Fix MkDocs configuration and GitHub Pages deployment

- Fix typo in site name (reproschema-py)
- Remove incorrect CNAME file
- Update GitHub workflow to use modern actions and proper permissions

Author: yibeichan

.github/workflows/deploy_mkdocs.yml

@@ -8,17 +8,21 @@ jobs:
   build:
     name: Deploy docs
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
     steps:
       - name: Checkout main
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+
+      - name: Install dependencies
+        run: |
+          pip install mkdocs
 
       - name: Deploy docs
-        uses: mhausenblas/mkdocs-deploy-gh-pages@master
-        # Or use mhausenblas/mkdocs-deploy-gh-pages@nomaterial to build without the mkdocs-material theme
-        env:
-          GITHUB_TOKEN: ${{ secrets.AUTO_TOKEN }}
-          CUSTOM_DOMAIN: https://repronim.github.io/reproschema-py/
-          CONFIG_FILE: mkdocs.yml
-          EXTRA_PACKAGES: build-base
-          # GITHUB_DOMAIN: github.myenterprise.com
-          # REQUIREMENTS: folder/requirements.txt
+        run: |
+          mkdocs gh-deploy --force --clean

.serena/project.yml

@@ -0,0 +1,68 @@
+# language of the project (csharp, python, rust, java, typescript, go, cpp, or ruby)
+#  * For C, use cpp
+#  * For JavaScript, use typescript
+# Special requirements:
+#  * csharp: Requires the presence of a .sln file in the project folder.
+language: python
+
+# whether to use the project's gitignore file to ignore files
+# Added on 2025-04-07
+ignore_all_files_in_gitignore: true
+# list of additional paths to ignore
+# same syntax as gitignore, so you can use * and **
+# Was previously called `ignored_dirs`, please update your config if you are using that.
+# Added (renamed) on 2025-04-07
+ignored_paths: []
+
+# whether the project is in read-only mode
+# If set to true, all editing tools will be disabled and attempts to use them will result in an error
+# Added on 2025-04-18
+read_only: false
+
+
+# list of tool names to exclude. We recommend not excluding any tools, see the readme for more details.
+# Below is the complete list of tools for convenience.
+# To make sure you have the latest list of tools, and to view their descriptions, 
+# execute `uv run scripts/print_tool_overview.py`.
+#
+#  * `activate_project`: Activates a project by name.
+#  * `check_onboarding_performed`: Checks whether project onboarding was already performed.
+#  * `create_text_file`: Creates/overwrites a file in the project directory.
+#  * `delete_lines`: Deletes a range of lines within a file.
+#  * `delete_memory`: Deletes a memory from Serena's project-specific memory store.
+#  * `execute_shell_command`: Executes a shell command.
+#  * `find_referencing_code_snippets`: Finds code snippets in which the symbol at the given location is referenced.
+#  * `find_referencing_symbols`: Finds symbols that reference the symbol at the given location (optionally filtered by type).
+#  * `find_symbol`: Performs a global (or local) search for symbols with/containing a given name/substring (optionally filtered by type).
+#  * `get_current_config`: Prints the current configuration of the agent, including the active and available projects, tools, contexts, and modes.
+#  * `get_symbols_overview`: Gets an overview of the top-level symbols defined in a given file.
+#  * `initial_instructions`: Gets the initial instructions for the current project.
+#     Should only be used in settings where the system prompt cannot be set,
+#     e.g. in clients you have no control over, like Claude Desktop.
+#  * `insert_after_symbol`: Inserts content after the end of the definition of a given symbol.
+#  * `insert_at_line`: Inserts content at a given line in a file.
+#  * `insert_before_symbol`: Inserts content before the beginning of the definition of a given symbol.
+#  * `list_dir`: Lists files and directories in the given directory (optionally with recursion).
+#  * `list_memories`: Lists memories in Serena's project-specific memory store.
+#  * `onboarding`: Performs onboarding (identifying the project structure and essential tasks, e.g. for testing or building).
+#  * `prepare_for_new_conversation`: Provides instructions for preparing for a new conversation (in order to continue with the necessary context).
+#  * `read_file`: Reads a file within the project directory.
+#  * `read_memory`: Reads the memory with the given name from Serena's project-specific memory store.
+#  * `remove_project`: Removes a project from the Serena configuration.
+#  * `replace_lines`: Replaces a range of lines within a file with new content.
+#  * `replace_symbol_body`: Replaces the full definition of a symbol.
+#  * `restart_language_server`: Restarts the language server, may be necessary when edits not through Serena happen.
+#  * `search_for_pattern`: Performs a search for a pattern in the project.
+#  * `summarize_changes`: Provides instructions for summarizing the changes made to the codebase.
+#  * `switch_modes`: Activates modes by providing a list of their names
+#  * `think_about_collected_information`: Thinking tool for pondering the completeness of collected information.
+#  * `think_about_task_adherence`: Thinking tool for determining whether the agent is still on track with the current task.
+#  * `think_about_whether_you_are_done`: Thinking tool for determining whether the task is truly completed.
+#  * `write_memory`: Writes a named memory (for future reference) to Serena's project-specific memory store.
+excluded_tools: []
+
+# initial prompt for the project. It will always be given to the LLM upon activating the project
+# (contrary to the memories, which are loaded on demand).
+initial_prompt: ""
+
+project_name: "reproschema-py"

CLAUDE.md

@@ -0,0 +1,86 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+ReproSchema Python library and CLI for working with ReproSchema format - a standardized way to represent assessments, questionnaires, and protocols used in research. The library provides validation, conversion utilities, and integrations with REDCap and FHIR.
+
+## Key Commands
+
+### Development Setup
+```bash
+# Install in development mode
+pip install -e .
+
+# Install with all development dependencies  
+pip install -e ".[dev]"
+
+# Run pre-commit hooks
+pre-commit install
+pre-commit run --all-files
+```
+
+### Testing
+```bash
+# Run tests with coverage
+pytest --cov=reproschema
+
+# Run specific test file
+pytest reproschema/tests/test_validate.py
+
+# Run tests in parallel
+pytest -n auto
+```
+
+### Linting and Formatting
+```bash
+# Format code with black
+black reproschema/
+
+# Run flake8 linter
+flake8 reproschema/
+
+# Sort imports
+isort reproschema/
+
+# Check spelling
+codespell
+```
+
+## Architecture
+
+### Core Modules
+
+- **reproschema/cli.py**: Main CLI entry point using Click framework. Provides commands for validation, conversion, migration.
+- **reproschema/models/model.py**: Pydantic models auto-generated from LinkML schema. DO NOT modify directly - changes should be made in ReproNim/reproschema repository.
+- **reproschema/validate.py**: Schema validation using PyShacl
+- **reproschema/redcap2reproschema.py**: Convert REDCap CSV to ReproSchema format
+- **reproschema/reproschema2redcap.py**: Convert ReproSchema to REDCap CSV format  
+- **reproschema/reproschema2fhir.py**: Convert ReproSchema to FHIR Questionnaire resources
+- **reproschema/output2redcap.py**: Process reproschema-ui output into REDCap CSV
+
+### Conversion Workflows
+
+1. **REDCap → ReproSchema**: Requires CSV data dictionary + YAML config file
+2. **ReproSchema → REDCap**: Takes protocol directory, outputs CSV
+3. **ReproSchema → FHIR**: Converts activities/items to FHIR Questionnaire
+4. **UI Output → REDCap**: Processes survey responses to REDCap format
+
+## CLI Commands
+
+- `reproschema validate <path>` - Validate ReproSchema format
+- `reproschema redcap2reproschema <csv> <yaml>` - Convert REDCap to ReproSchema
+- `reproschema reproschema2redcap <input_dir> <output_csv>` - Convert ReproSchema to REDCap
+- `reproschema reproschema2fhir <input_dir> <output_dir>` - Convert to FHIR
+- `reproschema output2redcap <input_dir> <output_dir>` - Process UI output
+- `reproschema migrate <path>` - Migrate to new schema version
+- `reproschema convert` - Convert between formats (jsonld, n-triples, turtle)
+
+## Important Notes
+
+- Python 3.10+ required
+- The Pydantic models in `reproschema/models/model.py` are auto-generated - DO NOT edit directly
+- All schema changes must be made in the LinkML source at ReproNim/reproschema repository
+- Uses pre-commit for code quality - commits may require running twice
+- Line length limit: 79 characters (enforced by black)

docs/CNAME

@@ -0,0 +1,56 @@
+# reproschema-py - Documentation
+
+## Inherits From
+→ Parent: ../../internal/CLAUDE.md (all shared practices apply)
+
+## Repository Purpose
+Python library for ReproSchema validation, conversion, and manipulation
+
+## Local Overrides
+- **Python**: 3.8+ (parent: 3.7+) - Need dataclasses and typing features
+- **Testing**: 90% coverage (parent: 80%) - Critical library requiring high reliability
+- **Type hints**: Required for all public APIs - Better IDE support and documentation
+
+## Tech Stack
+- Language: Python 3.8+
+- Validation: Pydantic
+- CLI: Click
+- Testing: pytest, pytest-cov
+
+## Key Commands
+```bash
+# Development
+pip install -e .
+pytest --cov=reproschema
+
+# CLI usage
+reproschema validate <path>
+reproschema redcap2reproschema <input> <output>
+```
+
+## Dependencies
+- **Depends on**: reproschema (core definitions)
+- **Used by**: reproschema-agents, reproschema-server
+- **External**: pydantic, click, jsonld
+
+## Current Focus
+- Active: FHIR converter implementation
+- Next: Optimize validation performance
+- Blocked: None
+
+## Recent Changes (Last 5)
+- 2025-01-29: Memory optimization → ./learnings/2025-01-memory.md
+- 2025-01-28: Added FHIR support → ./changes/2025-01-fhir.md
+
+## Local Patterns
+- CLI design → ./patterns/cli-architecture.md
+- Converter pattern → ./patterns/converter-design.md
+- Validation pipeline → ./patterns/validation-flow.md
+
+## Quick Links
+- PyPI: https://pypi.org/project/reproschema
+- CI: .github/workflows/test.yml
+- Issues: /issues?label=reproschema-py
+
+---
+*Line count: ~65 (target: < 100)*

internal/CLAUDE.md

@@ -0,0 +1,74 @@
+# ReproSchema Python Library - Repository Documentation
+
+## Inherits From
+- Parent: ../../internal/CLAUDE.md (all shared practices apply)
+
+## Repository-Specific Details
+
+### Purpose
+Python library for working with ReproSchema - provides validation, conversion, and manipulation tools for ReproSchema documents.
+
+### Local Overrides
+- **Python version**: Minimum Python 3.8 (not 3.7)
+- **Testing**: Use pytest exclusively, maintain 90% coverage (higher than parent requirement)
+- **Type hints**: Required for all public APIs
+
+### Unique Patterns
+- CLI tool in `reproschema/cli.py`
+- Conversion utilities for REDCap, FHIR, and other formats
+- Pydantic models for schema validation
+- Custom JSON-LD utilities
+
+### Dependencies on Other Repos
+- Depends on: reproschema (core schema definitions)
+- Used by: reproschema-agents, reproschema-server
+
+### Key Commands
+```bash
+# Install in development mode
+pip install -e .
+
+# Run tests with coverage
+pytest --cov=reproschema --cov-report=html
+
+# Validate a schema
+reproschema validate <path-to-schema>
+
+# Convert REDCap to ReproSchema
+reproschema redcap2reproschema <csv-file> <output-dir>
+
+# Convert ReproSchema to REDCap
+reproschema reproschema2redcap <input-dir> <output-csv>
+```
+
+### Development Workflow
+1. Write tests first (TDD approach)
+2. Implement features with type hints
+3. Run full test suite
+4. Update CLI help text if adding commands
+5. Update README with examples
+
+### Testing Strategy
+- Unit tests for all converters
+- Integration tests for CLI commands
+- Test with real-world schemas from reproschema-library
+- Mock external dependencies
+
+### Release Process
+1. Update CHANGELOG.md
+2. Bump version in pyproject.toml
+3. Ensure tests pass on all Python versions
+4. Create GitHub release
+5. Auto-publish to PyPI via GitHub Actions
+## Lessons Learned
+
+### Template for New Lessons
+```markdown
+### [YYYY-MM-DD] - [Brief Description]
+**Problem**: [What challenge we faced]
+**Solution**: [How we solved it]
+**Transferable to**: [Which other repos might benefit]
+**Status**: [Shared/Local-only/Under-evaluation]
+```
+
+<!-- Add new lessons above this line -->

internal/CLAUDE.md.backup

@@ -1,4 +1,4 @@
-site_name: reporschema-py
+site_name: reproschema-py
 nav:
   - Home: index.md
   - Installation: installation.md