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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["setuptools >= 61.0"]
build-backend = "setuptools.build_meta"
[project]
name = "bfabric"
description = "Python client for the B-Fabric WSDL API"
version = "1.13.13"
license = { text = "GPL-3.0" }
authors = [
{ name = "Christian Panse", email = "[email protected]" },
{ name = "Leonardo Schwarz", email = "[email protected]" },
{ name = "Aleksejs Fomins" },
{ name = "Marco Schmidt" },
{ name = "Maria d'Errico" },
{ name = "Witold Eryk Wolski" }
]
requires-python = ">=3.9"
dependencies = [
"suds >= 1.1.2",
"PyYAML >= 6.0",
"Flask >= 3.0.3",
"rich >= 13.7.1",
"zeep >= 4.2.1",
"polars-lts-cpu >= 0.20.25; platform_machine == 'x86_64' and platform_system == 'Darwin'",
"polars >= 0.20.25; platform_machine != 'x86_64' or platform_system != 'Darwin'",
"loguru>=0.7",
"pydantic>=2.9.2",
"eval_type_backport; python_version < '3.10'",
"python-dateutil >= 2.9.0",
"cyclopts >= 2.9.9",
#"platformdirs >= 4.3",
]
[project.optional-dependencies]
dev = [
"bfabric[doc,test]",
"black",
"isort",
"ruff",
"licensecheck",
"nox",
"uv",
]
doc = ["mkdocs", "mkdocs-material", "mkdocstrings[python]"]
test = ["pytest", "pytest-mock", "logot"]
typing = ["mypy", "types-requests", "lxml-stubs", "pandas-stubs", "types-python-dateutil"]
[project.urls]
Homepage = "https://github.com/fgcz/bfabricPy"
Repository = "https://github.com/fgcz/bfabricPy"
[project.scripts]
"bfabric_flask.py" = "bfabric_scripts.bfabric_flask:main"
#bfabric_feeder_resource_autoQC="bfabric_scripts.bfabric_feeder_resource_autoQC:main"
"bfabric_list_not_existing_storage_directories.py" = "bfabric_scripts.bfabric_list_not_existing_storage_directories:main"
"bfabric_list_not_available_proteomics_workunits.py" = "bfabric_scripts.bfabric_list_not_available_proteomics_workunits:main"
"bfabric_list_workunit_parameters.py" = "bfabric_scripts.bfabric_list_workunit_parameters:main"
"bfabric_upload_resource.py" = "bfabric_scripts.bfabric_upload_resource:main"
"bfabric_logthis.py" = "bfabric_scripts.bfabric_logthis:main"
"bfabric_setResourceStatus_available.py" = "bfabric_scripts.bfabric_setResourceStatus_available:main"
"bfabric_setExternalJobStatus_done.py" = "bfabric_scripts.bfabric_setExternalJobStatus_done:main"
"bfabric_setWorkunitStatus_available.py" = "bfabric_scripts.bfabric_setWorkunitStatus:main_available"
"bfabric_setWorkunitStatus_processing.py" = "bfabric_scripts.bfabric_setWorkunitStatus:main_processing"
"bfabric_setWorkunitStatus_failed.py" = "bfabric_scripts.bfabric_setWorkunitStatus:main_failed"
"bfabric_delete.py" = "bfabric_scripts.bfabric_delete:main"
"bfabric_read.py" = "bfabric_scripts.bfabric_read:main"
"bfabric_read_samples_of_workunit.py" = "bfabric_scripts.bfabric_read_samples_of_workunit:main"
"bfabric_read_samples_from_dataset.py" = "bfabric_scripts.bfabric_read_samples_from_dataset:main"
"bfabric_save_csv2dataset.py" = "bfabric_scripts.bfabric_save_csv2dataset:main"
"bfabric_save_dataset2csv.py" = "bfabric_scripts.bfabric_save_dataset2csv:main"
"bfabric_save_fasta.py" = "bfabric_scripts.bfabric_save_fasta:main"
"bfabric_save_importresource_sample.py" = "bfabric_scripts.bfabric_save_importresource_sample:main"
"bfabric_save_link_to_workunit.py" = "bfabric_scripts.bfabric_save_link_to_workunit:main"
#bfabric_save_resource="bfabric_scripts.bfabric_save_resource:main"
"bfabric_save_workunit_attribute.py" = "bfabric_scripts.bfabric_save_workunit_attribute:main"
"bfabric_save_workflowstep.py" = "bfabric_scripts.bfabric_save_workflowstep:main"
"bfabric_slurm_queue_status.py" = "bfabric_scripts.bfabric_slurm_queue_status:main"
"bfabric_save_resource_description.py" = "bfabric_scripts.bfabric_save_resource_description:main"
"bfabric-cli" = "bfabric_scripts.cli.__main__:app"
[tool.setuptools.package-data]
"*" = ["py.typed"]
[tool.uv]
reinstall-package = ["bfabric", "bfabric_scripts"]
[tool.black]
line-length = 120
target-version = ["py39"]
[tool.ruff]
line-length = 120
indent-width = 4
target-version = "py39"
[tool.ruff.lint]
select = ["ANN", "BLE", "D103", "E", "EXE", "F", "N", "PLW", "PTH", "SIM", "TCH", "UP", "W191"]
ignore = ["ANN101", "ANN102", "ANN401"]
[tool.ruff.lint.per-file-ignores]
"**/bfabric_scripts/**" = ["ALL"]
"**/wrapper_creator/**" = ["ALL"]
"**/examples/**" = ["ALL"]
"**/tests/**" = ["ALL"]
"noxfile.py" = ["ALL"]
[tool.licensecheck]
using = "PEP631"
[tool.pytest.ini_options]
logot_capturer = "logot.loguru.LoguruCapturer"
[tool.check-tests-structure]
sources_path = "src/bfabric"
tests_path = "tests/unit"
allow_missing_tests = true