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

package/dist/skills/bioresearcher-core/examples/template.md

@@ -1,49 +1,49 @@
-# Batch Data Summarization Task
-
-## Input File
-- Full path: `{file_path}`
-- Sheet name: `{sheet_name}`
-
-## Row Range
-- Batch number: {batch_number}
-- Start row: {row_start}
-- End row: {row_end}
-
-## Summarization Instructions
-
-Extract the following fields from each row:
-
-{instructions_json}
-
-## Output Format
-
-Your output must be a valid JSON file with this structure:
-
-```json
-{
-  "batch_number": {batch_number},
-  "row_count": <number_of_rows_processed>,
-  "summaries": [
-    {
-      "row_number": <row_number>,
-      <field_1>: "<extracted_value>",
-      <field_2>: "<extracted_value>"
-    }
-  ]
-}
-```
-
-**Important:** The JSON keys for extracted values must match the field names specified in the Summarization Instructions.
-
-## Instructions
-
-1. Read the specified row range from the input file using the `tableGetRange` tool
-2. For each row, extract the requested fields according to the instructions above
-3. Map the extracted values to the JSON keys specified in the instructions
-4. Generate concise summaries based on the extracted data
-5. Save your output to: `{output_file}`
-
-## Output File Path
-Full path: `{output_file}`
-
-**CRITICAL:** Write your final output as a markdown file (.md) containing ONLY the JSON object (no additional text or explanation).
+# Batch Data Summarization Task
+
+## Input File
+- Full path: `{file_path}`
+- Sheet name: `{sheet_name}`
+
+## Row Range
+- Batch number: {batch_number}
+- Start row: {row_start}
+- End row: {row_end}
+
+## Summarization Instructions
+
+Extract the following fields from each row:
+
+{instructions_json}
+
+## Output Format
+
+Your output must be a valid JSON file with this structure:
+
+```json
+{
+  "batch_number": {batch_number},
+  "row_count": <number_of_rows_processed>,
+  "summaries": [
+    {
+      "row_number": <row_number>,
+      <field_1>: "<extracted_value>",
+      <field_2>: "<extracted_value>"
+    }
+  ]
+}
+```
+
+**Important:** The JSON keys for extracted values must match the field names specified in the Summarization Instructions.
+
+## Instructions
+
+1. Read the specified row range from the input file using the `tableGetRange` tool
+2. For each row, extract the requested fields according to the instructions above
+3. Map the extracted values to the JSON keys specified in the instructions
+4. Generate concise summaries based on the extracted data
+5. Save your output to: `{output_file}`
+
+## Output File Path
+Full path: `{output_file}`
+
+**CRITICAL:** Write your final output as a markdown file (.md) containing ONLY the JSON object (no additional text or explanation).

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

@@ -1,215 +1,215 @@
-# Calculator Pattern
-
-In-workflow calculations using the calculator tool.
-
-## Overview
-
-Use the calculator tool for arithmetic operations in workflows. It's more reliable than manual calculations and provides consistent precision.
-
-## Tool: calculator
-
-```
-calculator(formula: string, precision: number = 3)
-```
-
-### Parameters
-- `formula`: Mathematical expression (string)
-- `precision`: Decimal places for result (0-15, default 3)
-
-### Return Format
-```json
-{
-  "formula": "(45 / 100) * 100",
-  "result": 45
-}
-```
-
-### Supported Operations
-
-| Operation | Symbol | Example |
-|-----------|--------|---------|
-| Addition | + | `2 + 3` |
-| Subtraction | - | `5 - 2` |
-| Multiplication | * | `3 * 4` |
-| Division | / | `10 / 2` |
-| Power | ^ | `2 ^ 3` |
-| Brackets | () | `(2 + 3) * 4` |
-| Scientific | e/E | `1e5`, `1.5e-3` |
-
-### Important Rules
-
-1. **MUST use explicit * for multiplication**: `2*(3)` NOT `2(3)`
-2. **Maximum precision**: 15 decimal places
-3. **Default precision**: 3 decimal places
-4. **No functions**: ceil, floor, sqrt not supported
-
-## Common Use Cases
-
-### Batch Calculations
-
-```
-# Calculate number of batches needed
-calculator(formula="ceil(100 / 30)", precision=0)
-# Note: ceil not supported, use workaround:
-calculator(formula="(100 + 30 - 1) / 30", precision=0)
-# Result: 4.333 -> Use ceiling logic in agent
-```
-
-### Progress Percentages
-
-```
-# Calculate completion percentage
-calculator(formula="(45 / 100) * 100", precision=1)
-# Result: 45
-
-# With variables in workflow
-completed = 67
-total = 120
-calculator(formula="({completed} / {total}) * 100", precision=1)
-# Result: 55.8
-```
-
-### Time Estimates
-
-```
-# Estimate remaining time
-remaining_items = 50
-items_per_minute = 10
-calculator(formula="50 / 10", precision=0)
-# Result: 5 minutes
-```
-
-### Data Size Calculations
-
-```
-# Calculate total rows across batches
-batch_size = 30
-num_batches = 4
-calculator(formula="30 * 4", precision=0)
-# Result: 120
-```
-
-## Ceiling/Floor Workarounds
-
-Since ceil/floor are not supported:
-
-### Ceiling
-```
-# ceil(a / b) = (a + b - 1) / b (for positive integers)
-# ceil(100 / 30)
-calculator(formula="(100 + 30 - 1) / 30", precision=0)
-# Result: 4.333 -> Agent interprets as 5
-```
-
-### Floor
-```
-# floor(a / b) = a / b (truncate decimal)
-# floor(100 / 30)
-calculator(formula="100 / 30", precision=0)
-# Result: 3.333 -> Agent interprets as 3
-```
-
-## Example Workflow
-
-### Calculate Batch Configuration
-
-```
-# Given
-total_rows = 250
-batch_size = 30
-
-# Calculate batches needed
-# ceil(250 / 30) = 9 batches
-batches_needed = calculator(
-    formula="(250 + 30 - 1) / 30",
-    precision=0
-)
-# Result: 9.3 -> Agent rounds up to 10
-
-# Calculate rows in last batch
-# 250 - (9 * 30) = 250 - 270 = -20 -> use 30
-# Actually: 250 - (8 * 30) = 250 - 240 = 10
-last_batch_rows = calculator(
-    formula="250 - (8 * 30)",
-    precision=0
-)
-# Result: 10
-```
-
-### Progress Tracking
-
-```
-# During batch processing
-completed = 0
-total = 10
-
-for batch in batches:
-    process(batch)
-    completed += 1
-    
-    # Calculate and report progress
-    percent = calculator(
-        formula="({completed} / {total}) * 100",
-        precision=0
-    )
-    report(f"Progress: {completed}/{total} ({percent}%)")
-```
-
-### Wave Timing
-
-```
-# Calculate expected completion time
-waves_remaining = 3
-seconds_per_wave = 45
-
-estimated_seconds = calculator(
-    formula="3 * 45",
-    precision=0
-)
-# Result: 135 seconds
-
-# Convert to minutes
-estimated_minutes = calculator(
-    formula="135 / 60",
-    precision=1
-)
-# Result: 2.3 minutes
-```
-
-## Error Handling
-
-### Invalid Formula
-```
-# Missing explicit multiplication
-calculator(formula="2(3)")
-# Error: "CALCULATOR ERROR: Invalid syntax: parentheses-less multiplication not allowed"
-```
-
-### Division by Zero
-```
-calculator(formula="10 / 0")
-# Error: "CALCULATOR ERROR: Division by zero"
-```
-
-### Invalid Characters
-```
-calculator(formula="2 + abc")
-# Error: "CALCULATOR ERROR: Formula contains invalid characters: a b c"
-```
-
-## Integration with Other Patterns
-
-| Pattern | Calculator Usage |
-|---------|-----------------|
-| `progress.md` | Calculate percentages |
-| `retry.md` | Calculate backoff delays |
-| `subagent-waves.md` | Calculate wave counts |
-| `table-tools.md` | Calculate row counts |
-
-## Best Practices
-
-1. **Use precision=0 for counts**: Integer results
-2. **Use precision=1 for percentages**: One decimal place
-3. **Always use explicit ***: Never implicit multiplication
-4. **Check for division by zero**: Validate divisors
-5. **Document formulas**: Explain what calculation does
+# Calculator Pattern
+
+In-workflow calculations using the calculator tool.
+
+## Overview
+
+Use the calculator tool for arithmetic operations in workflows. It's more reliable than manual calculations and provides consistent precision.
+
+## Tool: calculator
+
+```
+calculator(formula: string, precision: number = 3)
+```
+
+### Parameters
+- `formula`: Mathematical expression (string)
+- `precision`: Decimal places for result (0-15, default 3)
+
+### Return Format
+```json
+{
+  "formula": "(45 / 100) * 100",
+  "result": 45
+}
+```
+
+### Supported Operations
+
+| Operation | Symbol | Example |
+|-----------|--------|---------|
+| Addition | + | `2 + 3` |
+| Subtraction | - | `5 - 2` |
+| Multiplication | * | `3 * 4` |
+| Division | / | `10 / 2` |
+| Power | ^ | `2 ^ 3` |
+| Brackets | () | `(2 + 3) * 4` |
+| Scientific | e/E | `1e5`, `1.5e-3` |
+
+### Important Rules
+
+1. **MUST use explicit * for multiplication**: `2*(3)` NOT `2(3)`
+2. **Maximum precision**: 15 decimal places
+3. **Default precision**: 3 decimal places
+4. **No functions**: ceil, floor, sqrt not supported
+
+## Common Use Cases
+
+### Batch Calculations
+
+```
+# Calculate number of batches needed
+calculator(formula="ceil(100 / 30)", precision=0)
+# Note: ceil not supported, use workaround:
+calculator(formula="(100 + 30 - 1) / 30", precision=0)
+# Result: 4.333 -> Use ceiling logic in agent
+```
+
+### Progress Percentages
+
+```
+# Calculate completion percentage
+calculator(formula="(45 / 100) * 100", precision=1)
+# Result: 45
+
+# With variables in workflow
+completed = 67
+total = 120
+calculator(formula="({completed} / {total}) * 100", precision=1)
+# Result: 55.8
+```
+
+### Time Estimates
+
+```
+# Estimate remaining time
+remaining_items = 50
+items_per_minute = 10
+calculator(formula="50 / 10", precision=0)
+# Result: 5 minutes
+```
+
+### Data Size Calculations
+
+```
+# Calculate total rows across batches
+batch_size = 30
+num_batches = 4
+calculator(formula="30 * 4", precision=0)
+# Result: 120
+```
+
+## Ceiling/Floor Workarounds
+
+Since ceil/floor are not supported:
+
+### Ceiling
+```
+# ceil(a / b) = (a + b - 1) / b (for positive integers)
+# ceil(100 / 30)
+calculator(formula="(100 + 30 - 1) / 30", precision=0)
+# Result: 4.333 -> Agent interprets as 5
+```
+
+### Floor
+```
+# floor(a / b) = a / b (truncate decimal)
+# floor(100 / 30)
+calculator(formula="100 / 30", precision=0)
+# Result: 3.333 -> Agent interprets as 3
+```
+
+## Example Workflow
+
+### Calculate Batch Configuration
+
+```
+# Given
+total_rows = 250
+batch_size = 30
+
+# Calculate batches needed
+# ceil(250 / 30) = 9 batches
+batches_needed = calculator(
+    formula="(250 + 30 - 1) / 30",
+    precision=0
+)
+# Result: 9.3 -> Agent rounds up to 10
+
+# Calculate rows in last batch
+# 250 - (9 * 30) = 250 - 270 = -20 -> use 30
+# Actually: 250 - (8 * 30) = 250 - 240 = 10
+last_batch_rows = calculator(
+    formula="250 - (8 * 30)",
+    precision=0
+)
+# Result: 10
+```
+
+### Progress Tracking
+
+```
+# During batch processing
+completed = 0
+total = 10
+
+for batch in batches:
+    process(batch)
+    completed += 1
+    
+    # Calculate and report progress
+    percent = calculator(
+        formula="({completed} / {total}) * 100",
+        precision=0
+    )
+    report(f"Progress: {completed}/{total} ({percent}%)")
+```
+
+### Wave Timing
+
+```
+# Calculate expected completion time
+waves_remaining = 3
+seconds_per_wave = 45
+
+estimated_seconds = calculator(
+    formula="3 * 45",
+    precision=0
+)
+# Result: 135 seconds
+
+# Convert to minutes
+estimated_minutes = calculator(
+    formula="135 / 60",
+    precision=1
+)
+# Result: 2.3 minutes
+```
+
+## Error Handling
+
+### Invalid Formula
+```
+# Missing explicit multiplication
+calculator(formula="2(3)")
+# Error: "CALCULATOR ERROR: Invalid syntax: parentheses-less multiplication not allowed"
+```
+
+### Division by Zero
+```
+calculator(formula="10 / 0")
+# Error: "CALCULATOR ERROR: Division by zero"
+```
+
+### Invalid Characters
+```
+calculator(formula="2 + abc")
+# Error: "CALCULATOR ERROR: Formula contains invalid characters: a b c"
+```
+
+## Integration with Other Patterns
+
+| Pattern | Calculator Usage |
+|---------|-----------------|
+| `progress.md` | Calculate percentages |
+| `retry.md` | Calculate backoff delays |
+| `subagent-waves.md` | Calculate wave counts |
+| `table-tools.md` | Calculate row counts |
+
+## Best Practices
+
+1. **Use precision=0 for counts**: Integer results
+2. **Use precision=1 for percentages**: One decimal place
+3. **Always use explicit ***: Never implicit multiplication
+4. **Check for division by zero**: Validate divisors
+5. **Document formulas**: Explain what calculation does