pyproject.toml

[project]
name = "nmdc_schema"
dynamic = ["version"]
description = "Schema resources for the National Microbiome Data Collaborative (NMDC)"
readme = "README.md"
license = "MIT"
requires-python = ">=3.10,<4.0"
authors = [
    { name = "Bill Duncan", email = "wdduncan@gmail.com" },
    { name = "Chris Mungall", email = "cjmungall@lbl.gov" },
    { name = "Mark Andrew Miller", email = "MAM@lbl.gov" },
    { name = "Patrick Kalita", email = "pkalita@lbl.gov" },
    { name = "Sujay Patil", email = "spatil@lbl.gov" },
]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "Programming Language :: Python :: 3 :: Only",
]
keywords = ["NMDC", "schema", "metadata", "microbiome"]

# Upper bound policy (PR #2888): 1.0+ packages cap at next major, pre-1.0 at next minor.
dependencies = [
    "click>=8.0.0,<9.0.0",
    "click-log>=0.4.0,<0.5.0",
    "deprecated>=1.0.0,<2.0.0",
    "jsonasobj2>=1.0.0,<2.0.0",
    "jsonschema>=4.0.0,<5.0.0",
    "linkml>=1.9.0,<2.0.0",
    "linkml-runtime>=1.9.0,<2.0.0",
    "python-dotenv>=0.21.0,<2.0.0",
    "pyyaml>=6.0.0,<7.0.0",
    "rdflib>=6.2.0,<8.0.0",
    "requests>=2.0.0,<3.0.0",
    "pymdown-extensions>=10.16.1,<11.0.0",
    "pymongo>=4.7.2,<5.0.0",
]

[project.urls]
Homepage = "https://microbiomedata.github.io/nmdc-schema/"
Documentation = "https://microbiomedata.github.io/nmdc-schema/"
Repository = "https://github.com/microbiomedata/nmdc-schema"

# scripts should have click clis
# click parameters/options should be written out with hyphens
# click parameters/options should use consistent names
# only package-backed, stable CLIs should be listed in project.scripts
# prefer invoking repo-local scripts from Makefiles via `poetry run python src/scripts/<name>.py`
# use underscores to delimit file name
# use hyphens to delimit CLI alias
# scripts/aliases should be illustrated in a Makefile
# Makefile targets should make use of $< etc for input and $@ for output
# input and output files should use hyphens as delimiters in their names
# check usages of these features in other NMDC code before changing
# be intentional about output location: prefer destination by purpose (`docs/`, `local/`, `project/`, package artifacts), not a blanket `assets/` default
# cli entry points should probably all be main or cli unless there's a compelling reason to do otherwise

[project.scripts]
create-migrator = "nmdc_schema.migrators.cli.create_migrator:create_migrator"
run-migrator = "nmdc_schema.migrators.cli.run_migrator:run_migrator"
migration-recursion = "nmdc_schema.migration_recursion:main"
pure-export = "nmdc_schema.dump_single_modality:cli"
# Units analysis uses yq queries in units/Makefile (Python scripts removed)

[dependency-groups]
dev = [
    "autopep8>=2.2.0,<3.0.0",
    "bandit>=1.7.8,<2.0.0",
    "black>=26.3.1,<27.0.0",
    "exhaustion-check>=0.1.1,<0.2.0",  # for exhaustion-check, pretty-sort-yaml (also get-first-of-first)
    "fastjsonschema>=2.20.0,<3.0.0",
    "flake8>=7.0.0,<8.0.0",
    "isort>=5.13.2,<9.0.0",
    "mkdocs>=1.4.2,<2.0.0",
    "mkdocs-material>=9.0.12,<10.0.0",
    "mkdocs-mermaid2-plugin>=0.6.0,<2.0.0",
    "mkdocs-redirects>=1.2.1,<2.0.0",
    "mypy>=1.10.0,<2.0.0",
    "pandas>=2.2.3,<4.0.0",
    "psycopg2-binary>=2.9.10,<3.0.0",
    "pydocstyle>=6.3.0,<7.0.0",
    "pylint>=3.2.2,<5.0.0",
    "pyroma>=4.2,<6.0",
    "pytest>=8.4.2,<10.0.0",
    # We use `refscan` to generate diagrams of inter-collection relationships
    # and diagrams of inter-class relationships.
    # Reference: https://github.com/microbiomedata/refscan
    "refscan>=0.2.3,<0.5.0",
    "ruff>=0.4.7,<1.0.0",
    "schemasheets>=0.1.24,<0.5.0",
    "sheets-and-friends>=0.5.0,<0.6.0",  # for do_shuttle (and possibly more)
    "ucumvert>=0.2.2,<0.4.0",
    "vulture>=2.11,<3.0.0",
]
deps = [
    "deptry>=0.23.0,<1.0.0",
]

[tool.poetry]
version = "0.0.0"
packages = [
    { include = "nmdc_schema" },  # this is the package Poetry would have included by default
    { include = "migrators", from = "nmdc_schema" },
    { include = "adapters", from = "nmdc_schema/migrators" },
]

[tool.poetry-dynamic-versioning]
# We need poetry-dynamic-versioning to update the version in the src schema file,
# then generate project artifacts from that schema with the real version populated,
# and then perform any build or publish actions. Since this requires running
# `poetry dynamic-versioning` manually before `poetry build`, we set enable = false.
enable = false
vcs = "git"
style = "pep440"

[tool.poetry-dynamic-versioning.substitution]
files = [
    "src/schema/nmdc.yaml"
]
patterns = [
    "(^\\s*__version__\\s*(?::.*?)?=\\s*['\\\"])[^'\\\"]*(['\\\"])",
    "(^version:\\s*['\\\"]?)[^'\\\"]*?(['\\\"]?)$"
]

[build-system]
requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
build-backend = "poetry_dynamic_versioning.backend"

[tool.pytest.ini_options]
# Only run tests in tests/ directory to match original unittest discover behavior
# (excludes MongoDB integration tests and other tests outside tests/)
# Module independence is checked by check_schema_self_containment.py instead
testpaths = ["tests"]

[tool.deptry]
extend_exclude = [
    "nmdc_schema/nmdc_pydantic.py"
]
# These are transitive dependencies but we pin them directly
# to ensure users get security fixes from Dependabot alerts
per_rule_ignores = {DEP002 = ["pymdown-extensions"]}

# linkml 1.10.0+ monorepo includes linkml-runtime
[tool.deptry.package_module_name_map]
linkml = ["linkml", "linkml_runtime"]