.rs	chain_homotopy module visibility becomes pub(crate); secondary.rs drops in-file struct/impl definitions and re-exports concrete secondary lift types from their new module locations, adjusting imports accordingly.
SecondaryResolution implementation ext/src/resolution.rs	Adds SecondaryResolution<CC> with homotopy storage and intermediates cache; implements SecondaryLift (shift, max, composite, compute_intermediate) and adds new, homotopy, and e3_page methods.
SecondaryResolutionHomomorphism implementation ext/src/resolution_homomorphism.rs	Adds SecondaryResolutionHomomorphism<CC1, CC2> with SecondaryLift implementation, constructor/accessors, hom_k_with/hom_k for computing secondary homotopy maps, and product_nullhomotopy using an sseq quasi-inverse.
SecondaryChainHomotopy implementation ext/src/chain_complex/chain_homotopy.rs	Adds SecondaryChainHomotopy<S, T, U> wrapping a ChainHomotopy with secondary resolution homomorphisms and optional lambda maps; implements SecondaryLift and a validating new constructor with save-directory setup.

Sequence Diagram(s)

sequenceDiagram
  participant Caller
  participant SecondaryResolutionHomomorphism
  participant UnderlyingMap
  participant Sseq

  Caller->>SecondaryResolutionHomomorphism: product_nullhomotopy(lambda_part, sseq, b, class)
  SecondaryResolutionHomomorphism->>SecondaryResolutionHomomorphism: hom_k_with(class, lambda_part)
  SecondaryResolutionHomomorphism->>UnderlyingMap: hom_k(lambda_part)
  SecondaryResolutionHomomorphism->>Sseq: quasi_inverse for d2 differential
  Sseq-->>Caller: return resulting FpVector

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Estimated code review effort

🎯 5 (Critical) | ⏱️ ~120 minutes

Possibly related PRs

• SpectralSequences/sseq#226: The new SecondaryResolution::e3_page and SecondaryResolutionHomomorphism::{hom_k_with, hom_k, product_nullhomotopy} build directly on the stage-2 sseq::Sseq<2, sseq::Adams> API introduced there.
• SpectralSequences/sseq#241: Depends on the SecondaryChainHomotopy/SecondaryResolution/SecondaryResolutionHomomorphism composite/compute_intermediate machinery added here to implement SecondaryExtAlgebra's d2 differential.

Suggested reviewers

• hoodmane

A rabbit hops through code so deep,
Sorting secondary lifts while others sleep,
Homotopies tucked in modules new,
Re-exports gleam like morning dew,
Hop, hop, the lift is clean and true! 🐇✨

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title matches the main change: ext::secondary was split into separate modules and re-exports.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
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.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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[JoeyBF]

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