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refactor(sort): make --sort-stats run-scoped instead of a process-global static - #855

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Summary

SORT_STATS was a process-global AtomicBool gating the stat! diagnostics macro. Because fgumi-sort is a library, two sorts in one process with different --sort-stats settings clobbered each other's flag, and the two flag tests had to be serialized with a mutex to survive plain cargo test's thread-per-test model.

What changed

The flag now hangs off the sort's own state instead of a global. sort_stats is a field on RawExternalSorter (the sort-options struct, set via a .sort_stats(bool) builder from the CLI) and is copied into the SortPhaseTimer and SortWorkerPool that sorter builds — the two objects the stat! emitters already hold as self/pool. The macro takes the flag as its first argument (stat!(sort_stats, ...)); each emitter reads it from self.sort_stats / pool.sort_stats(), or takes a sort_stats: bool parameter where it is a free function. The global static, its set_sort_stats/sort_stats_enabled functions, and the SORT_STATS_LOCK test mutex are removed; the flag test is rewritten to check the run-scoped default and builder.

This removes both the library-concurrency hazard (concurrent sorts now keep independent settings) and the plain-cargo test race. Verified end-to-end: fgumi sort --sort-stats still emits the phase-timing diagnostics and a plain sort emits none. Full suite, clippy, and fmt pass.

Closes #849.

Risk: Sort diagnostics change when --sort-stats is enabled; grouping, consensus, sort order, corrected UMIs, and metrics output are none; unsafe changes and CLAUDE.md allowlist updates are none; memory bounds, queue capacity, and thread/backpressure policy changes are none.

Fix: Scope sort_stats to each RawExternalSorter run instead of process-global state. Propagate the setting through SortPhaseTimer and SortWorkerPool, remove the global state and test mutex, and add builder and end-to-end tests for enabled and default-disabled diagnostics.

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Walkthrough

The process-global statistics flag was replaced with run-scoped configuration. Sorter, timer, worker-pool, and diagnostic paths now use the configured value. Tests update worker-pool construction and verify disabled and enabled settings.

Changes

Sort statistics configuration

Layer / File(s) Summary
Run-scoped configuration
crates/fgumi-sort/src/lib.rs, crates/fgumi-sort/src/external.rs, src/lib/commands/sort.rs
The global setter and getter were removed. RawExternalSorter::sort_stats(bool) configures each run, and Sort::execute passes the command setting to the builder.
Phase and merge diagnostics
crates/fgumi-sort/src/external.rs
Timers, phase reporting, run formation, merge diagnostics, stall reports, and lifecycle reports use the run-scoped flag.
Worker-pool contract and validation
crates/fgumi-sort/src/worker_pool.rs, crates/fgumi-sort/src/bgzf_io.rs, crates/fgumi-sort/src/pooled_bam_writer.rs, crates/fgumi-sort/src/pooled_chunk_writer.rs, crates/fgumi-sort/src/phase1_keys.rs
SortWorkerPool::new accepts and stores the flag. Existing test constructions pass false. Sorter tests cover default and explicit configuration.

Estimated code review effort: 3 (Moderate) | ~25 minutes

Merge Risk: 🟡 Moderate · up to c6b9d

The refactor introduces new unsafe code without the repository-required safety justification and allowlist update, so the PR is not merge-ready until that documentation and approval requirement is addressed.

Suggested labels: fgumi sort

🚥 Pre-merge checks | ✅ 3
✅ Passed checks (3 passed)
Check name Status Explanation
Title check ✅ Passed The title follows Conventional Commit format and accurately describes the run-scoped sort statistics refactor.
Linked Issues check ✅ Passed The changes remove global sort-statistics state and propagate run-scoped configuration through the sorting pipeline as required by issue #849.
Out of Scope Changes check ✅ Passed The changes are limited to run-scoped sort-statistics propagation, related API updates, and necessary test adjustments.

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nh13 force-pushed the 849/nhomer/sort-stats-run-scoped branch from ac6ef1f to c6b9d38 Compare August 22, 2026 18:15
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nh13 deployed to github-actions August 22, 2026 18:15 — with GitHub Actions Active
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Codecov Report

❌ Patch coverage is 98.47328% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 94.66%. Comparing base (a46e71d) to head (5be9805).
⚠️ Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
crates/fgumi-sort/src/external.rs 98.18% 4 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #855      +/-   ##
==========================================
+ Coverage   94.57%   94.66%   +0.08%     
==========================================
  Files         193      193              
  Lines      119513   119792     +279     
==========================================
+ Hits       113033   113404     +371     
+ Misses       6480     6388      -92     

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Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (1)
crates/fgumi-sort/src/phase1_keys.rs (1)

119-136: 🔒 Security & Privacy | 🟠 Major | ⚡ Quick win

Keep this unsafe implementation in the approved allowlist.

prefetch_read_l1 adds new unsafe blocks in crates/fgumi-sort/src/phase1_keys.rs, which is not an approved fgumi-sort unsafe hot path. Move this code to an approved module, or add the required crate-root justification and CLAUDE.md unsafe-allowlist entry before merge. Local #[allow(unsafe_code)] does not meet that requirement.

As per coding guidelines, “any new unsafe block requires updating this section with a written justification.” As per path instructions, “For every unsafe block require a // SAFETY: comment … AND a corresponding entry in the unsafe allowlist in CLAUDE.md.”

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In `@crates/fgumi-sort/src/phase1_keys.rs` around lines 119 - 136, Handle the new
unsafe blocks in prefetch_read_l1 by moving the implementation to an approved
unsafe hot-path module, or by adding the required crate-root written
justification and corresponding CLAUDE.md unsafe-allowlist entry; retain the
existing SAFETY comments, since local #[allow(unsafe_code)] alone is
insufficient.

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Outside diff comments:
In `@crates/fgumi-sort/src/phase1_keys.rs`:
- Around line 119-136: Handle the new unsafe blocks in prefetch_read_l1 by
moving the implementation to an approved unsafe hot-path module, or by adding
the required crate-root written justification and corresponding CLAUDE.md
unsafe-allowlist entry; retain the existing SAFETY comments, since local
#[allow(unsafe_code)] alone is insufficient.

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📒 Files selected for processing (5)
  • crates/fgumi-sort/src/external.rs
  • crates/fgumi-sort/src/lib.rs
  • crates/fgumi-sort/src/phase1_keys.rs
  • crates/fgumi-sort/src/worker_pool.rs
  • src/lib/commands/sort.rs

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…bal static

`SORT_STATS` was a process-global `AtomicBool` gating the `stat!` diagnostics macro.
Because fgumi-sort is a library, two sorts in one process with different --sort-stats
settings clobbered each other's flag, and the two flag tests had to be serialized with
a mutex to survive plain `cargo test`'s thread-per-test model.

Hang the flag off the sort's own state instead of a global. `sort_stats` is now a field
on `RawExternalSorter` (the sort-options struct, set via a `.sort_stats(bool)` builder
from the CLI) and is copied into the `SortPhaseTimer` and `SortWorkerPool` that sorter
builds -- the two objects the `stat!` emitters already hold as `self`/`pool`. The macro
takes the flag as its first argument (`stat!(sort_stats, ...)`); each emitter reads it
from `self.sort_stats` / `pool.sort_stats()`, or takes a `sort_stats: bool` parameter
where it is a free function. The global static, its `set_sort_stats`/`sort_stats_enabled`
functions, and the `SORT_STATS_LOCK` test mutex are removed; the flag test is rewritten
to check the run-scoped default and builder.

This removes both the library-concurrency hazard (concurrent sorts now keep independent
settings) and the plain-`cargo test` race. Verified end-to-end: `fgumi sort --sort-stats`
still emits the phase-timing diagnostics and a plain sort emits none. Closes #849.
@nh13
nh13 force-pushed the 849/nhomer/sort-stats-run-scoped branch from c6b9d38 to 5be9805 Compare August 22, 2026 19:37
@nh13
nh13 deployed to github-actions August 22, 2026 19:37 — with GitHub Actions Active
@nh13
nh13 added this pull request to the merge queue Aug 22, 2026
Merged via the queue into main with commit 2ce643b Aug 22, 2026
16 checks passed
@nh13
nh13 deleted the 849/nhomer/sort-stats-run-scoped branch August 22, 2026 19:51
@nh13 nh13 mentioned this pull request Aug 22, 2026

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refactor(sort): make --sort-stats run-scoped instead of a process-global static

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