@yeyuan98/opencode-bioresearcher-plugin 1.4.0 → 1.5.0-alpha.0

package/dist/skills/bioresearcher-core/patterns/progress.md

@@ -1,127 +1,127 @@
-# Progress Pattern
-
-Track and report progress at configurable intervals during batch operations.
-
-## Overview
-
-Use this pattern when processing multiple items to provide user feedback on completion status.
-
-## Pattern Algorithm
-
-```
-1. Initialize: total = N, completed = 0, report_interval = M
-2. For each item:
-   a. Process item
-   b. completed += 1
-   c. If completed % report_interval == 0 OR completed == total:
-      - Use calculator: percent = (completed / total) * 100
-      - Report: "Progress: X/Y (Z%)"
-```
-
-## Parameters
-
-| Parameter | Default | Description |
-|-----------|---------|-------------|
-| `total` | Required | Total number of items to process |
-| `completed` | 0 | Items processed so far |
-| `report_interval` | 3 | Report every N items |
-
-## Tool: calculator
-
-```
-calculator(formula: string, precision: number = 3)
-```
-
-- Supported: +, -, *, /, ^, brackets, scientific notation
-- **MUST** use explicit * for multiplication: `2*(3)` not `2(3)`
-
-## Example: Batch Processing Progress
-
-```
-# Configuration
-total = 100
-completed = 0
-report_interval = 10
-
-# Processing loop
-for item in items:
-    process(item)
-    completed += 1
-    
-    if completed % report_interval == 0 or completed == total:
-        percent = calculator(formula="(completed / total) * 100", precision=1)
-        report("Progress: {completed}/{total} ({percent}%)")
-```
-
-## Example: Wave-Based Progress
-
-For subagent waves (3 subagents per wave):
-
-```
-# Configuration
-total_waves = 4
-completed_waves = 0
-total_batches = 12
-completed_batches = 0
-
-# After each wave completes
-completed_waves += 1
-completed_batches += 3
-percent = calculator(formula="({completed_batches} / {total_batches}) * 100")
-
-report("Progress: {completed_batches}/{total_batches} batches ({percent}%)")
-```
-
-## Progress Report Format
-
-Standard format for consistency:
-
-```
-Progress: X/Y batches completed (Z%)
-```
-
-Examples:
-- "Progress: 3/10 batches completed (30%)"
-- "Progress: 6/10 batches completed (60%)"
-- "Progress: 10/10 batches completed (100%)"
-
-## Percentage Calculation
-
-Use the calculator tool:
-
-```
-calculator(formula="(45 / 100) * 100", precision=1)
-# Returns: { "formula": "(45 / 100) * 100", "result": 45 }
-```
-
-## Example: Time Estimation
-
-```
-# Track start time and items per minute
-start_time = current_time()
-items_per_minute = 10
-
-# Calculate remaining time
-remaining_items = total - completed
-remaining_minutes = calculator(
-    formula="remaining_items / items_per_minute",
-    precision=0
-)
-
-report("Progress: {completed}/{total} ({percent}%) - ~{remaining_minutes} min remaining")
-```
-
-## Integration with Other Patterns
-
-| Pattern | Integration |
-|---------|-------------|
-| `retry.md` | Count retries in progress |
-| `subagent-waves.md` | Report after each wave |
-| `calculator.md` | Calculate percentages |
-
-## Best Practices
-
-1. **Report at meaningful intervals**: Not too frequent (spam) or too sparse (silent)
-2. **Include totals**: Always show X/Y format
-3. **Round percentages**: Use precision=0 or precision=1
-4. **Final report**: Always report 100% completion
+# Progress Pattern
+
+Track and report progress at configurable intervals during batch operations.
+
+## Overview
+
+Use this pattern when processing multiple items to provide user feedback on completion status.
+
+## Pattern Algorithm
+
+```
+1. Initialize: total = N, completed = 0, report_interval = M
+2. For each item:
+   a. Process item
+   b. completed += 1
+   c. If completed % report_interval == 0 OR completed == total:
+      - Use calculator: percent = (completed / total) * 100
+      - Report: "Progress: X/Y (Z%)"
+```
+
+## Parameters
+
+| Parameter | Default | Description |
+|-----------|---------|-------------|
+| `total` | Required | Total number of items to process |
+| `completed` | 0 | Items processed so far |
+| `report_interval` | 3 | Report every N items |
+
+## Tool: calculator
+
+```
+calculator(formula: string, precision: number = 3)
+```
+
+- Supported: +, -, *, /, ^, brackets, scientific notation
+- **MUST** use explicit * for multiplication: `2*(3)` not `2(3)`
+
+## Example: Batch Processing Progress
+
+```
+# Configuration
+total = 100
+completed = 0
+report_interval = 10
+
+# Processing loop
+for item in items:
+    process(item)
+    completed += 1
+    
+    if completed % report_interval == 0 or completed == total:
+        percent = calculator(formula="(completed / total) * 100", precision=1)
+        report("Progress: {completed}/{total} ({percent}%)")
+```
+
+## Example: Wave-Based Progress
+
+For subagent waves (3 subagents per wave):
+
+```
+# Configuration
+total_waves = 4
+completed_waves = 0
+total_batches = 12
+completed_batches = 0
+
+# After each wave completes
+completed_waves += 1
+completed_batches += 3
+percent = calculator(formula="({completed_batches} / {total_batches}) * 100")
+
+report("Progress: {completed_batches}/{total_batches} batches ({percent}%)")
+```
+
+## Progress Report Format
+
+Standard format for consistency:
+
+```
+Progress: X/Y batches completed (Z%)
+```
+
+Examples:
+- "Progress: 3/10 batches completed (30%)"
+- "Progress: 6/10 batches completed (60%)"
+- "Progress: 10/10 batches completed (100%)"
+
+## Percentage Calculation
+
+Use the calculator tool:
+
+```
+calculator(formula="(45 / 100) * 100", precision=1)
+# Returns: { "formula": "(45 / 100) * 100", "result": 45 }
+```
+
+## Example: Time Estimation
+
+```
+# Track start time and items per minute
+start_time = current_time()
+items_per_minute = 10
+
+# Calculate remaining time
+remaining_items = total - completed
+remaining_minutes = calculator(
+    formula="remaining_items / items_per_minute",
+    precision=0
+)
+
+report("Progress: {completed}/{total} ({percent}%) - ~{remaining_minutes} min remaining")
+```
+
+## Integration with Other Patterns
+
+| Pattern | Integration |
+|---------|-------------|
+| `retry.md` | Count retries in progress |
+| `subagent-waves.md` | Report after each wave |
+| `calculator.md` | Calculate percentages |
+
+## Best Practices
+
+1. **Report at meaningful intervals**: Not too frequent (spam) or too sparse (silent)
+2. **Include totals**: Always show X/Y format
+3. **Round percentages**: Use precision=0 or precision=1
+4. **Final report**: Always report 100% completion

package/dist/skills/bioresearcher-core/patterns/retry.md

@@ -1,110 +1,110 @@
-# Retry Pattern
-
-Retry failed operations with configurable delays and backoff.
-
-## Overview
-
-Use this pattern when operations may fail transiently (network issues, API rate limits, temporary resource unavailability).
-
-## Pattern Algorithm
-
-```
-1. Initialize: attempts = 0, max_attempts = N, delay = D, backoff_factor = B
-2. Attempt operation
-3. If success -> continue with workflow
-4. If failure:
-   a. attempts += 1
-   b. If attempts < max_attempts:
-      - Use blockingTimer(delay=D)
-      - delay = delay * backoff_factor
-      - Retry from step 2
-   c. If attempts >= max_attempts:
-      - Report failure or ask user via question tool
-```
-
-## Parameters
-
-| Parameter | Default | Description |
-|-----------|---------|-------------|
-| `max_attempts` | 3 | Maximum retry attempts |
-| `delay` | 2 | Initial wait time in seconds |
-| `backoff_factor` | 1 | Multiply delay after each failure (1 = constant delay) |
-
-## Tool: blockingTimer
-
-```
-blockingTimer(delay: number)
-```
-
-- Maximum delay: 300 seconds
-- Returns: "Timer completed: waited X seconds (actual elapsed: Ys)"
-
-## Example: Constant Delay Retry
-
-```
-# Retry configuration
-max_attempts = 3
-delay = 2
-attempts = 0
-
-# Attempt loop
-while attempts < max_attempts:
-    result = attempt_operation()
-    if result.success:
-        break
-    attempts += 1
-    if attempts < max_attempts:
-        blockingTimer(delay=2)  # Wait 2 seconds
-```
-
-## Example: Exponential Backoff Retry
-
-```
-# Retry configuration
-max_attempts = 4
-delay = 1
-backoff_factor = 2
-attempts = 0
-
-# Attempt loop
-while attempts < max_attempts:
-    result = attempt_operation()
-    if result.success:
-        break
-    attempts += 1
-    if attempts < max_attempts:
-        blockingTimer(delay=delay)
-        delay = delay * backoff_factor  # 1, 2, 4, 8...
-```
-
-## When to Use
-
-| Scenario | delay | backoff_factor | max_attempts |
-|----------|-------|----------------|--------------|
-| Network timeout | 2 | 1 | 3 |
-| API rate limit | 5 | 2 | 4 |
-| File lock | 1 | 1 | 5 |
-| Resource unavailable | 2 | 2 | 4 |
-
-## User Notification on Persistent Failure
-
-After all retries exhausted, use `question` tool:
-
-```
-question(questions=[{
-  "header": "Retry failed",
-  "question": "Operation failed after 3 attempts. How would you like to proceed?",
-  "options": [
-    {"label": "Retry now", "description": "Try one more time immediately"},
-    {"label": "Skip", "description": "Skip this item and continue"},
-    {"label": "Abort", "description": "Stop the entire workflow"}
-  ]
-}])
-```
-
-## Important Notes
-
-1. **Maximum delay**: blockingTimer caps at 300 seconds
-2. **Backoff calculation**: Use `calculator` tool if needed
-3. **State tracking**: Track attempts in your workflow state
-4. **Error logging**: Log failure reasons for debugging
+# Retry Pattern
+
+Retry failed operations with configurable delays and backoff.
+
+## Overview
+
+Use this pattern when operations may fail transiently (network issues, API rate limits, temporary resource unavailability).
+
+## Pattern Algorithm
+
+```
+1. Initialize: attempts = 0, max_attempts = N, delay = D, backoff_factor = B
+2. Attempt operation
+3. If success -> continue with workflow
+4. If failure:
+   a. attempts += 1
+   b. If attempts < max_attempts:
+      - Use blockingTimer(delay=D)
+      - delay = delay * backoff_factor
+      - Retry from step 2
+   c. If attempts >= max_attempts:
+      - Report failure or ask user via question tool
+```
+
+## Parameters
+
+| Parameter | Default | Description |
+|-----------|---------|-------------|
+| `max_attempts` | 3 | Maximum retry attempts |
+| `delay` | 2 | Initial wait time in seconds |
+| `backoff_factor` | 1 | Multiply delay after each failure (1 = constant delay) |
+
+## Tool: blockingTimer
+
+```
+blockingTimer(delay: number)
+```
+
+- Maximum delay: 300 seconds
+- Returns: "Timer completed: waited X seconds (actual elapsed: Ys)"
+
+## Example: Constant Delay Retry
+
+```
+# Retry configuration
+max_attempts = 3
+delay = 2
+attempts = 0
+
+# Attempt loop
+while attempts < max_attempts:
+    result = attempt_operation()
+    if result.success:
+        break
+    attempts += 1
+    if attempts < max_attempts:
+        blockingTimer(delay=2)  # Wait 2 seconds
+```
+
+## Example: Exponential Backoff Retry
+
+```
+# Retry configuration
+max_attempts = 4
+delay = 1
+backoff_factor = 2
+attempts = 0
+
+# Attempt loop
+while attempts < max_attempts:
+    result = attempt_operation()
+    if result.success:
+        break
+    attempts += 1
+    if attempts < max_attempts:
+        blockingTimer(delay=delay)
+        delay = delay * backoff_factor  # 1, 2, 4, 8...
+```
+
+## When to Use
+
+| Scenario | delay | backoff_factor | max_attempts |
+|----------|-------|----------------|--------------|
+| Network timeout | 2 | 1 | 3 |
+| API rate limit | 5 | 2 | 4 |
+| File lock | 1 | 1 | 5 |
+| Resource unavailable | 2 | 2 | 4 |
+
+## User Notification on Persistent Failure
+
+After all retries exhausted, use `question` tool:
+
+```
+question(questions=[{
+  "header": "Retry failed",
+  "question": "Operation failed after 3 attempts. How would you like to proceed?",
+  "options": [
+    {"label": "Retry now", "description": "Try one more time immediately"},
+    {"label": "Skip", "description": "Skip this item and continue"},
+    {"label": "Abort", "description": "Stop the entire workflow"}
+  ]
+}])
+```
+
+## Important Notes
+
+1. **Maximum delay**: blockingTimer caps at 300 seconds
+2. **Backoff calculation**: Use `calculator` tool if needed
+3. **State tracking**: Track attempts in your workflow state
+4. **Error logging**: Log failure reasons for debugging

package/dist/skills/bioresearcher-core/patterns/shell-commands.md

@@ -1,79 +1,79 @@
-# Shell Commands Pattern
-
-Generate shell commands using forward slashes for cross-platform compatibility.
-
-## Overview
-
-Forward slashes (`/`) work on all major platforms:
-- Unix-like (Linux, macOS): Native support
-- Windows (Git Bash): Native support
-- Windows (Python): Native support via `os.path`
-- Windows (cmd.exe): Supported in most contexts
-
-## Recommendation
-
-**Use forward slashes (`/`) universally** for maximum compatibility.
-
-## Examples
-
-### Python Script Execution
-```bash
-uv run python <skill_path>/script.py --input ./data/file.csv --output ./results/output.xlsx
-```
-
-### Directory Creation
-```bash
-mkdir -p .work/subdir1 .work/subdir2
-```
-
-### File Listing
-```bash
-ls -la ./work/outputs/
-```
-
-### For Loop
-```bash
-for file in file1.txt file2.txt file3.txt; do
-  uv run python <skill_path>/process.py "$file"
-done
-```
-
-### JSON String Arguments
-```bash
-uv run python script.py --data '{"key": "value"}'
-```
-
-### Environment Variables
-```bash
-export MY_VAR=value
-uv run python script.py
-```
-
-## Windows Edge Cases
-
-In rare cases, Windows cmd.exe may not support forward slashes:
-
-| Command | Forward Slash | Alternative |
-|---------|---------------|-------------|
-| `dir` | Works | `dir ./folder` |
-| `mkdir` | `mkdir -p` fails | Use Python: `python -c "import os; os.makedirs('./folder', exist_ok=True)"` |
-| `copy` | Works | `copy ./src/file.txt ./dest/` |
-| `del` | Works | `del ./folder/file.txt` |
-
-> **Note:** If using pure cmd.exe (not Git Bash), the `-p` flag for `mkdir` is not supported. Use Python's `os.makedirs()` instead.
-
-## Path Handling Guidelines
-
-1. **Always use forward slashes** (`/`) in paths
-2. **Quote paths with spaces** in all contexts
-3. **Use relative paths** from project root when possible
-4. **Python paths**: Forward slashes work on all platforms
-5. **Skill path placeholder**: Replace `<skill_path>` with actual path from skill tool output
-
-## Best Practices
-
-1. **Default to forward slashes** - works 99% of the time
-2. **Test on target platform** if edge cases suspected
-3. **Use Python alternatives** for complex file operations
-4. **Quote all paths** to handle spaces safely
-5. **Avoid cmd.exe-specific syntax** (like `^` line continuation)
+# Shell Commands Pattern
+
+Generate shell commands using forward slashes for cross-platform compatibility.
+
+## Overview
+
+Forward slashes (`/`) work on all major platforms:
+- Unix-like (Linux, macOS): Native support
+- Windows (Git Bash): Native support
+- Windows (Python): Native support via `os.path`
+- Windows (cmd.exe): Supported in most contexts
+
+## Recommendation
+
+**Use forward slashes (`/`) universally** for maximum compatibility.
+
+## Examples
+
+### Python Script Execution
+```bash
+uv run python <skill_path>/script.py --input ./data/file.csv --output ./results/output.xlsx
+```
+
+### Directory Creation
+```bash
+mkdir -p .work/subdir1 .work/subdir2
+```
+
+### File Listing
+```bash
+ls -la ./work/outputs/
+```
+
+### For Loop
+```bash
+for file in file1.txt file2.txt file3.txt; do
+  uv run python <skill_path>/process.py "$file"
+done
+```
+
+### JSON String Arguments
+```bash
+uv run python script.py --data '{"key": "value"}'
+```
+
+### Environment Variables
+```bash
+export MY_VAR=value
+uv run python script.py
+```
+
+## Windows Edge Cases
+
+In rare cases, Windows cmd.exe may not support forward slashes:
+
+| Command | Forward Slash | Alternative |
+|---------|---------------|-------------|
+| `dir` | Works | `dir ./folder` |
+| `mkdir` | `mkdir -p` fails | Use Python: `python -c "import os; os.makedirs('./folder', exist_ok=True)"` |
+| `copy` | Works | `copy ./src/file.txt ./dest/` |
+| `del` | Works | `del ./folder/file.txt` |
+
+> **Note:** If using pure cmd.exe (not Git Bash), the `-p` flag for `mkdir` is not supported. Use Python's `os.makedirs()` instead.
+
+## Path Handling Guidelines
+
+1. **Always use forward slashes** (`/`) in paths
+2. **Quote paths with spaces** in all contexts
+3. **Use relative paths** from project root when possible
+4. **Python paths**: Forward slashes work on all platforms
+5. **Skill path placeholder**: Replace `<skill_path>` with actual path from skill tool output
+
+## Best Practices
+
+1. **Default to forward slashes** - works 99% of the time
+2. **Test on target platform** if edge cases suspected
+3. **Use Python alternatives** for complex file operations
+4. **Quote all paths** to handle spaces safely
+5. **Avoid cmd.exe-specific syntax** (like `^` line continuation)