Merge remote-tracking branch 'origin/main' into qt_create_axes

manual_system_tests/dae_scan.py

@@ -1,8 +1,8 @@
 """Demonstration plan showing basic bluesky functionality."""
 
 import os
+from collections.abc import Generator
 from pathlib import Path
-from typing import Generator
 
 import bluesky.plan_stubs as bps
 import bluesky.plans as bp

manual_system_tests/interruption.py

@@ -1,7 +1,7 @@
 """Demonstration plan showing basic bluesky functionality."""
 
 import os
-from typing import Generator
+from collections.abc import Generator
 
 import bluesky.plan_stubs as bps
 from bluesky.utils import Msg

ruff.toml

@@ -2,35 +2,56 @@ line-length = 100
 indent-width = 4
 
 [lint]
+preview = true
 extend-select = [
     "N",     # pep8-naming
-    "D",     # pydocstyle (can use this later but for now causes too many errors)
+    "D",     # pydocstyle
     "I",     # isort (for imports)
     "E501",  # Line too long ({width} > {limit})
-    "E",
-    "F",
-	"W",
-    "ANN",
-	"ASYNC", # Asyncio-specific checks
-	"B",
-	"NPY",   # Numpy-specific rules
-	"RUF",   # Ruff-specific checks, include some useful asyncio rules
+    "E",     # Pycodestyle errors
+    "W",     # Pycodestyle warnings
+    "F",     # Pyflakes
+    "PL",    # Pylint
+    "B",     # Flake8-bugbear
+    "PIE",   # Flake8-pie
+    "ANN",   # Annotations
+    "ASYNC", # Asyncio-specific checks
+    "NPY",   # Numpy-specific rules
+    "RUF",   # Ruff-specific checks, include some useful asyncio rules
+    "FURB",  # Rules from refurb
+    "ERA",   # Commented-out code
+    "PT",    # Pytest-specific rules
+    "LOG",   # Logging-specific rules
+    "G",     # Logging-specific rules
+    "UP",    # Pyupgrade
+    "SLF",   # Private-member usage
+    "PERF",  # Performance-related rules
 ]
 ignore = [
     "D406",    # Section name should end with a newline ("{name}")
     "D407",    # Missing dashed underline after section ("{name}")
-	"D213",    # Incompatible with D212
-	"D203",    # Incompatible with D211
+    "D213",    # Incompatible with D212
+    "D203",    # Incompatible with D211
+    "B901",    # This is a standard, expected, pattern in bluesky
+    "PLR6301"  # Too noisy
 ]
 [lint.per-file-ignores]
 "tests/*" = [
-    "N802",
-    "D",   # Don't require method documentation for test methods
-    "ANN"  # Don't require tests to use type annotations
+    "N802",     # Allow test names to be long / not pep8
+    "D",        # Don't require method documentation for test methods
+    "ANN",      # Don't require tests to use type annotations
+    "PLR2004",  # Allow magic numbers in tests
+    "PLR0915",  # Allow complex tests
+    "PLR0914",  # Allow complex tests
+    "PLC2701",  # Allow tests to import "private" things
+    "SLF001",   # Allow tests to use "private" things
 ]
 "doc/conf.py" = [
     "D100"
 ]
 
 [lint.pep8-naming]
 extend-ignore-names = ["RE"]  # Conventional name used for RunEngine
+
+[lint.pylint]
+max-args = 6

src/ibex_bluesky_core/callbacks/document_logger.py

@@ -34,5 +34,5 @@ def __call__(self, name: str, document: dict[str, Any]) -> None:
 
         to_write: dict[str, Any] = {"type": name, "document": document}
 
-        with open(self.filename, "a") as outfile:
+        with open(self.filename, "a", encoding="utf8") as outfile:
             outfile.write(f"{json.dumps(to_write)}\n")

src/ibex_bluesky_core/callbacks/file_logger.py

@@ -65,7 +65,7 @@ def start(self, doc: RunStart) -> None:
         )
         header_data[START_TIME] = formatted_time
 
-        with open(self.filename, "a", newline="") as outfile:
+        with open(self.filename, "a", newline="", encoding="utf-8") as outfile:
             for key, value in header_data.items():
                 outfile.write(f"{key}: {value}\n")
 
@@ -102,7 +102,7 @@ def event(self, doc: Event) -> Event:
                 else value
             )
 
-        with open(self.filename, "a", newline="") as outfile:
+        with open(self.filename, "a", newline="", encoding="utf-8") as outfile:
             file_delimiter = ","
             if doc[SEQ_NUM] == 1:
                 # If this is the first event, write out the units before writing event data.

src/ibex_bluesky_core/callbacks/fitting/fitting_utils.py

@@ -30,7 +30,6 @@ def model(cls, *args: int) -> lmfit.Model:
             (x-values: NDArray, parameters: np.float64 -> y-values: NDArray)
 
         """
-        pass
 
     @classmethod
     @abstractmethod
@@ -47,7 +46,6 @@ def guess(
             (x-values: NDArray, y-values: NDArray -> parameters: Dict[str, lmfit.Parameter])
 
         """
-        pass
 
     @classmethod
     def fit(cls, *args: int) -> FitMethod:
@@ -198,8 +196,9 @@ class Polynomial(Fit):
     @classmethod
     def _check_degree(cls, args: tuple[int, ...]) -> int:
         """Check that polynomial degree is valid."""
-        degree = args[0] if args else 7
-        if not (0 <= degree <= 7):
+        max_degree = 7
+        degree = args[0] if args else max_degree
+        if not (0 <= degree <= max_degree):
             raise ValueError("The polynomial degree should be at least 0 and smaller than 8.")
         return degree
 

src/ibex_bluesky_core/callbacks/plotting.py

@@ -37,7 +37,7 @@ def __init__(
         """
         super().__init__(y=y, x=x, *args, **kwargs)  # noqa: B026
         if yerr is not None:
-            self.yerr, *others = get_obj_fields([yerr])
+            self.yerr, *_others = get_obj_fields([yerr])
         else:
             self.yerr = None
         self.yerr_data = []

src/ibex_bluesky_core/devices/__init__.py

@@ -5,7 +5,7 @@
 import binascii
 import os
 import zlib
-from typing import Type, TypeVar
+from typing import TypeVar
 
 from ophyd_async.core import SignalDatatype, SignalRW
 from ophyd_async.epics.core import epics_signal_rw
@@ -18,7 +18,7 @@ def get_pv_prefix() -> str:
     prefix = os.getenv("MYPVPREFIX")
 
     if prefix is None:
-        raise EnvironmentError("MYPVPREFIX environment variable not available - please define")
+        raise OSError("MYPVPREFIX environment variable not available - please define")
 
     return prefix
 
@@ -48,7 +48,7 @@ def compress_and_hex(value: str) -> bytes:
     return binascii.hexlify(compr)
 
 
-def isis_epics_signal_rw(datatype: Type[T], read_pv: str, name: str = "") -> SignalRW[T]:
+def isis_epics_signal_rw(datatype: type[T], read_pv: str, name: str = "") -> SignalRW[T]:
     """Make a RW signal with ISIS' PV naming standard ie. read_pv as TITLE, write_pv as TITLE:SP."""
     write_pv = f"{read_pv}:SP"
     return epics_signal_rw(datatype, read_pv, write_pv, name)

src/ibex_bluesky_core/devices/block.py

@@ -3,7 +3,7 @@
 import asyncio
 import logging
 from dataclasses import dataclass
-from typing import Callable, Generic, Type, TypeVar
+from typing import Callable, Generic, TypeVar
 
 from bluesky.protocols import Locatable, Location, Movable, Triggerable
 from ophyd_async.core import (
@@ -119,7 +119,7 @@ def __init__(self, prefix: str, name: str = "") -> None:
 class BlockR(StandardReadable, Triggerable, Generic[T]):
     """Device representing an IBEX readable block of arbitrary data type."""
 
-    def __init__(self, datatype: Type[T], prefix: str, block_name: str) -> None:
+    def __init__(self, datatype: type[T], prefix: str, block_name: str) -> None:
         """Create a new read-only block.
 
         Args:
@@ -154,7 +154,7 @@ class BlockRw(BlockR[T], Movable):
 
     def __init__(
         self,
-        datatype: Type[T],
+        datatype: type[T],
         prefix: str,
         block_name: str,
         *,
@@ -231,7 +231,7 @@ class BlockRwRbv(BlockRw[T], Locatable):
 
     def __init__(
         self,
-        datatype: Type[T],
+        datatype: type[T],
         prefix: str,
         block_name: str,
         *,
@@ -326,7 +326,7 @@ def __repr__(self) -> str:
         return f"{self.__class__.__name__}(name={self.name})"
 
 
-def block_r(datatype: Type[T], block_name: str) -> BlockR[T]:
+def block_r(datatype: type[T], block_name: str) -> BlockR[T]:
     """Get a local read-only block for the current instrument.
 
     See documentation of BlockR for more information.
@@ -335,7 +335,7 @@ def block_r(datatype: Type[T], block_name: str) -> BlockR[T]:
 
 
 def block_rw(
-    datatype: Type[T], block_name: str, *, write_config: BlockWriteConfig[T] | None = None
+    datatype: type[T], block_name: str, *, write_config: BlockWriteConfig[T] | None = None
 ) -> BlockRw[T]:
     """Get a local read-write block for the current instrument.
 
@@ -347,7 +347,7 @@ def block_rw(
 
 
 def block_rw_rbv(
-    datatype: Type[T], block_name: str, *, write_config: BlockWriteConfig[T] | None = None
+    datatype: type[T], block_name: str, *, write_config: BlockWriteConfig[T] | None = None
 ) -> BlockRwRbv[T]:
     """Get a local read/write/setpoint readback block for the current instrument.
 

src/ibex_bluesky_core/devices/dae/__init__.py

@@ -1,11 +1,11 @@
 """Utilities for the DAE device - mostly XML helpers."""
 
 from enum import Enum
-from typing import Any, Dict, List
+from typing import Any
 from xml.etree.ElementTree import Element
 
 
-def convert_xml_to_names_and_values(xml: Element) -> Dict[str, str]:
+def convert_xml_to_names_and_values(xml: Element) -> dict[str, str]:
     """Convert an XML element's children to a dict containing <Name>.text:<Val>.text."""
     names_and_values = dict()
     elements = get_all_elements_in_xml_with_child_called_name(xml)
@@ -16,7 +16,7 @@ def convert_xml_to_names_and_values(xml: Element) -> Dict[str, str]:
     return names_and_values
 
 
-def get_all_elements_in_xml_with_child_called_name(xml: Element) -> List[Element]:
+def get_all_elements_in_xml_with_child_called_name(xml: Element) -> list[Element]:
     """Find all elements with a "name" element, but ignore the first one as it's the root."""
     elements = xml.findall("*/Name/..")
     return elements
@@ -32,7 +32,7 @@ def _get_names_and_values(element: Element) -> tuple[Any, Any] | tuple[None, Non
 
 
 def set_value_in_dae_xml(
-    elements: List[Element], name: str, value: str | Enum | int | None | float
+    elements: list[Element], name: str, value: str | Enum | int | float | None
 ) -> None:
     """Find and set a value in the DAE XML, given a name and value.
 

src/ibex_bluesky_core/devices/dae/dae_period_settings.py

@@ -4,7 +4,6 @@
 import xml.etree.ElementTree as ET
 from dataclasses import dataclass
 from enum import Enum
-from typing import List
 from xml.etree.ElementTree import tostring
 
 from bluesky.protocols import Locatable, Location, Movable
@@ -58,13 +57,13 @@ class SinglePeriodSettings:
 class DaePeriodSettingsData:
     """Dataclass for the hardware period settings."""
 
-    periods_settings: List[SinglePeriodSettings] | None = None
-    periods_soft_num: None | int = None
+    periods_settings: list[SinglePeriodSettings] | None = None
+    periods_soft_num: int | None = None
     periods_type: PeriodType | None = None
     periods_src: PeriodSource | None = None
-    periods_file: None | str = None
-    periods_seq: None | int = None
-    periods_delay: None | int = None
+    periods_file: str | None = None
+    periods_seq: int | None = None
+    periods_delay: int | None = None
 
 
 def _convert_xml_to_period_settings(value: str) -> DaePeriodSettingsData:

src/ibex_bluesky_core/devices/dae/dae_tcb_settings.py

@@ -4,7 +4,6 @@
 import xml.etree.ElementTree as ET
 from dataclasses import dataclass
 from enum import Enum
-from typing import Dict
 from xml.etree.ElementTree import tostring
 
 from bluesky.protocols import Locatable, Location, Movable
@@ -66,14 +65,14 @@ class TimeRegimeRow:
 class TimeRegime:
     """Time regime - contains a dict(rows) which is row_number:TimeRegimeRow."""
 
-    rows: Dict[int, TimeRegimeRow]
+    rows: dict[int, TimeRegimeRow]
 
 
 @dataclass(kw_only=True)
 class DaeTCBSettingsData:
     """Dataclass for the DAE TCB settings."""
 
-    tcb_tables: Dict[int, TimeRegime] | None = None
+    tcb_tables: dict[int, TimeRegime] | None = None
     tcb_file: str | None = None
     time_unit: TimeUnit | None = None
     tcb_calculation_method: CalculationMethod | None = None

src/ibex_bluesky_core/devices/simpledae/__init__.py

@@ -51,9 +51,9 @@ def __init__(
 
         """
         self.prefix = prefix
-        self.controller: "Controller" = controller
-        self.waiter: "Waiter" = waiter
-        self.reducer: "Reducer" = reducer
+        self.controller: Controller = controller
+        self.waiter: Waiter = waiter
+        self.reducer: Reducer = reducer
 
         logger.info(
             "created simpledae with prefix=%s, controller=%s, waiter=%s, reducer=%s",
@@ -72,8 +72,7 @@ def __init__(
         # published when the top-level SimpleDae object is read.
         extra_readables = set()
         for strategy in [self.controller, self.waiter, self.reducer]:
-            for sig in strategy.additional_readable_signals(self):
-                extra_readables.add(sig)
+            extra_readables.update(strategy.additional_readable_signals(self))
         logger.info("extra readables: %s", list(extra_readables))
         self.add_readables(devices=list(extra_readables))
 

src/ibex_bluesky_core/devices/simpledae/controllers.py

@@ -83,7 +83,7 @@ async def start_counting(self, dae: "SimpleDae") -> None:
         await dae.controls.resume_run.trigger(wait=True, timeout=None)
         await wait_for_value(
             dae.run_state,
-            lambda v: v in [RunstateEnum.RUNNING, RunstateEnum.WAITING, RunstateEnum.VETOING],
+            lambda v: v in {RunstateEnum.RUNNING, RunstateEnum.WAITING, RunstateEnum.VETOING},
             timeout=10,
         )
 
@@ -130,7 +130,7 @@ async def start_counting(self, dae: "SimpleDae") -> None:
         await dae.controls.begin_run.trigger(wait=True, timeout=None)
         await wait_for_value(
             dae.run_state,
-            lambda v: v in [RunstateEnum.RUNNING, RunstateEnum.WAITING, RunstateEnum.VETOING],
+            lambda v: v in {RunstateEnum.RUNNING, RunstateEnum.WAITING, RunstateEnum.VETOING},
             timeout=10,
         )
 

src/ibex_bluesky_core/devices/simpledae/reducers.py

@@ -3,8 +3,9 @@
 import asyncio
 import logging
 import math
-from abc import ABCMeta, abstractmethod
-from typing import TYPE_CHECKING, Collection, Sequence
+from abc import ABC, abstractmethod
+from collections.abc import Collection, Sequence
+from typing import TYPE_CHECKING
 
 import scipp as sc
 from ophyd_async.core import (
@@ -41,7 +42,7 @@ async def sum_spectra(spectra: Collection[DaeSpectra]) -> sc.Variable | sc.DataA
     return summed_counts
 
 
-class ScalarNormalizer(Reducer, StandardReadable, metaclass=ABCMeta):
+class ScalarNormalizer(Reducer, StandardReadable, ABC):
     """Sum a set of user-specified spectra, then normalize by a scalar signal."""
 
     def __init__(self, prefix: str, detector_spectra: Sequence[int]) -> None: