apply stricter style

.github/workflows/python-package.yml

@@ -25,18 +25,18 @@ jobs:
                 os: [ubuntu-latest]
                 python-version: ['3.11', '3.12']
                 numpy-version: ['<2.0', '<2.1', '<2.2', '<3']
-                astropy-version: ['<6.1', '<7.0'] # , '<7.1'] 7 has an IERS issue
+                astropy-version: ['<6.1', '<7.0']  # , '<7.1'] 7 has an IERS issue
                 include:
                     # Close to current NERSC configuration.
                     - os: ubuntu-latest
                       python-version: '3.10'
                       numpy-version: '<1.23'
                       astropy-version: '<6.1'
                     # Stable, yet close to bleeding-edge.
-                    # - os: ubuntu-latest
-                    #   python-version: '3.13'
-                    #   numpy-version: '<3'
-                    #   astropy-version: '<7.1'
+                    - os: ubuntu-latest
+                      python-version: '3.13'
+                      numpy-version: '<3'
+                      astropy-version: '<7.0'  # not <7.1 yet, see above
 
         steps:
             - name: Checkout code

doc/index.rst

@@ -36,6 +36,7 @@ If you want to work with the dust utilities in :mod:`desiutil.dust`, you will
 need:
 
 * `SciPy <https://scipy.org>`_
+* `speclite <https://speclite.readthedocs.io/en/latest/>`_
 
 Contents
 ========

py/desiutil/annotate.py

@@ -465,11 +465,13 @@ def _options():
     parser.add_argument('-D', '--disable-comments', action='store_true', dest='disable_comments',
                         help='Do not add comments, even if they are defined in one of the inputs.')
     parser.add_argument('-e', '--extension', dest='extension', action='store', metavar='EXT', default='1',
-                        help="Update FITS extension EXT, which can be a number or an EXTNAME. If not specified, HDU 1 will be updated, which is standard for simple binary tables.")
+                        help=("Update FITS extension EXT, which can be a number or an EXTNAME. " +
+                              "If not specified, HDU 1 will be updated, which is standard for simple binary tables."))
     parser.add_argument('-o', '--overwrite', dest='overwrite', action='store_true',
                         help='Overwrite the input FITS file.')
     parser.add_argument('-T', '--truncate-comments', dest='truncate', action='store_true',
-                        help='Allow any long comments to be truncated when written out. Without this option, long comments will raise an error.')
+                        help=('Allow any long comments to be truncated when written out. ' +
+                              'Without this option, long comments will raise an error.'))
     parser.add_argument('-u', '--units', action='store', dest='units', metavar='UNITS',
                         help="UNITS should have the form COLUMN='unit':COLUMN='unit'.")
     parser.add_argument('-v', '--verbose', dest='verbose', action='store_true',

py/desiutil/depend.py

@@ -61,18 +61,14 @@
 #
 # default possible dependencies to check in add_dependencies()
 #
-possible_dependencies = [
-    'numpy', 'scipy', 'astropy', 'yaml', 'matplotlib',
-    'requests', 'fitsio', 'h5py', 'mpi4py', 'psycopg2', 'healpy',
-    'desiutil', 'desispec', 'desitarget', 'desimodel', 'desisim', 'desisurvey',
-    'specter', 'speclite', 'specsim', 'surveysim', 'redrock', 'desimeter',
-    'fiberassign', 'gpu_specter',
-    ]
-possible_envvars = [
-    'DESI_ROOT', 'DESI_SPECTRO_DATA', 'DESI_SPECTRO_REDUX', 'SPECPROD',
-    'DESI_SPECTRO_CALIB', 'DESI_BASIS_TEMPLATES',
-    'DESI_TARGET', 'DESIMODEL',
-    ]
+possible_dependencies = ['numpy', 'scipy', 'astropy', 'yaml', 'matplotlib',
+                         'requests', 'fitsio', 'h5py', 'mpi4py', 'psycopg2', 'healpy',
+                         'desiutil', 'desispec', 'desitarget', 'desimodel', 'desisim', 'desisurvey',
+                         'specter', 'speclite', 'specsim', 'surveysim', 'redrock', 'desimeter',
+                         'fiberassign', 'gpu_specter',]
+possible_envvars = ['DESI_ROOT', 'DESI_SPECTRO_DATA', 'DESI_SPECTRO_REDUX', 'SPECPROD',
+                    'DESI_SPECTRO_CALIB', 'DESI_BASIS_TEMPLATES',
+                    'DESI_TARGET', 'DESIMODEL',]
 
 
 def setdep(header, name, version):

py/desiutil/dust.py

@@ -526,12 +526,12 @@ def __init__(self, fname, scaling):
         self.lam_scal = header['LAM_SCAL']
         self.sign = header['LAM_NSGP']  # north = 1, south = -1
 
-    def ebv(self, l, b, interpolate):
+    def ebv(self, gal_l, gal_b, interpolate):
         """Project Galactic longitude/latitude to lambert pixels (See SFD98).
 
         Parameters
         ----------
-        l, b : :class:`numpy.ndarray`
+        gal_l, gal_b : :class:`numpy.ndarray`
             Galactic longitude and latitude.
         interpolate : :class:`bool`
             If ``True`` use bilinear interpolation to obtain values.
@@ -542,11 +542,11 @@ def ebv(self, l, b, interpolate):
             Reddening values.
         """
         x = (self.crpix1 - 1.0 +
-             self.lam_scal * np.cos(l) *
-             np.sqrt(1.0 - self.sign * np.sin(b)))
+             self.lam_scal * np.cos(gal_l) *
+             np.sqrt(1.0 - self.sign * np.sin(gal_b)))
         y = (self.crpix2 - 1.0 -
-             self.sign * self.lam_scal * np.sin(l) *
-             np.sqrt(1.0 - self.sign * np.sin(b)))
+             self.sign * self.lam_scal * np.sin(gal_l) *
+             np.sqrt(1.0 - self.sign * np.sin(gal_b)))
 
         # Get map values at these pixel coordinates.
         if interpolate:
@@ -652,10 +652,7 @@ def ebv(self, *args, **kwargs):
             frame = 'fk5'
 
         # compatibility: treat single argument 2-tuple as (RA, Dec)
-        if (
-                (len(args) == 1) and (type(args[0]) is tuple)
-                and (len(args[0]) == 2)
-        ):
+        if (len(args) == 1) and (type(args[0]) is tuple) and (len(args[0]) == 2):
             args = args[0]
 
         if len(args) == 1:
@@ -814,7 +811,9 @@ def _main():
     import matplotlib.pyplot as plt
 
     parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter,
-                                     description="Runs and displays a comparison between tabulated values of total to selective extinction ratios and values obtained with synthetic mags.")
+                                     description=("Runs and displays a comparison between " +
+                                                  "tabulated values of total to selective extinction " +
+                                                  "ratios and values obtained with synthetic mags."))
     args = parser.parse_args()
 
     plt.figure("reddening")

py/desiutil/iers.py

@@ -105,7 +105,8 @@ def freeze_iers(name='iers_frozen.ecsv', ignore_warnings=True):
     # to prevent any IERSRangeError being raised.
     class IERS_Frozen(astropy.utils.iers.IERS_B):
         def _check_interpolate_indices(self, indices_orig, indices_clipped,
-                                       max_input_mjd): pass
+                                       max_input_mjd):
+            pass
 
     # Create and register an instance of this class from the table.
     iers = IERS_Frozen(table)

py/desiutil/install.py

@@ -70,9 +70,7 @@
     'tilepicker': 'https://github.com/desihub/tilepicker',
     'timedomain': 'https://github.com/desihub/timedomain',
     'plate_layout': 'https://desi.lbl.gov/svn/code/focalplane/plate_layout',
-    'positioner_control':
-        'https://desi.lbl.gov/svn/code/focalplane/positioner_control',
-    }
+    'positioner_control': 'https://desi.lbl.gov/svn/code/focalplane/positioner_control'}
 
 
 #
@@ -109,8 +107,8 @@ def dependencies(modulefile):
         raise ValueError("Modulefile {0} does not exist!".format(modulefile))
     with open(modulefile) as m:
         lines = m.readlines()
-    return [l.strip().split()[2] for l in lines if
-            l.strip().startswith('module load')]
+    return [ln.strip().split()[2] for ln in lines if
+            ln.strip().startswith('module load')]
 
 
 class DesiInstallException(Exception):
@@ -605,8 +603,7 @@ def set_install_dir(self):
         if self.options.root is None and self.nersc is not None:
             self.options.root = self.default_nersc_dir()
 
-        if ((self.options.root is None or not os.path.isdir(self.options.root))
-                and not self.options.test):
+        if ((self.options.root is None or not os.path.isdir(self.options.root)) and not self.options.test):
             message = "Root install directory is missing or not set."
             self.log.critical(message)
             raise DesiInstallException(message)

py/desiutil/modules.py

@@ -183,18 +183,16 @@ def configure_module(product, version, product_root, working_dir=None, dev=False
     """
     if working_dir is None:
         working_dir = os.getcwd()
-    module_keywords = {
-        'name': product,
-        'version': version,
-        'product_root': product_root,
-        'needs_bin': '# ',
-        'needs_python': '# ',
-        'needs_trunk_py': '# ',
-        'trunk_py_dir': '/py',
-        'needs_ld_lib': '# ',
-        'needs_idl': '# ',
-        'pyversion': "python{0:d}.{1:d}".format(*sys.version_info)
-        }
+    module_keywords = {'name': product,
+                       'version': version,
+                       'product_root': product_root,
+                       'needs_bin': '# ',
+                       'needs_python': '# ',
+                       'needs_trunk_py': '# ',
+                       'trunk_py_dir': '/py',
+                       'needs_ld_lib': '# ',
+                       'needs_idl': '# ',
+                       'pyversion': "python{0:d}.{1:d}".format(*sys.version_info)}
     if os.path.isdir(os.path.join(working_dir, 'bin')):
         module_keywords['needs_bin'] = ''
     if os.path.isdir(os.path.join(working_dir, 'lib')):

py/desiutil/plots.py

@@ -92,7 +92,9 @@ def plot_slices(x, y, x_lo, x_hi, y_cut, num_slices=5, min_count=100, axis=None,
         axis.scatter(x, y, s=15, marker='.', lw=0, color='b', alpha=0.5, zorder=1)
 
     # Plot quantiles in slices with enough fits.
-    stepify = lambda y: np.vstack([y, y]).transpose().flatten()
+    def stepify(y):
+        return np.vstack([y, y]).transpose().flatten()
+
     y_m2 = stepify(limits[:, 0])
     y_m1 = stepify(limits[:, 1])
     y_med = stepify(limits[:, 2])
@@ -437,7 +439,7 @@ def projection_dec(self, dec):
     #
     base_tick_labels = np.array([150, 120, 90, 60, 30, 0, 330, 300, 270, 240, 210])
     base_tick_labels = np.remainder(base_tick_labels+360+ra_center, 360)
-    tick_labels = np.array(['{0}°'.format(l) for l in base_tick_labels])
+    tick_labels = np.array(['{0}°'.format(lab) for lab in base_tick_labels])
     #
     # Galactic plane.
     #
@@ -475,8 +477,8 @@ def projection_dec(self, dec):
     # Set RA labels.
     #
     labels = ax.get_xticklabels()
-    for l, item in enumerate(labels):
-        item.set_text(tick_labels[l])
+    for i, item in enumerate(labels):
+        item.set_text(tick_labels[i])
     ax.set_xticklabels(labels)
     #
     # Set axis labels.

py/desiutil/test/test_annotate.py

@@ -100,30 +100,32 @@ def test_find_key_name(self):
     def test_validate_unit(self):
         """Test function to validate units.
         """
-        m = "'ergs' did not parse as fits unit: At col 0, Unit 'ergs' not supported by the FITS standard. Did you mean erg?"
-        d = "'1/deg^2' did not parse as fits unit: Numeric factor not supported by FITS"
-        f = "'1/nanomaggy^2' did not parse as fits unit: Numeric factor not supported by FITS"
-        l = " If this is meant to be a custom unit, define it with 'u.def_unit'. To have it recognized inside a file reader or other code, enable it with 'u.add_enabled_units'. For details, see https://docs.astropy.org/en/latest/units/combining_and_defining.html"
+        erg = "'ergs' did not parse as fits unit: At col 0, Unit 'ergs' not supported by the FITS standard. Did you mean erg?"
+        deg = "'1/deg^2' did not parse as fits unit: Numeric factor not supported by FITS"
+        mag = "'1/nanomaggy^2' did not parse as fits unit: Numeric factor not supported by FITS"
+        cust_unit = (" If this is meant to be a custom unit, define it with 'u.def_unit'. " +
+                     "To have it recognized inside a file reader or other code, enable it with " +
+                     "'u.add_enabled_units'. For details, see https://docs.astropy.org/en/latest/units/combining_and_defining.html")
         c = validate_unit(None)
         self.assertIsNone(c)
         c = validate_unit('erg')
         self.assertIsNone(c)
         with self.assertWarns(FITSUnitWarning) as w:
             c = validate_unit('ergs', error=False)
-        self.assertEqual(str(w.warning), m + l)
+        self.assertEqual(str(w.warning), erg + cust_unit)
         self.assertIsNone(c)
         with self.assertWarns(FITSUnitWarning) as w:
             c = validate_unit('1/deg^2')
-        self.assertEqual(str(w.warning), d + l)
+        self.assertEqual(str(w.warning), deg + cust_unit)
         self.assertIsNone(c)
         c = validate_unit('nanomaggies', error=True)
         self.assertEqual(c, "'nanomaggies'")
         with self.assertRaises(ValueError) as e:
             c = validate_unit('ergs', error=True)
-        self.assertEqual(str(e.exception), m + l)
+        self.assertEqual(str(e.exception), erg + cust_unit)
         with self.assertRaises(ValueError) as e:
             c = validate_unit('1/nanomaggy^2', error=True)
-        self.assertEqual(str(e.exception), f + l)
+        self.assertEqual(str(e.exception), mag + cust_unit)
 
     @patch('desiutil.annotate.get_logger')
     def test_check_comment_length(self, mock_log):