@yeyuan98/opencode-bioresearcher-plugin 1.4.0 → 1.4.1

package/dist/skills/bioresearcher-core/README.md

@@ -1,210 +1,210 @@
-# BioResearcher Core
-
-Core library skill providing reusable patterns and utilities for BioResearcher skills.
-
-## Overview
-
-BioResearcher Core provides:
-- **Workflow patterns** for common operations (retry, progress, subagent waves)
-- **Data handling patterns** for JSON and table operations
-- **Python utilities** for template generation
-- **Tool-first architecture** using existing plugin tools
-
-## Installation
-
-No installation required. This skill uses only:
-- Existing plugin tools (jsonExtract, jsonValidate, etc.)
-- Python standard library
-
-## Quick Start
-
-### Load the Skill
-
-```
-skill bioresearcher-core
-```
-
-### Extract Skill Path
-
-From the `<skill_files>` section in the skill tool output, extract the `<skill_path>` value for use in commands.
-
-### Use a Pattern
-
-```
-Read <skill_path>/patterns/retry.md
-```
-
-### Run Python Script
-
-```bash
-uv run python <skill_path>/python/template.py generate-batches \
-  --template template.md \
-  --contexts contexts.json \
-  --output-dir ./outputs
-```
-
-## Available Patterns
-
-### Workflow Control
-
-| Pattern | Description | File |
-|---------|-------------|------|
-| Retry | Retry with backoff using blockingTimer | `patterns/retry.md` |
-| Progress | Track and report batch progress | `patterns/progress.md` |
-| Subagent Waves | Parallel subagent processing | `patterns/subagent-waves.md` |
-| Shell Commands | Cross-platform command generation | `patterns/shell-commands.md` |
-| User Confirmation | Request user confirmation | `patterns/user-confirmation.md` |
-
-### Data Handling
-
-| Pattern | Description | File |
-|---------|-------------|------|
-| JSON Tools | jsonExtract/jsonValidate/jsonInfer | `patterns/json-tools.md` |
-| Table Tools | Combine outputs with table tools | `patterns/table-tools.md` |
-| Data Exchange | Main/subagent communication | `patterns/data-exchange.md` |
-| Calculator | In-workflow calculations | `patterns/calculator.md` |
-
-## Available Tools
-
-These tools are always available without loading pattern files:
-
-### JSON Tools
-
-| Tool | Description |
-|------|-------------|
-| `jsonExtract` | Extract JSON from files |
-| `jsonValidate` | Validate JSON against schemas |
-| `jsonInfer` | Infer schemas from data |
-
-### Utility Tools
-
-| Tool | Description |
-|------|-------------|
-| `blockingTimer` | Blocking delays (0-300 seconds) |
-| `calculator` | Mathematical expressions |
-
-### Table Tools
-
-| Tool | Description |
-|------|-------------|
-| `tableCreateFile` | Create Excel/CSV from data |
-| `tableAppendRows` | Append rows to tables |
-
-## Python Utilities
-
-### Template Engine
-
-Location: `python/template.py`
-
-Commands:
-- `fill` - Generate single file from template
-- `generate-batches` - Generate multiple files from template
-- `escape` - Escape text for markdown
-
-See `python/template.md` for full documentation.
-
-## Examples
-
-### Example Files
-
-| File | Description |
-|------|-------------|
-| `examples/template.md` | Example template with placeholders |
-| `examples/contexts.json` | Example contexts for batch generation |
-| `examples/data-exchange-example.md` | Complete data exchange workflow |
-
-## Architecture
-
-### Tool-First Design
-
-This skill maximizes use of existing plugin tools:
-
-```
-┌─────────────────────────────────────────────────┐
-│              BioResearcher Core                  │
-├─────────────────────────────────────────────────┤
-│  Patterns (markdown)    │  Python Utilities     │
-│  - retry.md             │  - template.py        │
-│  - progress.md          │                       │
-│  - subagent-waves.md    │                       │
-│  - json-tools.md        │                       │
-│  - table-tools.md       │                       │
-│  - data-exchange.md     │                       │
-│  - calculator.md        │                       │
-│  - shell-commands.md    │                       │
-│  - user-confirmation.md │                       │
-├─────────────────────────┴───────────────────────┤
-│              Plugin Tools                        │
-│  jsonExtract │ jsonValidate │ jsonInfer         │
-│  blockingTimer │ calculator                      │
-│  tableCreateFile │ tableAppendRows              │
-└─────────────────────────────────────────────────┘
-```
-
-### Pattern Modules
-
-Each pattern is a self-contained markdown file:
-- Independent (no dependencies on other patterns)
-- Self-documenting (explains itself)
-- Minimal loading (agent reads only what it needs)
-
-## Integration with Other Skills
-
-### long-table-summary
-
-BioResearcher Core can be used by long-table-summary:
-- Use `jsonExtract` instead of manual JSON parsing
-- Use `jsonValidate` for schema validation
-- Apply retry/progress patterns
-- Use template.py for prompt generation
-
-### pubmed-weekly
-
-BioResearcher Core can be used by pubmed-weekly:
-- Apply retry pattern for download failures
-- Use shell-commands pattern for cross-platform support
-
-## Design Principles
-
-1. **Tool-first**: Use existing tools before creating Python scripts
-2. **Self-contained**: Each pattern is independent
-3. **Minimal dependencies**: Only Python standard library
-4. **Clear documentation**: Every file documents itself
-5. **Standard protocols**: JSON for data exchange
-
-## Directory Structure
-
-```
-plugin/skills/bioresearcher-core/
-├── SKILL.md                    # Routing document
-├── README.md                   # This file
-├── patterns/                   # Workflow patterns
-│   ├── retry.md
-│   ├── progress.md
-│   ├── subagent-waves.md
-│   ├── shell-commands.md
-│   ├── user-confirmation.md
-│   ├── json-tools.md
-│   ├── table-tools.md
-│   ├── data-exchange.md
-│   └── calculator.md
-├── python/                     # Python utilities
-│   ├── template.py
-│   └── template.md
-└── examples/                   # Example files
-    ├── template.md
-    ├── contexts.json
-    └── data-exchange-example.md
-```
-
-## Contributing
-
-When adding new patterns:
-1. Create self-contained markdown file in `patterns/`
-2. Follow existing pattern structure
-3. Include examples and error handling
-4. Update SKILL.md with new pattern reference
-
-## License
-
-Part of the BioResearcher plugin ecosystem.
+# BioResearcher Core
+
+Core library skill providing reusable patterns and utilities for BioResearcher skills.
+
+## Overview
+
+BioResearcher Core provides:
+- **Workflow patterns** for common operations (retry, progress, subagent waves)
+- **Data handling patterns** for JSON and table operations
+- **Python utilities** for template generation
+- **Tool-first architecture** using existing plugin tools
+
+## Installation
+
+No installation required. This skill uses only:
+- Existing plugin tools (jsonExtract, jsonValidate, etc.)
+- Python standard library
+
+## Quick Start
+
+### Load the Skill
+
+```
+skill bioresearcher-core
+```
+
+### Extract Skill Path
+
+From the `<skill_files>` section in the skill tool output, extract the `<skill_path>` value for use in commands.
+
+### Use a Pattern
+
+```
+Read <skill_path>/patterns/retry.md
+```
+
+### Run Python Script
+
+```bash
+uv run python <skill_path>/python/template.py generate-batches \
+  --template template.md \
+  --contexts contexts.json \
+  --output-dir ./outputs
+```
+
+## Available Patterns
+
+### Workflow Control
+
+| Pattern | Description | File |
+|---------|-------------|------|
+| Retry | Retry with backoff using blockingTimer | `patterns/retry.md` |
+| Progress | Track and report batch progress | `patterns/progress.md` |
+| Subagent Waves | Parallel subagent processing | `patterns/subagent-waves.md` |
+| Shell Commands | Cross-platform command generation | `patterns/shell-commands.md` |
+| User Confirmation | Request user confirmation | `patterns/user-confirmation.md` |
+
+### Data Handling
+
+| Pattern | Description | File |
+|---------|-------------|------|
+| JSON Tools | jsonExtract/jsonValidate/jsonInfer | `patterns/json-tools.md` |
+| Table Tools | Combine outputs with table tools | `patterns/table-tools.md` |
+| Data Exchange | Main/subagent communication | `patterns/data-exchange.md` |
+| Calculator | In-workflow calculations | `patterns/calculator.md` |
+
+## Available Tools
+
+These tools are always available without loading pattern files:
+
+### JSON Tools
+
+| Tool | Description |
+|------|-------------|
+| `jsonExtract` | Extract JSON from files |
+| `jsonValidate` | Validate JSON against schemas |
+| `jsonInfer` | Infer schemas from data |
+
+### Utility Tools
+
+| Tool | Description |
+|------|-------------|
+| `blockingTimer` | Blocking delays (0-300 seconds) |
+| `calculator` | Mathematical expressions |
+
+### Table Tools
+
+| Tool | Description |
+|------|-------------|
+| `tableCreateFile` | Create Excel/CSV from data |
+| `tableAppendRows` | Append rows to tables |
+
+## Python Utilities
+
+### Template Engine
+
+Location: `python/template.py`
+
+Commands:
+- `fill` - Generate single file from template
+- `generate-batches` - Generate multiple files from template
+- `escape` - Escape text for markdown
+
+See `python/template.md` for full documentation.
+
+## Examples
+
+### Example Files
+
+| File | Description |
+|------|-------------|
+| `examples/template.md` | Example template with placeholders |
+| `examples/contexts.json` | Example contexts for batch generation |
+| `examples/data-exchange-example.md` | Complete data exchange workflow |
+
+## Architecture
+
+### Tool-First Design
+
+This skill maximizes use of existing plugin tools:
+
+```
+┌─────────────────────────────────────────────────┐
+│              BioResearcher Core                  │
+├─────────────────────────────────────────────────┤
+│  Patterns (markdown)    │  Python Utilities     │
+│  - retry.md             │  - template.py        │
+│  - progress.md          │                       │
+│  - subagent-waves.md    │                       │
+│  - json-tools.md        │                       │
+│  - table-tools.md       │                       │
+│  - data-exchange.md     │                       │
+│  - calculator.md        │                       │
+│  - shell-commands.md    │                       │
+│  - user-confirmation.md │                       │
+├─────────────────────────┴───────────────────────┤
+│              Plugin Tools                        │
+│  jsonExtract │ jsonValidate │ jsonInfer         │
+│  blockingTimer │ calculator                      │
+│  tableCreateFile │ tableAppendRows              │
+└─────────────────────────────────────────────────┘
+```
+
+### Pattern Modules
+
+Each pattern is a self-contained markdown file:
+- Independent (no dependencies on other patterns)
+- Self-documenting (explains itself)
+- Minimal loading (agent reads only what it needs)
+
+## Integration with Other Skills
+
+### long-table-summary
+
+BioResearcher Core can be used by long-table-summary:
+- Use `jsonExtract` instead of manual JSON parsing
+- Use `jsonValidate` for schema validation
+- Apply retry/progress patterns
+- Use template.py for prompt generation
+
+### pubmed-weekly
+
+BioResearcher Core can be used by pubmed-weekly:
+- Apply retry pattern for download failures
+- Use shell-commands pattern for cross-platform support
+
+## Design Principles
+
+1. **Tool-first**: Use existing tools before creating Python scripts
+2. **Self-contained**: Each pattern is independent
+3. **Minimal dependencies**: Only Python standard library
+4. **Clear documentation**: Every file documents itself
+5. **Standard protocols**: JSON for data exchange
+
+## Directory Structure
+
+```
+plugin/skills/bioresearcher-core/
+├── SKILL.md                    # Routing document
+├── README.md                   # This file
+├── patterns/                   # Workflow patterns
+│   ├── retry.md
+│   ├── progress.md
+│   ├── subagent-waves.md
+│   ├── shell-commands.md
+│   ├── user-confirmation.md
+│   ├── json-tools.md
+│   ├── table-tools.md
+│   ├── data-exchange.md
+│   └── calculator.md
+├── python/                     # Python utilities
+│   ├── template.py
+│   └── template.md
+└── examples/                   # Example files
+    ├── template.md
+    ├── contexts.json
+    └── data-exchange-example.md
+```
+
+## Contributing
+
+When adding new patterns:
+1. Create self-contained markdown file in `patterns/`
+2. Follow existing pattern structure
+3. Include examples and error handling
+4. Update SKILL.md with new pattern reference
+
+## License
+
+Part of the BioResearcher plugin ecosystem.

package/dist/skills/bioresearcher-core/SKILL.md

@@ -1,128 +1,128 @@
----
-name: bioresearcher-core
-description: Core patterns and utilities for BioResearcher skills
-allowedTools:
-  - Read
-  - Write
-  - Bash
-  - jsonExtract
-  - jsonValidate
-  - jsonInfer
-  - blockingTimer
-  - calculator
-  - tableCreateFile
-  - tableAppendRows
-  - Question
-  - Task
----
-
-# BioResearcher Core
-
-This skill provides reusable patterns and utilities for BioResearcher skills.
-
-## Quick Start
-
-### Step 1: Load This Skill
-```
-skill bioresearcher-core
-```
-
-### Step 2: Extract Skill Path
-From the `<skill_files>` section in the skill tool output, extract the `<skill_path>` value.
-
-### Step 3: Use Resources
-- Read pattern: `Read <skill_path>/patterns/retry.md`
-- Run script: `uv run python <skill_path>/python/template.py ...`
-
-## Available Patterns
-
-### Workflow Control
-- `patterns/retry.md` - Retry with backoff using blockingTimer
-- `patterns/progress.md` - Progress tracking
-- `patterns/subagent-waves.md` - Parallel subagent processing
-- `patterns/shell-commands.md` - Unix/Windows command generation
-- `patterns/user-confirmation.md` - User confirmation
-
-### Data Handling
-- `patterns/json-tools.md` - Using jsonExtract/jsonValidate/jsonInfer
-- `patterns/table-tools.md` - Combining outputs with table tools
-- `patterns/data-exchange.md` - Main/subagent data exchange protocol
-- `patterns/calculator.md` - In-workflow calculations
-
-## Python Utilities
-- `python/template.md` - Template generation documentation
-
-## Direct Tools (No Loading Needed)
-
-These tools are always available without loading pattern files:
-
-### JSON Tools
-- `jsonExtract` - Extract JSON from files (handles markdown code blocks, raw JSON)
-- `jsonValidate` - Validate JSON against schemas (Draft-4, Draft-7, Draft-2020-12)
-- `jsonInfer` - Infer schemas from JSON data
-
-### Utility Tools
-- `blockingTimer` - Blocking delays (0-300 seconds)
-- `calculator` - Mathematical expressions (+, -, *, /, ^, brackets)
-
-### Table Tools
-- `tableCreateFile` - Create Excel/CSV files from data
-- `tableAppendRows` - Append rows to existing tables
-
-## Tool Signatures
-
-### jsonExtract
-```
-jsonExtract(file_path: string, return_all: boolean = false)
-Returns: { success, data, metadata: { method, dataType, fileSize } }
-```
-
-### jsonValidate
-```
-jsonValidate(data: string, schema: string)
-Returns: { success, valid, errors?, metadata: { errorCount, schemaFeatures } }
-```
-
-### jsonInfer
-```
-jsonInfer(data: string, strict: boolean = false)
-Returns: { success, data: JSONSchema, metadata: { inferredType, strictMode } }
-```
-
-### blockingTimer
-```
-blockingTimer(delay: number)
-Returns: "Timer completed: waited X seconds (actual elapsed: Ys)"
-```
-
-### calculator
-```
-calculator(formula: string, precision: number = 3)
-Returns: { formula, result }
-```
-
-### tableCreateFile
-```
-tableCreateFile(file_path: string, sheet_name: string = "Sheet1", data: array)
-Returns: { success, file_path, sheet_name, rows_created }
-```
-
-### tableAppendRows
-```
-tableAppendRows(file_path: string, sheet_name: string?, rows: array)
-Returns: { success, rows_appended }
-```
-
-## When to Use Each Pattern
-
-| Use Case | Pattern File |
-|----------|-------------|
-| Network/API failures | `patterns/retry.md` |
-| Batch processing progress | `patterns/progress.md` |
-| Parallel subagent execution | `patterns/subagent-waves.md` |
-| Cross-platform commands | `patterns/shell-commands.md` |
-| Destructive operations | `patterns/user-confirmation.md` |
-| JSON data extraction | `patterns/json-tools.md` |
-| Combining batch outputs | `patterns/table-tools.md` |
-| Subagent communication | `patterns/data-exchange.md` |
-| Progress calculations | `patterns/calculator.md` |
+---
+name: bioresearcher-core
+description: Core patterns and utilities for BioResearcher skills
+allowedTools:
+  - Read
+  - Write
+  - Bash
+  - jsonExtract
+  - jsonValidate
+  - jsonInfer
+  - blockingTimer
+  - calculator
+  - tableCreateFile
+  - tableAppendRows
+  - Question
+  - Task
+---
+
+# BioResearcher Core
+
+This skill provides reusable patterns and utilities for BioResearcher skills.
+
+## Quick Start
+
+### Step 1: Load This Skill
+```
+skill bioresearcher-core
+```
+
+### Step 2: Extract Skill Path
+From the `<skill_files>` section in the skill tool output, extract the `<skill_path>` value.
+
+### Step 3: Use Resources
+- Read pattern: `Read <skill_path>/patterns/retry.md`
+- Run script: `uv run python <skill_path>/python/template.py ...`
+
+## Available Patterns
+
+### Workflow Control
+- `patterns/retry.md` - Retry with backoff using blockingTimer
+- `patterns/progress.md` - Progress tracking
+- `patterns/subagent-waves.md` - Parallel subagent processing
+- `patterns/shell-commands.md` - Unix/Windows command generation
+- `patterns/user-confirmation.md` - User confirmation
+
+### Data Handling
+- `patterns/json-tools.md` - Using jsonExtract/jsonValidate/jsonInfer
+- `patterns/table-tools.md` - Combining outputs with table tools
+- `patterns/data-exchange.md` - Main/subagent data exchange protocol
+- `patterns/calculator.md` - In-workflow calculations
+
+## Python Utilities
+- `python/template.md` - Template generation documentation
+
+## Direct Tools (No Loading Needed)
+
+These tools are always available without loading pattern files:
+
+### JSON Tools
+- `jsonExtract` - Extract JSON from files (handles markdown code blocks, raw JSON)
+- `jsonValidate` - Validate JSON against schemas (Draft-4, Draft-7, Draft-2020-12)
+- `jsonInfer` - Infer schemas from JSON data
+
+### Utility Tools
+- `blockingTimer` - Blocking delays (0-300 seconds)
+- `calculator` - Mathematical expressions (+, -, *, /, ^, brackets)
+
+### Table Tools
+- `tableCreateFile` - Create Excel/CSV files from data
+- `tableAppendRows` - Append rows to existing tables
+
+## Tool Signatures
+
+### jsonExtract
+```
+jsonExtract(file_path: string, return_all: boolean = false)
+Returns: { success, data, metadata: { method, dataType, fileSize } }
+```
+
+### jsonValidate
+```
+jsonValidate(data: string, schema: string)
+Returns: { success, valid, errors?, metadata: { errorCount, schemaFeatures } }
+```
+
+### jsonInfer
+```
+jsonInfer(data: string, strict: boolean = false)
+Returns: { success, data: JSONSchema, metadata: { inferredType, strictMode } }
+```
+
+### blockingTimer
+```
+blockingTimer(delay: number)
+Returns: "Timer completed: waited X seconds (actual elapsed: Ys)"
+```
+
+### calculator
+```
+calculator(formula: string, precision: number = 3)
+Returns: { formula, result }
+```
+
+### tableCreateFile
+```
+tableCreateFile(file_path: string, sheet_name: string = "Sheet1", data: array)
+Returns: { success, file_path, sheet_name, rows_created }
+```
+
+### tableAppendRows
+```
+tableAppendRows(file_path: string, sheet_name: string?, rows: array)
+Returns: { success, rows_appended }
+```
+
+## When to Use Each Pattern
+
+| Use Case | Pattern File |
+|----------|-------------|
+| Network/API failures | `patterns/retry.md` |
+| Batch processing progress | `patterns/progress.md` |
+| Parallel subagent execution | `patterns/subagent-waves.md` |
+| Cross-platform commands | `patterns/shell-commands.md` |
+| Destructive operations | `patterns/user-confirmation.md` |
+| JSON data extraction | `patterns/json-tools.md` |
+| Combining batch outputs | `patterns/table-tools.md` |
+| Subagent communication | `patterns/data-exchange.md` |
+| Progress calculations | `patterns/calculator.md` |