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[build-system]

requires = ["hatchling", "hatch-vcs"]

build-backend = "hatchling.build"

[project]

name = "datajoint"

dynamic = ["version"]

dependencies = [

"numpy",

"pymysql>=0.7.2",

"deepdiff",

"pyparsing",

"pandas",

"tqdm",

"networkx",

"pydot",

"fsspec>=2023.1.0",

"pydantic-settings>=2.0.0",

"packaging",

]

requires-python = ">=3.10,<3.15"

authors = [

{name = "Dimitri Yatsenko", email = "[email protected]"},

{name = "Thinh Nguyen", email = "[email protected]"},

{name = "Raphael Guzman"},

{name = "Edgar Walker"},

{name = "DataJoint Contributors", email = "[email protected]"},

]

maintainers = [

{name = "Dimitri Yatsenko", email = "[email protected]"},

{name = "DataJoint Contributors", email = "[email protected]"},

]

# manually sync here: https://docs.datajoint.com/core/datajoint-python/latest/#welcome-to-datajoint-for-python

description = "The DataJoint Library for Python is a framework for scientific workflow management based on relational principles. It is built on the foundation of the relational data model and prescribes a consistent method for organizing, populating, computing, and querying data."

readme = "README.md"

license = {file = "LICENSE"}

keywords = [

"datajoint",

"data-pipelines",

"workflow-management",

"data-engineering",

"scientific-computing",

"neuroscience",

"research-software",

"data-integrity",

"reproducibility",

"declarative",

"etl",

"object-storage",

"schema-management",

"data-lineage",

"relational-model",

"mysql",

"postgresql",

]

# https://pypi.org/classifiers/

classifiers = [

"Programming Language :: Python",

"Programming Language :: Python :: 3.10",

"Programming Language :: Python :: 3.11",

"Programming Language :: Python :: 3.12",

"Programming Language :: Python :: 3.13",

"Programming Language :: Python :: 3.14",

"Development Status :: 5 - Production/Stable",

"Intended Audience :: Science/Research",

"Intended Audience :: Healthcare Industry",

"License :: OSI Approved :: Apache Software License",

"Topic :: Software Development :: Libraries :: Python Modules",

"Topic :: Scientific/Engineering",

"Topic :: Scientific/Engineering :: Bio-Informatics",

"Topic :: Scientific/Engineering :: Artificial Intelligence",

]

[project.urls]

Homepage = "https://docs.datajoint.com/"

Documentation = "https://docs.datajoint.com/"

Repository = "https://github.com/datajoint/datajoint-python"

"Bug Tracker" = "https://github.com/datajoint/datajoint-python/issues"

"Release Notes" = "https://github.com/datajoint/datajoint-python/releases"

[project.scripts]

dj = "datajoint.cli:cli"

datajoint = "datajoint.cli:cli"

[dependency-groups]

test = [

"pytest",

"pytest-cov",

"requests",

"faker",

"matplotlib",

"ipython",

"graphviz",

"testcontainers[mysql,minio,postgres]>=4.0",

"polars>=0.20.0",

"pyarrow>=14.0.0",

]

[project.optional-dependencies]

s3 = ["s3fs>=2023.1.0"]

gcs = ["gcsfs>=2023.1.0"]

azure = ["adlfs>=2023.1.0"]

postgres = ["psycopg2-binary>=2.9.0"]

polars = ["polars>=0.20.0"]

arrow = ["pyarrow>=14.0.0"]

viz = ["matplotlib", "ipython"]

test = [

"pytest",

"pytest-cov",

"requests",

"faker",

"matplotlib",

"ipython",

"s3fs>=2023.1.0",

"testcontainers[mysql,minio,postgres]>=4.0",

"psycopg2-binary>=2.9.0",

"polars>=0.20.0",

"pyarrow>=14.0.0",

]

dev = [

"pre-commit",

"ruff",

"codespell",

# including test

"pytest",

"pytest-cov",

"polars>=0.20.0",

"pyarrow>=14.0.0",

]

[tool.ruff]

# Equivalent to flake8 configuration

line-length = 127

target-version = "py310"

[tool.ruff.lint]

# Enable specific rule sets equivalent to flake8 configuration

select = [

"E", # pycodestyle errors

"W", # pycodestyle warnings

"F", # pyflakes

"C90", # mccabe complexity

]

# Ignore specific rules (equivalent to flake8 --ignore)

ignore = [

"E203", # whitespace before ':'

"E722", # bare except

]

# Per-file ignores (equivalent to flake8 --per-file-ignores)

[tool.ruff.lint.per-file-ignores]

"datajoint/diagram.py" = ["C901"] # function too complex

"tests/integration/test_blob_matlab.py" = ["E501"] # SQL hex strings cannot be broken across lines

[tool.ruff.lint.mccabe]

# Maximum complexity (equivalent to flake8 --max-complexity)

max-complexity = 62

[tool.ruff.format]

# Use black-compatible formatting

quote-style = "double"

indent-style = "space"

line-ending = "auto"

[tool.mypy]

python_version = "3.10"

ignore_missing_imports = true

# Start with lenient settings, gradually enable stricter checks

warn_return_any = false

warn_unused_ignores = false

disallow_untyped_defs = false

disallow_incomplete_defs = false

check_untyped_defs = true

# Modules with complete type coverage - strict checking enabled

[[tool.mypy.overrides]]

module = [

"datajoint.hash_registry",

"datajoint.errors",

"datajoint.hash",

]

disallow_untyped_defs = true

disallow_incomplete_defs = true

warn_return_any = true

# Modules excluded from type checking until fully typed

[[tool.mypy.overrides]]

module = [

"datajoint.admin",

"datajoint.autopopulate",

"datajoint.blob",

"datajoint.builtin_codecs",

"datajoint.cli",

"datajoint.codecs",

"datajoint.condition",

"datajoint.connection",

"datajoint.declare",

"datajoint.dependencies",

"datajoint.diagram",

"datajoint.expression",

"datajoint.gc",

"datajoint.heading",

"datajoint.jobs",

"datajoint.lineage",

"datajoint.logging",

"datajoint.migrate",

"datajoint.objectref",

"datajoint.preview",

"datajoint.schemas",

"datajoint.settings",

"datajoint.staged_insert",

"datajoint.storage",

"datajoint.table",

"datajoint.user_tables",

"datajoint.utils",

]

ignore_errors = true

[tool.hatch.version]

# Version is derived from the git tag at build time (hatch-vcs), so the tag is

# the single source of truth: `pip install [email protected]` reports X.Y.Z. The

# resolved version is written to the generated (git-ignored) src/datajoint/_version.py

# by the build hook below; src/datajoint/version.py reads it back at runtime.

source = "vcs"

[tool.hatch.build.hooks.vcs]

version-file = "src/datajoint/_version.py"

[tool.hatch.build.targets.wheel]

packages = ["src/datajoint"]

[tool.codespell]

skip = ".git,*.pdf,*.svg,*.csv,*.ipynb,*.drawio"

# Rever -- nobody knows

# numer -- numerator variable

# astroid -- Python library name (not "asteroid")

ignore-words-list = "rever,numer,astroid"

[tool.pytest.ini_options]

markers = [

"requires_mysql: marks tests as requiring MySQL database (deselect with '-m \"not requires_mysql\"')",

"requires_minio: marks tests as requiring MinIO object storage (deselect with '-m \"not requires_minio\"')",

"mysql: marks tests that run on MySQL backend (select with '-m mysql')",

"postgresql: marks tests that run on PostgreSQL backend (select with '-m postgresql')",

"backend_agnostic: marks tests that should pass on all backends (auto-marked for parameterized tests)",

]

[tool.pixi.workspace]

channels = ["conda-forge"]

platforms = ["linux-64", "osx-arm64", "linux-aarch64"]

[tool.pixi.pypi-dependencies]

datajoint = { path = ".", editable = true }

[tool.pixi.feature.test.pypi-dependencies]

datajoint = { path = ".", editable = true, extras = ["test"] }

[tool.pixi.feature.dev.pypi-dependencies]

datajoint = { path = ".", editable = true, extras = ["dev", "test"] }

# Pin the interpreter for the min/max supported versions so CI can exercise

# both ends of the requires-python range (see .github/workflows/test.yaml).

[tool.pixi.feature.py310.dependencies]

python = "3.10.*"

[tool.pixi.feature.py314.dependencies]

python = "3.14.*"

[tool.pixi.environments]

default = { solve-group = "default" }

dev = { features = ["dev"], solve-group = "default" }

test = { features = ["test"], solve-group = "default" }

# Version-pinned test environments (each solves independently — a solve-group

# cannot span different Python versions).

test-py310 = { features = ["test", "py310"] }

test-py314 = { features = ["test", "py314"] }

[tool.pixi.tasks]

# Tests use testcontainers - no manual setup required

test = "pytest tests/"

test-cov = "pytest --cov-report term-missing --cov=datajoint tests/"

# Optional: use external containers (docker-compose) instead of testcontainers

services-up = "docker compose up -d db minio"

services-down = "docker compose down"

test-external = { cmd = "DJ_USE_EXTERNAL_CONTAINERS=1 pytest tests/", depends-on = ["services-up"] }

[tool.pixi.dependencies]

python = ">=3.10,<3.15"

graphviz = ">=13.1.2,<14"

[tool.pixi.activation]

scripts=["activate.sh"]