[MAINT] Switch to pyproject.toml, enable ruff linting / formating, setup pre-commit

.github/workflows/lint_workflow.yml

@@ -1,4 +1,4 @@
-name: Lint workflow
+name: Lint
 
 on:
   push:
@@ -11,17 +11,20 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+
     steps:
-      - uses: actions/checkout@v2
-        with:
-          fetch-depth: '2'
-      - name: Setup Python
-        uses: actions/setup-python@v1
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: ${{ matrix.python-version }}
 
-      - name: Install Tox
-        run: pip install tox
+      - name: Install dependencies
+        run: |
+          python -m pip install pre-commit
 
-      - name: Run Pylint
-        run:  tox -e pylint-ci
+      - name: Lint
+        run: pre-commit run --all-files --show-diff-on-failure

.gitignore

@@ -26,6 +26,7 @@ __pycache__
 # Coverage reports
 htmlcov/*
 .coverage
+coverage.xml
 
 # check_pylint_diff
 .pylint_cache

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.14.14
+    hooks:
+      # Run the linter.
+      - id: ruff-check
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format

doc/pyproject.toml

@@ -0,0 +1,4 @@
+[tool.ruff]
+extend = "../pyproject.toml"
+# Exclude conf.py
+extend-exclude = ["conf.py"]

orangecontrib/spectroscopy/__init__.py

@@ -16,9 +16,10 @@ def get_sample_datasets_dir():
 try:
     import dask
     import dask.distributed
-    dask_client = dask.distributed.Client(processes=False, n_workers=2,
-                                          set_as_default=False,
-                                          dashboard_address=None)
+
+    dask_client = dask.distributed.Client(
+        processes=False, n_workers=2, set_as_default=False, dashboard_address=None
+    )
 except ImportError:
     dask = None
-    dask_client = None
+    dask_client = None

orangecontrib/spectroscopy/data.py

@@ -1,19 +1,28 @@
 # pylint: disable=unused-import
+# ruff: noqa: F401
 
 # import for compatibility before the restructure
 import Orange.data.io  # legacy import so that file readers are registered
-from orangecontrib.spectroscopy.io.util import \
-    _metatable_maplocs, _spectra_from_image, _spectra_from_image_2d,\
-    build_spec_table
+from orangecontrib.spectroscopy.io.util import (
+    _metatable_maplocs,
+    _spectra_from_image,
+    _spectra_from_image_2d,
+    build_spec_table,
+)
 
 from orangecontrib.spectroscopy.util import getx, spectra_mean
 
 # imports for workflow compatibility when a reader was explicitly selected
 # In the owfile settings, explicitly selected selected readers are stored with
 # full module and class name. Moving but not adding imports would show
 # the missing reader error.
-from orangecontrib.spectroscopy.io.agilent import AgilentImageReader, AgilentImageIFGReader,\
-    agilentMosaicReader, agilentMosaicIFGReader, agilentMosaicTileReader
+from orangecontrib.spectroscopy.io.agilent import (
+    AgilentImageReader,
+    AgilentImageIFGReader,
+    agilentMosaicReader,
+    agilentMosaicIFGReader,
+    agilentMosaicTileReader,
+)
 from orangecontrib.spectroscopy.io.ascii import AsciiColReader, AsciiMapReader
 from orangecontrib.spectroscopy.io.diamond import NXS_STXM_Diamond_I08
 from orangecontrib.spectroscopy.io.envi import EnviMapReader
@@ -25,6 +34,9 @@
 from orangecontrib.spectroscopy.io.omnic import OmnicMapReader, SPCReader, SPAReader
 from orangecontrib.spectroscopy.io.opus import OPUSReader
 from orangecontrib.spectroscopy.io.ptir import PTIRFileReader
-from orangecontrib.spectroscopy.io.soleil import SelectColumnReader, HDF5Reader_HERMES, \
-    HDF5Reader_ROCK
+from orangecontrib.spectroscopy.io.soleil import (
+    SelectColumnReader,
+    HDF5Reader_HERMES,
+    HDF5Reader_ROCK,
+)
 from orangecontrib.spectroscopy.io.wire import WiREReaders

orangecontrib/spectroscopy/io/__init__.py

@@ -10,8 +10,13 @@
 from .matlab import MatlabReader
 
 # Instrument-specific readers
-from .agilent import AgilentImageReader, AgilentImageIFGReader, agilentMosaicReader,\
-    agilentMosaicIFGReader, agilentMosaicTileReader
+from .agilent import (
+    AgilentImageReader,
+    AgilentImageIFGReader,
+    agilentMosaicReader,
+    agilentMosaicIFGReader,
+    agilentMosaicTileReader,
+)
 from .neaspec import NeaReader, NeaReaderGSF, NeaReaderMultiChannel
 from .omnic import OmnicMapReader, SPAReader, SPCReader
 from .opus import OPUSReader