chore: update dependencies and adapt to updated crate APIs

Bumps core dependencies including ndarray, rand, hashbrown, niffler, ureq, sysinfo, indicatif, lru, and remove_dir_all. Adapts source code to accommodate breaking changes by migrating RNG initialization, adjusting HTTP response handling, and replacing the fs4 crate with standard library file locking. Adds a planning document for query benchmarking and sparse index regression tests.
2026-08-20 13:45:41 +02:00
parent 32bcbd1465
commit 5a9d903e51
15 changed files with 365 additions and 511 deletions
@@ -55,6 +55,7 @@ nav:
      - Kmer filtering: implementation/filtering.md
      - Select command: implementation/select.md
      - obitaxonomy crate: implementation/obitaxonomy.md
+      - "Benchmark: query-path testing (discussion)": implementation/benchmark_query_testing.md
  - Architecture:
      - Sequences: architecture/sequences/invariant.md
      - Kmer index: architecture/index_architecture.md