-
Notifications
You must be signed in to change notification settings - Fork 0
/
pyproject.toml
169 lines (164 loc) · 5.58 KB
/
pyproject.toml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
[build-system]
build-backend = "setuptools.build_meta"
requires = [
"setuptools>=40.6.0",
"wheel",
]
[project]
name = "cryoemservices"
version = "0.5.4"
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>=10.2.3",
"marshmallow-sqlalchemy",
"mrcfile",
"numpy<2",
"pillow",
"plotly",
"pydantic>=2",
"readlif", # CLEM workflow
"starfile",
"stomp-py==8.1.0",
"tifffile", # CLEM workflow
"workflows",
"zocalo>=1",
]
[project.optional-dependencies]
dev = [
"bump-my-version",
"ipykernel",
"pre-commit",
"pytest",
"pytest-datafiles",
"pytest-mock",
]
[project.urls]
Bug-Tracker = "https://github.com/DiamondLightSource/cryoem-services/issues"
GitHub = "https://github.com/DiamondLightSource/cryoem-services"
[project.scripts]
"clem.align_and_merge" = "cryoemservices.cli.clem_align_and_merge:run"
"clem.lif_to_stack" = "cryoemservices.cli.clem_lif_to_stack:run"
"clem.tiff_to_stack" = "cryoemservices.cli.clem_tiff_to_stack:run"
"combine_star_files" = "cryoemservices.pipeliner_plugins.combine_star_files:main"
"cryoemservices.find_symmetry" = "cryoemservices.pipeliner_plugins.symmetry_finder:run"
"cryoemservices.reextract" = "cryoemservices.pipeliner_plugins.reextract:run"
"cryoemservices.resubmit_wrapper" = "cryoemservices.cli.resubmit_wrapper:run"
"relipy.link" = "cryoemservices.cli.project_linker: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"
Denoise = "cryoemservices.services.denoise:Denoise"
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"]
CLEMLIFToStack = "cryoemservices.wrappers.clem_process_raw_lifs:LIFToStackWrapper"
CLEMTIFFToStack = "cryoemservices.wrappers.clem_process_raw_tiffs:TIFFToStackWrapper"
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"