pyproject.toml

########################
### Project Metadata ###
########################
[project]
name = "examplepyapp"
description = "Example Python repo for neutrons"
dynamic = ["version"]
requires-python = ">=3.10"
license = { text = "MIT" }
keywords = ["neutrons", "example", "python"]
readme = "README.md"

dependencies = [
  # Dependencies available from both PyPI and conda should be listed here
  "numpy>=2.2.6,<3",
  "QtPy",
  "PyQt5",
  "pyqtgraph",
  # Dependencies only available from PyPI
  "bm3d-streak-removal>=0.2.0,<0.3",
  "pytest-playwright>=0.7.0,<0.11",
]

[project.optional-dependencies]
docs = ["sphinx", "sphinx_rtd_theme", "versioningit", "myst_parser"]

[project.scripts]
packagename-cli = "packagenamepy.packagename:main"

[project.gui-scripts]
packagenamepy = "packagenamepy.packagename:gui"

[project.urls]
homepage = "https://github.com/neutrons/python_project_template/"
repository = "https://github.com/neutrons/python_project_template/"
# documentation = add_url_to_readthedoc_here
issues = "https://github.com/neutrons/python_project_template/issues"

####################
### Build config ###
####################

[build-system]
build-backend = "hatchling.build"
requires = ["hatchling", "versioningit"]

[tool.hatch.version]
source = "versioningit"

[tool.hatch.build.hooks.versioningit-onbuild]
source-file = "src/packagenamepy/_version.py"
build-file = "packagenamepy/_version.py"

[tool.hatch.build]
artifacts = [
  "src/packagenamepy/_version.py",
  "src/packagenamepy/**/*.yml",
  "src/packagenamepy/**/*.yaml",
  "src/packagenamepy/**/*.ini",
]

[tool.hatch.build.targets.wheel]
packages = ["src/packagenamepy"]

[tool.versioningit.vcs]
method = "git"
default-tag = "0.1.0"

[tool.versioningit.next-version]
method = "minor"

[tool.versioningit.format]
distance = "{next_version}.dev{committer_date:%Y%m%d%H%M%S}"
# Since pixi builds currently require the package version to be set statically in pyproject.toml,
# and we solve that by temporarily changing pyproject.toml during build using the pixi tasks
# sync-version and reset-toml, then we need to ignore uncommitted changes in order for the wheel
# version to be consistent with the package version
dirty = "{version}"
distance-dirty = "{next_version}.dev{committer_date:%Y%m%d%H%M%S}"

[tool.versioningit.write]
file = "src/packagenamepy/_version.py"

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

[tool.pixi.workspace]
preview = ["pixi-build"] # Required until the build feature becomes stable
channels = [
  "conda-forge",
  "https://prefix.dev/pixi-build-backends", # Required for pixi build
]
platforms = ["linux-64", "osx-arm64"] # add additional platforms as needed
# If you don't need to map PyPI dependencies to conda, you can remove the `conda-pypi-map` section and the `pixi-mapping.json` file.
conda-pypi-map = { "conda-forge" = "pixi-mapping.json" }

## Dependency tables - https://pixi.sh/latest/reference/pixi_manifest/#the-dependencies-tables
## These tables override the dependencies listed in the [project] section

[tool.pixi.dependencies]
# Conda package dependencies
numpy = "*"
scipy = "*" # specify derivative dependencies here if you need them from conda
# GUI
pyqtgraph = "*"
qt = "*"
qtpy = "*"
pyqt = "*"
# Minimum versions that exclude known-vulnerable releases. These floors are kept
# deliberately (they keep a fresh environment off bad versions), but nothing in CI
# enforces or refreshes them any more -- the Grype scan in the conda-build job is
# report-only. Bump them if you want, but a stale floor will not fail a build.
h2 = ">=4.3.0"             # Known vulnerability in <4.3.0
brotli = ">=1.2.0"
urllib3 = ">=2.6.3"        # Known vulnerability in <2.6.3
filelock = ">=3.20.3"      # Known vulnerability in <3.20.3
virtualenv = ">=21.7.12"   # GHSA-94p9-xgh2-xp45, GHSA-9h9j-4vrj-gf7g
cryptography = ">=48.0.1"  # CVE-2026-26007, CVE-2026-39892, GHSA-537c-gmf6-5ccf
requests = ">=2.33.0"      # CVE-2026-25645
pillow = ">=12.3.0"        # CVE-2026-25990, CVE-2026-40192, PYSEC-2026-2255/2256/2257
msgpack-python = ">=1.2.1" # GHSA-6v7p-g79w-8964

[tool.pixi.pypi-dependencies]
# PyPI dependencies, including this package to allow local editable installs
examplepyapp = { path = ".", editable = true }
jaraco-context = ">=6.1.0"                     # CVE-2026-23949

# Pixi Build configuration - https://pixi.sh/latest/reference/pixi_manifest/#pixi-build

[tool.pixi.package.host-dependencies]
hatchling = "*"
versioningit = "*"

[tool.pixi.package.run-dependencies]
python = ">=3.10"
numpy = "*"
QtPy = "*"
pyqt = "*"
pyqtgraph = "*"

[tool.pixi.package]
name = "examplepyapp"
version = "0.0.0"     # placeholder, overwritten by sync-version

[tool.pixi.package.build]
backend = { name = "pixi-build-python", version = "*" }

# Environments and Features

[tool.pixi.environments]
default = { features = [
  "docs",
  "developer",
  "package",
  "test",
], solve-group = "default" }
jupyter = { features = ["developer", "jupyter"], solve-group = "jupyter" }

[tool.pixi.feature.test.dependencies]
pytest = ">=9.0.3"  # CVE-2025-71176 fixed in 9.0.3
pytest-cov = "*"
pytest-repeat = "*"
pytest-xdist = "*"

[tool.pixi.feature.package.dependencies]
twine = ">=6.1.0,<7" # for PyPI publishing
hatch = ">=1.16.5"   # for building wheels and sdist; >=1.16.5 supports virtualenv 21
versioningit = "*"

[tool.pixi.feature.package.pypi-dependencies]
toml-cli = "*"

[tool.pixi.feature.developer.dependencies]
pip = ">=26.0"     # CVE-2026-1703
pre-commit = "*"
ruff = "*"
versioningit = "*"

[tool.pixi.feature.docs.dependencies]
sphinx = "*"
sphinx_rtd_theme = "*"
myst-parser = "*"

[tool.pixi.feature.jupyter.dependencies]
jupyterlab = "*"
ipympl = "*"
ipywidgets = "*"

[tool.pixi.tasks]
# Documentation
build-docs = { cmd = 'sphinx-build -b html docs docs/_build', description = "Build documentation" }
test-docs = { cmd = "sphinx-build -M doctest docs docs/_build", description = "Test building the documentation" }
# Testing
test = { description = "Run the test suite", cmd = "pytest" }
# Packaging
pypi-sdist = { cmd = "hatch build -t sdist", description = "Build the source distribution (tar.gz)" }
pypi-wheel = { cmd = "hatch build -t wheel", description = "Build the wheel distribution" }
pypi-build = { description = "Build the packages for PyPI", depends-on = [
  "pypi-sdist",
  "pypi-wheel",
] }
pypi-publish = { cmd = "twine upload dist/*", description = "Publish the package to PyPI", depends-on = [
  "pypi-build",
] }
pypi-publish-test = { cmd = "twine upload --repository testpypi dist/*", description = "Publish the package to TestPyPI", depends-on = [
  "pypi-build",
] }
conda-build-command = { cmd = "pixi publish --target-channel ./local-channel", description = "Build the conda package command" }
conda-build = { description = "Build the conda package", depends-on = [
  "backup-toml",
  "sync-version",
  "conda-build-command",
  "reset-toml",
] }
conda-publish = { cmd = "pixi upload anaconda --owner neutrons *.conda", description = "Publish the .conda package to anaconda.org", depends-on = [
  "conda-build",
] }
# Cleaning
clean = { cmd = 'rm -rf .pytest_cache .ruff_cache **/*.egg-info **/dist **/__pycache__', description = "Clean up various caches and build artifacts" }
clean-conda = { cmd = "rm -f *.conda", description = "Clean the local .conda build artifacts" }
clean-docs = { cmd = "rm -rf docs/_build", description = "Clean up documentation build artifacts" }
clean-pypi = { cmd = "rm -rf dist", description = "Clean the PyPI build artifacts" }
clean-all = { description = "Clean all artifacts", depends-on = [
  "clean",
  "clean-conda",
  "clean-docs",
  "clean-pypi",
] }
# workaround for dynamic versioning
sync-version = { cmd = 'version=$(python -m versioningit); toml set tool.pixi.package.version "$version" --toml-path pyproject.toml', description = "Sync pyproject.toml version with Git version" }
backup-toml = { cmd = "cp pyproject.toml pyproject.toml.bak", description = "Backup the pyproject.toml file" }
reset-toml = { cmd = "cp pyproject.toml.bak pyproject.toml; rm pyproject.toml.bak", description = "Reset the pyproject.toml file to the original state" }

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

[tool.pytest.ini_options]
addopts = "-v --cov=packagenamepy --cov-report=term-missing --cov-report=xml"
pythonpath = [".", "src", "scripts"]
testpaths = ["tests"]
python_files = ["test*.py"]
norecursedirs = [
  ".git",
  "tmp*",
  "_tmp*",
  "__pycache__",
  "*dataset*",
  "*data_set*",
]
markers = ["mymarker: example markers goes here"]

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

[tool.ruff]
target-version = "py311"
line-length = 120
exclude = ["notebooks/**", "**/*.ipynb"]

[tool.ruff.lint]
select = ["A", "ARG", "ASYNC", "BLE", "C90", "E", "F", "I", "N", "UP032", "W"]
ignore = []

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

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