pyproject.toml

[build-system]
requires = ["flit_core >=3.4,<4"]
build-backend = "flit_core.buildapi"

[project]
name = "aiida-core"
dynamic = ["version"]  # read from aiida/__init__.py
description = "AiiDA is a workflow manager for computational science with a strong focus on provenance, performance and extensibility."
authors = [{name = "The AiiDA team", email = "developers@aiida.net"}]
readme = "README.md"
license = {file = "LICENSE.txt"}
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Framework :: AiiDA",
    "License :: OSI Approved :: MIT License",
    "Operating System :: POSIX :: Linux",
    "Operating System :: MacOS :: MacOS X",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3.8",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Topic :: Scientific/Engineering"
]
keywords = ["aiida", "workflows"]
requires-python = ">=3.8"
dependencies = [
    "alembic~=1.2",
    "archive-path~=0.4.2",
    "aio-pika~=6.6",
    "circus~=0.18.0",
    "click-config-file~=0.6.0",
    "click-spinner~=0.1.8",
    "click~=8.1",
    "disk-objectstore~=0.6.0",
    "graphviz~=0.13",
    "ipython~=7.20",
    "jinja2~=3.0",
    "jsonschema~=3.0",
    "kiwipy[rmq]~=0.7.7",
    "importlib-metadata~=4.3",
    "importlib-resources~=5.0;python_version<'3.9'",
    "numpy~=1.19",
    "paramiko~=2.7,>=2.7.2",
    "plumpy~=0.21.2",
    "pgsu~=0.2.1",
    "psutil~=5.6",
    "psycopg2-binary~=2.8",
    "pytz~=2021.1",
    "pyyaml~=6.0",
    "requests~=2.0",
    "sqlalchemy~=1.4.22",
    "tabulate~=0.8.5",
    "tqdm~=4.45",
    "upf_to_json~=0.9.2",
    "werkzeug<2.2",
    "wrapt~=1.11"
]

[project.urls]
Home = "http://www.aiida.net/"
Documentation = "https://aiida.readthedocs.io"
Source = "https://github.com/aiidateam/aiida-core"

[project.optional-dependencies]
ssh_kerberos = [
    "gssapi~=1.6",
    "pyasn1~=0.4.8"
]
rest = [
    "flask-cors~=3.0",
    "flask-restful~=0.3.7",
    "flask~=2.0",
    "pyparsing~=2.4",
    "python-memcached~=1.59",
    "seekpath~=1.9,>=1.9.3"
]
docs = [
    "pydata-sphinx-theme~=0.8.0",
    "sphinx~=4.1",
    "sphinxcontrib-details-directive~=0.1.0",
    "sphinx-copybutton~=0.5.0",
    "sphinx-design~=0.0.13",
    "sphinx-notfound-page~=0.5",
    "sphinxext-rediraffe~=0.2.4",
    "sphinx-sqlalchemy~=0.1.1",
    "sphinx-intl[transifex]~=2.0.1",
    "myst-nb~=0.17.0",
]
atomic_tools = [
    "PyCifRW~=4.4",
    "ase~=3.18",
    "matplotlib~=3.3,>=3.3.4",
    "pymatgen>=2022.1.20",
    "pymysql~=0.9.3",
    "seekpath~=1.9,>=1.9.3",
    "spglib>=1.14,<3.0"
]
notebook = [
    "jupyter-client~=6.1,<6.1.13",
    "jupyter~=1.0",
    "notebook~=6.1,>=6.1.5"
]
pre-commit = [
    "mypy==0.991",
    "packaging==20.3",
    "pre-commit~=2.2",
    "pylint~=2.11.1",
    "pylint-aiida~=0.1.1",
    "sqlalchemy[mypy]~=1.4.29",
    "tomli",
    "types-PyYAML",
]
tests = [
    "aiida-export-migration-tests==0.9.0",
    "pg8000~=1.13",
    "pgtest~=1.3,>=1.3.1",
    "pytest~=7.0",
    "pytest-asyncio~=0.12,<0.17",
    "pytest-timeout~=1.3",
    "pytest-cov~=2.7,<2.11",
    "pytest-rerunfailures~=9.1,>=9.1.1",
    "pytest-benchmark~=4.0",
    "pytest-regressions~=2.2",
    "pympler~=0.9",
    "coverage~=6.0",
    "sqlalchemy-utils~=0.37.2",
    "sphinx~=4.0",
    "docutils==0.16",
]
bpython = [
    "bpython~=0.18.0"
]

[project.scripts]
verdi = "aiida.cmdline.commands.cmd_verdi:verdi"
runaiida = "aiida.cmdline.commands.cmd_run:run"

[project.entry-points."aiida.calculations"]
"core.transfer" = "aiida.calculations.transfer:TransferCalculation"
"core.arithmetic.add" = "aiida.calculations.arithmetic.add:ArithmeticAddCalculation"
"core.templatereplacer" = "aiida.calculations.templatereplacer:TemplatereplacerCalculation"

[project.entry-points."aiida.calculations.importers"]
"core.arithmetic.add" = "aiida.calculations.importers.arithmetic.add:ArithmeticAddCalculationImporter"

[project.entry-points."aiida.calculations.monitors"]
"core.always_kill" = "aiida.calculations.monitors.base:always_kill"

[project.entry-points."aiida.cmdline.computer.configure"]
"core.local" = "aiida.transports.plugins.local:CONFIGURE_LOCAL_CMD"
"core.ssh" = "aiida.transports.plugins.ssh:CONFIGURE_SSH_CMD"

[project.entry-points."aiida.cmdline.data"]
"core.array" = "aiida.cmdline.commands.cmd_data.cmd_array:array"
"core.bands" = "aiida.cmdline.commands.cmd_data.cmd_bands:bands"
"core.cif" = "aiida.cmdline.commands.cmd_data.cmd_cif:cif"
"core.dict" = "aiida.cmdline.commands.cmd_data.cmd_dict:dictionary"
"core.remote" = "aiida.cmdline.commands.cmd_data.cmd_remote:remote"
"core.singlefile" = "aiida.cmdline.commands.cmd_data.cmd_singlefile:singlefile"
"core.structure" = "aiida.cmdline.commands.cmd_data.cmd_structure:structure"
"core.trajectory" = "aiida.cmdline.commands.cmd_data.cmd_trajectory:trajectory"
"core.upf" = "aiida.cmdline.commands.cmd_data.cmd_upf:upf"

[project.entry-points."aiida.cmdline.data.structure.import"]

[project.entry-points."aiida.data"]
"core.array" = "aiida.orm.nodes.data.array.array:ArrayData"
"core.array.bands" = "aiida.orm.nodes.data.array.bands:BandsData"
"core.array.kpoints" = "aiida.orm.nodes.data.array.kpoints:KpointsData"
"core.array.projection" = "aiida.orm.nodes.data.array.projection:ProjectionData"
"core.array.trajectory" = "aiida.orm.nodes.data.array.trajectory:TrajectoryData"
"core.array.xy" = "aiida.orm.nodes.data.array.xy:XyData"
"core.base" = "aiida.orm.nodes.data:BaseType"
"core.bool" = "aiida.orm.nodes.data.bool:Bool"
"core.cif" = "aiida.orm.nodes.data.cif:CifData"
"core.code" = "aiida.orm.nodes.data.code.legacy:Code"
"core.code.portable" = "aiida.orm.nodes.data.code.portable:PortableCode"
"core.code.installed" = "aiida.orm.nodes.data.code.installed:InstalledCode"
"core.code.containerized" = "aiida.orm.nodes.data.code.containerized:ContainerizedCode"
"core.dict" = "aiida.orm.nodes.data.dict:Dict"
"core.enum" = "aiida.orm.nodes.data.enum:EnumData"
"core.float" = "aiida.orm.nodes.data.float:Float"
"core.folder" = "aiida.orm.nodes.data.folder:FolderData"
"core.int" = "aiida.orm.nodes.data.int:Int"
"core.list" = "aiida.orm.nodes.data.list:List"
"core.jsonable" = "aiida.orm.nodes.data.jsonable:JsonableData"
"core.numeric" = "aiida.orm.nodes.data.numeric:NumericType"
"core.orbital" = "aiida.orm.nodes.data.orbital:OrbitalData"
"core.remote" = "aiida.orm.nodes.data.remote.base:RemoteData"
"core.remote.stash" = "aiida.orm.nodes.data.remote.stash.base:RemoteStashData"
"core.remote.stash.folder" = "aiida.orm.nodes.data.remote.stash.folder:RemoteStashFolderData"
"core.singlefile" = "aiida.orm.nodes.data.singlefile:SinglefileData"
"core.str" = "aiida.orm.nodes.data.str:Str"
"core.structure" = "aiida.orm.nodes.data.structure:StructureData"
"core.upf" = "aiida.orm.nodes.data.upf:UpfData"

[project.entry-points."aiida.groups"]
"core" = "aiida.orm.groups:Group"
"core.auto" = "aiida.orm.groups:AutoGroup"
"core.import" = "aiida.orm.groups:ImportGroup"
"core.upf" = "aiida.orm.groups:UpfFamily"

[project.entry-points."aiida.node"]
"data" = "aiida.orm.nodes.data.data:Data"
"process" = "aiida.orm.nodes.process.process:ProcessNode"
"process.calculation" = "aiida.orm.nodes.process.calculation.calculation:CalculationNode"
"process.calculation.calcfunction" = "aiida.orm.nodes.process.calculation.calcfunction:CalcFunctionNode"
"process.calculation.calcjob" = "aiida.orm.nodes.process.calculation.calcjob:CalcJobNode"
"process.workflow" = "aiida.orm.nodes.process.workflow.workflow:WorkflowNode"
"process.workflow.workchain" = "aiida.orm.nodes.process.workflow.workchain:WorkChainNode"
"process.workflow.workfunction" = "aiida.orm.nodes.process.workflow.workfunction:WorkFunctionNode"

[project.entry-points."aiida.parsers"]
"core.arithmetic.add" = "aiida.parsers.plugins.arithmetic.add:ArithmeticAddParser"
"core.templatereplacer" = "aiida.parsers.plugins.templatereplacer.parser:TemplatereplacerParser"

[project.entry-points."aiida.schedulers"]
"core.direct" = "aiida.schedulers.plugins.direct:DirectScheduler"
"core.lsf" = "aiida.schedulers.plugins.lsf:LsfScheduler"
"core.pbspro" = "aiida.schedulers.plugins.pbspro:PbsproScheduler"
"core.sge" = "aiida.schedulers.plugins.sge:SgeScheduler"
"core.slurm" = "aiida.schedulers.plugins.slurm:SlurmScheduler"
"core.torque" = "aiida.schedulers.plugins.torque:TorqueScheduler"

[project.entry-points."aiida.storage"]
"core.psql_dos" = "aiida.storage.psql_dos.backend:PsqlDosBackend"
"core.sqlite_temp" = "aiida.storage.sqlite_temp.backend:SqliteTempBackend"
"core.sqlite_zip" = "aiida.storage.sqlite_zip.backend:SqliteZipBackend"

[project.entry-points."aiida.transports"]
"core.local" = "aiida.transports.plugins.local:LocalTransport"
"core.ssh" = "aiida.transports.plugins.ssh:SshTransport"

[project.entry-points."aiida.tools.calculations"]

[project.entry-points."aiida.tools.dbexporters"]

[project.entry-points."aiida.tools.dbimporters"]
"core.cod" = "aiida.tools.dbimporters.plugins.cod:CodDbImporter"
"core.icsd" = "aiida.tools.dbimporters.plugins.icsd:IcsdDbImporter"
"core.materialsproject" = "aiida.tools.dbimporters.plugins.materialsproject:MaterialsProjectImporter"
"core.mpds" = "aiida.tools.dbimporters.plugins.mpds:MpdsDbImporter"
"core.mpod" = "aiida.tools.dbimporters.plugins.mpod:MpodDbImporter"
"core.nninc" = "aiida.tools.dbimporters.plugins.nninc:NnincDbImporter"
"core.oqmd" = "aiida.tools.dbimporters.plugins.oqmd:OqmdDbImporter"
"core.pcod" = "aiida.tools.dbimporters.plugins.pcod:PcodDbImporter"
"core.tcod" = "aiida.tools.dbimporters.plugins.tcod:TcodDbImporter"

[project.entry-points."aiida.tools.data.orbitals"]
"core.orbital" = "aiida.tools.data.orbital.orbital:Orbital"
"core.realhydrogen" = "aiida.tools.data.orbital.realhydrogen:RealhydrogenOrbital"

[project.entry-points."aiida.workflows"]
"core.arithmetic.multiply_add" = "aiida.workflows.arithmetic.multiply_add:MultiplyAddWorkChain"
"core.arithmetic.add_multiply" = "aiida.workflows.arithmetic.add_multiply:add_multiply"

[tool.flit.module]
name = "aiida"

[tool.flit.sdist]
exclude = [
    "docs/",
    "tests/",
]

[tool.pylint.master]
load-plugins = ["pylint_aiida"]

[tool.pylint.format]
max-line-length = 120

[tool.pylint.messages_control]
disable = [
    "bad-continuation",
    "consider-using-f-string",
    "cyclic-import",
    "duplicate-code",
    "import-outside-toplevel",
    "inconsistent-return-statements",
    "locally-disabled",
    "logging-fstring-interpolation",
    "no-else-raise",
    "raise-missing-from",
    "too-few-public-methods",
    "too-many-ancestors",
    "too-many-arguments",
    "too-many-instance-attributes",
    # this can be removed when https://github.com/PyCQA/astroid/issues/1015 is fixed
    "not-context-manager",
]

[tool.pylint.basic]
good-names = [
    "_",
    "x",
    "y",
    "z",
    "i",
    "j",
    "k",
    "dt",
    "pk",
    "fg",
    "tz",
    "nl",
    "TemplatereplacerCalculation",
    "ArithmeticAddCalculation",
    "MultiplyAddWorkChain"
]
no-docstring-rgx = "^_,setUp,tearDown"
docstring-min-length = 5

[tool.pylint.design]
max-locals = 20

[tool.pytest.ini_options]
minversion = "7.0"
addopts = "--benchmark-skip --durations=50 --cov-report xml --cov-append "
testpaths = [
    "tests",
]
filterwarnings = [
    "ignore::DeprecationWarning:babel:",
    "ignore::DeprecationWarning:frozendict:",
    "ignore::DeprecationWarning:sqlalchemy:",
    "ignore::DeprecationWarning:yaml:",
    "ignore::DeprecationWarning:pymatgen:",
    "ignore::DeprecationWarning:jsonbackend:",
    "ignore::DeprecationWarning:pkg_resources:",
    "ignore::pytest.PytestCollectionWarning",
    "default::ResourceWarning",
]
markers = [
    "nightly: long running tests that should rarely be affected and so only run nightly",
    "requires_rmq: requires a connection (on port 5672) to RabbitMQ",
    "sphinx: set parameters for the sphinx `app` fixture"
]

[tool.isort]
line_length = 120
force_sort_within_sections = true
# this configuration is compatible with yapf
multi_line_output = 3
include_trailing_comma = true

[tool.yapf]
based_on_style = "google"
column_limit = 120
dedent_closing_brackets = true
coalesce_brackets = true
align_closing_bracket_with_visual_indent = true
split_arguments_when_comma_terminated = true
indent_dictionary_value = false

[tool.mypy]
show_error_codes = true
scripts_are_modules = true
show_traceback = true
plugins = ["sqlalchemy.ext.mypy.plugin"]

# strictness
strict = true
# these options reduce the strictness and should eventually be removed
disallow_untyped_defs = false
disallow_untyped_calls = false
disallow_incomplete_defs = false
warn_return_any = false
disallow_any_generics = false
disallow_subclassing_any = false

[[tool.mypy.overrides]]
module = 'aiida'
implicit_reexport = true

[[tool.mypy.overrides]]
module = 'aiida.cmdline.commands.*'
disallow_untyped_decorators = false

[[tool.mypy.overrides]]
module = 'tests.*'
check_untyped_defs = false

[[tool.mypy.overrides]]
module = [
    'ase.*',
    'bpython.*',
    'bs4.*',
    'CifFile.*',
    'circus.*',
    'click_config_file.*',
    'click_spinner.*',
    'docutils.*',
    'flask_cors.*',
    'flask_restful.*',
    'graphviz.*',
    'importlib._bootstrap.*',
    'IPython.*',
    'jsonschema.*',
    'kiwipy.*',
    'matplotlib.*',
    'mayavi.*',
    'MySQLdb.*',
    'numpy.*',
    'paramiko.*',
    'pgsu.*',
    'pgtest.*',
    'phonopy.*',
    'psutil.*',
    'psycopg2.*',
    'pymatgen.*',
    'pymysql.*',
    'pyparsing.*',
    'pympler.*',
    'pytz.*',
    'requests.*',
    'ruamel.*',
    'scipy.*',
    'seekpath.*',
    'spglib.*',
    'sphinxcontrib.details.*',
    'sqlalchemy_utils.*',
    'tabulate.*',
    'tqdm.*',
    'wrapt.*',
    'upf_to_json.*',
]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = 'plumpy'
ignore_errors = true

[tool.tox]
legacy_tox_ini = """
[tox]
envlist = py38

[testenv]
usedevelop=True
deps =
    py38: -rrequirements/requirements-py-3.8.txt
    py39: -rrequirements/requirements-py-3.9.txt
    py310: -rrequirements/requirements-py-3.10.txt

[testenv:py{38,39,310}]
passenv =
    PYTHONASYNCIODEBUG
setenv =
    AIIDA_WARN_v3 = 1
    SQLALCHEMY_WARN_20 = 1
commands = pytest {posargs}

[testenv:py{38,39,310}-verdi]
passenv =
    AIIDA_TEST_BACKEND
setenv =
    AIIDA_PATH = {toxinidir}/.tox/.aiida
commands = verdi {posargs}

[testenv:py{38,39,310}-docs-{clean,update}]
description =
    clean: Build the documentation (remove any existing build)
    update: Build the documentation (modify any existing build)
passenv = RUN_APIDOC
setenv =
    update: RUN_APIDOC = False
changedir = docs
whitelist_externals = make
commands =
    clean: make clean
    make debug

[testenv:py{38,39,310}-docs-live]
# tip: remove apidocs before using this feature (`cd docs; make clean`)
description = Build the documentation and launch browser (with live updates)
deps =
    py38: -rrequirements/requirements-py-3.8.txt
    py39: -rrequirements/requirements-py-3.9.txt
    py310: -rrequirements/requirements-py-3.10.txt
    sphinx-autobuild
setenv =
    RUN_APIDOC = False
commands =
    sphinx-autobuild \
        --re-ignore build/.* \
        --port 0 --open-browser \
        -n -b {posargs:html} docs/source/ docs/build/{posargs:html}

[testenv:py{38,39,310}-pre-commit]
description = Run the pre-commit checks
extras = pre-commit
commands = pre-commit run {posargs}

[testenv:molecule]
description = Run the molecule containerised tests
skip_install = true
parallel_show_output = true
deps =
    ansible~=2.10.0
    docker~=4.2
    molecule[docker]~=3.1.0
setenv =
    MOLECULE_GLOB = .molecule/*/config_local.yml
passenv =
    AIIDA_TEST_BACKEND
    AIIDA_TEST_WORKERS
commands = molecule {posargs:test}
"""