6 Commits

Include renames

Author	SHA1	Message	Date
Eric Coissac	a63692b8c4	chore: update ci cache, document distance metrics, and bump version ... Updated CI workflow cache keys with a `v2` salt and `Cargo.lock` hash 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 the `obikmer` crate version to 1.1.42.	2026-08-11 17:12:28 +02:00
Eric Coissac	5f95e866f8	refactor: 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 direct `std::thread::available_parallelism()` calls across `obikindex` and `obikmer` with this centralized function. Bump `obikmer` version to 1.1.41.	2026-08-11 12:23:05 +02:00
Eric Coissac	fab4e0d6de	fix(ci): restrict workflow to PRs and improve release tagging ... Restrict the CI pipeline to pull request events only by removing the unconfigured push trigger and eliminating a duplicate pull_request block in the workflow file. Update the Makefile to suppress stderr from the aichat command and introduce a fallback release tag message for robust version tagging. Additionally, bump the obikmer crate version to 1.1.19.	2026-06-23 09:42:23 +02:00
Eric Coissac	9f1df96ea7	ci: restrict push trigger to main branch ... Replace the wildcard `['**']` in the push trigger with `['main']`. This prevents redundant pipeline runs on non-main branches during push events.	2026-06-22 16:58:44 +02:00
Eric Coissac	4e625afaba	refactor: update CI toolchain setup and optimize parallel indexing ... Update CI workflows to explicitly install the Rust toolchain via rustup and configure musl targets for deterministic static builds in Docker containers. Bump obikmer dependency to 0.1.3. Refactor obicompactvec to reduce peak memory usage by computing column sizes from filesystem metadata, add atomic writes, and implement cleanup guards. Replace parallel iteration patterns in obikindex with a structured PartitionRunner pipeline for simplified error handling and progress tracking.	2026-06-22 10:46:24 +02:00
Eric Coissac	a522c0907e	feat: add CI/CD workflows, release automation, and CLI version flag ... Adds Gitea Actions for continuous integration and tagged releases, including static musl binary compilation and artifact upload. Introduces a Makefile target to automate semantic version bumping and publishing. Bumps the package version to 0.1.1 and enables automatic `--version` output via Clap.	2026-06-22 10:36:40 +02:00