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• 5bdc0f826a Merge pull request 'fix: validate packed matrix columns before repacking' (#57) from push-vkqvorvsqnqx into main main coissac 2026-07-03 15:26:55 +00:00
• cd2f2f9417 fix: validate packed matrix columns before repacking v1.1.35 Eric Coissac 2026-07-03 17:16:36 +02:00
• 7844239a8e Merge pull request 'Push msotyzponsls' (#56) from push-msotyzponsls into main coissac 2026-07-03 11:28:49 +00:00
• 2b37e8aac4 fix(bitmatrix): explicitly compute diagonal entries for self-similarity v1.1.34 Eric Coissac 2026-07-03 13:01:39 +02:00
• 67b4e4da53 refactor(numa): replace flat runner with per-node activation channels Eric Coissac 2026-07-03 12:47:56 +02:00
• 66ab4c6db1 Merge pull request 'feat(numa): introduce I/O sampling to prevent activation stalls' (#55) from push-ooruxnkktvvz into main coissac 2026-07-02 09:36:19 +00:00
• f84dd539bf feat(numa): introduce I/O sampling to prevent activation stalls v1.1.33 Eric Coissac 2026-07-02 10:05:31 +02:00
• 6378734e1c Merge pull request 'fix(obisys): remove activation guard to always update metrics' (#54) from push-vkloynurrxzu into main coissac 2026-07-01 18:34:10 +00:00
• b3a617cce1 fix(obisys): remove activation guard to always update metrics v1.1.32 Eric Coissac 2026-07-01 19:49:23 +02:00
• 2080e5e8a9 Merge pull request 'ci: fix registry auth and bump obikmer to 1.1.30' (#53) from push-zxlknspoxknt into main coissac 2026-07-01 14:20:09 +00:00
• 45ed2bc9b8 ci: fix registry auth and bump obikmer to 1.1.30 v1.1.30 Eric Coissac 2026-07-01 14:30:23 +02:00
• aa126fd89d Merge pull request 'feat: simplify worker spawning logic and update macOS build workflow' (#52) from push-uvmlknmzqqnx into main coissac 2026-07-01 09:50:51 +00:00
• c612132763 feat: simplify worker spawning logic and update macOS build workflow v1.1.29 Eric Coissac 2026-07-01 11:35:06 +02:00
• 19660f8cd0 Merge pull request 'ci: update registry auth and improve adaptive worker scaling' (#51) from push-qlpywtroutvx into main coissac 2026-06-26 13:16:23 +00:00
• 7b07540a69 ci: update registry auth and improve adaptive worker scaling v1.1.27 Eric Coissac 2026-06-26 15:02:23 +02:00
• 89c43e28f5 Merge pull request 'ci: update release workflow and bump obikmer to 1.1.26' (#50) from push-npttlqpomtvz into main coissac 2026-06-24 13:55:40 +00:00
• b9b2e42ad2 ci: update release workflow and bump obikmer to 1.1.26 v1.1.26 Eric Coissac 2026-06-24 15:54:01 +02:00
• ca42fdff2f Merge pull request 'ci: update macOS ARM64 build workflow and bump obikmer version' (#49) from push-lllnsqlrqrut into main coissac 2026-06-23 13:15:20 +00:00
• 136cd89efb ci: update macOS ARM64 build workflow and bump obikmer version v1.1.25 Eric Coissac 2026-06-23 14:59:35 +02:00
• a4bbf607b7 Merge pull request 'Push kxsopnzprltv' (#48) from push-kxsopnzprltv into main coissac 2026-06-23 09:51:33 +00:00
• 9927100a1c chore: update obikmer to 1.1.24 v1.1.24 Eric Coissac 2026-06-23 11:12:32 +02:00
• 527258f822 ci: enforce macOS 11.0 deployment target for ARM builds Eric Coissac 2026-06-23 11:00:29 +02:00
• ef62f1947e Merge pull request 'chore: bump version to 1.1.21 and update obikindex features' (#47) from push-xwutoxpnxorz into main coissac 2026-06-23 08:31:31 +00:00
• d02316dcf6 chore: bump version to 1.1.21 and update obikindex features v1.1.21 Eric Coissac 2026-06-23 10:29:16 +02:00
• c323b3eaef Merge pull request 'Bump obikmer to 1.1.20 and update release workflow' (#46) from push-wpnywwlwxrps into main coissac 2026-06-23 08:03:58 +00:00
• b77d8e9ca0 Bump obikmer to 1.1.20 and update release workflow v1.1.20 Eric Coissac 2026-06-23 10:01:14 +02:00
• 7c5bab3694 Merge pull request 'fix(ci): restrict workflow to PRs and improve release tagging' (#45) from push-louqrszyuqpz into main coissac 2026-06-23 07:52:35 +00:00
• fab4e0d6de fix(ci): restrict workflow to PRs and improve release tagging v1.1.19 Eric Coissac 2026-06-23 09:39:45 +02:00
• 973a3f3d6e Merge pull request 'feat: add numa feature flag and automate release workflow' (#44) from push-uymxyvsyooro into main coissac 2026-06-23 07:22:33 +00:00
• 1a839a295a feat: add numa feature flag and automate release workflow v1.1.18 Eric Coissac 2026-06-23 08:50:18 +02:00
• 21a20ce7ca feat: automate release workflow and add optional NUMA support v1.1.17 Eric Coissac 2026-06-23 08:50:18 +02:00
• 1f0233d033 refactor: make hwlocality optional and streamline release workflow v1.1.16 Eric Coissac 2026-06-23 08:50:18 +02:00
• 2ea58703c7 Merge pull request 'Push zkptpswyxnvt' (#43) from push-zkptpswyxnvt into main coissac 2026-06-22 16:29:59 +00:00
• ac3ef106e7 refactor: implement adaptive worker scaling and infallible NUMA build v1.1.15 Eric Coissac 2026-06-22 18:04:56 +02:00
• 469e53b6f5 Add genomic distance benchmarking suite and test data Eric Coissac 2026-06-22 17:28:48 +02:00
• 9f1df96ea7 ci: restrict push trigger to main branch Eric Coissac 2026-06-22 16:57:56 +02:00
• 4e4cce2879 Merge pull request 'fix(ci): enable cross-compilation in release workflow and bump obikmer' (#42) from push-sxlpkrkyuttk into main coissac 2026-06-22 14:31:26 +00:00
• 68b05b93c4 fix(ci): enable cross-compilation in release workflow and bump obikmer v1.1.14 Eric Coissac 2026-06-22 16:28:52 +02:00
• 0a668cf8a6 Merge pull request 'chore: bump obikmer to 1.1.13 and fix Makefile revision tag' (#41) from push-qwzpxktnlyls into main coissac 2026-06-22 14:18:25 +00:00
• e6d6942e2f chore: bump obikmer to 1.1.13 and fix Makefile revision tag v1.1.13 Eric Coissac 2026-06-22 16:16:09 +02:00
• bf9c9aeacb Merge pull request 'chore: bump version to 1.1.12 and fix release workflow' (#40) from push-zmkxouxypspm into main coissac 2026-06-22 14:13:13 +00:00
• 22a65857a1 chore: bump version to 1.1.12 and fix release workflow Eric Coissac 2026-06-22 16:11:16 +02:00
• d16a867640 Merge pull request 'ci: bypass PEP 668 restrictions and update obikmer to 1.1.11' (#39) from push-mxysluysloxr into main v1.1.12 coissac 2026-06-22 13:52:51 +00:00
• 616050075f ci: bypass PEP 668 restrictions and update obikmer to 1.1.11 Eric Coissac 2026-06-22 15:41:11 +02:00
• e22afe9621 Merge pull request 'chore: bump obikmer to 1.1.9 and update release workflow' (#38) from push-noxuppsknsol into main v1.1.11 coissac 2026-06-22 13:32:50 +00:00
• bdfac71e65 chore: bump obikmer to 1.1.9 and update release workflow Eric Coissac 2026-06-22 15:30:32 +02:00
• a00bb37478 Merge pull request 'ci: switch to Zig build toolchain and bump obikmer to 1.1.7' (#37) from push-nvvqmzmrotxx into main v1.1.9 coissac 2026-06-22 13:20:12 +00:00
• d30a4efd9b ci: switch to Zig build toolchain and bump obikmer to 1.1.7 push-nvvqmzmrotxx Eric Coissac 2026-06-22 15:17:42 +02:00
• 6baf2e64ca Merge pull request 'chore: bump obikmer to 1.1.6 and automate git tagging' (#36) from push-yxmtknzsynpx into main v1.1.7 coissac 2026-06-22 13:01:06 +00:00
• c0a71a2d49 chore: bump obikmer to 1.1.6 and automate git tagging Eric Coissac 2026-06-22 14:58:37 +02:00
• a609c1af95 Merge pull request 'ci: streamline release workflow and bump obikmer to 0.1.4' (#35) from push-zokprynyqunu into main v1.1.6 coissac 2026-06-22 09:38:36 +00:00
• 3d32be8a83 ci: streamline release workflow and bump obikmer to 0.1.4 Eric Coissac 2026-06-22 11:36:39 +02:00
• c4c71dc892 Merge pull request 'Push mtzqmmrlmzzx' (#34) from push-mtzqmmrlmzzx into main coissac 2026-06-22 08:47:24 +00:00
• 4e625afaba refactor: update CI toolchain setup and optimize parallel indexing Eric Coissac 2026-06-22 10:40:50 +02:00
• a522c0907e feat: add CI/CD workflows, release automation, and CLI version flag push-vtvurtklymss Eric Coissac 2026-06-22 10:33:16 +02:00
• c1d6f277ce feat(select): add metrics reporting to selection methods Eric Coissac 2026-06-21 19:07:15 +02:00
• 9356be4ec0 feat: introduce obitaxonomy crate for hierarchical taxonomy parsing Eric Coissac 2026-06-21 10:37:50 +02:00
• c694e1f2b0 feat: add benchmark pipeline, expose APIs, and enforce strict paths Eric Coissac 2026-06-19 09:55:41 +02:00
• 280ca1f5a3 feat: add optimized new_ones constructor for all-ones bit vectors Eric Coissac 2026-06-19 09:23:44 +02:00
• 9abb2db92f refactor: replace explicit bit-setting loops with optimized bulk operations Eric Coissac 2026-06-19 09:20:14 +02:00
• 7c1efa9cbb feat: add vectorized column filters and optimize partitioner iteration Eric Coissac 2026-06-19 09:12:07 +02:00
• 4c4524766c feat(matrix): add partial group reductions and column persistence Eric Coissac 2026-06-18 07:34:29 +02:00
• 7eea71fdcd docs(obicompactvec): update API docs and algorithm descriptions Eric Coissac 2026-06-18 07:10:08 +02:00
• f91c5a3f79 refactor(obicompactvec): unify bit and int vector slice views Eric Coissac 2026-06-17 23:07:19 +02:00
• fb4962c4fe refactor: replace in-memory vectors with temp-file-backed storage Eric Coissac 2026-06-17 15:13:22 +02:00
• 1d38d87ff9 Add column group operations and mask_with trait Eric Coissac 2026-06-17 14:50:28 +02:00
• 93559c3294 feat: introduce unified column view types for bit and int matrices Eric Coissac 2026-06-17 14:48:31 +02:00
• 1f0d77d5bf docs: document compact vector implementation with Mermaid diagrams Eric Coissac 2026-06-17 14:24:57 +02:00
• eeba43ac4f docs: add technical reference for obicompactvec module Eric Coissac 2026-06-17 13:14:11 +02:00
• 7ed7b26039 perf: optimize vec arithmetic and add overflow tests Eric Coissac 2026-06-17 12:30:40 +02:00
• 26de90f18d feat: add iteration and aggregation to compact int vec Eric Coissac 2026-06-17 09:48:09 +02:00
• 497d250d8a refactor: replace byte-level bit iteration with 64-bit words Eric Coissac 2026-06-17 09:32:12 +02:00
• aa98e82875 refactor: introduce PackedIntCol view and use iterators Eric Coissac 2026-06-17 09:28:16 +02:00
• 5ff5b04d2d refactor: replace manual bit ops with BitSlice traits Eric Coissac 2026-06-17 09:19:30 +02:00
• df7b400fda perf: optimize aggregation with byte-level helpers and direct mmap Eric Coissac 2026-06-17 00:13:16 +02:00
• d1717688d2 refactor: extract matrix helpers and improve bit iteration ergonomics Eric Coissac 2026-06-16 23:36:25 +02:00
• cde6457eea feat: add memory vectors, slice traits, and column extraction methods Eric Coissac 2026-06-16 23:18:10 +02:00
• b6fcbc545f refactor: replace rayon with NUMA-aware PartitionRunner Eric Coissac 2026-06-15 15:45:04 +02:00
• 9578f991f4 Merge pull request 'Push pslsukyowzrp' (#32) from push-pslsukyowzrp into main coissac 2026-06-15 16:29:24 +00:00
• 1cd7916e06 refactor: replace rayon with NUMA-aware PartitionRunner Eric Coissac 2026-06-15 15:45:04 +02:00
• bc92dc4592 refactor: restructure partitioner with shared utilities and pipeline Eric Coissac 2026-06-15 14:01:43 +02:00
• a9567ad023 Merge pull request 'Push rtnzuqxzmkon' (#31) from push-rtnzuqxzmkon into main coissac 2026-06-15 09:40:35 +00:00
• 4a64718fd1 perf: replace partition processing with adaptive NUMA worker pool Eric Coissac 2026-06-15 11:30:46 +02:00
• 7a87e911b6 feat: introduce NUMA-aware PartitionRunner for adaptive parallelism Eric Coissac 2026-06-15 11:24:37 +02:00
• 313d73838a Merge pull request 'feat: add pipeline concurrency throttling and HPC build docs' (#30) from push-owwylwtskwzw into main coissac 2026-06-15 08:33:41 +00:00
• 175ea5bbd0 feat: add pipeline concurrency throttling and HPC build docs Eric Coissac 2026-06-15 10:26:40 +02:00
• c6ea0c53e3 Merge pull request 'feat: implement NUMA-aware worker pools for merge command' (#29) from push-wusvurukprsr into main coissac 2026-06-14 21:57:21 +00:00
• ea767376bd feat: implement NUMA-aware worker pools for merge command Eric Coissac 2026-06-14 23:40:09 +02:00
• f1d76f3203 Merge pull request 'refactor(merge): extract adaptive worker spawn logic' (#28) from push-yzruqtyqvopm into main coissac 2026-06-13 12:56:34 +00:00
• c4071eb450 refactor(merge): extract adaptive worker spawn logic Eric Coissac 2026-06-13 14:54:23 +02:00
• 817b02cbc1 Merge pull request 'Push zkspuxlpumpw' (#27) from push-zkspuxlpumpw into main coissac 2026-06-13 11:25:12 +00:00
• 547cb72d76 refactor: Enforce Rayon parallelism and fix merge_layer concurrency Eric Coissac 2026-06-13 13:18:16 +02:00
• 6d85387077 feat: add performance instrumentation and dynamic worker scaling Eric Coissac 2026-06-13 13:04:25 +02:00
• fb5b53dca9 Merge pull request 'Push ooxwzorvsqvy' (#26) from push-ooxwzorvsqvy into main coissac 2026-06-13 09:59:07 +00:00
• fddf630772 style: apply consistent formatting and whitespace normalization Eric Coissac 2026-06-13 11:41:14 +02:00
• bc14346f5f feat: add CPU-aware parallel worker pool for partition merging Eric Coissac 2026-06-13 11:32:12 +02:00
• fb8c6e427c refactor: pass Unitig objects directly instead of raw byte slices Eric Coissac 2026-06-13 10:46:35 +02:00
• 1f336fe496 refactor: replace mutex with channels for parallel debruijn processing Eric Coissac 2026-06-13 10:34:31 +02:00
• 5f98d2ef96 refactor: replace explicit collect with Unitig::from_nucleotides Eric Coissac 2026-06-13 10:09:07 +02:00
• 8b563d0804 refactor: migrate pipeline stages and improve graph processing Eric Coissac 2026-06-13 09:49:33 +02:00