pyproject.toml

[build-system]
requires = ["setuptools>=67.4.0", "gitpython>=3.1.0"]
build-backend = "setuptools.build_meta"

[tool.setuptools.packages.find]
where = ["."] # list of folders that the contains the packages. We need it to be at root due to flat-layout
include = ["biothings*"]  # package names should match these glob patterns
exclude = ["tests*"]  # exclude packages matching these glob patterns
namespaces = false  # to disable scanning PEP 420 namespaces (true by default)

[tool.setuptools.package-data]
"*" = ["*.md", "*.tpl", "*.json", "*.html", "config.py.sample", ".git_info"]

[tool.setuptools.dynamic]
version = {attr = "biothings.__version__"}

[project]
name="biothings"
dynamic = ["version"]    # version is dynamically generated from setup.py
authors = [
    {name = "The BioThings Team", email="dev@biothings.io"},
]
requires-python = ">=3.8"
description = "a toolkit for building high-performance data & knowledge APIs in biology"
readme = "README.md"
# license = "Apache-2.0"               # when we drop Python 3.8 support, we can use this new format
license = {text = "Apache-2.0"}        # this is an old format, but works for Python 3.8+
keywords = [
    "biology",
    "medicine",
    "annotation",
    "data",
    "knowledge",
    "web",
    "service",
    "api",
]
classifiers = [
    "Programming Language :: Python",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.8",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Development Status :: 5 - Production/Stable",
    "Operating System :: OS Independent",
    "Operating System :: POSIX",
    "Operating System :: MacOS :: MacOS X",
    "Operating System :: Microsoft :: Windows",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "Topic :: Utilities",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Software Development :: Libraries :: Python Modules",
    "Topic :: Software Development :: Libraries :: Application Frameworks",
]
dependencies = [
    "requests>=2.21.0",
    'tornado==6.1.0; python_version < "3.7.0"',
    'tornado==6.2.0; python_version == "3.7.0"',
    'tornado==6.4.2; python_version >= "3.8.0"',
    "gitpython>=3.1.0",
    "elasticsearch[async]>=7, <8; python_version < '3.7.0'",
    "elasticsearch-dsl>=7, <8; python_version < '3.7.0'",
    "elasticsearch[async]>=8, <9; python_version >= '3.7.0'",
    "elasticsearch-dsl>=8, <9; python_version >= '3.7.0'",
    'singledispatchmethod; python_version < "3.8.0"',
    'dataclasses; python_version < "3.7.0"',
    "jmespath>=0.7.1,<2.0.0",  # support jmespath query parameter
    "PyYAML>=5.1",
    "orjson>=3.6.1",  # a faster json lib supports inf/nan and datetime, v3.6.1 is the last version supports Python 3.6
]

[project.optional-dependencies]
# extra requirements for biothings.web
web_extra = [
    "msgpack>=0.6.1",  # support format=msgpack
    "sentry-sdk>=1.5.3",  # new sentry package
]
# extra requirements for biothings.web to use AWS OpenSearch
opensearch = [
    "boto3",  # for AWS OpenSearch connection
    "requests-aws4auth",  # for AWS OpenSearch connection
]
# minimal requirements for running biothings.hub, e.g. in CLI mode
hubcore = [
    "pymongo>=4.1.0,<5.0",  # support MongoDB 5.0 since v3.12.0
]
# extra requirements to run a full biothings.hub
hub = [
    "pymongo>=4.1.0,<5.0",
    "beautifulsoup4",  # used in dumper.GoogleDriveDumper
    "aiocron==1.8",  # setup scheduled jobs
    # "aiohttp==3.8.4",  # elasticsearch requires aiohttp>=3,<4
    "asyncssh>=2.19.0",  # needs libffi-dev installed (apt-get)
    # "pymongo>=4.1.0,<5.0",  # support MongoDB 5.0 since v3.12.0
    "psutil",
    "jsonpointer",  # for utils.jsonpatch
    "IPython",  # for interactive hub console
    "multiprocessing_on_dill",  # can replace pickler in concurrent.futures
    "dill",  # a pickle alternative with extra object type support
    "prettytable",  # diff report renderer
    "sockjs-tornado==1.0.7",  # websocket server for HubServer
    "jsonschema>=2.6.0",
    "pip",  # auto-install requirements from plugins
    # 'pandas==1.0.1',    # json with inf/nan and more to come (replaced by orjson below now)
    # 'orjson>=3.5.2',    # this is a faster json lib support inf/nan and datetime
    # "yapf",  # code reformatter, better results than autopep8
    "black",  # code formatter
    "boto3",  # for aws S3 access
    "requests-aws4auth",  # aws s3 auth requests for autohub
    'networkx>=2.1,<3.0; python_version >= "3.7.0"',  # datatransform
    'networkx>=2.1,<2.6; python_version < "3.7.0"',  # datatransform
    "biothings_client>=0.2.6",  # datatransform (api client)
    "cryptography>=38.0.3",  # for generate ssh keys, ssl cert.
    "pytest",  # to run hub api pytests
    "pydantic>=2.0",  # for source data validation
]
# minimal requirements for to run biothings CLI
cli = [
    "pymongo>=4.1.0,<5.0",  # support MongoDB 5.0 since v3.12.0
    "psutil",
    "jsonschema>=2.6.0",
    "typer>=0.12.1",  # required for CLI, also installs rich package
]
# if DockerContainerDumper is used, requires this Docker SDK for Python
docker = [
    "docker>=6.0.1",
]
# if DockerContainerDumper is used to connect to docker using ssh:// protocol, needs to install paramiko package
docker_ssh = [
    "docker[ssh]>=6.0.1",
]
# extra requirements to develop biothings
dev = [
    "aioresponses",
    "mongomock",
    "pytest-asyncio",
    "pytest-mock",
]
# extra requirements for building docs
docs = ["sphinx>=5.3.0", "sphinx_rtd_theme>=2.0.0", "sphinx_reredirects>=0.1.3"]


[project.urls]
homepage = "https://biothings.io"
source = "https://github.com/biothings/biothings.api"
documentation = "https://docs.biothings.io"
changelog = "https://github.com/biothings/biothings.api/blob/master/CHANGES.txt"
issues = "https://github.com/biothings/biothings.api/issues"

[project.scripts]
biothings-cli = "biothings.cli:main"

[tool.black]
line-length = 120
target-version = ['py38', 'py39', 'py310', 'py311', 'py312', 'py313']
extend-exclude = '''
# A regex preceded with ^/ will apply only to files and directories
# in the root of the project.
(
    # 3rd party code, don't touch
    "biothings/utils/jsondiff.py",
    "biothings/utils/jsonpatch.py",
    # deprecated code, don't touch
    "biothings/utils/parallel.py",
    "biothings/utils/parallel_mp.py",
    "biothings/utils/shelve.py",
    "biothings/hub/dataload/sync.py",
    "biothings/hub/dataload/validator.py",
)
'''

[tool.isort]
profile = "black"
combine_as_imports = true
line_length = 120
src_paths = ["."]

[tool.pytest.ini_options]
minversion = "6.2.5"

# Options
addopts = [
    "-rA",
    "-vv",
    "--doctest-modules",
    "--setup-show",
    "--capture=tee-sys",
    "--tb=line",
    "--durations=0",
    "--showlocals",
    "--strict-markers",
    "--color=yes",
    "--code-highlight=yes",
]

# Path
norecursedirs = [
    ".svn",
    ".git",
    "_build",
    "tmp*",
    "lib",
    "lib64",
    "tools",
    "tests/hub/dataplugin/data",
    "tests/hub/config/data",
    "tests/web/handlers/data",
]
testpaths = [
    "tests"
]

# Environment
env = []

markers = [
    "ReleaseNoteSrcBuildReaderAdapter",
    "ReleaseNoteSrcBuildReader",
    "ReleaseNoteSource",
    "ReleaseNoteTxt",
]

# Logging
log_cli = true
log_cli_level = "INFO"
log_cli_format = "%(asctime)s [%(levelname)] %(message)s"
log_cli_date_format = "%Y-%m-%d %H:%M:%S"