Update tutorials, workflows, and project configuration

[AndrewSazonov]

This PR introduces updates to documentation, tutorials, and CI/CD workflows, including:

Tutorials & Documentation

• Convert Python tutorial scripts to Jupyter notebooks using Jupytext.
• Strip notebook outputs and auto-rename cell IDs for clean version control.
• Update tutorial content and parameters for improved performance.
• Add documentation-specific dependencies (e.g., Jupytext).

CI/CD Workflows

• Standardize workflow and job naming for clarity.
• Add workflows for:
  • Automated release drafting
  • Security scanning
  • PR label verification
  • Old run cleanup
  • PyPI publishing
• Enhance package testing, including notebook testing with nbmake.
• Refine workflow scripts, YAML formatting, and dependency handling.

Project Configuration & Code Quality

• Update pyproject.toml configuration and dependencies.
• Apply and configure Ruff, YAPF, and Prettier formatting.
• Add SPDX license headers to all source files and update copyright.
• Introduce overwrite option to download_from_repository() utility.

[github-advanced-security]

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[github-advanced-security]

This pull request sets up GitHub code scanning for this repository. Once the scans have completed and the checks have passed, the analysis results for this pull request branch will appear on this overview. Once you merge this pull request, the 'Security' tab will show more code scanning analysis results (for example, for the default branch). Depending on your configuration and choice of analysis tool, future pull requests will be annotated with code scanning analysis results. For more information about GitHub code scanning, check out the documentation.

[github-advanced-security]

This pull request sets up GitHub code scanning for this repository. Once the scans have completed and the checks have passed, the analysis results for this pull request branch will appear on this overview. Once you merge this pull request, the 'Security' tab will show more code scanning analysis results (for example, for the default branch). Depending on your configuration and choice of analysis tool, future pull requests will be annotated with code scanning analysis results. For more information about GitHub code scanning, check out the documentation.

[Copilot]

Pull Request Overview

This PR introduces significant updates to documentation, tutorials, CI/CD workflows, and project configuration, focusing on improving the development experience and documentation quality for the EasyDiffraction library.

Key changes include:

• Conversion of Python tutorial scripts to Jupyter notebooks using Jupytext for better documentation integration
• Enhancement of CI/CD workflows with new automation features including security scanning, PR validation, and PyPI publishing
• Application of comprehensive code formatting and quality improvements using Ruff, YAPF, and Prettier across the codebase

Reviewed Changes

Copilot reviewed 142 out of 161 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
tutorials/*.py	Convert tutorial scripts to Jupytext format with installation checks for notebook compatibility
tutorials/*.ipynb	Generate corresponding Jupyter notebooks with clean metadata and numbered cell IDs
tools/update_spdx-headers.py	Add utility for managing SPDX license headers across source files
tools/run_notebooks.sh	Increase notebook execution timeout for better CI reliability
tools/create_mkdocs-yml.py	Apply code formatting improvements and better import organization
tests/unit_tests/*.py	Comprehensive code formatting updates using modern Python style guidelines

[Copilot]

The commented pip install command should either be uncommented to be functional or removed if not intended for use. Consider using a conditional installation approach or providing clear instructions in comments.

Suggested change

	# !pip install 'easydiffraction[visualization]'
	# If running in a notebook, install using IPython magic; otherwise, instruct the user.
	try:
	from IPython import get_ipython
	ipython = get_ipython()
	if ipython is not None:
	ipython.run_line_magic('pip', "install 'easydiffraction[visualization]'")
	except Exception:
	print("Please install 'easydiffraction[visualization]' manually using pip.")

[Copilot]

[nitpick] Trailing comma is now added consistently. This is good practice for Python function calls and improves version control diffs.

[Copilot]

Doubling the timeout from 300 to 600 seconds may indicate performance issues in the notebooks. Consider investigating if notebooks can be optimized rather than just increasing timeout limits.

Suggested change

	pytest --nbmake examples/ --ignore-glob='examples/*emcee*' --nbmake-timeout=600 --color=yes -n=auto
	pytest --nbmake examples/ --ignore-glob='examples/*emcee*' --nbmake-timeout=300 --color=yes -n=auto