|
1 | | -[build-system] |
2 | | -build-backend = "setuptools.build_meta" |
3 | | -requires = [ |
4 | | - "setuptools >= 40.6.0", |
5 | | - "wheel", |
6 | | -] |
7 | | - |
8 | | -[project] |
9 | | -name = "murfey" |
10 | | -version = "0.12.0" |
11 | | -description = "Client-Server architecture hauling Cryo-EM data" |
12 | | -readme = "README.md" |
13 | | -keywords = [ |
14 | | - "", |
15 | | -] |
16 | | -license = {file = "LICENSE"} |
17 | | -maintainers = [] |
18 | | -authors = [] |
19 | | -requires-python = ">=3.9" |
20 | | -classifiers = [ |
21 | | - "Development Status :: 3 - Alpha", |
22 | | - "Environment :: Console", |
23 | | - "Intended Audience :: Science/Research", |
24 | | - "License :: OSI Approved :: BSD License", |
25 | | - "Operating System :: OS Independent", |
26 | | - "Programming Language :: Python :: 3 :: Only", |
27 | | - "Programming Language :: Python :: 3.9", |
28 | | - "Programming Language :: Python :: 3.10", |
29 | | - "Programming Language :: Python :: 3.11", |
30 | | - "Programming Language :: Python :: 3.12", |
31 | | -] |
32 | | -dependencies = [ |
33 | | - "defusedxml", # For safely parsing XML files |
34 | | - "pydantic<2", # Locked to <2 by zocalo |
35 | | - "requests", |
36 | | - "rich", |
37 | | - "werkzeug", |
38 | | -] |
39 | | -[project.optional-dependencies] |
40 | | -cicd = [ |
41 | | - "pytest-cov", # Used by Azure Pipelines for PyTest coverage reports |
42 | | -] |
43 | | -client = [ |
44 | | - "procrunner", |
45 | | - "textual==0.42.0", |
46 | | - "websocket-client", |
47 | | - "xmltodict", |
48 | | -] |
49 | | -developer = [ |
50 | | - "bump2version", # Version control |
51 | | - "ipykernel", # Enable interactive coding with VS Code and Jupyter Notebook |
52 | | - "pre-commit", # Formatting, linting, type checking, etc. |
53 | | - "pytest", # Test code functionality |
54 | | -] |
55 | | -server = [ |
56 | | - # "matplotlib", # For visual statistical analysis of images |
57 | | - "cryptography", |
58 | | - "fastapi", |
59 | | - "ispyb", # Responsible for setting requirements for SQLAlchemy and mysql-connector-python; v10.0.0: sqlalchemy <2, mysql-connector-python >=8.0.32 |
60 | | - "jinja2", |
61 | | - "mrcfile", |
62 | | - "numpy", |
63 | | - "packaging", |
64 | | - "passlib", |
65 | | - "pillow", |
66 | | - "prometheus_client", |
67 | | - "python-jose[cryptography]", |
68 | | - "readlif", # Specific to cryo-CLEM workflow |
69 | | - "sqlmodel", |
70 | | - "stomp-py<=8.1.0", # 8.1.1 (released 2024-04-06) doesn't work with our project |
71 | | - "tifffile", # Specific to cryo-CLEM workflow |
72 | | - "uvicorn[standard]", |
73 | | - "zocalo", |
74 | | -] |
75 | | -[project.urls] |
76 | | -Bug-Tracker = "https://github.com/DiamondLightSource/python-murfey/issues" |
77 | | -Documentation = "https://github.com/DiamondLightSource/python-murfey" |
78 | | -GitHub = "https://github.com/DiamondLightSource/python-murfey" |
79 | | -[project.scripts] |
80 | | -murfey = "murfey.client:run" |
81 | | -"murfey.add_user" = "murfey.cli.add_user:run" |
82 | | -"murfey.create_db" = "murfey.cli.create_db:run" |
83 | | -"murfey.db_sql" = "murfey.cli.murfey_db_sql:run" |
84 | | -"murfey.decrypt_password" = "murfey.cli.decrypt_db_password:run" |
85 | | -"murfey.generate_key" = "murfey.cli.generate_crypto_key:run" |
86 | | -"murfey.generate_password" = "murfey.cli.generate_db_password:run" |
87 | | -"murfey.lif_to_tiff" = "murfey.cli.lif_to_tiff:run" |
88 | | -"murfey.server" = "murfey.server:run" |
89 | | -"murfey.sessions" = "murfey.cli.db_sessions:run" |
90 | | -"murfey.simulate" = "murfey.cli.dummy:run" |
91 | | -"murfey.spa_inject" = "murfey.cli.inject_spa_processing:run" |
92 | | -"murfey.spa_ispyb_entries" = "murfey.cli.spa_ispyb_messages:run" |
93 | | -"murfey.tiff_to_stack" = "murfey.cli.tiff_to_stack:run" |
94 | | -"murfey.transfer" = "murfey.cli.transfer:run" |
95 | | -[project.entry-points."murfey.workflows"] |
96 | | -"lif_to_tiff" = "murfey.workflows.lif_to_tiff:zocalo_cluster_request" |
97 | | -"tiff_to_stack" = "murfey.workflows.tiff_to_stack:zocalo_cluster_request" |
98 | | - |
99 | | -[tool.setuptools] |
100 | | -package-dir = {"" = "src"} |
101 | | -include-package-data = true |
102 | | -zip-safe = false |
103 | | - |
104 | | -[tool.setuptools.package-data] |
105 | | -"murfey.client.tui" = ["*.css"] |
106 | | - |
107 | | -[tool.setuptools.packages.find] |
108 | | -where = ["src", "tests"] |
109 | | - |
110 | | -[tool.isort] |
111 | | -profile = "black" |
112 | | - |
113 | | -[tool.flake8] |
114 | | -# Flake8-pyproject allows TOML file settings to be read into Flake8 |
115 | | -# URL: https://pypi.org/project/Flake8-pyproject/ |
116 | | -select = [ |
117 | | - "C4", |
118 | | - "E401", |
119 | | - "E711", |
120 | | - "E712", |
121 | | - "E713", |
122 | | - "E714", |
123 | | - "E721", |
124 | | - "E722", |
125 | | - "E901", |
126 | | - "F401", |
127 | | - "F402", |
128 | | - "F403", |
129 | | - "F405", |
130 | | - "F541", |
131 | | - "F631", |
132 | | - "F632", |
133 | | - "F633", |
134 | | - "F811", |
135 | | - "F812", |
136 | | - "F821", |
137 | | - "F822", |
138 | | - "F841", |
139 | | - "F901", |
140 | | - "W191", |
141 | | - "W291", |
142 | | - "W292", |
143 | | - "W293", |
144 | | - "W602", |
145 | | - "W603", |
146 | | - "W604", |
147 | | - "W605", |
148 | | - "W606", |
149 | | -] |
150 | | -ignore = [ |
151 | | - "E203", |
152 | | - "E266", |
153 | | - "E501", |
154 | | - "W503", |
155 | | -] |
156 | | -max-line-length = "88" |
157 | | - |
158 | | -[tool.pyproject-fmt] |
159 | | -inputs = "pyproject.toml" |
160 | | -check = false |
161 | | -indent = 4 |
162 | | -keep_full_version = true |
163 | | -max-supported-python = "3.12" |
164 | | - |
165 | | -[tool.pytest.ini_options] |
166 | | -addopts = "-ra" |
167 | | - |
168 | | -[tool.mypy] |
169 | | -disable_error_code = [ |
170 | | - "annotation-unchecked", # Notification that the bodies of untyped functions aren't checked. Not critical |
171 | | - "import-untyped", # Error for missing library stubs. Not critical |
172 | | -] |
| 1 | +[build-system] |
| 2 | +build-backend = "setuptools.build_meta" |
| 3 | +requires = [ |
| 4 | + "setuptools >= 40.6.0", |
| 5 | + "wheel", |
| 6 | +] |
| 7 | + |
| 8 | +[project] |
| 9 | +name = "murfey" |
| 10 | +version = "0.12.0" |
| 11 | +description = "Client-Server architecture hauling Cryo-EM data" |
| 12 | +readme = "README.md" |
| 13 | +keywords = [ |
| 14 | + "", |
| 15 | +] |
| 16 | +license = {file = "LICENSE"} |
| 17 | +maintainers = [] |
| 18 | +authors = [] |
| 19 | +requires-python = ">=3.9" |
| 20 | +classifiers = [ |
| 21 | + "Development Status :: 3 - Alpha", |
| 22 | + "Environment :: Console", |
| 23 | + "Intended Audience :: Science/Research", |
| 24 | + "License :: OSI Approved :: BSD License", |
| 25 | + "Operating System :: OS Independent", |
| 26 | + "Programming Language :: Python :: 3 :: Only", |
| 27 | + "Programming Language :: Python :: 3.9", |
| 28 | + "Programming Language :: Python :: 3.10", |
| 29 | + "Programming Language :: Python :: 3.11", |
| 30 | + "Programming Language :: Python :: 3.12", |
| 31 | +] |
| 32 | +dependencies = [ |
| 33 | + "defusedxml", # For safely parsing XML files |
| 34 | + "pydantic<2", # Locked to <2 by zocalo |
| 35 | + "requests", |
| 36 | + "rich", |
| 37 | + "werkzeug", |
| 38 | +] |
| 39 | +[project.optional-dependencies] |
| 40 | +cicd = [ |
| 41 | + "httpx", # Used by FastAPI tests |
| 42 | + "pytest-cov", # Used by Azure Pipelines for PyTest coverage reports |
| 43 | +] |
| 44 | +client = [ |
| 45 | + "procrunner", |
| 46 | + "textual==0.42.0", |
| 47 | + "websocket-client", |
| 48 | + "xmltodict", |
| 49 | +] |
| 50 | +developer = [ |
| 51 | + "bump2version", # Version control |
| 52 | + "ipykernel", # Enable interactive coding with VS Code and Jupyter Notebook |
| 53 | + "pre-commit", # Formatting, linting, type checking, etc. |
| 54 | + "pytest", # Test code functionality |
| 55 | +] |
| 56 | +server = [ |
| 57 | + # "matplotlib", # For visual statistical analysis of images |
| 58 | + "cryptography", |
| 59 | + "fastapi", |
| 60 | + "ispyb", # Responsible for setting requirements for SQLAlchemy and mysql-connector-python; v10.0.0: sqlalchemy <2, mysql-connector-python >=8.0.32 |
| 61 | + "jinja2", |
| 62 | + "mrcfile", |
| 63 | + "numpy", |
| 64 | + "packaging", |
| 65 | + "passlib", |
| 66 | + "pillow", |
| 67 | + "prometheus_client", |
| 68 | + "python-jose[cryptography]", |
| 69 | + "readlif", # Specific to cryo-CLEM workflow |
| 70 | + "sqlmodel", |
| 71 | + "stomp-py<=8.1.0", # 8.1.1 (released 2024-04-06) doesn't work with our project |
| 72 | + "tifffile", # Specific to cryo-CLEM workflow |
| 73 | + "uvicorn[standard]", |
| 74 | + "zocalo", |
| 75 | +] |
| 76 | +[project.urls] |
| 77 | +Bug-Tracker = "https://github.com/DiamondLightSource/python-murfey/issues" |
| 78 | +Documentation = "https://github.com/DiamondLightSource/python-murfey" |
| 79 | +GitHub = "https://github.com/DiamondLightSource/python-murfey" |
| 80 | +[project.scripts] |
| 81 | +murfey = "murfey.client:run" |
| 82 | +"murfey.add_user" = "murfey.cli.add_user:run" |
| 83 | +"murfey.create_db" = "murfey.cli.create_db:run" |
| 84 | +"murfey.db_sql" = "murfey.cli.murfey_db_sql:run" |
| 85 | +"murfey.decrypt_password" = "murfey.cli.decrypt_db_password:run" |
| 86 | +"murfey.generate_key" = "murfey.cli.generate_crypto_key:run" |
| 87 | +"murfey.generate_password" = "murfey.cli.generate_db_password:run" |
| 88 | +"murfey.lif_to_tiff" = "murfey.cli.lif_to_tiff:run" |
| 89 | +"murfey.server" = "murfey.server:run" |
| 90 | +"murfey.sessions" = "murfey.cli.db_sessions:run" |
| 91 | +"murfey.simulate" = "murfey.cli.dummy:run" |
| 92 | +"murfey.spa_inject" = "murfey.cli.inject_spa_processing:run" |
| 93 | +"murfey.spa_ispyb_entries" = "murfey.cli.spa_ispyb_messages:run" |
| 94 | +"murfey.tiff_to_stack" = "murfey.cli.tiff_to_stack:run" |
| 95 | +"murfey.transfer" = "murfey.cli.transfer:run" |
| 96 | +[project.entry-points."murfey.workflows"] |
| 97 | +"lif_to_tiff" = "murfey.workflows.lif_to_tiff:zocalo_cluster_request" |
| 98 | +"tiff_to_stack" = "murfey.workflows.tiff_to_stack:zocalo_cluster_request" |
| 99 | + |
| 100 | +[tool.setuptools] |
| 101 | +package-dir = {"" = "src"} |
| 102 | +include-package-data = true |
| 103 | +zip-safe = false |
| 104 | + |
| 105 | +[tool.setuptools.package-data] |
| 106 | +"murfey.client.tui" = ["*.css"] |
| 107 | + |
| 108 | +[tool.setuptools.packages.find] |
| 109 | +where = ["src", "tests"] |
| 110 | + |
| 111 | +[tool.isort] |
| 112 | +profile = "black" |
| 113 | + |
| 114 | +[tool.flake8] |
| 115 | +# Flake8-pyproject allows TOML file settings to be read into Flake8 |
| 116 | +# URL: https://pypi.org/project/Flake8-pyproject/ |
| 117 | +select = [ |
| 118 | + "C4", |
| 119 | + "E401", |
| 120 | + "E711", |
| 121 | + "E712", |
| 122 | + "E713", |
| 123 | + "E714", |
| 124 | + "E721", |
| 125 | + "E722", |
| 126 | + "E901", |
| 127 | + "F401", |
| 128 | + "F402", |
| 129 | + "F403", |
| 130 | + "F405", |
| 131 | + "F541", |
| 132 | + "F631", |
| 133 | + "F632", |
| 134 | + "F633", |
| 135 | + "F811", |
| 136 | + "F812", |
| 137 | + "F821", |
| 138 | + "F822", |
| 139 | + "F841", |
| 140 | + "F901", |
| 141 | + "W191", |
| 142 | + "W291", |
| 143 | + "W292", |
| 144 | + "W293", |
| 145 | + "W602", |
| 146 | + "W603", |
| 147 | + "W604", |
| 148 | + "W605", |
| 149 | + "W606", |
| 150 | +] |
| 151 | +ignore = [ |
| 152 | + "E203", |
| 153 | + "E266", |
| 154 | + "E501", |
| 155 | + "W503", |
| 156 | +] |
| 157 | +max-line-length = "88" |
| 158 | + |
| 159 | +[tool.pyproject-fmt] |
| 160 | +inputs = "pyproject.toml" |
| 161 | +check = false |
| 162 | +indent = 4 |
| 163 | +keep_full_version = true |
| 164 | +max-supported-python = "3.12" |
| 165 | + |
| 166 | +[tool.pytest.ini_options] |
| 167 | +addopts = "-ra" |
| 168 | + |
| 169 | +[tool.mypy] |
| 170 | +disable_error_code = [ |
| 171 | + "annotation-unchecked", # Notification that the bodies of untyped functions aren't checked. Not critical |
| 172 | + "import-untyped", # Error for missing library stubs. Not critical |
| 173 | +] |
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