release 1.5.0

.copier-answers.yml

@@ -2,7 +2,7 @@
 _commit: 8bdcedc
 _src_path: gh:/EasyScience/EasyProjectTemplate
 description: A reflectometry python package built on the EasyScience framework.
-max_python: '3.12'
+max_python: '3.13'
 min_python: '3.9'
 orgname: EasyScience
 packagename: easyreflectometry

.github/copilot-instructions.md

@@ -0,0 +1,181 @@
+# 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 **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` (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/         # BornAgain calculator (not yet functional)
+├── 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

.github/workflows/documentation-build.yml

@@ -23,6 +23,16 @@ jobs:
   # This workflow contains a single job called "build"
   build_documentation:
     runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
+    permissions:
+      contents: read    # to clone the repository
+      pages: write      # to deploy to Pages
+      id-token: write   # to verify the deployment originates from an appropriate source
+
     steps:
     - name: Checkout
       uses: actions/checkout@master
@@ -34,16 +44,21 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.11
+        python-version: 3.12
     - name: Install Pandoc, repo and dependencies
       run: |
         sudo apt install pandoc
+        sudo apt install libcairo2-dev
         pip install sphinx==8.1.3
         pip install . '.[dev,docs]'
+
+    - name: Install Jupyter kernel
+      run: |
+        python -m ipykernel install --user --name=python3
+
     - name: Build and Commit
-      uses: sphinx-notes/pages@master
+      uses: sphinx-notes/pages@v3
       with:
-        install_requirements: false
         sphinx_version: 8.1.3
         documentation_path: docs/src
     - name: Push changes

.github/workflows/ossar-analysis.yml

@@ -13,7 +13,7 @@ jobs:
   OSSAR-Scan:
     # OSSAR runs on windows-latest.
     # ubuntu-latest and macos-latest support coming soon
-    runs-on: windows-latest
+    runs-on: windows-2022
 
     steps:
       # Checkout your code repository to scan

.github/workflows/python-ci.yml

@@ -8,8 +8,6 @@
 # - build the package
 # - check the package
 #
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
 name: CI using pip
 
 on: [push, pull_request]
@@ -30,8 +28,8 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ['3.11', '3.12']
-        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ['3.11', '3.12', '3.13']
+        os: [ubuntu-latest, macos-latest, windows-2022]
 
     runs-on: ${{ matrix.os }}
     if: "!contains(github.event.head_commit.message, '[ci skip]')"
@@ -50,19 +48,24 @@ jobs:
     - name: Install dependencies
       run: pip install -e '.[dev]'
 
-    - name: Test with tox
+    - name: Test with pytest and coverage
       run: |
-        pip install tox tox-gh-actions coverage
-        tox
+        pip install pytest pytest-cov
+        pytest --cov=src/easyreflectometry tests --cov-branch --cov-report=xml:coverage-unit.xml
 
-    - name: Upload coverage
-      uses: codecov/codecov-action@v3
+    - name: Upload coverage reports to Codecov
+      # only on ubuntu to avoid multiple uploads
+      if: runner.os == 'Linux'
+      uses: codecov/codecov-action@v5
       with:
-        name: Pytest coverage
-        env_vars: OS,PYTHON,GITHUB_ACTIONS,GITHUB_ACTION,GITHUB_REF,GITHUB_REPOSITORY,GITHUB_HEAD_REF,GITHUB_RUN_ID,GITHUB_SHA,COVERAGE_FILE
-      env:
-        OS: ${{ matrix.os }}
-        PYTHON: ${{ matrix.python-version }}
+        name: unit-tests-job
+        flags: unittests
+        files: ./coverage-unit.xml
+        fail_ci_if_error: true
+        verbose: true
+        token: ${{ secrets.CODECOV_TOKEN }}
+        slug: EasyScience/EasyReflectometryLib
+
 
   Package_Testing:
 

.github/workflows/python-package.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.11','3.12']
+        python-version: ['3.11','3.12','3.13']
     if: "!contains(github.event.head_commit.message, '[ci skip]')"
 
     steps:

CONTRIBUTING.rst

@@ -102,7 +102,7 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.md.
-3. The pull request should work for Python, 3.11 and 3.12, and for PyPy. Check
+3. The pull request should work for Python, 3.11, 3.12, and 3.13, and for PyPy. Check
    https://travis-ci.com/easyScience/EasyReflectometryLib/pull_requests
    and make sure that the tests pass for all supported Python versions.
 

docs/src/api/api.rst

@@ -19,6 +19,15 @@ Sample is build from assemblies.
 
    sample
 
+Project
+=======
+Project provides a higher-level interface for managing models, experiments, and ORSO import.
+
+.. toctree::
+   :maxdepth: 1
+
+   project
+
 Assemblies
 ==========
 Assemblies are collections of layers that are used to represent a specific physical setup.

docs/src/api/project.rst

@@ -0,0 +1,4 @@
+.. automodule:: easyreflectometry.project
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/src/tutorials/advancedfitting/multi_contrast.ipynb

@@ -251,7 +251,7 @@
     ")\n",
     "d13d2o.constrain_area_per_molecule = True\n",
     "d13d2o.conformal_roughness = True\n",
-    "d13d2o.constrain_solvent_roughness(d2o_layer)"
+    "d13d2o.constrain_solvent_roughness(d2o_layer.roughness)"
    ]
   },
   {
@@ -291,7 +291,7 @@
     ")\n",
     "d70d2o.constrain_area_per_molecule = True\n",
     "d70d2o.conformal_roughness = True\n",
-    "d70d2o.constrain_solvent_roughness(d2o_layer)"
+    "d70d2o.constrain_solvent_roughness(d2o_layer.roughness)"
    ]
   },
   {
@@ -331,7 +331,7 @@
     ")\n",
     "d83acmw.constrain_area_per_molecule = True\n",
     "d83acmw.conformal_roughness = True\n",
-    "d83acmw.constrain_solvent_roughness(acmw_layer)"
+    "d83acmw.constrain_solvent_roughness(acmw_layer.roughness)"
    ]
   },
   {
@@ -341,8 +341,8 @@
    "source": [
     "## Introducing constraints\n",
     "\n",
-    "Then to ensure that the structure (thicknesss, area per molecule, etc.) is kept the same between the different contrasts we constain these (`layer2` is the head layer and `layer1`, which the neutron are incident on first are the tail layer). \n",
-    "The `constrain_multiple_contrast` method allows this, not that is it important that a chain of constraints is produced, one constraining the next. "
+    "To ensure that the structure (thicknesss, area per molecule, etc.) is kept the same between the different contrasts we constrain these (`layer2` is the head layer and `layer1`, which the neutron are incident on first are the tail layer). \n",
+    "The `constrain_multiple_contrast` method allows this, note that it is important that a chain of constraints is produced, one constraining the next. "
    ]
   },
   {
@@ -352,12 +352,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# These four lines should be removed in future\n",
-    "d70d2o.head_layer.area_per_molecule_parameter.enabled = True\n",
-    "d70d2o.tail_layer.area_per_molecule_parameter.enabled = True\n",
-    "d83acmw.head_layer.area_per_molecule_parameter.enabled = True\n",
-    "d83acmw.tail_layer.area_per_molecule_parameter.enabled = True\n",
-    "\n",
     "d70d2o.constrain_multiple_contrast(d13d2o)\n",
     "d83acmw.constrain_multiple_contrast(d70d2o)"
    ]
@@ -571,7 +565,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.9"
+   "version": "3.12.11"
   }
  },
  "nbformat": 4,