Standardize code conventions and modernize naming

[johnh2o2]

Audit and update code to use modern Python and CUDA conventions. Standardize function and class naming, improve type hinting where useful, and ensure code is internally consistent. Develop or update CONTRIBUTING guidelines to help maintain standards going forward.

[johnh2o2]

v1.0 status. A CONTRIBUTING.md with development setup, test, and style guidance ships in the release. The renaming/standardization half is explicitly deferred: renaming public API (e.g. eebls_*) immediately before a major release would churn every downstream script for purely cosmetic gain. If a rename happens it should land early in a major cycle (v2.0) with deprecation aliases. Leaving open, re-scoped to that.

[johnh2o2]

Release triage for PR #69 (cuvarbase 1.0.1, source 6b6c48945160).

This issue remains open and is listed as related follow-up in PR #69; it is intentionally excluded from automatic closure.

The owner’s June 12 comment explicitly re-scoped public API naming changes to a later major cycle with deprecation aliases. Current eebls_* entry points and compatibility names remain intentional. Remaining: carry out the separately planned naming/consistency work with a migration and deprecation strategy; this release does not complete that portion.

Evidence: contributor naming and style guidance · compatibility surface protected by tests