chore: release v0.3.0

CHANGELOG.md

@@ -4,6 +4,62 @@ All notable changes to this project will be documented in this file.
 
 ## [Unreleased]
 
+## [0.3.0] - 2026-06-10
+
+### Bug Fixes
+
+- Make root crate build cleanly with `--no-default-features` ([#314](https://github.com/fulcrumgenomics/fgumi/pull/314))
+- Deterministic MoleculeId numbering via opt-in MI Assign stage ([#319](https://github.com/fulcrumgenomics/fgumi/pull/319))
+- Address remaining review feedback from PR #323 ([#325](https://github.com/fulcrumgenomics/fgumi/pull/325))
+- [**breaking**] Require SS:template-coordinate ([#337](https://github.com/fulcrumgenomics/fgumi/pull/337))
+- Drop dense (max_ab × max_ba) grid that OOMs on cfDNA hot spots ([#359](https://github.com/fulcrumgenomics/fgumi/pull/359))
+- Accept --compression-level 0 for uncompressed BAM ([#360](https://github.com/fulcrumgenomics/fgumi/pull/360)) ([#361](https://github.com/fulcrumgenomics/fgumi/pull/361))
+- Use 128-bit composite hash for read-name keys ([#369](https://github.com/fulcrumgenomics/fgumi/pull/369))
+
+### Documentation
+
+- Use absolute URLs for logo images ([#324](https://github.com/fulcrumgenomics/fgumi/pull/324))
+- Recommend uncompressed BAM input for streaming pipelines ([#362](https://github.com/fulcrumgenomics/fgumi/pull/362))
+
+### Features
+
+- Zstd as the default temp-spill codec ([#341](https://github.com/fulcrumgenomics/fgumi/pull/341))
+- --parallel-group-min-templates with per-strategy auto thresholds ([#371](https://github.com/fulcrumgenomics/fgumi/pull/371))
+- Variable-width template-coordinate sort key, zero-copy merge, and slimmer arena ([#375](https://github.com/fulcrumgenomics/fgumi/pull/375))
+- Add host-aware --max-memory to pipeline commands ([#381](https://github.com/fulcrumgenomics/fgumi/pull/381))
+
+### Miscellaneous Tasks
+
+- Add publish dry-run to catch release-blocking bugs pre-merge ([#312](https://github.com/fulcrumgenomics/fgumi/pull/312))
+- Add codecov.yml with project coverage threshold ([#374](https://github.com/fulcrumgenomics/fgumi/pull/374))
+- Bump codecov-action to v6.0.2 to fix upload GPG verification ([#383](https://github.com/fulcrumgenomics/fgumi/pull/383))
+
+### Performance
+
+- Cache UMI tag position in DecodedRecord to avoid duplicate aux scan ([#343](https://github.com/fulcrumgenomics/fgumi/pull/343))
+- Single-pass aux scan captures UMI position ([#334](https://github.com/fulcrumgenomics/fgumi/pull/334)) ([#351](https://github.com/fulcrumgenomics/fgumi/pull/351))
+- Bypass libdeflater for deflate stored blocks ([#366](https://github.com/fulcrumgenomics/fgumi/pull/366))
+- Pin flate2 zlib-rs backend to restore fast FASTQ decompression ([#387](https://github.com/fulcrumgenomics/fgumi/pull/387))
+
+### Refactor
+
+- Validate and consolidate SAM tag identifiers via SamTag ([#316](https://github.com/fulcrumgenomics/fgumi/pull/316))
+- Extract fgumi-bam-io and fgumi-sort workspace crates ([#323](https://github.com/fulcrumgenomics/fgumi/pull/323))
+- Migrate hand-rolled rejects writers to first-class secondary_output ([#332](https://github.com/fulcrumgenomics/fgumi/pull/332))
+- Typed CodecConsensusError replaces substring matching ([#342](https://github.com/fulcrumgenomics/fgumi/pull/342))
+- Replace dead Binomial::new Err arm with expect ([#363](https://github.com/fulcrumgenomics/fgumi/pull/363))
+- Delegate ConsensusOutput heap-size estimate to owning type ([#368](https://github.com/fulcrumgenomics/fgumi/pull/368))
+- Demote algorithm-internal info! logs to debug ([#367](https://github.com/fulcrumgenomics/fgumi/pull/367))
+
+### Testing
+
+- In-process Command::execute for Phase 1 commands ([#352](https://github.com/fulcrumgenomics/fgumi/pull/352)) ([#353](https://github.com/fulcrumgenomics/fgumi/pull/353))
+- In-process Command::execute for Phase 2 commands ([#352](https://github.com/fulcrumgenomics/fgumi/pull/352)) ([#354](https://github.com/fulcrumgenomics/fgumi/pull/354))
+- In-process Command::execute for Phase 4 commands ([#352](https://github.com/fulcrumgenomics/fgumi/pull/352)) ([#356](https://github.com/fulcrumgenomics/fgumi/pull/356))
+- In-process follow-ups from Opus/Sonnet review of #352 ([#357](https://github.com/fulcrumgenomics/fgumi/pull/357))
+
+<!-- generated by git-cliff -->
+
 ### Documentation
 
 - Recommend uncompressed BAM (`bwa-mem3 mem --bam=0`) as the preferred `fgumi zipper` input format for streaming pipelines, with SAM kept as a fallback for aligners that can't emit BAM. Replaced the misleading "BAM input is discouraged" `warn!` on the stdin-BAM path with a neutral `info!`, and dropped the equivalent warning on the file-BAM path. Updated `zipper` CLI help/long_about and the getting-started, best-practices, performance-tuning, and migration-from-fgbio guides accordingly.