v3.0.0

haddock-runner v3.0.0

Major Changes

Complete Rewrite in Rust 🦀

This release represents a complete rewrite of haddock-runner from Go to Rust, bringing significant improvements in performance, safety, and maintainability.

Technical Changes

Architecture

• Language: Migrated from Go to Rust
• Error Handling: Using Rust's anyhow::Result pattern throughout
• Configuration: Using serde for YAML parsing with proper deserialization
• Modular Design: Clear separation of concerns with dedicated modules

Job Management

• Job Restart Logic: Added automatic detection and handling of incomplete jobs
• Status Tracking: Enhanced job status monitoring with Done, Incomplete, and Unknown states
• Automatic Cleanup: Incomplete jobs are automatically cleaned and re-setup

Configuration Format

The new YAML format supports:

general:
  max_concurrent: 100
  ncores: 1
  execution: slurm  # or local
  mol_suffixes: [_r_u, _l_u, _x_u]
  input_list: path/to/input_list.txt # relative paths now available
  work_dir: path/to/work_dir

scenarios:
  - name: scenario-name
    workflow:
      topoaa:
        autohis: true
      rigidbody:
        sampling: 10
        ambig_fname: _ti.tbl
      # ... additional workflow steps

Command Line Interface

• --setup flag for setup-only mode
• --debug flag for verbose logging

Build System

• Cargo-based build with optimized release profiles
• Rust 1.92+ required
• Cross-platform compilation support

Migration Notes

Breaking Changes

1. Configuration Format: Completely new YAML structure
2. Binary Name: Now haddock-runner (was same in Go version)
3. Input Validation: More strict validation of paths and configurations
4. Shape File Handling: Removed shape_suffix configuration option - shape files must now be specified in mol_suffixes

Compatibility

• Supports only HADDOCK3.0 workflows
• Maintains same core functionality as Go version
• Improved error messages and logging

Performance Improvements

• Faster job creation and setup
• More efficient file handling
• Better memory management
• Optimized concurrent execution

Development Changes

• Comprehensive test suite
• Better documentation with doc comments
• Type-safe development
• Modern Rust toolchain integration

v2.0.1

What's Changed

• Bump golang.org/x/text from 0.27.0 to 0.29.0 by @dependabot[bot] in #164
• specify end of string anchor in topparRegex by @rvhonorato in #166

Full Changelog: v2.0.0...v2.0.1

v2.0.0

What's Changed

• add error message for empty parameters by @rvhonorato in #162
• check if modules in the order field are defined as modules and vice-versa by @rvhonorato in #163

💥breaking changes 💥
empty definitions now need to have an object:

-        emref:
+        emref: {}

Full Changelog: v1.13.2...v2.0.0

v1.13.2

What's Changed

• disable nested execution by @rvhonorato in #159

Full Changelog: v1.13.1...v1.13.2

v1.13.1

What's Changed

-- Quick bugfix by changing how early the code checks if the benchmark folder is present or not

• Hotfix by @rvhonorato in #158

Full Changelog: v1.13.0...v1.13.1

v1.13.0

What's Changed

• Bump golang.org/x/text from 0.25.0 to 0.26.0 by @dependabot[bot] in #151
• Bump golang.org/x/text from 0.26.0 to 0.27.0 by @dependabot[bot] in #152
• add -setup option by @rvhonorato in #155
• update docs by @rvhonorato in #156

Full Changelog: v1.12.3...v1.13.0

v1.12.3

What's Changed

• Bump golang.org/x/text from 0.22.0 to 0.23.0 by @dependabot in #143
• Fix documentation typos by @cvnoort in #144
• Bump github.com/golang/glog from 1.2.4 to 1.2.5 by @dependabot in #146
• Bump golang.org/x/text from 0.23.0 to 0.24.0 by @dependabot in #145
• Bump golang.org/x/text from 0.24.0 to 0.25.0 by @dependabot in #147
• Update module-struct by @rvhonorato in #149

New Contributors

• @cvnoort made their first contribution in #144

Full Changelog: v1.12.2...v1.12.3

v1.12.2

What's Changed

• Bump golang.org/x/text from 0.21.0 to 0.22.0 by @dependabot in #139
• Skip shapeRegex matching if ssuf is empty by @rvhonorato in #141
• bump version by @rvhonorato in #142

Full Changelog: v1.12.1...v1.12.2

v1.12.1

What's Changed

• Bump github.com/golang/glog from 1.2.3 to 1.2.4 in the go_modules group by @dependabot in #138
• Update toppar regex by @rvhonorato in #137

Full Changelog: v1.12.0...v1.12.1

v1.12.0

What's Changed

• Bump golang.org/x/text from 0.20.0 to 0.21.0 by @dependabot in #133
• add HETATM support to CreateEnsemble by @rvhonorato in #135

Full Changelog: v1.11.0...v1.12.0