Upgrade python version to 3.12 and fix linting errors

.github/workflows/test.yml

@@ -15,6 +15,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: astral-sh/ruff-action@v3
         with:
+          version: "latest"
           args: "check --fix-only --exit-non-zero-on-fix"
       - uses: pre-commit-ci/lite-action@v1.1.0
         if: always()
@@ -27,7 +28,7 @@ jobs:
     strategy:
       matrix:
         os: [macos-latest, ubuntu-latest, windows-latest]
-        python-version: ['3.10', '3.11', '3.12']
+        python-version: ['3.12']
       fail-fast: false
 
     env:

.gitignore

@@ -25,6 +25,10 @@
 /dist
 .mplconfig
 
+# INSTALL.md recommends a venv that should not be committed
+venv
+.venv
+
 # doc build
 /docs/sphinx-docs/build
 
@@ -42,6 +46,3 @@ tests.log
 /installers/dist
 *.exe
 sasdata/_version.py
-
-# Local pre-commit hooks
-.pre-commit-config.yaml

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+default_install_hook_types: [pre-commit, pre-push]
+
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.1
+    hooks:
+      # Run the linter, applying any available fixes
+      - id: ruff-check
+        stages: [ pre-commit, pre-push ]
+        args: [ --fix-only ]

conftest.py

@@ -0,0 +1,11 @@
+import pytest
+
+
+def pytest_addoption(parser):
+    parser.addoption(
+        "--show_plots", action="store_true", default=False, help="Display diagnostic plots during tests"
+    )
+
+@pytest.fixture
+def show_plots(request):
+    return request.config.getoption("--show_plots")

pyproject.toml

@@ -20,7 +20,7 @@ dynamic = [
 ]
 description = "Sas Data Loader application"
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.12"
 license = { text = "BSD-3-Clause" }
 authors = [
     {name = "SasView Team", email = "developers@sasview.org"},
@@ -118,3 +118,28 @@ testpaths = [
 norecursedirs = [
   "sasdata",
 ]
+
+[tool.ruff]
+line-length = 120
+
+[tool.ruff.lint]
+# The ruff rules are available at: https://docs.astral.sh/ruff/rules/
+select = ["E",       # pycodestyle errors
+          "F",       # pyflakes
+          "I",       # isort
+          "UP",      # pyupgrade
+          "W",       # pycodestyle warnings
+          "SIM118",  # Use `key in dict` instead of `key in dict.keys()`
+          "SIM300"]  # Yoda condition detected
+
+
+ignore = ["E501",    # line too long (leave to formatter)
+          "UP008",   # Use `super()` instead of `super(__class__, self)`
+          "UP031"]   # Use format specifiers instead of percent format
+
+[tool.ruff.lint.isort.sections]
+# Group all SasView and SasModels imports into a separate section.
+"sas" = ["sas", "sasmodels"]
+
+[tool.ruff.lint.isort]
+section-order = ["future", "standard-library", "third-party", "sas", "first-party", "local-folder"]

requirements.txt

@@ -4,3 +4,16 @@ lxml
 
 # Calculation
 numpy
+scipy
+
+# Unit testing
+pytest
+unittest-xml-reporting
+
+# Documentation (future)
+sphinx
+html5lib
+
+# Other stuff
+matplotlib
+pre-commit

sasdata/data_util/formatnum.py

@@ -9,9 +9,9 @@
 where the number in parenthesis is the uncertainty in the last two digits of v.
 
 :func:`format_uncertainty` uses the compact format by default, but this
-can be changed to use the expanded +/- format by setting 
+can be changed to use the expanded +/- format by setting
 format_uncertainty.compact to False.
-    
+
 The formatted string uses only the number of digits warranted by
 the uncertainty in the measurement.
 
@@ -37,7 +37,9 @@
 formatter.compact flag.
 """
 import math
+
 import numpy as np
+
 __all__ = ['format_uncertainty', 'format_uncertainty_pm',
            'format_uncertainty_compact']
 
@@ -85,7 +87,7 @@ class UncertaintyFormatter:
     True or False.  The default is True.
     """
     compact = True
-    
+
     def __call__(self, value, uncertainty):
         """
         Given *value* and *uncertainty*, return a string representation.
@@ -140,7 +142,7 @@ def _format_uncertainty(value, uncertainty, compact):
         # Extreme cases: zeros before value or after error
         # The value is ###.###(##)e#, ##.####(##)e# or #.#####(##)e#
         pass
-    
+
     # Force engineering notation, with exponent a multiple of 3
     val_place = int(math.floor(val_place / 3.)) * 3
 
@@ -279,7 +281,7 @@ def test_compact():
     assert value_str(-np.inf,None) == "-inf"
     assert value_str(np.inf,None) == "inf"
     assert value_str(np.nan,None) == "NaN"
-    
+
     # bad or missing uncertainty
     assert value_str(-1.23567,np.nan) == "-1.23567"
     assert value_str(-1.23567,-np.inf) == "-1.23567"
@@ -410,7 +412,7 @@ def test_pm():
     assert value_str(-np.inf,None) == "-inf"
     assert value_str(np.inf,None) == "inf"
     assert value_str(np.nan,None) == "NaN"
-    
+
     # bad or missing uncertainty
     assert value_str(-1.23567,np.nan) == "-1.23567"
     assert value_str(-1.23567,-np.inf) == "-1.23567"
@@ -432,8 +434,9 @@ def main():
     test_compact()
     test_pm()
     test_default()
-    
+
     import doctest
     doctest.testmod()
 
-if __name__ == "__main__": main()
+if __name__ == "__main__":
+    main()

sasdata/data_util/loader_exceptions.py

@@ -2,7 +2,6 @@
 Exceptions specific to loading data.
 """
 
-from typing import Optional
 
 
 class NoKnownLoaderException(Exception):
@@ -11,7 +10,7 @@ class NoKnownLoaderException(Exception):
     extension of the loaded file. This exception should only be thrown by
     loader.py.
     """
-    def __init__(self, e: Optional[str] = None):
+    def __init__(self, e: str | None = None):
         self.message = e
 
 
@@ -20,7 +19,7 @@ class DefaultReaderException(Exception):
     Exception for files with no associated reader. This should be thrown by
     default readers only to tell Loader to try the next reader.
     """
-    def __init__(self, e: Optional[str] = None):
+    def __init__(self, e: str | None = None):
         self.message = e
 
 
@@ -29,7 +28,7 @@ class FileContentsException(Exception):
     Exception for files with an associated reader, but with no loadable data.
     This is useful for catching loader or file format issues.
     """
-    def __init__(self, e: Optional[str] = None):
+    def __init__(self, e: str | None = None):
         self.message = e
 
 
@@ -39,5 +38,5 @@ class DataReaderException(Exception):
     along the way.
     Any exceptions of this type should be put into the datainfo.errors
     """
-    def __init__(self, e: Optional[str] = None):
+    def __init__(self, e: str | None = None):
         self.message = e

sasdata/data_util/manipulations.py

@@ -20,8 +20,8 @@
 
 # TODO: copy the meta data from the 2D object to the resulting 1D object
 import math
+
 import numpy as np
-from typing import Optional, Union
 
 from sasdata.dataloader.data_info import Data1D, Data2D
 
@@ -41,7 +41,7 @@ def position_and_wavelength_to_q(dx: float, dy: float, detector_distance: float,
     return (4.0 * math.pi / wavelength) * math.sin(theta)
 
 
-def get_q_compo(dx: float, dy: float, detector_distance: float, wavelength: float, compo: Optional[str] = None) -> float:
+def get_q_compo(dx: float, dy: float, detector_distance: float, wavelength: float, compo: str | None = None) -> float:
     """
     This reduces tiny error at very large q.
     Implementation of this func is not started yet.<--ToDo
@@ -102,7 +102,7 @@ def get_pixel_fraction_square(x: float, x_min: float, x_max: float) -> float:
         return 1.0
 
 
-def get_intercept(q: float, q_0: float, q_1: float) -> Union[float, None]:
+def get_intercept(q: float, q_0: float, q_1: float) -> float | None:
     """
     Returns the fraction of the side at which the
     q-value intercept the pixel, None otherwise.
@@ -235,7 +235,7 @@ def get_dq_data(data2d: Data2D) -> np.array:
 ################################################################################
 
 
-def reader2D_converter(data2d: Optional[Data2D] = None) -> Data2D:
+def reader2D_converter(data2d: Data2D | None = None) -> Data2D:
     """
     convert old 2d format opened by IhorReader or danse_reader
     to new Data2D format

sasdata/data_util/nxsunit.py

@@ -45,11 +45,12 @@
 
 import math
 import re
-from typing import Dict, Union, TypeVar, Tuple, Sequence, Optional, List
+from collections.abc import Sequence
+from typing import TypeVar
 
 __all__ = ['Converter', 'standardize_units']
 T = TypeVar('T')
-ConversionType = Union[float, Tuple[float, float]]
+ConversionType = float | tuple[float, float]
 DIMENSIONS = {}  # type: Dict[str, Dict[str, ConversionType]]
 AMBIGUITIES = {}  # type: Dict[str, str]
 PREFIX = dict(peta=1e15, tera=1e12, giga=1e9, mega=1e6, kilo=1e3, deci=1e-1, centi=1e-2, milli=1e-3, mili=1e-3,
@@ -60,7 +61,7 @@
 # Limited form of units for returning objects of a specific type.
 # Maybe want to do full units handling with e.g., pyre's
 # unit class. For now lets keep it simple.  Note that
-def _build_metric_units(unit: str, abbr: str) -> Dict[str, float]:
+def _build_metric_units(unit: str, abbr: str) -> dict[str, float]:
     """
     Construct standard SI names for the given unit.
     Builds e.g.,
@@ -89,7 +90,7 @@ def _build_metric_units(unit: str, abbr: str) -> Dict[str, float]:
     return units
 
 
-def _build_plural_units(**kw: Dict[str, ConversionType]) -> Dict[str, ConversionType]:
+def _build_plural_units(**kw: dict[str, ConversionType]) -> dict[str, ConversionType]:
     """
     Construct names for the given units.  Builds singular and plural form.
     """
@@ -99,7 +100,7 @@ def _build_plural_units(**kw: Dict[str, ConversionType]) -> Dict[str, Conversion
     return units
 
 
-def _build_degree_units(name: str, symbol: str, conversion: ConversionType) -> Dict[str, ConversionType]:
+def _build_degree_units(name: str, symbol: str, conversion: ConversionType) -> dict[str, ConversionType]:
     """
     Builds variations on the temperature unit name, including the degree
     symbol or the word degree.
@@ -118,7 +119,7 @@ def _build_degree_units(name: str, symbol: str, conversion: ConversionType) -> D
 
 
 def _build_inv_n_units(names: Sequence[str], conversion: ConversionType,
-                       n: int = 2) -> Dict[str, ConversionType]:
+                       n: int = 2) -> dict[str, ConversionType]:
     """
     Builds variations on inverse x to the nth power units, including 1/x^n, invx^n, x^-n and x^{-n}.
     """
@@ -132,7 +133,7 @@ def _build_inv_n_units(names: Sequence[str], conversion: ConversionType,
     return units
 
 
-def _build_inv_n_metric_units(unit: str, abbr: str, n: int = 2) -> Dict[str, ConversionType]:
+def _build_inv_n_metric_units(unit: str, abbr: str, n: int = 2) -> dict[str, ConversionType]:
     """
     Using the return from _build_metric_units, build inverse to the nth power variations on all units
     (1/x^n, invx^n, x^{-n} and x^-n)
@@ -265,7 +266,7 @@ def _build_all_units():
     DIMENSIONS['dimensionless'] = unknown
 
 
-def standardize_units(unit: Union[str, None]) -> List[str]:
+def standardize_units(unit: str | None) -> list[str]:
     """
     Convert supplied units to a standard format for maintainability
     :param unit: Raw unit as supplied
@@ -301,7 +302,7 @@ def standardize_units(unit: Union[str, None]) -> List[str]:
     return _format_unit_structure(unit)
 
 
-def _format_unit_structure(unit: Optional[str] = None) -> List[str]:
+def _format_unit_structure(unit: str | None = None) -> list[str]:
     """
     Format units a common way
     :param unit: Unit string to be formatted
@@ -373,7 +374,7 @@ def units(self) -> str:
     def units(self, unit: str):
         self._units = standardize_units(unit)
 
-    def __init__(self, units: Optional[str] = None, dimension: Optional[List[str]] = None):
+    def __init__(self, units: str | None = None, dimension: list[str] | None = None):
         self.units = units if units is not None else 'a.u.'  # type: str
 
         # Lookup dimension if not given
@@ -398,20 +399,20 @@ def __init__(self, units: Optional[str] = None, dimension: Optional[List[str]] =
         self.scalebase = base[0]
         self.scaleoffset = base[1]
 
-    def scale(self, units: str = "", value: T = None) -> Union[List[float], T]:
+    def scale(self, units: str = "", value: T = None) -> list[float] | T:
         """Scale the given value using the units string supplied"""
         units = standardize_units(units) if units is not None else ['']
         base = self._get_scale_for_units(units)
         value = self._scale_with_offset(value, base)
         return value
 
-    def _scale_with_offset(self, value: float, scale_base: Tuple[float, float]) -> float:
+    def _scale_with_offset(self, value: float, scale_base: tuple[float, float]) -> float:
         """Scale the given value and add the offset using the units string supplied"""
         inscale, inoffset = self.scalebase, self.scaleoffset
         outscale, outoffset = scale_base
         return (value + outoffset) * inscale / outscale - inoffset
 
-    def _get_scale_for_units(self, units: List[str]):
+    def _get_scale_for_units(self, units: list[str]):
         """Protected method to get scale factor and scale offset as a combined value"""
         base = (1.0, 0.0)
         for scalemap, unit in zip(self.scalemap, units):
@@ -423,7 +424,7 @@ def _get_scale_for_units(self, units: List[str]):
             base = (base[0] * unit_scale[0], base[1] + unit_scale[1])
         return base
 
-    def get_compatible_units(self) -> List[str]:
+    def get_compatible_units(self) -> list[str]:
         """Return a list of compatible units for the current Convertor object"""
         unique_units = []
         conv_list = []
@@ -436,7 +437,7 @@ def get_compatible_units(self) -> List[str]:
             unique_units = [x for _, x in sorted(zip(conv_list, unique_units))]
         return unique_units
 
-    def __call__(self, value: T, units: Optional[str] = "") -> Union[List[float], T]:
+    def __call__(self, value: T, units: str | None = "") -> list[float] | T:
         # Note: calculating a*1 rather than simply returning a would produce
         # an unnecessary copy of the array, which in the case of the raw
         # counts array would be bad.  Sometimes copying and other times