Apply basic code style checks to test configuration files

.pre-commit-config.yaml

@@ -67,7 +67,6 @@ repos:
             jwst/persistence/.* |
             jwst/photom/.* |
             jwst/refpix/.* |
-            jwst/regtest/.* |
             jwst/resample/.* |
             jwst/reset/.* |
             jwst/residual_fringe/.* |
@@ -82,9 +81,7 @@ repos:
             jwst/tso_photometry/.* |
             jwst/wfs_combine/.* |
             jwst/white_light/.* |
-            jwst/conftest.py |
-            .*/tests/.* |
-            setup.py |
-            pytest_jwst/.* |
-            docs/.*
+            docs/.* |
+            jwst/regtest/test_.* |
+            .*/tests/test_.*
           )$

.ruff.toml

@@ -8,6 +8,7 @@ exclude = [
     "build",
     "*.ipynb",
     "**/tests/test_*.py",
+    "**/regtest/test_*.py",
 ]
 line-length = 100
 
@@ -18,10 +19,6 @@ quote-style = "double"
 indent-style = "space"
 docstring-code-format = true
 exclude = [
-    "jwst/step.py",
-    "jwst/__init__.py",
-    "jwst/conftest.py",
-    "pytest_jwst/**.py",
     "jwst/assign_wcs/**.py",
     "jwst/associations/**.py",
     "jwst/background/**.py",
@@ -44,7 +41,6 @@ exclude = [
     "jwst/persistence/**.py",
     "jwst/photom/**.py",
     "jwst/refpix/**.py",
-    "jwst/regtest/**.py",
     "jwst/resample/**.py",
     "jwst/reset/**.py",
     "jwst/residual_fringe/**.py",
@@ -55,7 +51,6 @@ exclude = [
     "jwst/srctype/**.py",
     "jwst/straylight/**.py",
     "jwst/superbias/**.py",
-    "jwst/tests/**.py",
     "jwst/tso_photometry/**.py",
     "jwst/wfs_combine/**.py",
     "jwst/white_light/**.py",
@@ -115,13 +110,18 @@ ignore-fully-untyped = true  # Turn off annotation checking for fully untyped co
 "**/tests/**.py" = [
     "D104", # missing docstring in public package
 ]
+"jwst/conftest.py" = [
+    "SLF", "ARG", "PTH",
+    "B003", # Assigning to os.environ does not clear the environment
+]
+"**/regtest/**.py" = [ # conftest, regtestdata, and sdp_pools_source
+    "SLF", "ARG", "PTH",
+    "A002", # builtin variable shadowing
+    "S101", # use of assert
+]
 "jwst/associations/tests*" = [
     "F841", # unused variable
 ]
-"jwst/step.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
-"jwst/__init__.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
-"jwst/conftest.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
-"pytest_jwst/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
 "jwst/assign_wcs/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
 "jwst/associations/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
 "jwst/background/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
@@ -144,7 +144,6 @@ ignore-fully-untyped = true  # Turn off annotation checking for fully untyped co
 "jwst/persistence/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
 "jwst/photom/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
 "jwst/refpix/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
-"jwst/regtest/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
 "jwst/resample/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
 "jwst/reset/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
 "jwst/residual_fringe/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
@@ -155,7 +154,6 @@ ignore-fully-untyped = true  # Turn off annotation checking for fully untyped co
 "jwst/srctype/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
 "jwst/straylight/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
 "jwst/superbias/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
-"jwst/tests/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
 "jwst/tso_photometry/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
 "jwst/wfs_combine/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
 "jwst/white_light/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]

jwst/__init__.py

@@ -1,3 +1,5 @@
+"""Process JWST data with Python."""
+
 import re
 
 from importlib.metadata import version
@@ -7,6 +9,6 @@
 _regex_git_hash = re.compile(r".*\+g(\w+)")
 __version_commit__ = ""
 if "+" in __version__:
-    commit = _regex_git_hash.match(__version__).groups()  # type: ignore
+    commit = _regex_git_hash.match(__version__).groups()  # type: ignore[union-attr]
     if commit:
         __version_commit__ = commit[0]

jwst/conftest.py

@@ -1,28 +1,40 @@
-"""Project default for pytest"""
+"""Set project defaults and add fixtures for pytest."""
+
 import os
 import tempfile
 import pytest
 import inspect
 from pathlib import Path
 
-from jwst.associations import (AssociationRegistry, AssociationPool)
+from jwst.associations import AssociationRegistry, AssociationPool
 from jwst.associations.tests.helpers import t_path
 
 
 @pytest.fixture
 def jail_environ():
-    """Lock changes to the environment"""
+    """Lock changes to the environment."""
     original = os.environ.copy()
     try:
         yield
     finally:
         os.environ = original
 
 
-@pytest.fixture(scope='session')
+@pytest.fixture(scope="session")
 def full_pool_rules(request):
-    """Setup to use the full example pool and registry"""
-    pool_fname = t_path('data/mega_pool.csv')
+    """
+    Set up the full example pool and registry.
+
+    Returns
+    -------
+    pool: AssociationPool
+        The full example pool as read from data/mega_pool.csv.
+    rules: AssociationRegistry
+        The registry of available associations.
+    pool_fname: str
+        The full test path to mega_pool.csv.
+    """
+    pool_fname = t_path("data/mega_pool.csv")
     pool = AssociationPool.read(pool_fname)
     rules = AssociationRegistry()
 
@@ -46,20 +58,32 @@ def mk_tmp_dirs():
 
 @pytest.fixture
 def slow(request):
-    """Setup slow fixture for tests to identify if --slow
-    has been specified
     """
-    return request.config.getoption('--slow')
+    Set up slow fixture for tests to identify if --slow has been specified.
+
+    Returns
+    -------
+    bool
+        True if --slow has been specified, False otherwise.
+    """
+    return request.config.getoption("--slow")
 
 
 @pytest.fixture(scope="module")
 def tmp_cwd_module(request, tmp_path_factory):
-    """Run test in a pristine temporary working directory, scoped to module.
-    This allows a fixture using it to produce files in a
+    """
+    Set up fixture to run test in a pristine temporary working directory, scoped to module.
+
+    This allows a test using this fixture to produce files in a
     temporary directory, and then have the tests access them.
+
+    Yields
+    ------
+    tmp_path
+        The temporary directory path.
     """
     old_dir = os.getcwd()
-    path = request.module.__name__.split('.')[-1]
+    path = request.module.__name__.split(".")[-1]
     if request._parent_request.fixturename is not None:
         path = path + "_" + request._parent_request.fixturename
     newpath = tmp_path_factory.mktemp(path)
@@ -81,12 +105,14 @@ def tmp_cwd(tmp_path):
 
 @pytest.hookimpl(trylast=True)
 def pytest_configure(config):
-    terminal_reporter = config.pluginmanager.getplugin('terminalreporter')
-    config.pluginmanager.register(TestDescriptionPlugin(terminal_reporter), 'testdescription')
+    """Add the test description plugin to the pytest configuration."""
+    terminal_reporter = config.pluginmanager.getplugin("terminalreporter")
+    config.pluginmanager.register(TestDescriptionPlugin(terminal_reporter), "testdescription")
 
 
 class TestDescriptionPlugin:
-    """Pytest plugin to print the test docstring when `pytest -vv` is used.
+    """
+    Pytest plugin to print the test docstring when `pytest -vv` is used.
 
     This plug-in was added to support JWST instrument team testing and
     reporting for the JWST calibration pipeline.
@@ -97,20 +123,21 @@ def __init__(self, terminal_reporter):
         self.desc = None
 
     def pytest_runtest_protocol(self, item):
+        """Get the docstring for the test."""
         try:
-            # Get the docstring for the test
             self.desc = inspect.getdoc(item.obj)
         except AttributeError:
             self.desc = None
 
     @pytest.hookimpl(hookwrapper=True, tryfirst=True)
     def pytest_runtest_logstart(self, nodeid, location):
+        """Print the test docstring when `pytest -vv` is used."""
         # When run as `pytest` or `pytest -v`, no change in behavior
         if self.terminal_reporter.verbosity <= 1:
             yield
         # When run as `pytest -vv`, `pytest -vvv`, etc, print the test docstring
         else:
-            self.terminal_reporter.write('\n')
+            self.terminal_reporter.write("\n")
             yield
             if self.desc:
-                self.terminal_reporter.write(f'\n{self.desc} ')
+                self.terminal_reporter.write(f"\n{self.desc} ")

jwst/extract_1d/soss_extract/tests/conftest.py

@@ -164,7 +164,7 @@ def throughput():
     """
 
     def filter_function(wl, wl_max):
-        """Set free parameters to roughly mimic throughput functions on main."""
+        # Set free parameters to roughly mimic throughput functions on main.
         maxthru = 0.4
         thresh = 0.01
         scaling = 0.3

jwst/pipeline/tests/helpers.py

@@ -22,15 +22,14 @@ def update_asn_basedir(asn_file, root=None):
 
     Parameters
     ----------
-    asn_file: str
+    asn_file : str
         The original association file
-
-    root: str
+    root : str
         The root directory where the data actually resides
 
     Returns
     -------
-    updated_asn_path: str
+    updated_asn_path : str
         The updated association file path
     """
     if root is None:

jwst/ramp_fitting/tests/check_gls_stats.py

@@ -22,7 +22,41 @@ def setup_inputs(
     gain=1,
     deltatime=1,
 ):
-    """Set up data."""
+    """
+    Set up the input data.
+
+    Parameters
+    ----------
+    ngroups : int
+        Number of groups in the ramp.
+    readnoise : float
+        Read noise.
+    nints : int
+        Number of integrations.
+    nrows : int
+        Number of rows in the image.
+    ncols : int
+        Number of columns in the image.
+    gain : float
+        Gain.
+    deltatime : float
+        Time between groups.
+
+    Returns
+    -------
+    model1 : RampModel
+        Data model.
+    gdq : ndarray
+        Group data quality array.
+    rnoise : ReadnoiseModel
+        Read noise data model.
+    pixdq : ndarray
+        Pixel data quality array.
+    err : ndarray
+        Error array.
+    gain : GainModel
+        Gain data model.
+    """
     times = np.array(list(range(ngroups)), dtype=np.float64) * deltatime
     gain = np.ones(shape=(nrows, ncols), dtype=np.float64) * gain
     err = np.ones(shape=(nints, ngroups, nrows, ncols), dtype=np.float64)
@@ -63,7 +97,23 @@ def setup_inputs(
 
 
 def simple_ramp(fit_method="OLS", ngroups=10, cr_group=None):
-    """Create a simple ramp."""
+    """
+    Create a simple ramp.
+
+    Parameters
+    ----------
+    fit_method : str
+        Fitting method.
+    ngroups : int
+        Number of groups in the ramp.
+    cr_group : int
+        Group with a cosmic ray.
+
+    Returns
+    -------
+    slopes : ndarray
+        Fitted slopes.
+    """
     # Here given a 10 group ramp with an exact slope of 20/group.
     # The output slope should be 20.
     slope_per_group = 20.0

jwst/regtest/__init__.py

@@ -0,0 +1 @@
+"""JWST pipeline regression tests."""