MAINT: Test using ruff with minimal changes to defaults

scipp · Apr 16, 2024 · e1e46f0 · e1e46f0
1 parent f041c9b
commit e1e46f0
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -13,34 +13,13 @@ repos:
       - id: trailing-whitespace
         args: [ --markdown-linebreak-ext=md ]
         exclude: '\.svg'
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-        name: isort (python)
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 23.11.0
-    hooks:
-      - id: black
   - repo: https://github.com/kynan/nbstripout
     rev: 0.6.0
     hooks:
       - id: nbstripout
         types: [ "jupyter" ]
         args: [ "--drop-empty-cells",
                 "--extra-keys 'metadata.language_info.version cell.metadata.jp-MarkdownHeadingCollapsed cell.metadata.pycharm'" ]
-  - repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
-    hooks:
-      - id: flake8
-        types: ["python"]
-        additional_dependencies: ["flake8-bugbear==23.9.16"]
-  - repo: https://github.com/pycqa/bandit
-    rev: 1.7.5
-    hooks:
-      - id: bandit
-        additional_dependencies: ["bandit[toml]"]
-        args: ["-c", "pyproject.toml"]
   - repo: https://github.com/codespell-project/codespell
     rev: v2.2.6
     hooks:
@@ -57,3 +36,11 @@ repos:
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
       - id: text-unicode-replacement-char
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.7
+    hooks:
+      - id: ruff
+        types_or: [ python, pyi, jupyter ]
+        args: [ --fix]
+      - id: ruff-format
+        types_or: [ python, pyi]
diff --git a/docs/conf.py b/docs/conf.py
@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 import doctest
 import os
 import sys
@@ -8,9 +6,9 @@
 sys.path.insert(0, os.path.abspath('.'))
 
 # General information about the project.
-project = u'ESSsans'
-copyright = u'2024 Scipp contributors'
-author = u'Scipp contributors'
+project = 'ESSsans'
+copyright = '2024 Scipp contributors'
+author = 'Scipp contributors'
 
 html_show_sourcelink = True
 

diff --git a/docs/user-guide/common/beam-center-finder.ipynb b/docs/user-guide/common/beam-center-finder.ipynb
@@ -25,11 +25,11 @@
    },
    "outputs": [],
    "source": [
-    "import scipp as sc\n",
     "import plopp as pp\n",
     "import sciline\n",
-    "from ess import sans\n",
+    "import scipp as sc\n",
     "from ess import isissans as isis\n",
+    "from ess import sans\n",
     "from ess.sans.types import *"
    ]
   },
@@ -377,7 +377,7 @@
     "p.ax.axhline(0, color='cyan')\n",
     "p.ax.plot(0, 0, '+', color='k', ms=10)\n",
     "dx = 0.25\n",
-    "style = dict(ha='center', va='center', color='w')\n",
+    "style = {'ha': 'center', 'va': 'center', 'color': 'w'}\n",
     "p.ax.text(dx, dx, 'North-East', **style)\n",
     "p.ax.text(-dx, dx, 'North-West', **style)\n",
     "p.ax.text(dx, -dx, 'South-East', **style)\n",
@@ -402,15 +402,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "kwargs = dict(\n",
-    "    data=masked,\n",
-    "    norm=pipeline.compute(NormWavelengthTerm[SampleRun]),\n",
-    "    graph=pipeline.compute(sans.conversions.ElasticCoordTransformGraph),\n",
-    "    q_bins=params[sans.beam_center_finder.BeamCenterFinderQBins],\n",
-    "    wavelength_bins=params[WavelengthBins],\n",
-    "    transform=pipeline.compute(LabFrameTransform[SampleRun]),\n",
-    "    pixel_shape=pipeline.compute(DetectorPixelShape[SampleRun]),\n",
-    ")"
+    "kwargs = {\n",
+    "    'data': masked,\n",
+    "    'norm': pipeline.compute(NormWavelengthTerm[SampleRun]),\n",
+    "    'graph': pipeline.compute(sans.conversions.ElasticCoordTransformGraph),\n",
+    "    'q_bins': params[sans.beam_center_finder.BeamCenterFinderQBins],\n",
+    "    'wavelength_bins': params[WavelengthBins],\n",
+    "    'transform': pipeline.compute(LabFrameTransform[SampleRun]),\n",
+    "    'pixel_shape': pipeline.compute(DetectorPixelShape[SampleRun]),\n",
+    "}"
    ]
   },
   {

diff --git a/docs/user-guide/isis/sans2d.ipynb b/docs/user-guide/isis/sans2d.ipynb
@@ -22,11 +22,11 @@
    },
    "outputs": [],
    "source": [
-    "import scipp as sc\n",
-    "import sciline\n",
     "import plopp as pp\n",
-    "from ess import sans\n",
+    "import sciline\n",
+    "import scipp as sc\n",
     "from ess import isissans as isis\n",
+    "from ess import sans\n",
     "from ess.sans.types import *"
    ]
   },
@@ -102,11 +102,10 @@
     "providers = (\n",
     "    sans.providers + isis.providers + isis.data.providers + isis.sans2d.providers\n",
     ")\n",
-    "providers = providers + (\n",
-    "    isis.data.transmission_from_background_run,\n",
-    "    isis.data.transmission_from_sample_run,\n",
-    "    sans.beam_center_from_center_of_mass,\n",
-    ")\n",
+    "providers = (*providers,\n",
+    "             isis.data.transmission_from_background_run,\n",
+    "             isis.data.transmission_from_sample_run,\n",
+    "             sans.beam_center_from_center_of_mass)\n",
     "\n",
     "pipeline = sciline.Pipeline(providers=providers, params=params)"
    ]
@@ -248,7 +247,7 @@
     ")\n",
     "parts = (CleanSummedQ[SampleRun, Numerator], CleanSummedQ[SampleRun, Denominator])\n",
     "iofqs = (IofQ[SampleRun], IofQ[BackgroundRun], BackgroundSubtractedIofQ)\n",
-    "keys = monitors + (MaskedData[SampleRun],) + parts + iofqs\n",
+    "keys = (*monitors, MaskedData[SampleRun], *parts, *iofqs)\n",
     "\n",
     "results = pipeline.compute(keys)\n",
     "\n",

diff --git a/docs/user-guide/isis/zoom.ipynb b/docs/user-guide/isis/zoom.ipynb
@@ -42,10 +42,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import scipp as sc\n",
     "import sciline\n",
-    "from ess import sans\n",
+    "import scipp as sc\n",
     "from ess import isissans as isis\n",
+    "from ess import sans\n",
     "from ess.sans.types import *"
    ]
   },
@@ -131,11 +131,10 @@
    "outputs": [],
    "source": [
     "providers = sans.providers + isis.providers + (isis.io.read_xml_detector_masking,)\n",
-    "providers = providers + (\n",
-    "    isis.data.transmission_from_background_run,\n",
-    "    isis.data.transmission_from_sample_run,\n",
-    "    sans.beam_center_from_center_of_mass,\n",
-    ")\n",
+    "providers = (*providers,\n",
+    "             isis.data.transmission_from_background_run,\n",
+    "             isis.data.transmission_from_sample_run,\n",
+    "             sans.beam_center_from_center_of_mass)\n",
     "pipeline = sciline.Pipeline(providers, params=params)\n",
     "pipeline.set_param_series(PixelMaskFilename, masks)"
    ]
@@ -159,8 +158,8 @@
    "outputs": [],
    "source": [
     "try:\n",
+    "    import ess.isissans.mantidio  # noqa: F401\n",
     "    from mantid import ConfigService\n",
-    "    import ess.isissans.mantidio\n",
     "\n",
     "    cfg = ConfigService.Instance()\n",
     "    cfg.setLogLevel(3)  # Silence verbose load via Mantid\n",
@@ -169,7 +168,6 @@
     "    for provider in isis.mantidio.providers:\n",
     "        pipeline.insert(provider)\n",
     "except ImportError:\n",
-    "    import ess.isissans.io\n",
     "\n",
     "    for provider in isis.data.providers:\n",
     "        pipeline.insert(provider)"
@@ -236,7 +234,7 @@
     ")\n",
     "parts = (CleanSummedQ[SampleRun, Numerator], CleanSummedQ[SampleRun, Denominator])\n",
     "iofqs = (IofQ[SampleRun],)\n",
-    "keys = monitors + (MaskedData[SampleRun],) + parts + iofqs\n",
+    "keys = (*monitors, MaskedData[SampleRun], *parts, *iofqs)\n",
     "\n",
     "results = pipeline.compute(keys)\n",
     "\n",

diff --git a/docs/user-guide/loki/loki-direct-beam.ipynb b/docs/user-guide/loki/loki-direct-beam.ipynb
@@ -38,14 +38,11 @@
    },
    "outputs": [],
    "source": [
-    "import numpy as np\n",
-    "import scipp as sc\n",
-    "import sciline\n",
-    "import scippneutron as scn\n",
     "import plopp as pp\n",
-    "from ess import sans\n",
-    "from ess import loki\n",
+    "import sciline\n",
+    "import scipp as sc\n",
     "from ess import isissans as isis\n",
+    "from ess import loki, sans\n",
     "from ess.sans.types import *"
    ]
   },
@@ -252,8 +249,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from scipp.scipy.interpolate import interp1d\n",
     "from ess.loki.data import get_path\n",
+    "from scipp.scipy.interpolate import interp1d\n",
     "\n",
     "Iq_theory = sc.io.load_hdf5(get_path('PolyGauss_I0-50_Rg-60.h5'))\n",
     "f = interp1d(Iq_theory, 'Q')\n",

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,9 +1,9 @@
 [build-system]
+build-backend = "setuptools.build_meta"
 requires = [
   "setuptools>=68",
-  "setuptools_scm[toml]>=8.0",
+  "setuptools_scm[toml]>=8",
 ]
-build-backend = "setuptools.build_meta"
 
 [project]
 name = "esssans"
@@ -12,17 +12,14 @@ authors = [{ name = "Scipp contributors" }]
 license = { file = "LICENSE" }
 readme = "README.md"
 classifiers = [
-    "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: BSD License",
-    "Natural Language :: English",
-    "Operating System :: OS Independent",
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",
-    "Topic :: Scientific/Engineering",
-    "Typing :: Typed",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: BSD License",
+  "Natural Language :: English",
+  "Operating System :: OS Independent",
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.10",
+  "Topic :: Scientific/Engineering",
+  "Typing :: Typed",
 ]
 requires-python = ">=3.10"
 
@@ -31,25 +28,46 @@ requires-python = ">=3.10"
 # Make sure to list one dependency per line.
 dependencies = [
   "dask",
-  "graphviz",
   "essreduce",
+  "graphviz",
   "plopp",
   "pythreejs",
   "sciline>=24.4.1",
-  "scipp>=23.8.0",
-  "scippneutron>=23.9.0",
-  "scippnexus>=23.12.1",  # 23.12.0 and below deadlock in threaded use
+  "scipp>=23.8",
+  "scippneutron>=23.9",
+  "scippnexus>=23.12.1", # 23.12.0 and below deadlock in threaded use
 ]
 
-dynamic = ["version"]
+dynamic = [
+  "version",
+]
 
 [project.urls]
 "Bug Tracker" = "https://github.com/scipp/esssans/issues"
 "Documentation" = "https://scipp.github.io/esssans"
 "Source" = "https://github.com/scipp/esssans"
-
 [tool.setuptools_scm]
 
+[tool.ruff.lint]
+select = ["B", "C4", "DTZ", "E",  "F", "FA",
+          "G", "I", "S", "T20", "PERF", "PGH",
+          "PT", "PYI", "RUF", "UP", "W"]
+ignore = [
+    "E111", "E114", "E117", "D206", "D300",  # conflict with ruff format
+    "UP006", "UP035", "UP007"] # FIXME: this breaks the tests
+pydocstyle.convention = "numpy"
+
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["I"]
+# Assert in tests are fine
+"tests/*" = ["S101"]
+# Blocked by https://github.com/scipp/esssans/issues/95
+"*.ipynb" = ["F403", "F405"]
+"docs/*" = ["T201"]  # printing is ok for demonstration purposes
+
+[tool.ruff.format]
+quote-style = "preserve"
+
 [tool.pytest.ini_options]
 minversion = "7.0"
 addopts = """
@@ -65,18 +83,6 @@ filterwarnings = [
   'ignore:\n            Sentinel is not a public part of the traitlets API:DeprecationWarning',
 ]
 
-[tool.bandit]
-# Excluding tests because bandit doesn't like `assert`.
-exclude_dirs = ["docs/conf.py", "tests"]
-
-[tool.black]
-skip-string-normalization = true
-
-[tool.isort]
-skip_gitignore = true
-profile = "black"
-known_first_party = ["esssans"]
-
 [tool.mypy]
 strict = true
 ignore_missing_imports = true

diff --git a/requirements/make_base.py b/requirements/make_base.py
@@ -24,10 +24,7 @@ def write_dependencies(dependency_name: str, dependencies: List[str]) -> None:
     path = Path(f"{dependency_name}.in")
     if path.exists():
         sections = path.read_text().split(CUSTOM_AUTO_SEPARATOR)
-        if len(sections) > 1:
-            custom = sections[0]
-        else:
-            custom = ""
+        custom = sections[0] if len(sections) > 1 else ""
     else:
         custom = ""
     with path.open("w") as f:

diff --git a/src/ess/isissans/general.py b/src/ess/isissans/general.py
@@ -3,6 +3,7 @@
 """
 Providers for the ISIS instruments.
 """
+
 import scipp as sc
 
 from ..sans.types import (
@@ -48,7 +49,7 @@ def data_to_tof(
 
 
 def monitor_to_tof(
-    da: ConfiguredReducibleMonitor[RunType, MonitorType]
+    da: ConfiguredReducibleMonitor[RunType, MonitorType],
 ) -> TofMonitor[RunType, MonitorType]:
     """Dummy conversion of monitor data to time-of-flight data.
     The monitor data already has a time-of-flight coordinate."""

diff --git a/src/ess/isissans/io.py b/src/ess/isissans/io.py
@@ -3,6 +3,7 @@
 """
 File loading functions for ISIS data, NOT using Mantid.
 """
+
 from typing import NewType
 
 import scipp as sc
@@ -43,9 +44,9 @@ def read_xml_detector_masking(
     filename:
         Path to the XML file.
     """
-    import xml.etree.ElementTree as ET  # nosec
+    import xml.etree.ElementTree as ET
 
-    tree = ET.parse(filename)  # nosec
+    tree = ET.parse(filename)  # noqa: S314
     root = tree.getroot()
 
     masked_detids = []