Migrate to using Ruff for formatting and linting (#679)

* Migrated to using Ruff for linting and formatting
* Applied Ruff formatting changes
* Deleted 'transfer' CLI file

Author: tieneupin

.pre-commit-config.yaml

@@ -45,53 +45,15 @@ repos:
         name: Formatting the pyproject.toml file
         additional_dependencies: ["tox>=4.9"]
 
-  # Automatic source code formatting
-  - repo: https://github.com/psf/black
-    rev: 24.3.0 # Released 2024-03-15
+  # Format and lint using Ruff
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.0
     hooks:
-      - id: black
-        name: Formatting Python scripts according to Black
-        args: [--safe, --quiet]
-
-  # Automatically sort imports
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.13.2 # Released 2023-12-13
-    hooks:
-      - id: isort
-        name: Tidying Python imports via Isort
-        args: [
-            #'-a', 'from __future__ import annotations',        # 3.7-3.11
-            "--rm",
-            "from __future__ import absolute_import", # -3.0
-            "--rm",
-            "from __future__ import division", # -3.0
-            "--rm",
-            "from __future__ import generator_stop", # -3.7
-            "--rm",
-            "from __future__ import generators", # -2.3
-            "--rm",
-            "from __future__ import nested_scopes", # -2.2
-            "--rm",
-            "from __future__ import print_function", # -3.0
-            "--rm",
-            "from __future__ import unicode_literals", # -3.0
-            "--rm",
-            "from __future__ import with_statement", # -2.6
-          ]
-
-  # 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
-    hooks:
-      - id: flake8
-        name: Running Flake8 linter on Python files
-        additional_dependencies: [
-            # Added Flake8-pyproject plugin for .toml compatibility
-            "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
-          ]
+      - id: ruff
+        name: Running Ruff linter
+        args: ["--fix"]
+      - id: ruff-format
+        name: Running Ruff formatter
 
   # Type checking
   - repo: https://github.com/pre-commit/mirrors-mypy

pyproject.toml

@@ -121,53 +121,26 @@ zip-safe = false
 [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 = [
+[tool.ruff]
+line-length = 88
+lint.extend-ignore = ["E203", "E266", "E501", "E731", "E741"]
+lint.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",
+    "E4", "E7", "E9",
+    "F",
+    "I",
+    "W6",
 ]
-max-line-length = "88"
+fix = true
+
+[tool.ruff.lint.isort]
+known-first-party = ["murfey"]
+combine-as-imports = true
+
+[tool.ruff.format]
+quote-style="double"
+indent-style="space"
+line-ending="auto"
 
 [tool.pyproject-fmt]
 inputs = "pyproject.toml"

src/murfey/cli/generate_route_manifest.py

@@ -68,7 +68,6 @@ def is_implicitly_resolved(value: str) -> bool:
 
 
 def find_routers(name: str) -> dict[str, APIRouter]:
-
     def _extract_routers_from_module(module: ModuleType):
         routers = {}
         for name, obj in inspect.getmembers(module):
@@ -115,7 +114,6 @@ def _extract_routers_from_module(module: ModuleType):
 
 
 def get_route_manifest(routers: dict[str, APIRouter]):
-
     manifest = {}
 
     for router_name, router in routers.items():

src/murfey/cli/inject_spa_processing.py

@@ -173,7 +173,6 @@ def run():
             / str(ppath.stem + "_motion_corrected.mrc")
         )
         if proc_params:
-
             detached_ids = [c.id for c in collected_ids]
 
             if not mrc_out.parent.exists():

src/murfey/cli/spa_ispyb_messages.py

@@ -14,8 +14,7 @@
     DataCollectionGroup,
     ProcessingJob,
 )
-from sqlmodel import Session as MurfeySession
-from sqlmodel import create_engine, select
+from sqlmodel import Session as MurfeySession, create_engine, select
 
 from murfey.client.contexts.spa import _get_xml_list_index
 from murfey.server.feedback import _murfey_id, _register

src/murfey/cli/transfer.py

@@ -65,7 +65,6 @@ def _get_image_elements(root: ET.Element) -> List[ET.Element]:
     def _find_elements_recursively(
         node: ET.Element,
     ) -> Generator[ET.Element, None, None]:
-
         # Find items labelled "Element" under current node
         elem_list = node.findall("./Children/Element")
         if len(elem_list) < 1:  # Try alternative path for top-level of XML tree
@@ -103,7 +102,6 @@ def post_transfer(
         environment: Optional[MurfeyInstanceEnvironment] = None,
         **kwargs,
     ) -> bool:
-
         super().post_transfer(transferred_file, environment=environment, **kwargs)
 
         # Process files generated by "auto-save" acquisition mode
@@ -188,7 +186,6 @@ def post_transfer(
 
             # Process XLIF files
             if transferred_file.suffix == ".xlif":
-
                 # Skip processing of "_histo" histogram XLIF files
                 if transferred_file.stem.endswith("_histo"):
                     logger.debug(

src/murfey/client/contexts/clem.py

@@ -71,7 +71,6 @@ def _get_pulse_segments(
     def __rich_console__(
         self, console: Console, options: ConsoleOptions
     ) -> RenderResult:
-
         width = min(self.width or options.max_width, options.max_width)
         ascii = options.ascii_only
         if self.pulse:

src/murfey/client/tui/progress.py

@@ -193,7 +193,6 @@ def __init__(
         self._context = SPAModularContext
 
     def compose(self):
-
         machine_data = capture_get(
             base_url=str(self.app._environment.url.geturl()),
             router_name="session_control.router",
@@ -1013,7 +1012,7 @@ def compose(self):
                                     name_root += st
                                 if dest_num:
                                     dest = str(
-                                        dest_path.parent / f"{name_root}{dest_num+1}"
+                                        dest_path.parent / f"{name_root}{dest_num + 1}"
                                     )
                                 else:
                                     dest = str(dest_path.parent / f"{name_root}2")

src/murfey/client/tui/screens.py

@@ -23,8 +23,7 @@
 from murfey.server.murfey_db import murfey_db, url
 from murfey.util.api import url_path_for
 from murfey.util.config import get_security_config
-from murfey.util.db import MurfeyUser as User
-from murfey.util.db import Session as MurfeySession
+from murfey.util.db import MurfeyUser as User, Session as MurfeySession
 
 # Set up logger
 logger = getLogger("murfey.server.api.auth")
@@ -147,7 +146,7 @@ def validate_session_against_visit(session_id: int, visit: str):
 
 
 async def validate_instrument_token(
-    token: Annotated[str, Depends(instrument_oauth2_scheme)]
+    token: Annotated[str, Depends(instrument_oauth2_scheme)],
 ):
     """
     Used by the backend routers to check the incoming instrument server token.
@@ -334,7 +333,6 @@ def validate_user(username: str, password: str) -> bool:
 
 
 def create_access_token(data: dict, token: str = "") -> str:
-
     # If authenticating with password, auth URL needs a 'mint_session_token' endpoint
     if security_config.auth_type == "password":
         if auth_url and data.get("session"):
@@ -420,6 +418,6 @@ async def mint_session_token(session_id: MurfeySessionIDFrontend, db=murfey_db):
 
 @router.get("/validate_token")
 async def simple_token_validation(
-    token: Annotated[str, Depends(validate_instrument_token)]
+    token: Annotated[str, Depends(validate_instrument_token)],
 ):
     return {"valid": True}