diffraction-lib/pixi.toml at master · easyscience/diffraction-lib · GitHub

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###########

# WORKSPACE

###########

[workspace]

# Supported platforms for the lock file (pixi.lock)

platforms = [

'win-64',

# Set minimum supported version for glibc to be 2.35 to ensure packages

# like `crysfml` that only have wheels for glibc 2.35+

# (manylinux_2_35_x86_64) are used.

#libc = { family = 'glibc', version = '2.35' }

{ platform = 'linux-64', glibc = '2.35' },

# Set minimum supported version for macOS to be 14.0 to ensure packages

# like `scipp` that only have wheels for macOS 14.0+ (macosx_14_0_arm64)

# are used instead of building from source. This is a workaround for

# Pixi, see https://github.com/prefix-dev/pixi/issues/5667

{ platform = 'osx-arm64', macos = '14.0' },

]

# Channels for fetching packages

channels = ['nodefaults', 'conda-forge']

##########

# FEATURES

##########

# Default features:

[activation.env]

PYTHONIOENCODING = 'utf-8'

# Non-default features:

# Set specific Python versions to be used in CI testing.

[feature.py-min.dependencies]

python = '3.12.*'

[feature.py-max.dependencies]

python = '3.14.*'

# Development dependencies for local development and testing with

# editable installations.

[feature.dev.dependencies]

nodejs = '*' # Required for Prettier (non-Python formatting)

jupyterlab = '*' # Jupyter notebooks

ipython = '*' # Interactive Python shell

pixi-kernel = '*' # Pixi Jupyter kernel

ipykernel = '*' # Jupyter kernel base; required for pixi-kernel

gsl = '*' # GNU Scientific Library; required for diffpy.pdffit2

tectonic = '*' # LaTeX engine for PDF report generation

lychee = '*' # Link checker for documentation

[feature.dev.pypi-dependencies]

pip = '*'

#pycrysfml = { version = ">=0.4.0", index = "https://easyscience.github.io/pypi/" }

#cryspy = { git = "https://github.com/ikibalin/cryspy.git", branch = "fix-tof-lorentz-half-angle" }

easydiffraction = { path = '.', editable = true, extras = ['dev'] }

# User-like behavior for testing with pip-installed dependencies instead

# of editable installations.

[feature.user.dependencies]

jupyterlab = '*' # Jupyter notebooks

ipython = '*' # Interactive Python shell

pixi-kernel = '*' # Pixi Jupyter kernel

[feature.user.pypi-dependencies]

pip = '*'

easydiffraction = '*'

##############

# ENVIRONMENTS

##############

[environments]

# The `default` feature is always included in all environments.

# Additional features can be specified per environment.

# Specific environments for CI testing with different Python versions.

py-312-env = { features = ['py-min', 'dev'] }

py-314-env = { features = ['py-max', 'dev'] }

# The `default` environment is developer-oriented for local development

# and testing with editable installation of the current package.

default = { features = ['py-max', 'dev'] }

# The `user` environment allows testing with pip-installed dependencies

# instead of editable installation of the current package.

user = { features = ['py-max', 'user'] }

#######

# TASKS

#######

[tasks]

##################

# 🧪 Testing Tasks

##################

unit-tests = 'python -m pytest tests/unit/ --color=yes -v'

functional-tests = 'python -m pytest tests/functional/ --color=yes -v'

integration-tests = 'python -m pytest tests/integration/ --color=yes -n auto -v'

# Run nightly-tier tests across the suite (benchmarks have their own task

# because pytest-benchmark does not run under xdist).

nightly-tests = 'python -m pytest tests/ -m nightly --ignore=tests/benchmarks --color=yes -n auto -v'

# Performance benchmarks, per experiment type; writes benchmark.json for

# the nightly CI artifact. Informational (no regression gate yet).

benchmarks = 'python -m pytest tests/benchmarks/ --benchmark-only --benchmark-json=benchmark.json --color=yes -v'

# Remove previously saved tutorial output projects (the slug-named

# projects/* directories) so the tutorial-output checks cannot pass against a

# stale artifact from an earlier run. Downloaded project archives

# (projects/proj-*) are preserved so they need not be re-downloaded.

clean-tutorial-projects = { cmd = 'python tools/clean_tutorial_projects.py', env = { EASYDIFFRACTION_ARTIFACT_ROOT = 'tmp/tutorials' } }

script-tests = { cmd = 'python -m pytest tools/test_scripts.py --color=yes -n auto -v', depends-on = [

'clean-tutorial-projects',

], env = { EASYDIFFRACTION_ARTIFACT_ROOT = 'tmp/tutorials' } }

notebook-tests = { cmd = 'python -m pytest --nbmake docs/docs/tutorials/ docs/docs/verification/ --nbmake-timeout=1200 --color=yes -n auto -v', depends-on = [

'clean-tutorial-projects',

], env = { EASYDIFFRACTION_ARTIFACT_ROOT = 'tmp/tutorials' } }

# Parse the analysis.edi of every saved tutorial project and assert its

# refined fit results against tests/tutorials/baseline.json. Run only after

# the tutorials have been executed (script-tests or notebook-tests), so the

# saved projects exist under tmp/tutorials/projects/.

tutorial-output-tests = { cmd = 'python -m pytest tests/tutorials/ --color=yes -v', env = { EASYDIFFRACTION_ARTIFACT_ROOT = 'tmp/tutorials' } }

# Run the tutorials and then verify their saved outputs in a single step.

script-tests-checked = { cmd = 'python -m pytest tests/tutorials/ --color=yes -v', depends-on = [

'script-tests',

], env = { EASYDIFFRACTION_ARTIFACT_ROOT = 'tmp/tutorials' } }

notebook-tests-checked = { cmd = 'python -m pytest tests/tutorials/ --color=yes -v', depends-on = [

'notebook-tests',

], env = { EASYDIFFRACTION_ARTIFACT_ROOT = 'tmp/tutorials' } }

test = { depends-on = ['unit-tests', 'functional-tests'] }

# Full local gate before opening a PR: every static check, unit coverage,

# all tests, tutorial execution + output verification (as scripts AND

# notebooks), and a strict documentation build (which validates the built

# site's nav/links). Steps run sequentially because the tutorial tasks

# share tmp/tutorials/projects/. Slow but comprehensive — run `pixi run

# fix` first to auto-format.

all = 'pixi run check && pixi run unit-tests-coverage && pixi run functional-tests && pixi run integration-tests && pixi run script-tests-checked && pixi run notebook-tests-checked && pixi run docs-build-local'

###########

# ✔️ Checks

###########

pyproject-check = 'python -m validate_pyproject pyproject.toml'

docstring-lint-check = 'pydoclint --quiet src/'

notebook-lint-check = 'nbqa ruff docs/docs/tutorials/ docs/docs/verification/'

py-lint-check = 'ruff check src/ tests/ docs/docs/tutorials/ docs/docs/verification/'

py-format-check = 'ruff format --check src/ tests/ docs/docs/tutorials/ docs/docs/verification/'

nonpy-format-check = 'npx prettier --list-different --config=prettierrc.toml --ignore-unknown .'

nonpy-format-check-modified = 'python tools/nonpy_prettier_modified.py'

test-structure-check = 'python tools/test_structure_check.py'

# Spelling over docs and source (config in [tool.codespell]).

spell-check = 'codespell docs src tools README.md CONTRIBUTING.md'

# Local/relative documentation link integrity (offline; external URL

# checking is deferred, see issue 114). Config in lychee.toml.

link-check = 'lychee --config lychee.toml docs/docs README.md CONTRIBUTING.md'

check = 'pre-commit run --hook-stage manual --all-files'

##########

# 🛠️ Fixes

##########

docstring-transform = 'pixi run docstripy src/ -s=numpy -w'

docstring-format-fix = 'format-docstring src/'

notebook-lint-fix = 'nbqa ruff --fix docs/docs/tutorials/ docs/docs/verification/'

py-lint-fix = 'ruff check --fix src/ tests/ docs/docs/tutorials/ docs/docs/verification/'

py-lint-fix-unsafe = 'ruff check --fix --unsafe-fixes src/ tests/ docs/docs/tutorials/ docs/docs/verification/'

py-format-fix = 'ruff format src/ tests/ docs/docs/tutorials/ docs/docs/verification/'

nonpy-format-fix = 'npx prettier --write --list-different --config=prettierrc.toml --ignore-unknown .'

nonpy-format-fix-modified = 'python tools/nonpy_prettier_modified.py --write'

update-package-diagrams = 'python tools/generate_package_docs.py'

success-message = 'echo "✅ All auto-formatting steps completed successfully!"'

fix = { depends-on = [

#'param-docstring-fix', # ED only

'docstring-format-fix',

'py-format-fix',

'py-lint-fix',

'nonpy-format-fix',

'notebook-lint-fix',

'update-package-diagrams',

'success-message',

] }

####################

# 🧮 Code Complexity

####################

complexity-check = 'radon cc -s src/'

complexity-check-json = 'radon cc -s -j src/'

maintainability-check = 'radon mi src/'

maintainability-check-json = 'radon mi -j src/'

raw-metrics = 'radon raw -s src/'

raw-metrics-json = 'radon raw -s -j src/'

#############

# 📊 Coverage

#############

unit-tests-coverage = 'pixi run unit-tests --cov=src/easydiffraction --cov-report=term-missing'

functional-tests-coverage = 'pixi run functional-tests --cov=src/easydiffraction --cov-report=term-missing'

integration-tests-coverage = 'pixi run integration-tests --cov=src/easydiffraction --cov-report=term-missing'

docstring-coverage = 'interrogate -c pyproject.toml src/easydiffraction'

cov = { depends-on = ['docstring-coverage', 'unit-tests-coverage'] }

########################

# 📓 Notebook Management

########################

python = { cmd = 'python', env = { EASYDIFFRACTION_ARTIFACT_ROOT = 'tmp/tutorials' } }

tutorial = { cmd = 'python', env = { EASYDIFFRACTION_ARTIFACT_ROOT = 'tmp/tutorials' } }

tutorial-benchmarks = { cmd = 'python tools/benchmark_tutorials.py', env = { EASYDIFFRACTION_ARTIFACT_ROOT = 'tmp/tutorials' } }

jupyter = { cmd = 'jupyter', env = { EASYDIFFRACTION_ARTIFACT_ROOT = 'tmp/tutorials' } }

notebook-convert = 'jupytext docs/docs/tutorials/*.py docs/docs/verification/*.py --from py:percent --to ipynb'

notebook-strip = 'nbstripout docs/docs/tutorials/*.ipynb docs/docs/verification/*.ipynb'

notebook-tweak = 'python tools/tweak_notebooks.py docs/docs/tutorials/ docs/docs/verification/'

notebook-exec = { cmd = 'python -m pytest --nbmake docs/docs/tutorials/ docs/docs/verification/ --overwrite --color=yes -n auto -v', env = { EASYDIFFRACTION_ARTIFACT_ROOT = 'tmp/tutorials', EASYDIFFRACTION_FIGURE_EMBED_MODE = 'shared' } }

notebook-exec-ci = { cmd = 'python -m pytest --nbmake docs/docs/tutorials/ docs/docs/verification/ --nbmake-timeout=1200 --overwrite --color=yes -n auto -v', env = { EASYDIFFRACTION_ARTIFACT_ROOT = '.', EASYDIFFRACTION_FIGURE_EMBED_MODE = 'shared' } }

# Execute and overwrite outputs for the verification notebooks only (the

# verification-page subset of notebook-exec); nbmake runs every page, and

# a known-bad page is gated by its in-notebook known_discrepancy flag.

verification-exec = { cmd = 'python -m pytest --nbmake docs/docs/verification/ --overwrite --color=yes -n auto -v', env = { EASYDIFFRACTION_ARTIFACT_ROOT = 'tmp/tutorials', EASYDIFFRACTION_FIGURE_EMBED_MODE = 'shared' } }

notebook-prepare = { depends-on = [

'notebook-convert',

'notebook-tweak',

'notebook-strip',

] }

########################

# 📚 Documentation Tasks

########################

docs-vars = "JUPYTER_PLATFORM_DIRS=1 PYTHONWARNINGS='ignore::RuntimeWarning'"

docs-pre = 'pixi run docs-vars python -m mkdocs'

# Copy the canonical Three.js snapshot into the (git-ignored) docs

# assets before any build/serve so MkDocs can serve it.

docs-sync-vendored-js = 'python tools/sync_docs_vendored_js.py'

docs-serve = { cmd = 'pixi run docs-pre serve -f docs/mkdocs.yml', depends-on = [

'docs-sync-vendored-js',

] }

docs-serve-dirty = 'pixi run docs-serve --dirty'

# Strict build (fails on broken nav / internal references); used for the

# deploy and the CI docs check. Tutorials are not executed (mkdocs-jupyter

# execute: false). docs-serve is intentionally left non-strict.

docs-build = { cmd = 'pixi run docs-pre build --strict -f docs/mkdocs.yml', depends-on = [

'docs-sync-vendored-js',

] }

# Inherits --strict; --no-directory-urls makes the built site browsable

# from disk (used by `all` so you can inspect it after verifying).

docs-build-local = 'pixi run docs-build --no-directory-urls'

docs-inventory-check = 'python -c "from pathlib import Path; p = Path(\"docs/site/objects.inv\"); raise SystemExit(0 if p.is_file() and p.stat().st_size > 0 else \"missing or empty docs/site/objects.inv\")"'

docs-deploy-pre = 'mike deploy -F docs/mkdocs.yml --push --branch gh-pages --update-aliases --alias-type copy'

docs-set-default-pre = 'mike set-default -F docs/mkdocs.yml --push --branch gh-pages'

docs-update-assets = 'python tools/update_docs_assets.py'

# Vendored JavaScript runtimes (Plotly cartesian bundle + Three.js).

# vendor-update-js re-fetches the pinned versions; vendor-check-js is a

# no-network drift guard for CI.

vendor-update-js = 'python tools/bump_vendored_js.py'

vendor-check-js = 'python tools/bump_vendored_js.py --check'

##############################

# 📦 Template Management Tasks

##############################

copier-copy = 'copier copy gh:easyscience/templates . --data-file ../diffraction/.copier-answers.yml --data template_type=lib'

copier-recopy = 'copier recopy --data-file ../diffraction/.copier-answers.yml --data template_type=lib'

copier-update = 'copier update --data-file ../diffraction/.copier-answers.yml --data template_type=lib'

#####################

# 🪝 Pre-commit Hooks

#####################

pre-commit-clean = 'pre-commit clean'

pre-commit-install = 'pre-commit install --hook-type pre-commit --hook-type pre-push --overwrite'

pre-commit-uninstall = 'pre-commit uninstall --hook-type pre-commit --hook-type pre-push'

pre-commit-setup = { depends-on = [

'pre-commit-clean',

'pre-commit-uninstall',

'pre-commit-install',

] }

#################

# 🐙️ GitHub Tasks

#################

repo-wiki = 'gh api -X PATCH repos/easyscience/diffraction-lib -f has_wiki=false'

repo-discussions = 'gh api -X PATCH repos/easyscience/diffraction-lib -f has_discussions=true'

repo-description = "gh api -X PATCH repos/easyscience/diffraction-lib -f description='Diffraction data analysis'"

repo-homepage = "gh api -X PATCH repos/easyscience/diffraction-lib -f homepage='https://easyscience.github.io/diffraction-lib'"

repo-config = { depends-on = [

'repo-wiki',

'repo-discussions',

'repo-description',

'repo-homepage',

] }

master-protection = 'gh api -X POST repos/easyscience/diffraction-lib/rulesets --input .github/configs/rulesets-master.json'

develop-protection = 'gh api -X POST repos/easyscience/diffraction-lib/rulesets --input .github/configs/rulesets-develop.json'

gh-pages-protection = 'gh api -X POST repos/easyscience/diffraction-lib/rulesets --input .github/configs/rulesets-gh-pages.json'

branch-protection = { depends-on = [

'master-protection',

'develop-protection',

'gh-pages-protection',

] }

pages-deployment = 'gh api -X POST repos/easyscience/diffraction-lib/pages --input .github/configs/pages-deployment.json'

github-labels = 'python tools/update_github_labels.py'

#########################

# ⚖️ SPDX License Headers

#########################

license-remove = 'python tools/license_headers.py remove src/ tests/ --exclude-from-pyproject-toml tool.ruff.exclude'

license-add = 'python tools/license_headers.py add src/ tests/ --exclude-from-pyproject-toml tool.ruff.exclude'

license-check = 'python tools/license_headers.py check src/ tests/ --exclude-from-pyproject-toml tool.ruff.exclude'

####################################

# 🚀 Other Development & Build Tasks

####################################

default-build = 'python -m build'

dist-build = 'python -m build --wheel --outdir dist'

npm-config = 'npm config set registry https://registry.npmjs.org/'

prettier-install = 'npm install --no-save --no-audit --no-fund prettier prettier-plugin-toml'

clean-pycache = "find . -type d -name '__pycache__' -prune -exec rm -rf '{}' +"

post-install = { depends-on = [

'npm-config',

'prettier-install',

#'pre-commit-setup',

] }

##########################

# 🔗 Main Package Shortcut

##########################

easydiffraction = 'python -m easydiffraction'

diffraction-lib/pixi.toml at master · easyscience/diffraction-lib · GitHub

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