feat: Add Claude skill for generating Allotropy parsers (#1160)

## Summary
- Adds a Claude skill to help developers quickly generate complete
Allotropy instrument parsers from example input files
- The skill analyzes files, suggests appropriate schemas, and generates
all necessary boilerplate code
- Includes three main scripts: analyze_file.py, list_schemas.py, and
create_parser.py

## Features
- **File Analysis**: Automatically detects file format and suggests
appropriate Allotrope schema based on content
- **Schema Discovery**: Lists all available schemas with filtering and
shows example parsers
- **Parser Generation**: Creates complete parser structure with reader,
structure, tests, and all required files
- **Smart Detection**: Recognizes measurement types (absorbance, CT
values, pH, etc.) to suggest the right schema

## Files Added
- `.claude/skills/parser-generator/skill.md` - Main skill definition for
Claude
- `.claude/skills/parser-generator/README.md` - Documentation for using
the skill
- `.claude/skills/parser-generator/scripts/analyze_file.py` - Analyzes
input files and suggests schemas
- `.claude/skills/parser-generator/scripts/list_schemas.py` - Lists
available Allotrope schemas
- `.claude/skills/parser-generator/scripts/create_parser.py` - Generates
complete parser structure
- `.claude/.ruff.toml` - Ruff configuration for Claude skill scripts

## Usage
1. Analyze a file: `python
.claude/skills/parser-generator/scripts/analyze_file.py <file>`
2. List schemas: `python
.claude/skills/parser-generator/scripts/list_schemas.py [filter]`
3. Generate parser: `python
.claude/skills/parser-generator/scripts/create_parser.py <name>
"<Display Name>"`

## Test Plan
- [x] Tested file analysis on Excel files (Exp6.xlsx)
- [x] Tested schema listing with filtering
- [x] All linting checks pass
- [x] Scripts are executable

This skill will significantly speed up the process of adding new
instrument parsers to the allotropy library.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

---------

Co-authored-by: Claude Opus 4.1 <noreply@anthropic.com>

Author: nathan-stender

.claude/.ruff.toml

@@ -0,0 +1,7 @@
+# Ruff configuration for Claude skills
+# These are CLI scripts, so print statements are allowed
+
+extend-ignore = ["T201", "T203", "E501"]  # Allow print, pprint, and long lines in skills
+
+[per-file-ignores]
+"skills/*/scripts/*.py" = ["T201", "T203", "FBT001", "FBT002"]  # Allow print and boolean args in skill scripts

.claude/skills/parser-generator/README.md

@@ -0,0 +1,120 @@
+# Allotropy Parser Generator Skill
+
+This Claude skill helps you generate complete Allotropy instrument parsers from example input files. It analyzes file structure, auto-detects appropriate Allotrope schemas, and generates fully functional parser code.
+
+## Installation
+
+This skill is already installed in the `.claude/skills/parser-generator/` directory.
+
+## Usage with Claude
+
+When working with Claude in this repository, you can invoke the parser generator skill by saying:
+
+- "Use the parser-generator skill to create a new parser"
+- "Analyze this file and suggest a schema" (with a file path)
+- "Generate a parser for [instrument name]"
+- "/parser-generator" (if configured as a slash command)
+
+## Manual Usage
+
+You can also run the scripts directly:
+
+### 1. Analyze an Input File
+
+```bash
+python .claude/skills/parser-generator/scripts/analyze_file.py <path_to_file>
+```
+
+This will analyze the file and suggest an appropriate schema based on the content.
+
+### 2. List Available Schemas
+
+```bash
+# List all schemas
+python .claude/skills/parser-generator/scripts/list_schemas.py
+
+# Filter schemas
+python .claude/skills/parser-generator/scripts/list_schemas.py plate
+
+# Verbose output with paths
+python .claude/skills/parser-generator/scripts/list_schemas.py --verbose
+```
+
+### 3. Generate a Parser
+
+```bash
+python .claude/skills/parser-generator/scripts/create_parser.py \
+  <parser_name> \
+  "<Display Name>" \
+  --schema <schema_path> \
+  --example <example_file>
+```
+
+Example:
+```bash
+python .claude/skills/parser-generator/scripts/create_parser.py \
+  beckman_pharmspec \
+  "Beckman Coulter PharmSpec" \
+  --schema adm/plate_reader/BENCHLING/2024/06/plate_reader \
+  --example ~/Downloads/pharmspec_data.xlsx
+```
+
+## Generated Files
+
+The skill creates a complete parser structure:
+
+```
+src/allotropy/parsers/{parser_name}/
+├── __init__.py                    # Module exports
+├── {parser_name}_parser.py        # Main parser class
+├── {parser_name}_reader.py        # File reading logic
+└── {parser_name}_structure.py     # Data structures
+
+tests/parsers/{parser_name}/
+├── __init__.py
+├── test_{parser_name}_parser.py   # Test file
+└── testdata/
+    └── example.xlsx               # Test data
+```
+
+## Workflow
+
+1. **Analyze** your example file to detect the schema
+2. **List** available schemas if you need to override
+3. **Generate** the parser with the create script
+4. **Implement** the TODO sections in the generated code
+5. **Test** the parser with your example data
+6. **Register** the parser in `parser_factory.py`
+
+## Supported File Formats
+
+- Excel files (.xlsx, .xls)
+- CSV files (.csv)
+- Tab-delimited files (.txt, .tsv)
+- Text files with sections
+
+## Schema Detection
+
+The skill detects schemas based on keywords in the file:
+
+- **plate-reader**: absorbance, fluorescence, luminescence, well, plate
+- **pcr**: ct, cq, cycle, amplification, target
+- **cell-counting**: viability, cell count, density
+- **spectrophotometry**: wavelength, spectrum, nm
+- **solution-analyzer**: pH, osmolality, particle size
+- **binding-affinity**: ka, kd, kon, koff, resonance
+
+## Tips
+
+- Always start with `analyze_file.py` to understand your input format
+- Look at similar existing parsers for patterns
+- Use the existing utility functions in `allotropy.parsers.utils`
+- Test with real data files early and often
+- Start with `WORKING_DRAFT` release state
+
+## Troubleshooting
+
+- **Schema not detected**: Manually specify with `list_schemas.py`
+- **Parser already exists**: Choose a different name or delete existing
+- **Import errors**: Make sure you're in the allotropy repository
+- **Test failures**: Check that your Data structure matches the schema