From 97bc22518fb5e44d78a2198a30ef60daec9a92cf Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 18 Oct 2025 10:06:04 +0000
Subject: [PATCH 1/4] Initial plan


From e6fbfe5eed1a2b3e76a437106e7667172e7dce03 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 18 Oct 2025 10:11:13 +0000
Subject: [PATCH 2/4] Add GitHub Copilot instructions for EasyReflectometryLib

Co-authored-by: rozyczko <8266281+rozyczko@users.noreply.github.com>
---
 .github/copilot-instructions.md | 168 ++++++++++++++++++++++++++++++++
 1 file changed, 168 insertions(+)
 create mode 100644 .github/copilot-instructions.md

diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
new file mode 100644
index 00000000..a8036ef2
--- /dev/null
+++ b/.github/copilot-instructions.md
@@ -0,0 +1,168 @@
+# GitHub Copilot Instructions for EasyReflectometryLib
+
+## Project Overview
+
+EasyReflectometryLib is a reflectometry Python package built on the EasyScience framework. It provides tools for reflectometry analysis and modeling.
+
+## Development Environment
+
+- **Python Versions**: 3.11, 3.12
+- **Supported Platforms**: Linux (ubuntu-latest), macOS (macos-latest), Windows (windows-latest)
+- **Package Manager**: pip
+- **Build System**: hatchling with setuptools-git-versioning
+
+## Code Style and Formatting
+
+### Ruff Configuration
+- Use **Ruff** for linting and formatting (configured in `pyproject.toml`)
+- Maximum line length: 127 characters
+- Quote style: single quotes for strings
+- Import style: force single-line imports
+- To fix issues automatically: `python -m ruff . --fix`
+
+### Code Quality Standards
+- Follow PEP 8 guidelines
+- Use type hints where appropriate
+- Write clear, self-documenting code with meaningful variable names
+- Maintain consistency with existing code patterns in the repository
+
+### Linting Rules
+The project uses Ruff with the following rule sets:
+- `E9`, `F63`, `F7`, `F82`: Critical flake8 rules
+- `E`: pycodestyle errors
+- `F`: Pyflakes
+- `I`: isort (import sorting)
+- `S`: flake8-bandit (security checks)
+
+Special notes:
+- Asserts are allowed in test files (`*test_*.py`)
+- Init module imports are ignored
+- Exclude `docs` directory from linting
+
+## Testing
+
+### Test Framework
+- Use **pytest** for all tests
+- Test coverage should be tracked with **pytest-cov**
+- Aim for comprehensive test coverage
+- Tests are located in the `tests/` directory
+
+### Running Tests
+```bash
+# Install dev dependencies
+pip install -e '.[dev]'
+
+# Run tests with coverage
+pytest --cov --cov-report=xml
+
+# Run tests using tox (for multiple Python versions)
+pip install tox tox-gh-actions
+tox
+```
+
+### Test Guidelines
+- Write unit tests for all new functionality
+- Include tests when fixing bugs to prevent regression
+- Test files should match the pattern `test_*.py`
+- Use descriptive test function names that explain what is being tested
+- Follow the existing test structure and patterns in the repository
+
+## Security
+
+- Follow flake8-bandit security guidelines (enabled via Ruff `S` rules)
+- Be cautious with user input and file operations
+- Do not commit secrets or sensitive information
+- Review security implications of all changes
+
+## Documentation
+
+### Docstring Style
+- Include docstrings for all public modules, classes, and functions
+- Use clear, concise descriptions
+- Document parameters, return values, and exceptions
+
+### Documentation Build
+- Documentation is built using Sphinx (version 8.1.3)
+- Source files are in the `docs/` directory
+- Use MyST parser for Markdown support
+- Include code examples in documentation where appropriate
+
+## Dependencies
+
+### Core Dependencies
+- easyscience (EasyScience framework)
+- scipp (Scientific computing)
+- refnx, refl1d (Reflectometry calculations)
+- orsopy (Data format support)
+- bumps (Optimization)
+
+### Adding New Dependencies
+- Only add dependencies when absolutely necessary
+- Add to appropriate section in `pyproject.toml`:
+  - `dependencies` for core runtime dependencies
+  - `dev` for development tools
+  - `docs` for documentation building
+- Document why the dependency is needed
+
+## Git and Version Control
+
+### Commit Messages
+- Write clear, descriptive commit messages
+- Use present tense ("Add feature" not "Added feature")
+- Reference issue numbers when applicable
+
+### Branch Workflow
+- Create feature branches from the main branch
+- Use descriptive branch names (e.g., `feature/add-new-calculator`, `bugfix/fix-reflection-calculation`)
+- Keep changes focused and atomic
+
+## Pull Request Guidelines
+
+1. Include tests for new functionality
+2. Update documentation if adding or changing features
+3. Ensure all CI checks pass:
+   - Code consistency (Ruff)
+   - Code testing (pytest on all supported platforms/versions)
+   - Package building
+4. Code should work on Python 3.11, 3.12 and all supported platforms
+5. Write a clear PR description explaining the changes
+
+## Project Structure
+
+```
+src/easyreflectometry/     # Main package source code
+├── calculators/           # Calculator implementations (refnx, refl1d, bornagain)
+├── model/                 # Reflectometry models
+├── sample/                # Sample structures and materials
+├── special/               # Special calculations and parsing
+├── summary/               # Summary generation
+└── project.py             # Main project interface
+
+tests/                     # Test suite
+docs/                      # Documentation source
+```
+
+## Best Practices
+
+1. **Minimal Changes**: Make the smallest possible changes to accomplish the task
+2. **Don't Break Existing Code**: Maintain backward compatibility unless explicitly required
+3. **Test Before Committing**: Always run tests and linting before pushing
+4. **Follow Existing Patterns**: Look at similar code in the repository for guidance
+5. **Ask When Uncertain**: If unsure about an approach, ask for clarification
+
+## CI/CD Pipeline
+
+The project uses GitHub Actions for continuous integration:
+- **Code Consistency**: Runs Ruff linting on all pushes and PRs
+- **Code Testing**: Runs pytest across multiple Python versions and platforms
+- **Package Testing**: Validates package building and installation
+- **Coverage**: Uploads test coverage to Codecov
+
+All CI checks must pass before merging PRs.
+
+## Special Notes
+
+- The project is part of the EasyScience ecosystem
+- Built on top of established reflectometry libraries (refnx, refl1d)
+- Focuses on providing a user-friendly interface for reflectometry analysis
+- Maintains compatibility with multiple calculator backends

From edb3b3ad808e25d3088f50728540fdc5adfcece1 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 18 Oct 2025 10:15:25 +0000
Subject: [PATCH 3/4] Address code review feedback for Copilot instructions

Co-authored-by: rozyczko <8266281+rozyczko@users.noreply.github.com>
---
 .github/copilot-instructions.md | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
index a8036ef2..4eaf3252 100644
--- a/.github/copilot-instructions.md
+++ b/.github/copilot-instructions.md
@@ -78,13 +78,25 @@ tox
 
 ### Docstring Style
 - Include docstrings for all public modules, classes, and functions
+- Use **Sphinx/reStructuredText style** docstrings (`:param`, `:type`, `:return`, `:rtype`)
 - Use clear, concise descriptions
 - Document parameters, return values, and exceptions
+- Example format:
+  ```python
+  """
+  Brief description of the function.
+
+  :param param_name: description of parameter
+  :type param_name: type
+  :return: description of return value
+  :rtype: return_type
+  """
+  ```
 
 ### Documentation Build
 - Documentation is built using Sphinx (version 8.1.3)
 - Source files are in the `docs/` directory
-- Use MyST parser for Markdown support
+- Use myst_parser (MyST parser) for Markdown support
 - Include code examples in documentation where appropriate
 
 ## Dependencies
@@ -131,7 +143,8 @@ tox
 
 ```
 src/easyreflectometry/     # Main package source code
-├── calculators/           # Calculator implementations (refnx, refl1d, bornagain)
+├── calculators/           # Calculator implementations (refnx, refl1d)
+│   └── bornagain/         # BornAgain calculator (not yet functional)
 ├── model/                 # Reflectometry models
 ├── sample/                # Sample structures and materials
 ├── special/               # Special calculations and parsing

From ca314ec4fc2d7b739678ce2bdce656b5c9640441 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 18 Oct 2025 10:16:07 +0000
Subject: [PATCH 4/4] Fix formatting of myst_parser package name

Co-authored-by: rozyczko <8266281+rozyczko@users.noreply.github.com>
---
 .github/copilot-instructions.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
index 4eaf3252..881b2c53 100644
--- a/.github/copilot-instructions.md
+++ b/.github/copilot-instructions.md
@@ -96,7 +96,7 @@ tox
 ### Documentation Build
 - Documentation is built using Sphinx (version 8.1.3)
 - Source files are in the `docs/` directory
-- Use myst_parser (MyST parser) for Markdown support
+- Use `myst_parser` (MyST parser) for Markdown support
 - Include code examples in documentation where appropriate
 
 ## Dependencies