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pyproject.toml
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pyproject.toml
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[build-system]
build-backend = "setuptools.build_meta"
requires = [
"setuptools>=40.6.0",
"wheel",
]
[project]
name = "cryoemservices"
version = "0.3.4"
description = "Services for CryoEM processing"
readme = "README.md"
keywords = [
"cryoem-services",
]
license = { file = "LICENSE" }
authors = [
{ name = "Diamond Light Source - Data Analysis et al.", email = "[email protected]" },
]
requires-python = ">=3.8"
classifiers = [
"Development Status :: 3 - Alpha",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: BSD License",
"Natural Language :: English",
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
]
dependencies = [
"defusedxml", # CLEM workflow
"gemmi==0.6.5",
"healpy",
"icebreaker-em",
"importlib-metadata",
"ispyb",
"marshmallow-sqlalchemy",
"mrcfile",
"numpy<2",
"pillow",
"plotly",
"pydantic==1.10.7",
"readlif", # CLEM workflow
"starfile",
"stomp-py==8.1.0",
"tifffile", # CLEM workflow
"workflows",
"zocalo==0.32.0",
]
[project.optional-dependencies]
dev = [
"bump2version",
"ipykernel",
"pre-commit",
"pytest",
]
[project.urls]
Bug-Tracker = "https://github.com/DiamondLightSource/cryoem-services/issues"
GitHub = "https://github.com/DiamondLightSource/cryoem-services"
[project.scripts]
"clem.lif_to_stack" = "cryoemservices.cli.lif_to_stack:run"
"clem.tiff_to_stack" = "cryoemservices.cli.tiff_to_stack:run"
"combine_star_files" = "cryoemservices.pipeliner_plugins.combine_star_files:main"
"cryoemservices.reextract" = "cryoemservices.pipeliner_plugins.reextract:run"
"cryoemservices.resubmit_wrapper" = "cryoemservices.cli.resubmit_wrapper:run"
[project.entry-points."ccpem_pipeliner.jobs"]
"combine_star_files_job" = "cryoemservices.pipeliner_plugins.combine_star_job:ProcessStarFiles"
[project.entry-points."cryoemservices.services.cluster.schedulers"]
slurm = "cryoemservices.services.cluster_submission:submit_to_slurm"
[project.entry-points."cryoemservices.services.images.plugins"]
"mrc_central_slice" = "cryoemservices.services.images_plugins:mrc_central_slice"
"mrc_to_apng" = "cryoemservices.services.images_plugins:mrc_to_apng"
"mrc_to_jpeg" = "cryoemservices.services.images_plugins:mrc_to_jpeg"
"picked_particles" = "cryoemservices.services.images_plugins:picked_particles"
[project.entry-points."workflows.services"]
BFactor = "cryoemservices.services.bfactor_setup:BFactor"
CTFFind = "cryoemservices.services.ctffind:CTFFind"
ClusterSubmission = "cryoemservices.services.cluster_submission:ClusterSubmission"
CrYOLO = "cryoemservices.services.cryolo:CrYOLO"
DenoiseSlurm = "cryoemservices.services.denoise_slurm:DenoiseSlurm"
Extract = "cryoemservices.services.extract:Extract"
ExtractClass = "cryoemservices.services.extract_class:ExtractClass"
ISPyB = "cryoemservices.services.ispyb:EMISPyB"
IceBreaker = "cryoemservices.services.icebreaker:IceBreaker"
Images = "cryoemservices.services.images:Images"
MembrainSeg = "cryoemservices.services.membrain_seg:MembrainSeg"
MotionCorr = "cryoemservices.services.motioncorr:MotionCorr"
NodeCreator = "cryoemservices.services.node_creator:NodeCreator"
PostProcess = "cryoemservices.services.postprocess:PostProcess"
SelectClasses = "cryoemservices.services.select_classes:SelectClasses"
SelectParticles = "cryoemservices.services.select_particles:SelectParticles"
TomoAlign = "cryoemservices.services.tomo_align:TomoAlign"
TomoAlignSlurm = "cryoemservices.services.tomo_align_slurm:TomoAlignSlurm"
[project.entry-points."zocalo.services.dispatcher.filters"]
ispyb = "cryoemservices.util.dispatcher_tools:ispyb_filter"
[project.entry-points."zocalo.services.dispatcher.ready_for_processing"]
ispyb = "cryoemservices.util.dispatcher_tools:ready_for_processing"
[project.entry-points."zocalo.wrappers"]
Class2D = "cryoemservices.wrappers.class2d_wrapper:Class2DWrapper"
Class3D = "cryoemservices.wrappers.class3d_wrapper:Class3DWrapper"
Refine3D = "cryoemservices.wrappers.refine3d_wrapper:Refine3DWrapper"
[tool.setuptools]
package-dir = { "" = "src" }
include-package-data = true
zip-safe = false
[tool.setuptools.packages.find]
where = [ "src" ]
[tool.isort]
profile = "black"
[tool.flake8]
select = [
"C4", # flake8-comprehensions, https://github.com/adamchainz/flake8-comprehensions
"E401",
"E711",
"E712",
"E713",
"E714",
"E721",
"E722",
"E901",
"F401",
"F402",
"F403",
"F405",
"F541",
"F631",
"F632",
"F633",
"F811",
"F812",
"F821",
"F822",
"F841",
"F901",
"W191",
"W291",
"W292",
"W293",
"W602",
"W603",
"W604",
"W605",
"W606",
]
ignore = [
"E203",
"E266",
"E501",
"W503",
]
max-line-length = "88"
[tool.pyproject-fmt]
indent = 4
keep_full_version = true
max_supported_python = "3.11"