Adjust style checks to align with jwst

.pre-commit-config.yaml

@@ -1,6 +1,8 @@
+exclude: ".*\\.asdf$"
+
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-added-large-files
       - id: check-ast
@@ -15,49 +17,20 @@ repos:
       # - id: end-of-file-fixer
       # - id: trailing-whitespace
 
-  - repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.10.0
-    hooks:
-      - id: rst-directive-colons
-      - id: rst-inline-touching-normal
-      - id: text-unicode-replacement-char
-
-  # - repo: https://github.com/codespell-project/codespell
-  #   rev: v2.2.5
-  #   hooks:
-  #     - id: codespell
-  #       args: ["--write-changes"]
-  #       additional_dependencies:
-  #         - tomli
-
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.1.5"
+    rev: 'v0.6.8'
     hooks:
       - id: ruff
-        args: ["--fix", "--show-fixes"]
+        args: ["--fix"]
       # - id: ruff-format
 
-  - repo: https://github.com/MarcoGorelli/cython-lint
-    rev: v0.15.0
+  - repo: https://github.com/PyCQA/bandit
+    rev: 1.7.10
     hooks:
-      - id: cython-lint
-      # - id: double-quote-cython-strings
+      - id: bandit
+        args: ["-r", "-ll", "src", "tests"]
 
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-        name: isort (cython)
-        types: [cython]
-
-  - repo: https://github.com/adamchainz/blacken-docs
-    rev: 1.16.0
+  - repo: https://github.com/MarcoGorelli/cython-lint
+    rev: v0.16.2
     hooks:
-      - id: blacken-docs
-        additional_dependencies:
-          - black==22.12.0
-
-  # - repo: https://github.com/pre-commit/mirrors-prettier
-  #   rev: "v3.0.1"
-  #   hooks:
-  #     - id: prettier
+      - id: cython-lint

changes/295.general.rst

@@ -0,0 +1 @@
+Adjust code style checks.

pyproject.toml

@@ -120,69 +120,12 @@ src = [
 ]
 
 [tool.ruff.lint]
-select = [
-    #"F",      # Pyflakes (part of default flake8)
-    #"W", "E", # pycodestyle (part of default flake8)
-    #"I",      # isort (import sorting)
-    # "N",      # pep8-naming
-    #"D",      # pydocstyle (docstring style guide)
-    #"UP",     # pyupgrade (upgrade code to modern python)
-    "YTT",    # flake8-2020 (system version info)
-    "ANN",    # flake8-annotations (best practices for type annotations)
-    #"S",      # flake8-bandit (security checks)
-    "BLE",    # flake8-blind-except (prevent blind except statements)
-    #"B",      # flake8-bugbear (prevent common gotcha bugs)
-    "A",      # flake8-builtins (prevent shadowing of builtins)
-    "C4",     # flake8-comprehensions (best practices for comprehensions)
-    "T10",    # flake8-debugger (prevent debugger statements in code)
-    #"EM",     # flake8-errormessages (best practices for error messages)
-    "FA",     # flake8-future-annotations (correct usage future annotations)
-    "ISC",    # flake8-implicit-str-concat (prevent implicit string concat)
-    "ICN",    # flake8-import-conventions (enforce import conventions)
-    #"G",      # flake8-logging-format (best practices for logging)
-    "INP",    # flake8-no-pep420 (prevent use of PEP420, i.e. implicit name spaces)
-    #"PIE",    # flake8-pie (misc suggested improvement linting)
-    # "T20",    # flake8-print (prevent print statements in code)
-    #"PT",     # flake8-pytest-style (best practices for pytest)
-    #"Q",      # flake8-quotes (best practices for quotes)
-    "RSE",    # flake8-raise (best practices for raising exceptions)
-    #"RET",    # flake8-return (best practices for return statements)
-    #"SLF",    # flake8-self (prevent private member access)
-    "SLOT",   # flake8-slots (require __slots__ for immutable classes)
-    #"SIM",    # flake8-simplify (suggest simplifications to code where possible)
-    "TID",    # flake8-tidy-imports (prevent banned api and best import practices)
-    "TCH",    # flake8-type-checking (move type checking imports into type checking blocks)
-    "INT",    # flake8-gettext (when to use printf style strings)
-    # "ARG",    # flake8-unused-arguments (prevent unused arguments)
-    #"PTH",    # flake8-use-pathlib (prefer pathlib over os.path)
-    # "ERA",    # eradicate (remove commented out code)
-    "PGH",    # pygrep (simple grep checks)
-    #"PL",     # pylint (general linting, flake8 alternative)
-    #"TRY",    # tryceratops (linting for try/except blocks)
-    "FLY",    # flynt (f-string conversion where possible)
-    #"NPY",    # NumPy-specific checks (recommendations from NumPy)
-    #"PERF",   # Perflint (performance linting)
-    "LOG",
-    #"RUF",    # ruff specific checks
+extend-select = [
+    "I",  # isort
 ]
 ignore = [
-    "ISC001", # interferes with formatter
-    "PLR0912", # Too many branches
-    "PLR0913", # Too many arguments
-    "PLR0915", # Too many statements
-    "PLR2004", # Magic value used in comparison
-    "ANN101", # Missing type annotation for self in method
-    "ANN102", # Missing type annotation for cls in classmethod
-
-    # Pydocstyle (to fix over time
-    "D100", # Undocumented public module
-    "D101", # Undocumented public class
-    "D102", # Undocumented public method
-    "D103", # Undocumented public function
-    "D104", # Undocumented public package
-    "D205", # 1 blank line required between summary line and description
-    "D401", # First line of docstring should be in imperative mood
-    "D404", # First word of docstring should not be This
+    # "E741", # ambiguous variable name (O/0, l/I, etc.)
+    # "E722", # Do not use bare `except`
 ]
 exclude = [
     "docs",
@@ -192,18 +135,6 @@ exclude = [
     ".eggs",
 ]
 
-[tool.ruff.lint.extend-per-file-ignores]
-"tests/*.py" = [
-    "S101",
-    "D",
-]
-
-[tool.ruff.lint.pydocstyle]
-convention = "numpy"
-
-[tool.ruff.lint.flake8-annotations]
-ignore-fully-untyped = true  # Turn of annotation checking for fully untyped code
-
 [tool.mypy]
 python_version = "3.12"
 warn_return_any = true

src/stcal/alignment/util.py

@@ -4,8 +4,8 @@
 import functools
 import logging
 import re
-from typing import TYPE_CHECKING
 import warnings
+from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
     from collections.abc import Callable, Sequence

src/stcal/jump/jump.py

@@ -3,12 +3,10 @@
 import time
 import warnings
 
-import numpy as np
-import cv2 as cv
 import astropy.stats as stats
-
-from astropy.convolution import Ring2DKernel
-from astropy.convolution import convolve
+import cv2 as cv
+import numpy as np
+from astropy.convolution import Ring2DKernel, convolve
 
 from . import constants
 from . import twopoint_difference as twopt
@@ -760,7 +758,6 @@ def extend_ellipses(
             saty, satx = np.where(sat_pix == sat_flag)
             jump_ellipse[saty, satx] = 0
             out_gdq_cube[intg, flg_grp, :, :] = np.bitwise_or(gdq_cube[intg, flg_grp, :, :], jump_ellipse)
-    diff_cube = out_gdq_cube - gdq_cube
     return out_gdq_cube, num_ellipses
 
 def find_last_grp(grp, ngrps, num_grps_masked):

src/stcal/jump/twopoint_difference.py

@@ -2,7 +2,6 @@
 import warnings
 
 import numpy as np
-import warnings
 from astropy import stats
 
 log = logging.getLogger(__name__)
@@ -490,7 +489,6 @@ def calc_med_first_diffs(in_first_diffs):
         return np.nan
 
     if first_diffs.ndim == 2:  # in the case where input is a single pixel
-        nansum = np.sum(np.isnan(first_diffs), axis=(0, 1))
         num_usable_diffs = first_diffs.size - np.sum(np.isnan(first_diffs), axis=(0, 1))
         if num_usable_diffs >= 4:  # if 4+, clip largest and return median
             mask = np.ones_like(first_diffs).astype(bool)
@@ -500,7 +498,6 @@ def calc_med_first_diffs(in_first_diffs):
         elif num_usable_diffs == 3:  # if 3, no clipping just return median
             return np.nanmedian(first_diffs)
         elif num_usable_diffs == 2:  # if 2, return diff with minimum abs
-            TEST = np.nanargmin(np.abs(first_diffs))
             diff_min_idx = np.nanargmin(first_diffs)
             location = np.unravel_index(diff_min_idx, first_diffs.shape)
             return first_diffs[location]

src/stcal/outlier_detection/utils.py

@@ -1,18 +1,18 @@
 """
 Utility functions for outlier detection routines
 """
-import warnings
 
+import logging
+
+import gwcs
 import numpy as np
 from astropy.stats import sigma_clip
 from drizzle.cdrizzle import tblot
 from scipy import ndimage
 from skimage.util import view_as_windows
-import gwcs
 
 from stcal.alignment.util import wcs_bbox_from_shape
 
-import logging
 log = logging.getLogger(__name__)
 log.setLevel(logging.DEBUG)
 

src/stcal/ramp_fitting/likely_algo_classes.py

@@ -278,6 +278,9 @@
             Bias of the best-fit count rate from using cvec plus the observed
             resultants to estimate the covariance matrix.
         """
+
+        from .likely_fit import fit_ramps
+
         alpha = countrates[np.newaxis, :] * self.alpha_phnoise[:, np.newaxis]
         alpha += sig**2 * self.alpha_readnoise[:, np.newaxis]
         beta = countrates[np.newaxis, :] * self.beta_phnoise[:, np.newaxis]
@@ -291,8 +294,6 @@
         # try to avoid problems with roundoff error
         da_incr = da * (countrates[np.newaxis, :] + sig**2)
 
-        dalpha = da_incr * self.alpha_phnoise[:, np.newaxis]
-        dbeta = da_incr * self.beta_phnoise[:, np.newaxis]
         result_high_a = fit_ramps(z, self, sig, countrateguess=countrates + da_incr)
         # finite difference approximation to dw/da
 

src/stcal/ramp_fitting/likely_fit.py

@@ -1,20 +1,13 @@
 #! /usr/bin/env python
 
 import logging
-import multiprocessing
-import time
-import scipy
-import sys
 import warnings
 
-from multiprocessing import cpu_count
-from pprint import pprint
-
 import numpy as np
+import scipy
 
-from . import ramp_fit_class, utils
-from .likely_algo_classes import IntegInfo, RampResult, Covar
-
+from . import utils
+from .likely_algo_classes import Covar, IntegInfo, RampResult
 
 DELIM = "=" * 80
 SQRT2 = np.sqrt(2)

src/stcal/ramp_fitting/ols_fit.py

@@ -2,16 +2,15 @@
 
 import logging
 import multiprocessing
+import sys
 import time
 import warnings
 from multiprocessing import cpu_count
-import sys
 
 import numpy as np
 
-from .slope_fitter import ols_slope_fitter  # c extension
 from . import ramp_fit_class, utils
-
+from .slope_fitter import ols_slope_fitter  # c extension
 
 log = logging.getLogger(__name__)
 log.setLevel(logging.DEBUG)

src/stcal/ramp_fitting/ramp_fit.py

@@ -19,9 +19,9 @@
 from astropy import units as u
 
 from . import (
-    gls_fit,    # used only if algorithm is "GLS"
-    likely_fit, # used only if algorithm is "LIKELY"
-    ols_fit,    # used only if algorithm is "OLS"
+    gls_fit,  # used only if algorithm is "GLS"
+    likely_fit,  # used only if algorithm is "LIKELY"
+    ols_fit,  # used only if algorithm is "OLS"
     ramp_fit_class,
 )
 
@@ -261,9 +261,9 @@ def ramp_fit_data(
     # a minimum of a four group ramp is needed.
     ngroups = ramp_data.data.shape[1]
     if algorithm.upper() == "LIKELY" and ngroups < likely_fit.LIKELY_MIN_NGROUPS:
-        log.info(f"When selecting the LIKELY ramp fitting algorithm the"
-                  " ngroups needs to be a minimum of {likely_fit.LIKELY_MIN_NGROUPS},"
-                  " but ngroups = {ngroups}.  Due to this, the ramp fitting algorithm"
+        log.info("When selecting the LIKELY ramp fitting algorithm the"
+                  f" ngroups needs to be a minimum of {likely_fit.LIKELY_MIN_NGROUPS},"
+                  f" but ngroups = {ngroups}.  Due to this, the ramp fitting algorithm"
                   " is being changed to OLS_C")
         algorithm = "OLS_C"
 

src/stcal/ramp_fitting/ramp_fit_class.py

@@ -209,10 +209,10 @@
 
     def dbg_print_pixel_info(self, row, col):
         print("-" * 80)
-        print(f"    data")
+        print("    data")
         for integ in range(self.data.shape[0]):
             print(f"[{integ}] {self.data[integ, :, row, col]}")
-        print(f"    groupdq")
+        print("    groupdq")
         for integ in range(self.data.shape[0]):
             print(f"[{integ}] {self.groupdq[integ, :, row, col]}")
         # print(f"    err :\n{self.err[:, :, row, col]}")
@@ -280,8 +280,8 @@
 
         # XXX Make this a separate function
         delimiter = "-" * 40
-        fd.write(f"{indent}# {delimiter}\n\n");
-        fd.write(f"{indent}# ({row}, {col})\n\n");
+        fd.write(f"{indent}# {delimiter}\n\n")
+        fd.write(f"{indent}# ({row}, {col})\n\n")
 
         nints = self.data.shape[0]
 

src/stcal/ramp_fitting/utils.py

@@ -6,7 +6,6 @@
 
 import numpy as np
 
-
 log = logging.getLogger(__name__)
 log.setLevel(logging.DEBUG)
 

tests/outlier_detection/test_utils.py

@@ -1,20 +1,20 @@
 import warnings
 
 import gwcs
-import pytest
 import numpy as np
+import pytest
 import scipy.signal
 from astropy.modeling import models
 
 from stcal.outlier_detection.utils import (
     _abs_deriv,
+    calc_gwcs_pixmap,
     compute_weight_threshold,
     flag_crs,
     flag_resampled_crs,
     gwcs_blot,
-    calc_gwcs_pixmap,
-    reproject,
     medfilt,
+    reproject,
 )