Clean up linting and tool configs (#1547)

.pre-commit-config.yaml

@@ -21,37 +21,13 @@ repos:
 - repo: https://github.com/pre-commit/pygrep-hooks
   rev: v1.10.0
   hooks:
-    - id: python-check-blanket-noqa
-    - id: python-check-mock-methods
     - id: rst-directive-colons
     - id: rst-inline-touching-normal
     - id: text-unicode-replacement-char
 
-- repo: https://github.com/asottile/pyupgrade
-  rev: 'v3.19.0'
-  hooks:
-    - id: pyupgrade
-      args: ["--py38-plus"]
-
 - repo: https://github.com/astral-sh/ruff-pre-commit
   rev: 'v0.8.0'
   hooks:
     - id: ruff
-      args: ["--fix"]
-
-- repo: https://github.com/pycqa/isort
-  rev: 5.13.2
-  hooks:
-    - id: isort
-
-- repo: https://github.com/psf/black
-  rev: 24.10.0
-  hooks:
-    - id: black
-
-- repo: https://github.com/PyCQA/bandit
-  rev: 1.7.10
-  hooks:
-    - id: bandit
-      args: ["-c", "pyproject.toml"]
-      additional_dependencies: ["bandit[toml]"]
+      args: ["--fix", "--show-fixes"]
+    - id: ruff-format

docs/conf.py

@@ -14,17 +14,12 @@
 import importlib
 import os
 import sys
+import tomllib
 from distutils.version import LooseVersion
 from pathlib import Path
 
 import sphinx
 import stsci_rtd_theme
-
-if sys.version_info < (3, 11):
-    import tomli as tomllib
-else:
-    import tomllib
-
 from sphinx.ext.autodoc import AttributeDocumenter
 
 from romancal.stpipe import RomanStep
@@ -106,14 +101,6 @@ def check_sphinx_version(expected_version):
 
 intersphinx_disabled_reftypes = ["*"]
 
-if sys.version_info[0] == 2:
-    intersphinx_mapping["python"] = ("http://docs.python.org/2/", None)
-    intersphinx_mapping["pythonloc"] = (
-        "http://docs.python.org/",
-        os.path.abspath(
-            os.path.join(os.path.dirname(__file__), "local/python2_local_links.inv")
-        ),
-    )
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom

docs/exts/numfig.py

@@ -56,7 +56,8 @@ def doctree_resolved(app, doctree, docname):
         if app.builder.name != "latex" and app.config.number_figures:
             for cap in figure_info.traverse(caption):
                 cap[0] = Text(
-                    "%s %d: %s" % (app.config.figure_caption_prefix, i, cap[0])
+                    "%s %d: %s"  # noqa: UP031
+                    % (app.config.figure_caption_prefix, i, cap[0])
                 )
 
         for id in figure_info["ids"]:

pyproject.toml

@@ -15,17 +15,18 @@ classifiers = [
 dependencies = [
     "asdf >=3.3.0",
     "asdf-astropy >=0.5.0",
-    "astropy >=5.3.0",
+    "astropy >=6.0.0",
     "crds >=11.16.16",
-    "gwcs >=0.21.0",
+    # "gwcs >=0.21.0",
+    "gwcs @ git+https://github.com/spacetelescope/gwcs.git@master",
     "jsonschema >=4.8",
     "numpy >=1.24",
     "photutils >=1.13.0",
     "pyparsing >=2.4.7",
     "requests >=2.26",
     # "roman_datamodels>=0.22.0,<0.23.0",
     "roman_datamodels @ git+https://github.com/spacetelescope/roman_datamodels.git",
-    "scipy >=1.11",
+    "scipy >=1.14.1",
     # "stcal>=1.10.0,<1.11.0",
     "stcal @ git+https://github.com/spacetelescope/stcal.git@main",
     # "stpipe >=0.7.0,<0.8.0",
@@ -57,7 +58,6 @@ docs = [
     "sphinx-rtd-theme",
     "stsci-rtd-theme",
     "sphinx-autobuild",
-    "tomli; python_version <=\"3.11\"",
 ]
 test = [
     "ci-watson >=0.5.0",
@@ -121,7 +121,7 @@ zip-safe = false
 ]
 
 [tool.pytest.ini_options]
-minversion = 4.6
+minversion = 6.0
 norecursedirs = [
     "docs/_build",
     "romancal/scripts",
@@ -139,9 +139,14 @@ doctest_plus = "enabled"
 doctest_rst = "enabled"
 text_file_format = "rst"
 log_cli_level = "info"
+xfail_strict = true
 addopts = [
+    "--color=yes",      # color test output
+    "--doctest-rst",    # enable doctests
     "--doctest-ignore-import-errors",
-    "--color=yes",
+    "--strict-config",  # fail on unknown config options
+    "--strict-markers", # fail on unknown markers
+    "-ra",              # Show summary of all failures/errorsproduct_names
 ]
 markers = [
     "soctests: run only the SOC tests in the suite.",
@@ -173,30 +178,19 @@ exclude_lines = [
     "if __name__ == \"__main__\":",
 ]
 
-[tool.bandit]
-skips = [
-    "B101",
-    "B307",
-    "B404",
-    "B603",
-]
-exclude_dirs = [
-    "romancal/regtest/scripts",
-]
-
-[tool.isort]
-profile = "black"
-filter_files = true
-line_length = 88
-
-[tool.black]
-line-length = 88
-force-exclude = "^/(\n  (\n      \\.eggs\n    | \\.git\n    | \\.pytest_cache\n    | \\.tox\n  )/\n)\n"
-
 [tool.ruff]
 line-length = 88
 
+
 [tool.ruff.lint]
+extend-select = [
+    "UP",   # PyUpgrade
+    "I",    # isort
+    "B",    # BugBear
+    "S",    # Bandit
+    "RUF",  # ruff specific
+    "NPY",  # Numpy lint
+]
 exclude = [
     "jdocs",
     ".tox",
@@ -206,14 +200,20 @@ exclude = [
 ignore = [
     "E741", # ambiguous variable name
 ]
-extend-select = [
-    "NPY",
-]
 
 [tool.ruff.lint.extend-per-file-ignores]
 "romancal/associations/__init__.py" = [
     "E402",
 ]
+"romancal/**/tests/**.py" = [
+    "S101" # Bandit: Use of assert detected (fine in test files)
+]
+"romancal/**/test/**.py" = [
+    "S101" # Bandit: Use of assert detected (fine in test files)
+]
+"romancal/regtest/**.py" = [
+    "S101" # Bandit: Use of assert detected (fine in test files)
+]
 
 [tool.cibuildwheel.macos]
 archs = [

romancal/assign_wcs/assign_wcs_step.py

@@ -3,7 +3,10 @@
 
 """
 
+from __future__ import annotations
+
 import logging
+from typing import TYPE_CHECKING
 
 import gwcs.coordinate_frames as cf
 from astropy import coordinates as coord
@@ -16,6 +19,9 @@
 from . import pointing
 from .utils import add_s_region, wcs_bbox_from_shape
 
+if TYPE_CHECKING:
+    from typing import ClassVar
+
 log = logging.getLogger(__name__)
 log.setLevel(logging.DEBUG)
 
@@ -28,7 +34,7 @@ class AssignWcsStep(RomanStep):
 
     class_alias = "assign_wcs"
 
-    reference_file_types = ["distortion"]
+    reference_file_types: ClassVar = ["distortion"]
 
     def process(self, input):
         reference_file_names = {}

romancal/assign_wcs/utils.py

@@ -1,6 +1,5 @@
 import functools
 import logging
-from typing import List, Tuple, Union
 
 import numpy as np
 from astropy.coordinates import SkyCoord
@@ -44,8 +43,8 @@ def wcs_from_footprints(
     pscale=None,
     rotation=None,
     shape=None,
-    ref_pixel: Tuple[float, float] = None,
-    ref_coord: Tuple[float, float] = None,
+    ref_pixel: tuple[float, float] | None = None,
+    ref_coord: tuple[float, float] | None = None,
 ):
     """
     Create a WCS from a list of input data models.
@@ -217,9 +216,9 @@ def wcs_from_footprints(
 
 def compute_scale(
     wcs: WCS,
-    fiducial: Union[tuple, np.ndarray],
-    disp_axis: int = None,
-    pscale_ratio: float = None,
+    fiducial: tuple | np.ndarray,
+    disp_axis: int | None = None,
+    pscale_ratio: float | None = None,
 ) -> float:
     """Compute scaling transform.
 
@@ -282,7 +281,7 @@ def compute_scale(
 
 def calc_rotation_matrix(
     roll_ref: float, v3i_yang: float, vparity: int = 1
-) -> List[float]:
+) -> list[float]:
     """Calculate the rotation matrix.
 
     Parameters

romancal/associations/association.py

@@ -1,4 +1,4 @@
-""" Main module for associations """
+"""Main module for associations"""
 
 import json
 import logging

romancal/associations/association_io.py

@@ -66,7 +66,9 @@ def load(cls, serialized):
             asn = loader(serialized)
         except Exception as err:
             logger.debug(f'Error unserializing: "{err}"')
-            raise AssociationNotValidError(f'Container is not JSON: "{serialized}"')
+            raise AssociationNotValidError(
+                f'Container is not JSON: "{serialized}"'
+            ) from err
 
         return asn
 
@@ -132,7 +134,9 @@ def load(cls, serialized):
             asn = yaml_lib.safe_load(serialized)
         except Exception as err:
             logger.debug(f'Error unserializing: "{err}"')
-            raise AssociationNotValidError(f'Container is not YAML: "{serialized}"')
+            raise AssociationNotValidError(
+                f'Container is not YAML: "{serialized}"'
+            ) from err
         return asn
 
     @staticmethod

romancal/associations/lib/constraint.py

@@ -1,5 +1,4 @@
-"""Constraints
-"""
+"""Constraints"""
 
 import abc
 import collections
@@ -139,7 +138,7 @@ def __iter__(self):
         yield self
 
     def __repr__(self):
-        result = f"{self.__class__.__name__}({str(self.__dict__)})"
+        result = f"{self.__class__.__name__}({self.__dict__!s})"
         return result
 
     def __str__(self):
@@ -600,7 +599,7 @@ class Constraint:
                       'value': 'a_value',
                       'name': 'simple',
                       'matched': False})
-    """  # noqa: E501
+    """
 
     def __init__(
         self,
@@ -639,8 +638,8 @@ def __init__(
             self.constraints = [init]
         else:
             raise TypeError(
-                "Invalid initialization value type {}.\nValid types are"
-                " `SimpleConstraint`, `Constraint`,\nor subclass.".format(type(init))
+                f"Invalid initialization value type {type(init)}.\nValid types are"
+                " `SimpleConstraint`, `Constraint`,\nor subclass."
             )
 
         # Give some defaults real meaning.
@@ -664,10 +663,10 @@ def dup_names(
             and all the constraints that define that name.
         """
         attrs = self.get_all_attr("name")
-        constraints, names = zip(*attrs)
+        constraints, names = zip(*attrs, strict=False)
         dups = [name for name, count in collections.Counter(names).items() if count > 1]
         result = collections.defaultdict(list)
-        for name, constraint in zip(names, constraints):
+        for name, constraint in zip(names, constraints, strict=False):
             if name in dups:
                 result[name].append(constraint)
 

romancal/associations/lib/decorators.py

@@ -10,7 +10,7 @@
 
 from functools import wraps
 
-__all__ = ["memoize", "singleton", "memoize_attr_check"]
+__all__ = ["memoize", "memoize_attr_check", "singleton"]
 
 
 def _make_key(args, kwargs):

romancal/associations/lib/diff.py

@@ -1,4 +1,4 @@
-""""Diff and compare associations"""
+""" "Diff and compare associations"""
 
 import logging
 import re
@@ -267,9 +267,9 @@ def compare_membership(left, right):
             )
         )
 
-    for left_idx, left_product in enumerate(products_left):
+    for left_product in products_left:
         left_product_name = components(left_product["name"])
-        for right_idx, right_product in enumerate(products_right):
+        for right_product in products_right:
             if components(right_product["name"]) != left_product_name:
                 continue
             try: