oxo-call 0.11.0

Model-intelligent orchestration for CLI bioinformatics — call any tool with LLM intelligence
Documentation 
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# history

Browse past command runs with exit codes and timestamps.

## Synopsis

```
oxo-call history list  [-n <N>] [--tool <TOOL>]
oxo-call history clear [-y]
```

## Subcommands

### `history list`

Show recent command history:

```bash
# Last 20 commands (default)
oxo-call history list

# Last 50 commands
oxo-call history list -n 50

# Filter by tool name
oxo-call history list --tool samtools
```

### `history clear`

Clear all command history:

```bash
oxo-call history clear
oxo-call history clear -y  # Skip confirmation
```

## History Entry Format

Each history entry includes:

- **ID**: Unique UUID
- **Tool**: The CLI tool that was executed
- **Task**: The natural language task description
- **Command**: The full generated command
- **Exit code**: The process exit code
- **Timestamp**: When the command was executed
- **Dry-run flag**: Whether it was a dry-run or real execution
- **Provenance** (new): Reproducibility metadata recorded alongside each command:
  - `tool_version`: Version string from `<tool> --version`
  - `docs_hash`: Fingerprint of the documentation used in the LLM prompt
  - `skill_name`: Name of the matched skill file (if any)
  - `model`: LLM model identifier that generated the command

Provenance fields are displayed below each history entry when available:

```
ok       samtools     0        2025-06-01 12:00:00          samtools sort -o sorted.bam input.bam
         [ver=samtools 1.21, model=gpt-4o-mini, skill=samtools, docs=a1b2c3d4]
```

## Storage

History is stored as JSONL (JSON Lines) at:

- Linux: `~/.local/share/oxo-call/history.jsonl`
- macOS: `~/Library/Application Support/io.traitome.oxo-call/history.jsonl`