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Changelog#

All notable changes to oxo-flow are documented in this file.

The format follows Keep a Changelog and this project adheres to Semantic Versioning.

Changelog entries are automatically generated by git-cliff from conventional commit messages.

0.6.1 — 2026-05-24#

Bug Fixes#

  • Replace silent checkpoint save failures with tracing warnings (@ShixiangWang)
  • Resource detection, checkpoint skip, error cascade, and validation improvements (@ShixiangWang)
  • Workspace tests use tempdir for CI reliability (@ShixiangWang)
  • Allow ':' in rule names and add include E2E tests (@ShixiangWang)
  • Parse conda env name from YAML content, not file stem (@ShixiangWang)

Documentation#

Features#

  • Subprocess-based dynamic plugin loading (@ShixiangWang)
  • Full plugin system with discovery, TOML integration, signatures (@ShixiangWang)
  • Retry persistence, plugin traits, i18n reports, input tests (@ShixiangWang)
  • Output verification with sizes, watch --run flag (@ShixiangWang)
  • History command, clean confirmation, plugin design doc (@ShixiangWang)
  • Dry-run execution hint, deadlock diagnosis improvement (@ShixiangWang)
  • Auto-create output dirs, watch dry-run, error test coverage (@ShixiangWang)
  • Progress ETA, dry-run input status, colored diff, error tests (@ShixiangWang)
  • Dry-run resource summary, output verification, deprecated cleanup (@ShixiangWang)
  • Input file existence check and --quiet banner suppression (@ShixiangWang)
  • Enhance dry-run output and update CITATION.cff (@ShixiangWang)
  • Transform operator tests and complete priority items (@ShixiangWang)
  • Resource exhaustion hints and enhanced test command (@ShixiangWang)
  • Env error hints, web crate tests, and improved init template (@ShixiangWang)
  • Improve oxo-flow init template with shell reference and China mirrors (@ShixiangWang)

Maintenance#

Other Changes#

0.6.0 — 2026-05-21#

Bug Fixes#

  • Landing page rendering, badges, and stale content (@ShixiangWang)
  • Publish command crash and documentation accuracy (@ShixiangWang)

Documentation#

Maintenance#

Other Changes#

0.5.5 — 2026-05-20#

Bug Fixes#

  • Resolve bugs found by 30-user simulation testing (@ShixiangWang)
  • Resolve critical bugs, integrate security code, add tests, update deps, and fix README (@ShixiangWang)

Documentation#

Features#

  • Auto-create output directories and add dry-run shell safety checks (@ShixiangWang)

Maintenance#

Other Changes#

Styling#

  • Fix cargo fmt formatting in output directory creation (@ShixiangWang)

0.5.4 — 2026-05-19#

CI/CD#

  • Remove Venus from build/publish/release pipeline (@ShixiangWang)

Documentation#

Maintenance#

Other Changes#

0.5.3 — 2026-05-18#

Bug Fixes#

  • Resolve clippy errors for Rust 1.95 and update test (@ShixiangWang)
  • Include schema file within CLI crate to fix cargo package build (#42) (@Copilot) (#42)

Documentation#

Features#

  • rule: Add Dir variant to FilePatterns for directory input (@ShixiangWang)
  • executor: Implement optional rule skip logic (@ShixiangWang)
  • rule: Add optional field for skip-on-missing behavior (@ShixiangWang)
  • format: Add validation for undefined env_group references (@ShixiangWang)
  • config: Add env_groups for shared environments (@ShixiangWang)
  • executor: Add auto-scaling helper functions (@ShixiangWang)
  • rule: Add AutoScale type for resource auto-scaling (@ShixiangWang)
  • config: Add reference_dir field with auto-derivation (@ShixiangWang)
  • cli: Implement --as-include validation mode (@ShixiangWang)
  • cli: Add --as-include flag to validate command (@ShixiangWang)
  • core: Enhance clinical workflow support and permissive wildcard expansion (@ShixiangWang)

Maintenance#

Testing#

0.5.2 — 2026-05-18#

Bug Fixes#

  • Suppress rustls-webpki audit warnings from aws-sdk-s3 transitive deps (@ShixiangWang)
  • Allow $(…) in shell templates; validate wildcard injection; fix dry-run when; fix example workflows (#40) (@Copilot) (#40)

Documentation#

Features#

  • 100% resolution of 40-user comprehensive testing — security, storage, CLI, docs (@ShixiangWang)
  • Achieve 100% resolution of 100-user comprehensive review (@ShixiangWang)
  • Resolve top 10 priority actions from 100-user comprehensive review (@ShixiangWang)
  • Switch to rustls, optimize hot paths, update docs and deps (@ShixiangWang)
  • Comprehensive 30-expert review, dependency upgrades, performance optimizations, and documentation updates (@ShixiangWang)
  • Implement Phase 9.6 roadmap items and performance optimizations (@ShixiangWang)
  • 30-expert user journey review, performance optimizations, and documentation improvements (@ShixiangWang)
  • Implement named inputs and outputs for rules (@ShixiangWang)
  • Address simulated user reviews and comprehensive optimization (@ShixiangWang)

Maintenance#

Other Changes#

Performance#

  • Optimize wildcard expansion engine and consolidate Phase 9.6 (@ShixiangWang)

0.5.1 — 2026-05-17#

Bug Fixes#

  • cli: Add 'default' alias for profile show and 'check' alias for config stats (@ShixiangWang)
  • docs: Add pairs_file/pairs_pattern/sample_groups_file to how-to guides (@ShixiangWang)
  • docs: Use absolute GitHub URLs for example workflow links (@ShixiangWang)

Documentation#

Features#

  • batch: Implement true parallel execution with Semaphore (@ShixiangWang)
  • config: Add pairs_pattern for auto-discovering pairs from filesystem (@ShixiangWang)
  • config: Add pairs_file and sample_groups_file support (@ShixiangWang)
  • ci: Auto-update docs version references on version bump (@ShixiangWang)

Maintenance#

0.5.0 — 2026-05-16#

Bug Fixes#

  • Correct cargo-audit config format (@ShixiangWang)
  • Address all issues from 30-expert review (@ShixiangWang)
  • venus: Add interpreter_map to generated workflow metadata (@ShixiangWang)
  • security: Relax shell validation for &&, ||, and pipes (@ShixiangWang)
  • executor: Remove duplicate resource release on failure (@ShixiangWang)
  • Simplify build_script_command to avoid clippy warning (@ShixiangWang)

CI/CD#

Documentation#

Features#

  • cli: Add batch subcommand for parallel task execution (@ShixiangWang)
  • Complete rule lifecycle hooks, environment injection, and custom interpreters (@ShixiangWang)
  • config: Fix namespace prefixing for depends_on in included rules (@ShixiangWang)
  • cli: Add progress bar for run command execution tracking (@ShixiangWang)
  • cli: Add --pending-timeout option to cluster submit (@ShixiangWang)
  • cli: Add --orphans option to clean command (@ShixiangWang)
  • lint: Add hook command safety validation (W020-W022) (@ShixiangWang)
  • executor: Implement script execution with interpreter detection and sequential shell+script (@ShixiangWang)
  • Add interpreter and interpreter_map fields for script execution (@ShixiangWang)
  • Add disk space pre-flight check and resource summary (@ShixiangWang)
  • scheduler: Implement ResourceHint memory estimation (@ShixiangWang)
  • executor: Add structured logging for resource allocation (@ShixiangWang)
  • cluster: Enhance GPU spec translation for SLURM/PBS/SGE (@ShixiangWang)
  • scheduler: Add system capacity validation with warnings (@ShixiangWang)
  • executor: Add process group timeout and cleanup on failure (@ShixiangWang)
  • executor: Use sysinfo for cross-platform memory detection (@ShixiangWang)
  • Add sysinfo, nix, fs2 dependencies for resource management (@ShixiangWang)
  • core: Implement unified transform operator for scatter-gather (@ShixiangWang)

Maintenance#

Other Changes#

Refactoring#

  • Add #[must_use] attributes to interpreter functions (@ShixiangWang)

Testing#

  • batch: Add comprehensive unit tests and update docs nav (@ShixiangWang)
  • executor: Add tests for interpreter detection and script execution (@ShixiangWang)

0.4.2 — 2026-05-16#

Bug Fixes#

  • validation: Exempt pairs/sample_groups wildcards from E003 (@ShixiangWang)
  • web: Replace panic with graceful error handling in executor (@ShixiangWang)
  • cli: Apply defaults and templates in dry-run and debug commands (@ShixiangWang)
  • cli: Properly return exit codes on cluster command failures and handle empty checkpoints (@ShixiangWang)

Documentation#

Features#

Maintenance#

Other Changes#

0.4.1 — 2026-05-16#

Bug Fixes#

  • executor: Implement retry loop and hooks execution (@ShixiangWang)

Maintenance#

0.4.0 — 2026-05-16#

Bug Fixes#

  • Expand placeholders in cluster submit scripts (@ShixiangWang)
  • Address critical bugs from user simulation testing (@ShixiangWang)
  • Remove unused helper functions and fix unused_mut warning (@ShixiangWang)
  • Add async mutex guard for thread-safe database initialization (@ShixiangWang)
  • Use process-specific temp database for tests (@ShixiangWang)
  • Resolve test database initialization race condition (@ShixiangWang)
  • Walltime tests and add 'd' suffix support (@ShixiangWang)
  • Add partition field to Resources Default and update tests (@ShixiangWang)
  • web: Resolve modal CSS priority issue and complete UI functions (@ShixiangWang)

Documentation#

Features#

  • Implement persistent checkpointing, fix modular includes, and reduce TOML noise (@ShixiangWang)
  • Add 81 new comprehensive tests for oxo-flow (145 total, covering CLI, core, Venus, bioinformatics) (#39) (@Copilot) (#39)
  • clinical: SHA-256 checksums and provenance persistence (@ShixiangWang)
  • validation: Integrate validate_format() and secret scanning (@ShixiangWang)
  • container: Add GPU support for container generation (@ShixiangWang)
  • cluster: Add GPU directives, per-rule walltime, modules, logs (@ShixiangWang)
  • bioinformatics: Address bioinformatics expert review (@ShixiangWang)
  • web: Implement critical Web API enhancements (@ShixiangWang)
  • Implement advanced user features (@ShixiangWang)
  • Address all issues from junior user review and generalize terminology (@ShixiangWang)
  • Implement WC-01 tumor-normal pairing, WC-02 sample groups, WF-01 conditional rules (#38) (@Copilot) (#38)
  • Make workflow argument optional for run and dry-run commands (@ShixiangWang)
  • Target-based partial workflow execution for run and dry-run (#37) (@Copilot) (#37)
  • Implement 20-persona dev plan Phase 1 and enhance CLI security/usability (@ShixiangWang)
  • Add ANSI colors and fix box alignment in ASCII graph output (@ShixiangWang)
  • cli: Add ASCII terminal graph output for oxo-flow graph (@ShixiangWang)
  • web: Complete industrial-grade Web UI system (Phase 10) (@ShixiangWang)

Maintenance#

Other Changes#

0.3.1 — 2026-05-13#

Bug Fixes#

  • Address all 32 review issues across security, code quality, pipeline correctness, and docs (#34) (@Copilot) (#34)

Documentation#

Features#

  • web: Add request and active workflow metrics with frontend auto-refresh (@ShixiangWang)

Maintenance#

Other Changes#

Refactoring#

0.3.0 — 2026-04-07#

Bug Fixes#

  • Template variable substitution, DOT graph labels, and optional env check workflow (@Copilot)

Documentation#

Features#

  • Enhance error types, re-export public API, docs update (@Copilot)
  • wildcard: Add regex constraint validation and pattern-to-regex file discovery (@Copilot)
  • Add reference database tracking, data lineage, and extended job states (@Copilot)
  • core: Add GpuSpec, ResourceHint, and new Rule fields with builder methods (@Copilot)

Maintenance#

Other Changes#

  • Merge pull request #32 from Traitome/copilot/update-oxo-flow-evaluation-report (@Copilot) (#32)
  • Merge pull request #30 from Traitome/copilot/oxo-flow-project-evaluation-report (@ShixiangWang) (#30)
  • Add debug subcommand and project root detection utility (@Copilot)
  • Initial plan (@Copilot)
  • Merge pull request #28 from Traitome/copilot/fix-template-variable-replacement-bug (@ShixiangWang) (#28)
  • Initial plan (@Copilot)

Refactoring#

  • Address code review comments - use imported HashMap and all_known_backends() (@Copilot)

0.2.0 — 2026-04-06#

Bug Fixes#

  • Path traversal protection in touch, overflow protection in duration parsing (@Copilot)

CI/CD#

  • Add Windows ARM64, i686 Windows, and ARMv7 Linux release targets (@Copilot)

Documentation#

Features#

  • Add Rule depends_on/retry_delay/workdir/hooks, DAG critical_path, format diff/lint codes (@Copilot)

Maintenance#

Other Changes#

  • Merge pull request #26 from Traitome/copilot/add-ci-automation-release-support (@ShixiangWang) (#26)
  • Merge pull request #21 from Traitome/copilot/fix-267392264-1201351505-31179d07-4ceb-4491-a557-c277d32cfe31 (@ShixiangWang) (#21)
  • Add comprehensive tests for new features (@Copilot)
  • Fix summary statistics to match actual opinion counts (89 total) (@Copilot)
  • Add comprehensive expert panel evaluation TODO.md (@Copilot)
  • Initial plan (@Copilot)

0.1.3 — 2026-04-06#

Bug Fixes#

  • Rename venus crate to oxo-flow-venus to avoid crates.io name conflict (@Copilot)

Documentation#

Maintenance#

Other Changes#

  • Merge pull request #25 from Traitome/copilot/update-package-name-to-oxo-flow-venus (@ShixiangWang) (#25)
  • Initial plan (@Copilot)

0.1.2 — 2026-04-06#

Bug Fixes#

  • Add version to workspace path deps for crates.io publishing (@Copilot)

Documentation#

Maintenance#

Other Changes#

0.1.1 — 2026-04-06#

CI/CD#

  • Replace deprecated macos-13 with macos-latest cross-compiling to x86_64 (@Copilot)
  • Fix release and crates.io publish being blocked by cancelled builds (@Copilot)

Documentation#

  • Fix number formatting (1 000 → 1,000) (@Copilot)
  • Update landing page to accurately reflect repository state (@Copilot)

Maintenance#

Other Changes#

0.1.0 — 2026-04-06#

Bug Fixes#

  • Address code review feedback - XSS, event handling, credential docs (@Copilot)
  • Address code review feedback - improve test comments, fix bismark path, add escape docs (@Copilot)

Build#

  • Use workspace version inheritance for all crates, update CI sync-version (@Copilot)

CI/CD#

  • Skip heavy build jobs on pull_request events to prevent slow/cancelled runs (@Copilot)
  • Optimize CI workflow for reliable builds and crates.io publishing (@Copilot)

Documentation#

  • Add missing documentation files referenced in TODO.md (@Copilot)
  • Replace TODO.md with comprehensive 30-expert evaluation report (@Copilot)
  • Update TODO.md to mark completed items (@Copilot)
  • Add complete documentation website with MkDocs Material, landing page, tutorials, command reference, and architecture docs (@Copilot)
  • Fix grammar in quickstart tutorial (@Copilot)
  • Create complete documentation website (@Copilot)
  • Add CHANGELOG, CITATION, CODE_OF_CONDUCT, CONTRIBUTING, cliff.toml, and CI/CD pipeline (@Copilot)

Features#

  • web: Add in-memory rate limiter and graceful shutdown (@Copilot)
  • container: Add multi-stage builds, rootless support, healthcheck, and docker run command (@Copilot)
  • core: Add type system features - WorkflowState, RuleBuilder, newtypes, clinical types (@Copilot)
  • Integrate oxo-license, add auth/login system, export/cluster CLI subcommands (@Copilot)
  • core: Add comprehensive enhancements to oxo-flow-core (@Copilot)
  • Enhance scientific messaging, add gallery to README/docs, add CLI integration tests (@Copilot)
  • Add workflow gallery with 8 examples from basic to multi-omics, docs, and tests (@Copilot)
  • Remove all Snakemake references, establish innovation-first messaging (@Copilot)
  • Add validation, provenance, diagnostics, and DAG metrics improvements (@Copilot)
  • web: Add embedded frontend, new API endpoints, SSE, and base path support (@Copilot)
  • cli: Add Format, Lint, Profile, and Config subcommands (@Copilot)
  • core: Add resolve_includes, execution group validation, conditional execution, schema verification, and enhanced formatting (@Copilot)
  • Add scatter/gather, when, temp/protected output, input_function, retries, include, execution groups (@Copilot)
  • Add format module for .oxoflow validation, linting, and formatting (@Copilot)
  • Add request ID middleware, export endpoint, and CLI retry/timeout flags (@Copilot)
  • Add priority scheduling, clinical report sections, and CNV/MSI/TMB pipeline steps (@Copilot)
  • executor: Implement retry logic, timeout enforcement, and output validation (@Copilot)
  • core: Add error variants, apply_defaults, parallel_groups, rule validate (@Copilot)
  • cli: Enhance clean, init, add completions and verbose flag (@Copilot)
  • container: Add pixi support, extra_packages, compose file, and improved singularity defs (@Copilot)
  • web: Add CORS, run, version, and clean endpoints (@Copilot)
  • venus: Add VenusPipelineBuilder and .oxoflow generation (@Copilot)
  • web: Add full REST API with validate, parse, DAG, dry-run, and report endpoints (@Copilot)
  • report: Add Tera template engine and clinical report components (@Copilot)
  • Add cluster execution backends and executor checkpointing (@Copilot)
  • environment: Add setup/teardown commands, cache keys, and EnvironmentCache (@Copilot)
  • Initialize oxo-flow project with core library, CLI, web, and venus pipeline (@Copilot)

Maintenance#

Other Changes#

  • Merge pull request #16 from Traitome/copilot/resolve-todo-issues (@ShixiangWang) (#16)
  • Add 303 implementation notes to TODO.md; update README, CONTRIBUTING docs (@Copilot)
  • Phase 7: Add 32 new tests (clinical types, builder, security, stress, format, container) (@Copilot)
  • Add validation and security features to oxo-flow-core (@Copilot)
  • Add core safety attributes: forbid(unsafe_code), CLI flags, #[must_use] (@Copilot)
  • Initial plan (@Copilot)
  • Merge pull request #13 from Traitome/copilot/optimize-ci-workflow-release-files (@ShixiangWang) (#13)
  • Merge pull request #14 from Traitome/copilot/collect-feedback-from-experts (@ShixiangWang) (#14)
  • Add comprehensive TODO.md with 300+ expert opinions from 30 simulated domain experts (@Copilot)
  • Merge pull request #11 from Traitome/copilot/create-oxo-flow-system-design (@ShixiangWang) (#11)
  • Merge pull request #10 from Traitome/copilot/create-oxo-flow-system-design (@ShixiangWang) (#10)
  • Add comprehensive TODO.md with 300 expert review items across 30 domain perspectives (@Copilot)
  • Merge pull request #9 from Traitome/copilot/implement-oxo-flow-system-design (@ShixiangWang) (#9)
  • Add TODO.md with 30 expert opinions (150 action items) (@Copilot)
  • Delete TODO.md (@ShixiangWang)
  • Merge pull request #8 from Traitome/copilot/update-workflow-gallery-and-documentation (@ShixiangWang) (#8)
  • Merge pull request #7 from Traitome/copilot/update-roadmap-implementation-again (@ShixiangWang) (#7)
  • Add ..Default::default() to all Rule constructors for new fields (@Copilot)
  • Initial plan (@Copilot)
  • Merge pull request #5 from Traitome/copilot/update-roadmap-and-implement-features (@ShixiangWang) (#5)
  • Replace README.md with comprehensive documentation (@Copilot)
  • Add binary targets for oxo-flow-web and venus, create dual license files (@Copilot)
  • Merge pull request #4 from Traitome/copilot/update-roadmap-and-release-process (@ShixiangWang) (#4)
  • Add TODO.md with 30-expert evaluation and action items (@Copilot)
  • Update (@ShixiangWang)
  • Merge pull request #3 from Traitome/copilot/implement-oxo-flow-core-library (@ShixiangWang) (#3)
  • Add paired_tumor_normal example, integration tests, and root package for workspace-level tests (@Copilot)
  • 30-expert evaluation: comprehensive upgrades - error variants, config defaults, DAG parallel groups, rule validation, executor retry/timeout, priority scheduling, clinical reports, Venus CNV/MSI/TMB, web export/request-ID, CLI retry/timeout flags, examples, integration tests - 231 tests passing (@Copilot)
  • Comprehensive multi-expert evaluation upgrades: executor env integration, Venus FilterMutectCalls/Strelka2, web API CORS/run/clean/version endpoints, container multi-stage builds, CLI clean/completions/init enhancements, Venus pipeline files, 200 tests passing (@Copilot)
  • Add comprehensive tests for web, venus, and environment modules (@Copilot)
  • Add FilterMutectCalls, Strelka2, known_sites to Venus pipeline (@Copilot)
  • Add environment integration to executor and retry/timeout config fields (@Copilot)
  • Merge pull request #2 from Traitome/copilot/update-roadmap-with-expert-feedback (@ShixiangWang) (#2)
  • Phase 7-8: Venus pipeline builder, CLI status/clean commands, enhanced example workflow, ROADMAP update (@Copilot)
  • Merge pull request #1 from Traitome/copilot/add-core-library-oxo-flow (@ShixiangWang) (#1)
  • Initial commit (@ShixiangWang)

Testing#

  • Add 30 CLI binary integration tests for oxo-flow, venus, and oxo-flow-web (@Copilot)