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v1.2.2
Stablecoissac released this
2026-08-17 11:33:43 +00:00 | 1 commits to main since this releasechore: bump obikmer to 1.2.1 and disable obikindex default features
Updates the obikmer lockfile version to 1.2.1 and configures the obikindex dependency to explicitly disable default features. These are manifest and lockfile adjustments that do not modify source code or alter application behavior.
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v1.2.1
Stable2026-08-17 10:34:46 +00:00 | 3 commits to main since this releasechore: disable default features for obikindex
Explicitly sets
default-features = falsefor theobikindexdependency to ensure no default features are activated during dependency resolution and compilation.Downloads
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v1.2.0
Stable2026-08-17 09:40:57 +00:00 | 6 commits to main since this releaseAdd TNT configuration directives and tree export commands to script
Updates the generated TNT script with configuration parameters and appends tree management commands for saving and exporting results. Modifications are strictly limited to string literals written to the output stream.
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v1.1.44
Stable2026-08-11 21:04:49 +00:00 | 53 commits to main since this releasefix: resolve test race conditions, add logging, and fix CI deadlock
Re-enables the
numafeature in CI workflows to prevent container/cgroup deadlocks while preserving validation correctness. Fixes concurrent test race conditions by replacing thread-local parameter storage with process-wide atomics and mutex locks. Integratestracing-subscriberfor structured logging and adds thread-ID tracking to debug worker lifecycles. Additionally bumps the crate version, updates.gitignore, documents experimental evolutionary distance pipelines, and refactors hardcoded test constants.Downloads
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v1.1.43
Stable2026-08-11 16:27:19 +00:00 | 55 commits to main since this releaseci: disable numa feature, bump obikmer, and document Sankoff costs
Disable the
numadefault feature in CI build and test steps to prevent container environment deadlocks, and add comments explaining the cache key salt bump (v2) to mitigate incremental compilation corruption. Document a 16-state Sankoff cost matrix derived from set-edit distances, including substitution, gain/loss, and context-disappearance costs compatible with TNT's interface. Bumpobikmercrate version to 1.1.43.Downloads
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v1.1.42
Stable2026-08-11 15:12:57 +00:00 | 57 commits to main since this releasechore: update ci cache, document distance metrics, and bump version
Updated CI workflow cache keys with a
v2salt andCargo.lockhash to prevent stale incremental compilation caches and deadlocks, while updating restore keys and documenting interrupted job state. Introduced a 3-way ordinal distance metric framework that replaces ambiguous IUPAC encoding with explicit k-mer scoring, bridging pairwise methods to character-based phylogenetics via Sankoff parsimony. Bumped theobikmercrate version to 1.1.42.Downloads
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v1.1.41
Stable2026-08-11 10:23:36 +00:00 | 59 commits to main since this releaserefactor: centralize CPU core detection using cgroup-aware utility
Introduce
obisys::effective_parallelism()to read Linux cgroup v1/v2 CPU quotas from sysfs, preventing thread pool oversubscription in containerized environments. Replace directstd::thread::available_parallelism()calls acrossobikindexandobikmerwith this centralized function. Bumpobikmerversion to 1.1.41.Downloads
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v1.1.40
Stable2026-08-10 23:01:39 +00:00 | 61 commits to main since this releasefeat: add multi-genome SNP pseudo-alignment and CLI export
Introduces a
SnpAlignmentstruct and helper methods to construct per-genome SNP pseudo-alignments from sibling k-mer data, filtering monomorphic families and encoding bases as IUPAC ambiguity codes. Exposes the type at the crate root for simplified imports. Adds a--snpCLI flag to compute and export these alignments as an IUPAC-coded FASTA file. Updates theory documentation to propose a multi-genome framing approach for joint phylogenetic inference, resolving pairwise correspondence ambiguities through positional homology and partial coverage thresholds. Bumps crate version to 1.1.40.Downloads
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v1.1.39
Stable2026-07-08 17:37:26 +00:00 | 70 commits to main since this releaserefactor: remove equivalence class folding from entropy pipeline
Removes circular-reverse complement machinery and explicit k-mer canonicalization across the entropy pipeline. Frequency tallying and Shannon entropy computation now operate directly on raw k-mer values, eliminating prior score inflation and alignment-dependent artifacts while preserving orientation invariance. Updates build scripts to generate normalized lookup tables for k-mer lengths 1–6, restricts the public API to
EntropyTracker, and bumps crate versions. Documentation is updated to reflect the simplified raw-value approach and revised module structure.Downloads
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v1.1.38
Stable2026-07-08 10:15:27 +00:00 | 74 commits to main since this releaseBump obikmer version to 1.1.38 and add memory footprint logging
Updates Cargo.toml version from 1.1.37 to 1.1.38. Adds explicit memory footprint estimation for the
by_partitionk-mer dedup HashMap by computing capacity-based byte sizes for map slots and stored descriptors. These metrics are logged viadebug!to track actual memory pressure during chunk processing.Downloads