diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 00200fe5..053d1bf7 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -3,7 +3,7 @@
repos:
# Syntax validation and some basic sanity checks
- repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v4.5.0 # Released 2023-10-09
+ rev: v4.6.0 # Released 2024-04-06
# rev input based on version tag format in repo (e.g. with or without 'v')
hooks:
- id: check-added-large-files
@@ -26,15 +26,22 @@ repos:
# Format the pyproject.toml file
- repo: https://github.com/tox-dev/pyproject-fmt
- rev: 1.7.0 # Released 2024-01-22
+ rev: 1.8.0 # Released 2024-04-17 | Latest version that retains ability to group project keys under sub-tables
hooks:
- id: pyproject-fmt
name: Formatting the pyproject.toml file
additional_dependencies: ["tox>=4.9"]
+ # args: [
+ # "--check",
+ # "--keep-full-version",
+ # "--max-supported-python", "3.11",
+ # "--indent", "8",
+ # "./pyproject.toml",
+ # ]
# Automatic source code formatting
- repo: https://github.com/psf/black
- rev: 24.3.0 # Released 2024-03-15
+ rev: 24.8.0 # Released 2024-08-02
hooks:
- id: black
name: Formatting Python scripts according to Black
@@ -69,20 +76,20 @@ repos:
# Linting
- repo: https://github.com/PyCQA/flake8
# Release history: https://flake8.pycqa.org/en/latest/release-notes/index.html
- rev: 7.0.0 # Released 2024-01-05
+ rev: 7.1.1 # Released 2024-08-04
hooks:
- id: flake8
name: Running Flake8 linter on Python files
additional_dependencies: [
- # Added Flake8-pyproject plugin for .toml compatibility
+ # Added Flake8-pyproject plugin for .toml compatibility | URL: https://github.com/john-hen/Flake8-pyproject
"Flake8-pyproject==1.2.3", # Released 2023-03-21
# flake8-comprehensions URL: https://github.com/adamchainz/flake8-comprehensions
- "flake8-comprehensions==3.14.0", # Released 2023-07-10
+ "flake8-comprehensions==3.15.0", # Released 2024-06-29
]
# Type checking
- repo: https://github.com/pre-commit/mirrors-mypy
- rev: v1.9.0 # Released 2024-03-09
+ rev: v1.11.1 # Released 2024-07-31
hooks:
- id: mypy
name: Checking types in Python scripts using MyPy
diff --git a/pyproject.toml b/pyproject.toml
index 0f4986e2..e210b2e9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,168 +1,166 @@
-[build-system]
-build-backend = "setuptools.build_meta"
-requires = [
- "setuptools >= 40.6.0",
- "wheel",
-]
-
-[project]
-name = "murfey"
-version = "0.12.2"
-description = "Client-Server architecture hauling Cryo-EM data"
-readme = "README.md"
-keywords = [
- "",
-]
-license = {file = "LICENSE"}
-maintainers = []
-authors = []
-requires-python = ">=3.9"
-classifiers = [
- "Development Status :: 3 - Alpha",
- "Environment :: Console",
- "Intended Audience :: Science/Research",
- "License :: OSI Approved :: BSD License",
- "Operating System :: OS Independent",
- "Programming Language :: Python :: 3 :: Only",
- "Programming Language :: Python :: 3.9",
- "Programming Language :: Python :: 3.10",
- "Programming Language :: Python :: 3.11",
- "Programming Language :: Python :: 3.12",
-]
-dependencies = [
- "defusedxml", # For safely parsing XML files
- "pydantic<2", # Locked to <2 by zocalo
- "requests",
- "rich",
- "werkzeug",
-]
-[project.optional-dependencies]
-cicd = [
- "pytest-cov", # Used by Azure Pipelines for PyTest coverage reports
-]
-client = [
- "procrunner",
- "textual==0.42.0",
- "websocket-client",
- "xmltodict",
-]
-developer = [
- "bump2version", # Version control
- "ipykernel", # Enable interactive coding with VS Code and Jupyter Notebook
- "pre-commit", # Formatting, linting, type checking, etc.
- "pytest", # Test code functionality
-]
-server = [
- # "matplotlib", # For visual statistical analysis of images
- "cryptography",
- "fastapi[standard]",
- "ispyb", # Responsible for setting requirements for SQLAlchemy and mysql-connector-python; v10.0.0: sqlalchemy <2, mysql-connector-python >=8.0.32
- "jinja2",
- "mrcfile",
- "numpy",
- "packaging",
- "passlib",
- "pillow",
- "prometheus_client",
- "python-jose[cryptography]",
- "sqlmodel",
- "stomp-py<=8.1.0", # 8.1.1 (released 2024-04-06) doesn't work with our project
- "uvicorn[standard]",
- "zocalo",
-]
-[project.urls]
-Bug-Tracker = "https://github.com/DiamondLightSource/python-murfey/issues"
-Documentation = "https://github.com/DiamondLightSource/python-murfey"
-GitHub = "https://github.com/DiamondLightSource/python-murfey"
-[project.scripts]
-murfey = "murfey.client:run"
-"murfey.add_user" = "murfey.cli.add_user:run"
-"murfey.create_db" = "murfey.cli.create_db:run"
-"murfey.db_sql" = "murfey.cli.murfey_db_sql:run"
-"murfey.decrypt_password" = "murfey.cli.decrypt_db_password:run"
-"murfey.generate_key" = "murfey.cli.generate_crypto_key:run"
-"murfey.generate_password" = "murfey.cli.generate_db_password:run"
-"murfey.server" = "murfey.server:run"
-"murfey.sessions" = "murfey.cli.db_sessions:run"
-"murfey.simulate" = "murfey.cli.dummy:run"
-"murfey.spa_inject" = "murfey.cli.inject_spa_processing:run"
-"murfey.spa_ispyb_entries" = "murfey.cli.spa_ispyb_messages:run"
-"murfey.transfer" = "murfey.cli.transfer:run"
-[project.entry-points."murfey.workflows"]
-"lif_to_stack" = "murfey.workflows.lif_to_stack:zocalo_cluster_request"
-"tiff_to_stack" = "murfey.workflows.tiff_to_stack:zocalo_cluster_request"
-
-[tool.setuptools]
-package-dir = {"" = "src"}
-include-package-data = true
-zip-safe = false
-
-[tool.setuptools.package-data]
-"murfey.client.tui" = ["*.css"]
-
-[tool.setuptools.packages.find]
-where = ["src", "tests"]
-
-[tool.isort]
-profile = "black"
-
-[tool.flake8]
-# Flake8-pyproject allows TOML file settings to be read into Flake8
-# URL: https://pypi.org/project/Flake8-pyproject/
-select = [
- "C4",
- "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]
-inputs = "pyproject.toml"
-check = false
-indent = 4
-keep_full_version = true
-max-supported-python = "3.12"
-
-[tool.pytest.ini_options]
-addopts = "-ra"
-
-[tool.mypy]
-disable_error_code = [
- "annotation-unchecked", # Notification that the bodies of untyped functions aren't checked. Not critical
- "import-untyped", # Error for missing library stubs. Not critical
-]
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = [
+ "setuptools >= 40.6.0",
+ "wheel",
+]
+
+[project]
+name = "murfey"
+version = "0.12.2"
+description = "Client-Server architecture hauling Cryo-EM data"
+readme = "README.md"
+keywords = [
+ "",
+]
+license = {file = "LICENSE"}
+maintainers = []
+authors = []
+requires-python = ">=3.9"
+classifiers = [
+ "Development Status :: 3 - Alpha",
+ "Environment :: Console",
+ "Intended Audience :: Science/Research",
+ "License :: OSI Approved :: BSD License",
+ "Operating System :: OS Independent",
+ "Programming Language :: Python :: 3 :: Only",
+ "Programming Language :: Python :: 3.9",
+ "Programming Language :: Python :: 3.10",
+ "Programming Language :: Python :: 3.11",
+]
+dependencies = [
+ "defusedxml", # Used for safely extracting XML elements
+ "importlib-metadata", # Needed in both client and server for Python >3.9
+ "pydantic<2", # Fixed to <2 by zocalo in [server] dependencies
+ "requests",
+ "rich",
+ "werkzeug",
+]
+[project.optional-dependencies]
+cicd = [
+ "pytest-cov", # Used by Azure Pipelines for PyTest coverage reports
+]
+client = [
+ "procrunner",
+ "textual", # ==0.42.0", # importlib-metadata a former dependency of theirs
+ "websocket-client",
+ "xmltodict",
+]
+developer = [
+ "bump2version", # Version control
+ "ipykernel", # Enable interactive coding with VS Code and Jupyter Notebook
+ "pre-commit", # Formatting, linting, type checking, etc.
+ "pytest", # Test code functionality
+]
+server = [
+ "cryptography",
+ "fastapi[standard]",
+ "ispyb", # Responsible for setting requirements for SQLAlchemy and mysql-connector-python; v10.0.0: sqlalchemy <2, mysql-connector-python >=8.0.32
+ "jinja2",
+ "mrcfile",
+ "numpy<2", # Locked numpy to <2 while other dependencies catch up
+ "packaging",
+ "passlib",
+ "pillow",
+ "prometheus_client",
+ "python-jose[cryptography]",
+ "sqlalchemy[postgresql]<2", # Installs psycopg2 dependency
+ "sqlmodel",
+ "stomp-py", # <=8.1.0", # 8.1.1 (released 2024-04-06) doesn't work with our project # 8.1.2 seems ok
+ "uvicorn[standard]",
+ "zocalo",
+]
+[project.urls]
+Bug-Tracker = "https://github.com/DiamondLightSource/python-murfey/issues"
+Documentation = "https://github.com/DiamondLightSource/python-murfey"
+GitHub = "https://github.com/DiamondLightSource/python-murfey"
+[project.scripts]
+murfey = "murfey.client:run"
+"murfey.add_user" = "murfey.cli.add_user:run"
+"murfey.create_db" = "murfey.cli.create_db:run"
+"murfey.db_sql" = "murfey.cli.murfey_db_sql:run"
+"murfey.decrypt_password" = "murfey.cli.decrypt_db_password:run"
+"murfey.generate_key" = "murfey.cli.generate_crypto_key:run"
+"murfey.generate_password" = "murfey.cli.generate_db_password:run"
+"murfey.server" = "murfey.server:run"
+"murfey.sessions" = "murfey.cli.db_sessions:run"
+"murfey.simulate" = "murfey.cli.dummy:run"
+"murfey.spa_inject" = "murfey.cli.inject_spa_processing:run"
+"murfey.spa_ispyb_entries" = "murfey.cli.spa_ispyb_messages:run"
+"murfey.transfer" = "murfey.cli.transfer:run"
+[project.entry-points."murfey.workflows"]
+"lif_to_stack" = "murfey.workflows.lif_to_stack:zocalo_cluster_request"
+"tiff_to_stack" = "murfey.workflows.tiff_to_stack:zocalo_cluster_request"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+include-package-data = true
+zip-safe = false
+
+[tool.setuptools.package-data]
+"murfey.client.tui" = ["*.css"]
+
+[tool.setuptools.packages.find]
+where = ["src", "tests"]
+
+[tool.isort]
+profile = "black"
+
+[tool.flake8]
+# Flake8-pyproject allows TOML file settings to be read into Flake8
+# URL: https://pypi.org/project/Flake8-pyproject/
+select = [
+ "C4",
+ "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"
+
+[tool.pytest.ini_options]
+addopts = "-ra"
+
+[tool.mypy]
+disable_error_code = [
+ "annotation-unchecked", # Notification that the bodies of untyped functions aren't checked. Not critical
+ "import-untyped", # Error for missing library stubs. Not critical
+]
diff --git a/src/murfey/server/__init__.py b/src/murfey/server/__init__.py
index 7b2431ea..cac38616 100644
--- a/src/murfey/server/__init__.py
+++ b/src/murfey/server/__init__.py
@@ -81,8 +81,8 @@
class ExtendedRecord(NamedTuple):
- record: Base
- record_params: List[Base]
+ record: Base # type: ignore
+ record_params: List[Base] # type: ignore
class JobIDs(NamedTuple):
@@ -2908,7 +2908,7 @@ def _register(record, header: dict, **kwargs):
@_register.register # type: ignore
-def _(record: Base, header: dict, **kwargs):
+def _(record: Base, header: dict, **kwargs): # type: ignore
if not _transport_object:
logger.error(
f"No transport object found when processing record {record}. Message header: {header}"
diff --git a/src/murfey/server/murfey_db.py b/src/murfey/server/murfey_db.py
index cafcfaf9..6aaa03fd 100644
--- a/src/murfey/server/murfey_db.py
+++ b/src/murfey/server/murfey_db.py
@@ -22,7 +22,7 @@ def url(machine_config: MachineConfig | None = None) -> str:
def get_murfey_db_session(
machine_config: MachineConfig | None = None,
-) -> Session:
+) -> Session: # type: ignore
_url = url(machine_config)
if machine_config and not machine_config.sqlalchemy_pooling:
engine = create_engine(_url, poolclass=NullPool)