v0.8.0

0.8.0 — 2026-06-14

Bug Fixes

• Resolve all audit findings — Makefile tabs, suite.py shadowing, version refs, Snakemake (@ShixiangWang)

Documentation

• Add CONTRIBUTING.md and SECURITY.md (@ShixiangWang)
• Overhaul landing page — AI Companion, current API, React stack (@ShixiangWang)
• Overhaul README — AI Companion, current API, clean duplicates (@ShixiangWang)
• Deployment guide, AI provider env vars, UI polish (@ShixiangWang)
• Add cloud storage reference doc, update LIMITATIONS.md and nav (@ShixiangWang)
• Update CHANGELOG.md for v0.7.0 [skip ci] (@github-actions[bot])

Features

• AI config API, runtime provider switching, Docker deployment, UI polish (@ShixiangWang)
• Docker deployment, custom AI URLs, frontend serving (@ShixiangWang)
• AI provider abstraction with Claude/OpenAI/Ollama support (@ShixiangWang)
• AI-native pipeline platform with structured results and web frontend (@ShixiangWang)
• core: Implement real S3/GCS storage backends, expand webhook & plugin tests, add benchmarks (@ShixiangWang)

Maintenance

• Bump version to 0.8.0 [skip ci] (@github-actions[bot])
• Add remaining frontend config files (@ShixiangWang)

Other Changes

• Feat/v0.8 deterministic core (#45) (@ShixiangWang) (#45)
• Add macro/comparative benchmarks, bump version to 0.8.0 (@ShixiangWang)

Performance

• bench: Restructure benchmarks into modular suite with 35 micro-benchmarks (@ShixiangWang)

v0.7.0

0.7.0 — 2026-05-25

Bug Fixes

• Resolve doc/code discrepancies found in consistency audit (@ShixiangWang)
• Use serde serialization for format_workflow, fix example workflows (@ShixiangWang)
• Resolve all remaining code audit issues across core, web, and plugin (@ShixiangWang)
• --as-include skips E010, fix double GPU flag, escape report HTML, respect rule retries (@ShixiangWang)
• Respect rule-level retries field in execution retry loop (@ShixiangWang)
• Complete security patterns, validate export/package format args (@ShixiangWang)
• Resolve 5 feature gaps from production readiness audit (@ShixiangWang)
• Wildcard constraints filter instead of fail, optional rules warn on missing input (@ShixiangWang)
• Improve target resolution UX and environment listing, fix CI issues (@ShixiangWang)
• web: Resolve 6 bugs from production readiness audit (@ShixiangWang)
• Resolve CLI unwrap risks and Core config expect improvements (@ShixiangWang)
• web: Comprehensive test-driven fixes for 9 issues found (@ShixiangWang)
• container: Add CMD to Dockerfile for better UX (@ShixiangWang)
• container: Add cargo install + fallback to Singularity def oxo-flow installation (@ShixiangWang)
• container: Use cargo install + GitHub release fallback for Dockerfiles (@ShixiangWang)
• web: Prevent XSS via workflow name in onclick handlers (@ShixiangWang)

Documentation

• Complete rewrite of JSON Schema, fix all CLI and format doc gaps (@ShixiangWang)
• Add missing rule fields, env_groups, genome_build to workflow format spec (@ShixiangWang)
• web: Add multi-user web system design specification (@ShixiangWang)
• web: Add security model and DELETE endpoint to web API docs (@ShixiangWang)
• Update CHANGELOG.md for v0.6.1 [skip ci] (@github-actions[bot])

Features

• Light theme, license upload web UI, and CLI license command (@ShixiangWang)
• web: Embed default academic license with commercial notice (@ShixiangWang)
• web: Comprehensive multi-user web system with User Mgmt, HPC, Templates (@ShixiangWang)
• web: Add HPC scheduler integration for Slurm/PBS monitoring (@ShixiangWang)
• web: Add scheduled workflow runs with cron support (@ShixiangWang)
• web: Add P2 Enterprise Governance and Template Library features (@ShixiangWang)
• web: Modularize handlers and add maud templates (@ShixiangWang)
• web: Add optional id field to SaveWorkflowRequest for upsert support (@ShixiangWang)
• container: Add oxo-flow binary installation to Dockerfile and Singularity def (@ShixiangWang)
• web: Add New Workflow button, auto-clear save name, UX polish (@ShixiangWang)
• web: Add Dockerfile export button and modal to editor (@ShixiangWang)
• web: Replace prompt() login with modal sign-in form (@ShixiangWang)
• web: Add workflow deletion, SSE live updates, and editor templates (@ShixiangWang)
• web: Add CLI arg parsing to web binary, update full API docs (@ShixiangWang)
• web: Add GET /api/workflows/saved/{id} endpoint and Load-to-Editor (@ShixiangWang)
• web: Professional dark-themed Command Center SPA frontend (@ShixiangWang)
• web: Full workflow lifecycle API, workspace isolation, and 20-user simulation (@ShixiangWang)

Maintenance

• Bump version to 0.7.0 [skip ci] (@github-actions[bot])
• Fix all 16 unused-variable warnings in simulation_20users (@ShixiangWang)
• Fix make ci - remove orphan comments, fix clippy warnings (@ShixiangWang)
• web: Remove 15 orphan doc comments after handler dedup (@ShixiangWang)
• Remove e2e-playwright test suite (@ShixiangWang)
• Update e2e gitignore for logs and lock file (@ShixiangWang)
• Update Cargo.lock for web crate clap dependency (@ShixiangWang)

Refactoring

• web: Remove 1101 dup lines, dead maud templates, partials (@ShixiangWang)
• web: Remove 31 duplicate handlers, add DAG viz + template CRUD UI (@ShixiangWang)
• web: Split frontend into index.html + app.js (@ShixiangWang)

Testing

• web: Add Playwright E2E tests for multi-user web system (@ShixiangWang)
• web: Add 20 real-world user scenario tests from expert perspectives (@ShixiangWang)
• container: Add tests for oxo-flow install in Dockerfile and Singularity def (@ShixiangWang)
• web: Add E2E lifecycle tests for save/load/delete and full run cycle (@ShixiangWang)

v0.6.1

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

• Fix README accuracy, serve base_path passthrough, and broken links (@ShixiangWang)
• Add missing history command reference page (@ShixiangWang)
• Update plugin-system.md to reflect full implementation (@ShixiangWang)
• Fix plugin-system.md to reflect actual implementation status (@ShixiangWang)
• Update command count to 31 (added history command) (@ShixiangWang)
• Add CLI reference pages for all 29 commands (@ShixiangWang)
• Update CHANGELOG.md for v0.6.0 [skip ci] (@github-actions[bot])

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

• Bump version to 0.6.1 [skip ci] (@github-actions[bot])
• Fix stale version references and documentation consistency (@ShixiangWang)

Other Changes

• Update (@ShixiangWang)

v0.6.0

0.6.0 — 2026-05-21

Bug Fixes

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

Documentation

• Add BLIT citation and optimize landing page badges (@ShixiangWang)
• Refactor clinical reporting and synchronize CLI commands in README (@ShixiangWang)
• Update CHANGELOG.md for v0.5.5 [skip ci] (@github-actions[bot])

Maintenance

• Bump version to 0.6.0 [skip ci] (@github-actions[bot])

Other Changes

• Test/real data validation (#43) (@ShixiangWang) (#43)

v0.5.5

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

• Fix remaining stale subcommand count and add cargo install instruction (@ShixiangWang)
• Update CHANGELOG.md for v0.5.4 [skip ci] (@github-actions[bot])

Features

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

Maintenance

• Bump version to 0.5.5 [skip ci] (@github-actions[bot])

Other Changes

• Consolidate AI agent docs into AGENTS.md (@ShixiangWang)
• Update README.md (@ShixiangWang)

Styling

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

v0.5.4

0.5.4 — 2026-05-19

CI/CD

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

Documentation

• Add Venus extraction design spec (@ShixiangWang)
• Update CHANGELOG.md for v0.5.3 [skip ci] (@github-actions[bot])

Maintenance

• Bump version to 0.5.4 [skip ci] (@github-actions[bot])
• Completely remove Venus from oxo-flow repository (@ShixiangWang)
• Remove Venus CLI integration tests, gitignore oxo-flow-venus (@ShixiangWang)
• Remove Venus integration tests after extraction (@ShixiangWang)
• Extract Venus into standalone repository oxo-flow-venus (@ShixiangWang)

Other Changes

• Update Cargo.lock (@ShixiangWang)

v0.5.3

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

• Add missing documentation for optional rules, directory input, and E010 test (@ShixiangWang)
• Document new features in README (@ShixiangWang)
• Update CHANGELOG for new features (@ShixiangWang)
• Add implementation plan for oxo-flow optimizations (@ShixiangWang)
• Add oxo-flow optimizations design spec (@ShixiangWang)
• Add circRNA pipeline implementation plan (@ShixiangWang)
• Add circRNA pipeline design specification (@ShixiangWang)
• Update CHANGELOG.md for v0.5.2 [skip ci] (@github-actions[bot])

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

• Bump version to 0.5.3 [skip ci] (@github-actions[bot])
• Fix clippy warnings and ensure CI passes (@ShixiangWang)

Testing

• config: Add tests for reference_dir derivation (@ShixiangWang)
• cli: Add tests for --as-include validation (@ShixiangWang)

v0.5.2

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

• Audit and clean up documentation, resolve implementation inconsistencies (@ShixiangWang)
• Clean up and fix issues in all .md files (#41) (@Copilot) (#41)
• Update CHANGELOG.md for v0.5.1 [skip ci] (@github-actions[bot])

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

• Bump version to 0.5.2 [skip ci] (@github-actions[bot])
• Fix lint and formatting issues from CI (@ShixiangWang)

Other Changes

• Add auth, CORS & schema; remove reviews (@ShixiangWang)

Performance

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

v0.5.1

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

• Add metadata field to pairs table documentation (@ShixiangWang)
• Update CHANGELOG.md for v0.5.0 [skip ci] (@github-actions[bot])

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

• Bump version to 0.5.1 [skip ci] (@github-actions[bot])

v0.5.0

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

• Block pipeline on security audit failures (@ShixiangWang)

Documentation

• Update version references from 0.4.1 to 0.4.2 (@ShixiangWang)
• Update CLI subcommand count and add batch references (@ShixiangWang)
• Add 30-expert comprehensive assessment report (@ShixiangWang)
• Docs update (@ShixiangWang)
• Add 30-expert assessment report (@ShixiangWang)
• Improve quickstart graph visualization section (@ShixiangWang)
• Fix duplicate [rules.resources] TOML syntax error (@ShixiangWang)
• Add script execution and all missing Rule fields to workflow format reference (@ShixiangWang)
• Add non-shell language support design spec (@ShixiangWang)
• Add resource management section to workflow format reference (@ShixiangWang)
• Create resource tuning best practices guide (@ShixiangWang)
• Add resource management implementation plan (@ShixiangWang)
• Add resource management review design spec (@ShixiangWang)
• Update CHANGELOG.md for v0.4.2 [skip ci] (@github-actions[bot])
• design: Add transform operator design spec (@ShixiangWang)

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

• Bump version to 0.5.0 [skip ci] (@github-actions[bot])
• Ignore hello.txt from example workflow output (@ShixiangWang)

Other Changes

• Remove Windows CI job and platform references (@ShixiangWang)
• Update README.md (@ShixiangWang)
• Add oxo-flow logo SVGs (@ShixiangWang)
• Add cargo audit configuration (@ShixiangWang)
• executor: Validate interpreter paths for safety (@ShixiangWang)
• executor: Block absolute paths outside workdir (@ShixiangWang)
• executor: Validate hook commands for injection prevention (@ShixiangWang)
• executor: Add validate_shell_safety to block dangerous patterns (@ShixiangWang)
• Add pre_exec hook and cleanup/resource changes (@ShixiangWang)
• Merge branch 'main' of https://github.com/Traitome/oxo-flow (@ShixiangWang)

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)