Merge pull request #73 from LSSTDESC/u/jrbogart/flake

U/jrbogart/flake
LSSTDESC · Oct 14, 2023 · 66cd16d · 66cd16d
2 parents 7c68b00 + c30f271
commit 66cd16d
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Showing 23 changed files with 442 additions and 407 deletions.
diff --git a/.gitignore b/.gitignore
@@ -66,3 +66,6 @@ target/
 
 # local sandbox
 local/
+
+# local flake8  running
+.flake8
diff --git a/skycatalogs/catalog_creator.py b/skycatalogs/catalog_creator.py
diff --git a/skycatalogs/objects/base_object.py b/skycatalogs/objects/base_object.py
@@ -1,15 +1,9 @@
 from collections.abc import Sequence, Iterable
 from collections import namedtuple
 import os
-import gzip
 import itertools
 import numpy as np
-import astropy.units as u
-import warnings
-from dust_extinction.parameter_averages import F19
 import galsim
-import logging
-from galsim.errors import GalSimRangeError
 
 from skycatalogs.utils.translate_utils import form_object_string
 from skycatalogs.utils.config_utils import Config
@@ -26,6 +20,8 @@
 LSST_BANDS = ('ugrizy')
 
 # global for easy access for code run within mp
+
+
 def load_lsst_bandpasses():
     '''
     Read in lsst bandpasses from standard place, trim, and store in global dict
@@ -40,17 +36,17 @@ def load_lsst_bandpasses():
 
         if os.path.exists(bp_dir):
             BaseObject._bp_path = bp_dir
-            #logger.info(f'Using rubin sim dir {rubin_sim_dir}')
+            # logger.info(f'Using rubin sim dir {rubin_sim_dir}')
         else:
             bp_dir = os.path.join(os.getenv('HOME'), 'rubin_sim_data',
-                                   'throughputs', 'baseline')
-            #logger.info(f'Using rubin sim dir rubin_sim_data under HOME')
+                                  'throughputs', 'baseline')
+            # logger.info(f'Using rubin sim dir rubin_sim_data under HOME')
             if os.path.exists(bp_dir):
                 BaseObject._bp_path = bp_dir
             else:
-                #logger.info('Using galsim built-in bandpasses')
+                # logger.info('Using galsim built-in bandpasses')
                 bp_dir = None
-                fname_fmt = 'LSST_{band}.dat'
+
     for band in LSST_BANDS:
         if bp_dir:
             bp_full_path = os.path.join(bp_dir, f'total_{band}.dat')
@@ -60,22 +56,25 @@ def load_lsst_bandpasses():
 
         # Mirror behavior in imsim.RubinBandpass:
         # https://github.com/LSSTDESC/imSim/blob/main/imsim/bandpass.py#L9
-        # Trim the edges to avoid 1.e-4 values out to very high and low wavelengths.
+        # Trim the edges to avoid 1.e-4 values out to very high and low
+        # wavelengths.
         bp = bp.truncate(relative_throughput=1.e-3)
-        # Remove wavelength values selectively for improved speed but preserve flux integrals.
+        # Remove wavelength values selectively for improved speed but
+        # preserve flux integrals.
         bp = bp.thin()
         bp = bp.withZeropoint('AB')
         lsst_bandpasses[band] = bp
 
     return lsst_bandpasses
 
+
 class BaseObject(object):
     '''
     Abstract base class for static (in position coordinates) objects.
     Likely need a variant for SSO.
     '''
 
-    _bp500 = galsim.Bandpass(galsim.LookupTable([499, 500, 501],[0, 1, 0]),
+    _bp500 = galsim.Bandpass(galsim.LookupTable([499, 500, 501], [0, 1, 0]),
                              wave_type='nm').withZeropoint('AB')
 
     def __init__(self, ra, dec, id, object_type, belongs_to, belongs_index,
@@ -103,7 +102,6 @@ def __init__(self, ra, dec, id, object_type, belongs_to, belongs_index,
         # All objects also include redshift information. Also MW extinction,
         # but extinction is by subcomponent for galaxies
 
-
     @property
     def ra(self):
         return self._ra
@@ -122,7 +120,8 @@ def object_type(self):
 
     @property
     def redshift(self):
-        if self._redshift:        return self._redshift
+        if self._redshift:
+            return self._redshift
         if self._belongs_to:
             self._redshift = self.get_native_attribute('redshift')
         return self._redshift
@@ -173,7 +172,7 @@ def get_sed_metadata(self, **kwargs):
         '''
         raise NotImplementedError
 
-    def get_instcat_entry(self, band = 'r', component=None):
+    def get_instcat_entry(self, band='r', component=None):
         '''
         Return the string corresponding to instance catalog line
         Parameters:
@@ -204,7 +203,6 @@ def _get_sed(self, component=None, resolution=None, mjd=None):
 
         raise NotImplementedError('Must be implemented by BaseObject subclass if needed')
 
-
     def write_sed(self, sed_file_path, component=None, resolution=None,
                   mjd=None):
         sed, _ = self._get_sed(component=component, resolution=None, mjd=None)
@@ -284,11 +282,11 @@ def get_total_observer_sed(self, mjd=None):
         components.
         """
         sed = None
-        for sed_component in self.get_observer_sed_components(mjd=mjd).values():
+        for sed_cmp in self.get_observer_sed_components(mjd=mjd).values():
             if sed is None:
-                sed = sed_component
+                sed = sed_cmp
             else:
-                sed += sed_component
+                sed += sed_cmp
 
         return sed
 
@@ -318,7 +316,7 @@ def get_fluxes(self, bandpasses, mjd=None):
         return [sed.calculateFlux(b) for b in bandpasses]
 
     def get_LSST_flux(self, band, sed=None, cache=True, mjd=None):
-        if not band in LSST_BANDS:
+        if band not in LSST_BANDS:
             return None
         att = f'lsst_flux_{band}'
 
@@ -463,7 +461,8 @@ def get_native_attribute(self, attribute_name):
         exists.
         '''
         val = getattr(self, attribute_name, None)
-        if val is not None: return val
+        if val is not None:
+            return val
 
         for r in self._rdrs:
             if attribute_name in r.columns:
@@ -510,7 +509,7 @@ def get_native_attributes_iterator(self, attribute_names):
         -------
         iterator which returns df for a chunk of values of the attributes
         '''
-        pass        #    for now
+        pass        # for now
 
     # implement Sequence methods
     def __contains__(self, obj):
@@ -519,7 +518,7 @@ def __contains__(self, obj):
         ----------
         obj can be an (object id) or of type BaseObject
         '''
-        if type(obj) == type(10):
+        if isinstance(obj, int):
             id = obj
         else:
             if isinstance(obj, BaseObject):
@@ -531,8 +530,8 @@ def __contains__(self, obj):
     def __len__(self):
         return len(self._id)
 
-    #def __iter__(self):   Standard impl based on __getitem__ should be ok
-    #def __reversed__(self):   Default implementation ok
+    # def __iter__(self):   Standard impl based on __getitem__ should be ok
+    # def __reversed__(self):   Default implementation ok
 
     def __getitem__(self, key):
         '''
@@ -556,7 +555,7 @@ def __getitem__(self, key):
         elif type(key) == slice:
             if key.start is None:
                 key.start = 0
-            ixdata = [i for i in range(min(key.stop,len(self._ra)))]
+            ixdata = [i for i in range(min(key.stop, len(self._ra)))]
             ixes = itertools.islice(ixdata, key.start, key.stop, key.step)
             return [self._object_class(self._ra[i], self._dec[i], self._id[i],
                                        object_type, self, i)
@@ -568,15 +567,15 @@ def __getitem__(self, key):
                                        object_type, self, i)
                     for i in key[0]]
 
-
     def get_partition_id(self):
         return self._partition_id
 
     def count(self, obj):
         '''
         returns # of occurrences of obj.  It can only be 0 or 1
         '''
-        if self.__contains__(obj): return 1
+        if self.__contains__(obj):
+            return 1
         return 0
 
     def index(self, obj):
@@ -585,6 +584,7 @@ def index(self, obj):
         '''
         return self._id.index(obj.id)
 
+
 LocatedCollection = namedtuple('LocatedCollection',
                                ['collection', 'first_index', 'upper_bound'])
 '''
@@ -595,6 +595,7 @@ def index(self, obj):
       so upper_bound for one collection = first_index in the next
 '''
 
+
 class ObjectList(Sequence):
     '''
     Keep track of a list of ObjectCollection objects, but from user
@@ -642,13 +643,13 @@ def get_collections(self):
         return constituent ObjectCollection objects in a list
         '''
         collections = []
-        for  e in self._located:
+        for e in self._located:
             collections.append(e.collection)
 
         return collections
 
-
     # implement Sequence methods
+
     def __contains__(self, obj):
         '''
         Parameters
@@ -665,8 +666,8 @@ def __contains__(self, obj):
     def __len__(self):
         return self._total_len
 
-    #def __iter__(self):   Standard impl based on __getitem__ should be ok??
-    #def __reversed__(self):   Default implementation ok??
+    # def __iter__(self):   Standard impl based on __getitem__ should be ok??
+    # def __reversed__(self):   Default implementation ok??
 
     def __getitem__(self, key):
         '''
@@ -709,7 +710,7 @@ def __getitem__(self, key):
                     sub = [elem - e.first_index for elem in key_list if elem >= e.first_index and elem < e.upper_bound]
                     to_return += e.collection[(sub,)]
 
-                    start_ix +=len(sub)
+                    start_ix += len(sub)
                     if start_ix >= len(key_list):
                         break
                     start = key_list[start_ix]

diff --git a/skycatalogs/objects/gaia_object.py b/skycatalogs/objects/gaia_object.py
@@ -1,8 +1,8 @@
 import os
-import sys
 import warnings
 from functools import wraps
 import itertools
+from collections.abc import Iterable
 from pathlib import PurePath
 import numpy as np
 import erfa
@@ -60,6 +60,7 @@ class GaiaObject(BaseObject):
     _stellar_temperature = _TEMP_FUNC
     _gaia_bp_bandpass = _GAIA_BP
     _wavelengths = np.arange(250, 1250, 5, dtype=float)
+
     def __init__(self, obj_pars, parent_collection, index):
         """
         Parameters
@@ -92,9 +93,9 @@ def __init__(self, obj_pars, parent_collection, index):
                 # Convert from flux units of nJy to AB mag for the bp passband,
                 # which we will use to normalize the SED.
                 self.bp_mag = -2.5*np.log10(bp_flux*1e-9) + 8.90
-            except galsim.errors.GalSimRangeError as ex:
+            except galsim.errors.GalSimRangeError:
                 self.stellar_temp = None
-            except RuntimeError as rex:
+            except RuntimeError:
                 self.stellar_temp = None
 
     def blambda(self, wl):
@@ -126,16 +127,21 @@ def get_gsobject_components(self, gsparams=None, rng=None):
     def set_use_lut(self, use_lut):
         self.use_lut = use_lut
 
+
 class GaiaCollection(ObjectCollection):
     # Class methods
     _gaia_config = None
-    def set_config(config):
+
+    @classmethod
+    def set_config(cls, config):
         GaiaCollection._gaia_config = config
 
-    def get_config():
+    @classmethod
+    def get_config(cls):
         return GaiaCollection._gaia_config
 
     @ignore_erfa_warnings
+    @staticmethod
     def load_collection(region, skycatalog, mjd=None):
         if isinstance(region, Disk):
             ra = lsst.geom.Angle(region.ra, lsst.geom.degrees)
@@ -229,13 +235,14 @@ def __getitem__(self, key):
             return GaiaObject(self.df.iloc[key], self, key)
 
         elif type(key) == slice:
-            ixdata = [i for i in range(min(key.stop,len(self._id)))]
+            ixdata = [i for i in range(min(key.stop, len(self._id)))]
             ixes = itertools.islice(ixdata, key.start, key.stop, key.step)
             return [self._object_class(self.df.iloc[i], self, i) for i in ixes]
 
         elif type(key) == tuple and isinstance(key[0], Iterable):
             #  check it's a list of int-like?
-            return [self._object_class(self.df.iloc[i], self, i) for i in key[0]]
+            return [self._object_class(self.df.iloc[i], self,
+                                       i) for i in key[0]]
 
     def __len__(self):
         return len(self.df)
diff --git a/skycatalogs/objects/galaxy_object.py b/skycatalogs/objects/galaxy_object.py
@@ -2,11 +2,14 @@
 import galsim
 
 from .base_object import BaseObject
+from skycatalogs.utils.translate_utils import form_object_string
 
 __all__ = ['GalaxyObject']
 
+
 class GalaxyObject(BaseObject):
     _type_name = 'galaxy'
+
     def _get_sed(self, component=None, resolution=None):
         '''
         Return sed and mag_norm for a galaxy component or for a star
@@ -25,7 +28,7 @@ def _get_sed(self, component=None, resolution=None):
             raise ValueError(f'Cannot fetch SED for component type {component}')
 
         th_val = self.get_native_attribute(f'sed_val_{component}')
-        if  th_val is None:   #  values for this component are not in the file
+        if th_val is None:   # values for this component are not in the file
             raise ValueError(f'{component} not part of this catalog')
 
         # if values are all zeros or nearly no point in trying to convert
@@ -46,11 +49,11 @@ def get_wl_params(self):
         """Return the weak lensing parameters, g1, g2, mu."""
         gamma1 = self.get_native_attribute('shear_1')
         gamma2 = self.get_native_attribute('shear_2')
-        kappa =  self.get_native_attribute('convergence')
+        kappa = self.get_native_attribute('convergence')
         # Compute reduced shears and magnification.
         g1 = gamma1/(1. - kappa)    # real part of reduced shear
         g2 = gamma2/(1. - kappa)    # imaginary part of reduced shear
-        mu = 1./((1. - kappa)**2 - (gamma1**2 + gamma2**2)) # magnification
+        mu = 1./((1. - kappa)**2 - (gamma1**2 + gamma2**2))  # magnification
         return g1, g2, mu
 
     def get_total_observer_sed(self, mjd=None):
@@ -67,7 +70,6 @@ def get_total_observer_sed(self, mjd=None):
         sed *= mu
         return sed
 
-
     def get_gsobject_components(self, gsparams=None, rng=None):
 
         if gsparams is not None:
@@ -123,7 +125,7 @@ def get_observer_sed_component(self, component, mjd=None, resolution=None):
 
         return sed
 
-    def get_instcat_entry(self, band = 'r', component=None):
+    def get_instcat_entry(self, band='r', component=None):
         '''
         Return the string corresponding to instance catalog line
         Parameters: