pyproject.toml.bk

########################
### Project Metadata ###
########################
# Note: This is a notebook collection project, not a Python package
[project]
name = "python-notebooks-development"
description = "Python notebooks for neutron imaging beamlines at ORNL"
version = "0.1.0"
requires-python = "==3.12"
license = { text = "MIT" }
readme = "README.md"

[project.urls]
homepage = "https://github.com/ornlneutronimaging/python_notebooks"
repository = "https://github.com/ornlneutronimaging/python_notebooks"
documentation = "https://neutronimaging.pages.ornl.gov/tutorial/"
issues = "https://github.com/ornlneutronimaging/python_notebooks/issues"

###################
### Pixi config ###
###################

[tool.pixi.workspace]
channels = ["neutronimaging", "conda-forge", "oncat"]
platforms = ["linux-64"]

# Base dependencies (always included)
[tool.pixi.dependencies]
python = "3.12.*"
requests = "*"
requests-oauthlib = "*"

# ============================================
# Feature: Scientific Computing
# ============================================
[tool.pixi.feature.scientific]
[tool.pixi.feature.scientific.dependencies]
astropy = "*"
scipy = "*"
pandas = "*"
scikit-image = "*"
h5py = "*"
lmfit = "*"
pillow = "*"
neunorm = "*"

# ============================================
# Feature: Supporting Libraries
# ============================================
[tool.pixi.feature.support]
[tool.pixi.feature.support.dependencies]
poco = "*"

# ============================================
# Feature: Visualization
# ============================================
[tool.pixi.feature.viz]
[tool.pixi.feature.viz.dependencies]
matplotlib = "*"
plotly = "*"
dash = "*"

# ============================================
# Feature: Jupyter and Notebooks
# ============================================
[tool.pixi.feature.jupyter]
[tool.pixi.feature.jupyter.dependencies]
jupyterlab = "*"
ipympl = "*"
ipywidgets = "*"
jupytext = "*"
nbstripout = "*"
ipython = "*"

[tool.pixi.feature.jupyter.tasks]
lab = "jupyter lab --NotebookApp.nbserver_extensions=\"{'jupyterlab':True}\""
notebook = "jupyter notebook"
lab-build = "jupyter lab build --dev-build=False --minimize=True"
lab-clean = "jupyter lab clean --all"
lab-rebuild = { depends-on = ["lab-clean", "lab-build"] }

# ============================================
# Feature: Excel Support
# ============================================
[tool.pixi.feature.excel]
[tool.pixi.feature.excel.dependencies]
xlrd = "*"
openpyxl = "*"
xlsxwriter = "*"

# ============================================
# Feature: Qt and GUI
# ============================================
[tool.pixi.feature.gui]
[tool.pixi.feature.gui.dependencies]
qt = "*"
qtpy = "*"
pyqt = "*"
pyqtgraph = "*"

# ============================================
# Feature: Utilities
# ============================================
[tool.pixi.feature.utils]
[tool.pixi.feature.utils.dependencies]
inflect = "*"
werkzeug = "*"
tqdm = "*"
pyoncat = "*"

# ============================================
# Feature: Testing
# ============================================
[tool.pixi.feature.test]
[tool.pixi.feature.test.dependencies]
pytest = "*"
pytest-cov = "*"

[tool.pixi.feature.test.tasks]
test = "pytest notebooks/tests/ -v"
test_imports = "pytest notebooks/tests/test_imports.py -v"

# ============================================
# Feature: Development
# ============================================
[tool.pixi.feature.dev]
[tool.pixi.feature.dev.dependencies]
pre-commit = "*"
ruff = "*"
pip-audit = "*"

[tool.pixi.feature.dev.tasks]
lint = "ruff check notebooks/"
format = "ruff format notebooks/"
clean_notebooks = "python notebooks/_before_and_after_github_script.py -b"
restore_notebooks = "python notebooks/_before_and_after_github_script.py -a"
# Non-blocking audit - just warns about vulnerabilities
audit = "pip-audit --local || echo 'Warning: Some vulnerabilities found. Consider updating dependencies.'"

# ============================================
# PyPI Dependencies (all environments)
# ============================================
[tool.pixi.pypi-dependencies]
# tdcsophiread = { path = "/SNS/VENUS/shared/zhangc/wheels/tdcsophiread-3.0.2-cp312-abi3-linux_x86_64.whl" }
# neunorm = "*"
changepy = { git = "https://github.com/JeanBilheux/changepy" }
# ipywe = "*"
neutronbraggedge = "*"
sectorizedradialprofile = "*"
imagingreso = "*"
# tdcsophiread = { path = "/SNS/VENUS/shared/zhangc/wheels/tdcsophiread-3.0.2-cp312-abi3-linux_x86_64.whl" }

# ============================================
# Environments
# ============================================
[tool.pixi.environments]
# Default environment includes all features
default = { features = [
  "scientific",
  "support",
  "viz",
  "jupyter",
  "excel",
  "gui",
  "utils",
  "test",
], solve-group = "default" }

# Development environment includes everything plus dev tools
dev = { features = [
  "scientific",
  "support",
  "viz",
  "jupyter",
  "excel",
  "gui",
  "utils",
  "test",
  "dev",
], solve-group = "default" }

# Minimal environment for CI/CD or lightweight usage
minimal = { features = [
  "scientific",
  "utils",
  "test",
], solve-group = "minimal" }

# Jupyter-only environment
jupyter = { features = [
  "scientific",
  "viz",
  "jupyter",
  "utils",
], solve-group = "jupyter" }

# ============================================
# Global Tasks (available in all environments)
# ============================================
[tool.pixi.tasks]
# Installation check
check = "python util/installation_check.py"

# Combined test task
test_all = { depends-on = ["test_imports", "test"] }

# Clean all caches and build artifacts
clean = 'rm -rf .pytest_cache .ruff_cache **/__pycache__ notebooks/**/.ipynb_checkpoints'

##############
### Pytest ###
##############

[tool.pytest.ini_options]
# Adjusted for notebook testing
addopts = "-v"
pythonpath = [".", "notebooks"]
testpaths = ["notebooks/tests"]
python_files = ["test*.py"]
norecursedirs = [
  ".git",
  "tmp*",
  "_tmp*",
  "__pycache__",
  "*dataset*",
  "*data_set*",
  ".ipynb_checkpoints",
]
# Add markers for different test categories
markers = [
  "slow: marks tests as slow (deselect with '-m \"not slow\"')",
  "integration: marks tests as integration tests",
  "unit: marks tests as unit tests",
]

############
### Ruff ###
############

[tool.ruff]
target-version = "py311"
line-length = 120
# Exclude notebooks from direct linting (we'll handle them separately if needed)
exclude = [
  "*.ipynb",
  ".ipynb_checkpoints",
  "__pycache__",
  ".git",
  ".ruff_cache",
  ".pytest_cache",
]

[tool.ruff.lint]
# Selected rules appropriate for scientific notebooks
select = [
  "E",   # pycodestyle errors
  "F",   # pyflakes
  "I",   # isort
  "N",   # pep8-naming
  "W",   # pycodestyle warnings
  "UP",  # pyupgrade
  "B",   # flake8-bugbear
  "C4",  # flake8-comprehensions
  "NPY", # NumPy-specific rules
  "PD",  # pandas-vet
]
ignore = [
  "E501",  # line too long (handled by formatter)
  "N802",  # function names should be lowercase (scientific computing often uses math notation)
  "N803",  # argument names should be lowercase
  "N806",  # variable in function should be lowercase
  "PD901", # avoid using 'df' as variable name (common in notebooks)
]

[tool.ruff.lint.isort]
known-first-party = ["__code"]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
line-ending = "auto"