U/jrbogart/fix ci

.github/workflows/ci.yml

@@ -28,10 +28,10 @@ jobs:
                 shell: bash -l {0}
 
         steps:
-            - uses: actions/checkout@v3
+            - uses: actions/checkout@v4
 
             - name: Setup conda
-              uses: conda-incubator/setup-miniconda@v2
+              uses: conda-incubator/setup-miniconda@v3
               with:
                   activate-environment: stack
                   python-version: ${{ matrix.py }}

etc/conda_requirements.txt

@@ -3,4 +3,4 @@
 stackvana>=0.2023.32
 gitpython
 dust_extinction
-sncosmo
+# sncosmo

skycatalogs/catalog_creator.py

@@ -257,7 +257,9 @@ def __init__(self, parts, area_partition=None, skycatalog_root=None,
         _cosmo_cat = 'cosmodc2_v1.1.4_image_addon_knots'
         _diffsky_cat = 'roman_rubin_2023_v1.1.2_elais'
         _star_db = '/global/cfs/cdirs/lsst/groups/SSim/DC2/dc2_stellar_healpixel.db'
-        _sn_db = '/global/cfs/cdirs/lsst/groups/SSim/DC2/cosmoDC2_v1.1.4/sne_cosmoDC2_v1.1.4_MS_DDF_healpix.db'
+        # _sn_db = '/global/cfs/cdirs/lsst/groups/SSim/DC2/cosmoDC2_v1.1.4/sne_cosmoDC2_v1.1.4_MS_DDF_healpix.db'
+        _sn_db = None
+
 
         _star_parquet = '/global/cfs/cdirs/descssim/postDC2/UW_star_catalog'
 
@@ -284,8 +286,8 @@ def __init__(self, parts, area_partition=None, skycatalog_root=None,
                 self._galaxy_truth = _diffsky_cat
 
         self._sn_truth = sn_truth
-        if self._sn_truth is None:
-            self._sn_truth = _sn_db
+        # if self._sn_truth is None:
+        #     self._sn_truth = _sn_db
 
         self._sn_object_type = sn_object_type
 
@@ -856,7 +858,8 @@ def create_pointsource_catalog(self):
             self._logger.debug(f'Point sources. Starting on pixel {p}')
             self.create_pointsource_pixel(p, arrow_schema,
                                           star_cat=self._star_truth,
-                                          sn_cat=self._sn_truth)
+                                          sn_cat=None)
+            # sn_cat=self._sn_truth)
             self._logger.debug(f'Completed pixel {p}')
 
     def create_pointsource_pixel(self, pixel, arrow_schema, star_cat=None,
@@ -911,43 +914,44 @@ def create_pointsource_pixel(self, pixel, arrow_schema, star_cat=None,
             writer.write_table(out_table)
 
         if sn_cat:
-            # Get data for this pixel
-            cols = ','.join(['snid_in as id', 'snra_in as ra',
-                             'sndec_in as dec', 'galaxy_id as host_galaxy_id'])
-
-            params = ','.join(['z_in as z', 't0_in as t0, x0_in as x0',
-                               'x1_in as x1', 'c_in as c'])
-
-            q1 = f'select {cols} from sne_params where hpid={pixel} '
-            q2 = f'select {params} from sne_params where hpid={pixel} '
-            with sqlite3.connect(sn_cat) as conn:
-                sn_df = pd.read_sql_query(q1, conn)
-                params_df = pd.read_sql_query(q2, conn)
-
-            nobj = len(sn_df['ra'])
-            if nobj > 0:
-                sn_df['object_type'] = np.full((nobj,), self._sn_object_type)
-
-                sn_df['MW_rv'] = make_MW_extinction_rv(sn_df['ra'],
-                                                       sn_df['dec'])
-                sn_df['MW_av'] = make_MW_extinction_av(sn_df['ra'],
-                                                       sn_df['dec'])
-
-                # Add fillers for columns not relevant for sn
-                sn_df['sed_filepath'] = np.full((nobj), '')
-                sn_df['magnorm'] = np.full((nobj,), None)
-                sn_df['mura'] = np.full((nobj,), None)
-                sn_df['mudec'] = np.full((nobj,), None)
-                sn_df['radial_velocity'] = np.full((nobj,), None)
-                sn_df['parallax'] = np.full((nobj,), None)
-                sn_df['variability_model'] = np.full((nobj,), 'salt2_extended')
-
-                # Form array of struct from params_df
-                sn_df['salt2_params'] = params_df.to_records(index=False)
-                out_table = pa.Table.from_pandas(sn_df, schema=arrow_schema)
-                self._logger.debug('Created arrow table from sn dataframe')
-
-                writer.write_table(out_table)
+            sn_cat = None
+            # # Get data for this pixel
+            # cols = ','.join(['snid_in as id', 'snra_in as ra',
+            #                  'sndec_in as dec', 'galaxy_id as host_galaxy_id'])
+
+            # params = ','.join(['z_in as z', 't0_in as t0, x0_in as x0',
+            #                    'x1_in as x1', 'c_in as c'])
+
+            # q1 = f'select {cols} from sne_params where hpid={pixel} '
+            # q2 = f'select {params} from sne_params where hpid={pixel} '
+            # with sqlite3.connect(sn_cat) as conn:
+            #     sn_df = pd.read_sql_query(q1, conn)
+            #     params_df = pd.read_sql_query(q2, conn)
+
+            # nobj = len(sn_df['ra'])
+            # if nobj > 0:
+            #     sn_df['object_type'] = np.full((nobj,), self._sn_object_type)
+
+            #     sn_df['MW_rv'] = make_MW_extinction_rv(sn_df['ra'],
+            #                                            sn_df['dec'])
+            #     sn_df['MW_av'] = make_MW_extinction_av(sn_df['ra'],
+            #                                            sn_df['dec'])
+
+            #     # Add fillers for columns not relevant for sn
+            #     sn_df['sed_filepath'] = np.full((nobj), '')
+            #     sn_df['magnorm'] = np.full((nobj,), None)
+            #     sn_df['mura'] = np.full((nobj,), None)
+            #     sn_df['mudec'] = np.full((nobj,), None)
+            #     sn_df['radial_velocity'] = np.full((nobj,), None)
+            #     sn_df['parallax'] = np.full((nobj,), None)
+            #     sn_df['variability_model'] = np.full((nobj,), 'salt2_extended')
+
+            #     # Form array of struct from params_df
+            #     sn_df['salt2_params'] = params_df.to_records(index=False)
+            #     out_table = pa.Table.from_pandas(sn_df, schema=arrow_schema)
+            #     self._logger.debug('Created arrow table from sn dataframe')
+
+            #     writer.write_table(out_table)
 
         writer.close()
         if self._provenance == 'yaml':
@@ -1094,8 +1098,8 @@ def write_config(self, overwrite=False, path_only=False):
         config.add_key('knots_magnitude_cut', self._knots_mag_cut)
 
         inputs = {'galaxy_truth': self._galaxy_truth}
-        if self._sn_truth:
-            inputs['sn_truth'] = self._sn_truth
+        # if self._sn_truth:
+        #     inputs['sn_truth'] = self._sn_truth
         if self._star_truth:
             inputs['star_truth'] = self._star_truth
         if self._sso_truth:

skycatalogs/skyCatalogs.py

@@ -22,7 +22,7 @@
 from skycatalogs.utils.sed_tools import MilkyWayExtinction
 from skycatalogs.utils.config_utils import Config
 from skycatalogs.utils.shapes import Box, Disk, PolygonalRegion
-from skycatalogs.objects.sncosmo_object import SncosmoObject, SncosmoCollection
+### from skycatalogs.objects.sncosmo_object import SncosmoObject, SncosmoCollection
 from skycatalogs.objects.star_object import StarObject
 from skycatalogs.objects.galaxy_object import GalaxyObject
 from skycatalogs.objects.diffsky_object import DiffskyObject
@@ -387,11 +387,11 @@ def __init__(self, config, mp=False, skycatalog_root=None, verbose=False,
                                               object_class=GaiaObject,
                                               collection_class=GaiaCollection,
                                               custom_load=True)
-        if 'sncosmo' in config['object_types']:
-            self.cat_cxt.register_source_type(
-                'sncosmo',
-                object_class=SncosmoObject,
-                collection_class=SncosmoCollection)
+        # if 'sncosmo' in config['object_types']:
+        #     self.cat_cxt.register_source_type(
+        #         'sncosmo',
+        #         object_class=SncosmoObject,
+        #         collection_class=SncosmoCollection)
         if 'star' in config['object_types']:
             self.cat_cxt.register_source_type('star',
                                               object_class=StarObject)
@@ -700,7 +700,8 @@ def get_object_type_by_hp(self, hp, object_type, region=None, mjd=None,
         elif object_type in ['snana']:
             columns = ['id', 'ra', 'dec', 'start_mjd', 'end_mjd']
             id_name = 'id'
-        elif object_type in ['star', 'sncosmo']:
+        # elif object_type in ['star', 'sncosmo']:
+        elif object_type in ['star']:
             columns = ['object_type', 'id', 'ra', 'dec']
             id_name = 'id'
         elif object_type in ['sso']:
@@ -907,15 +908,18 @@ def open_catalog(config_file, mp=False, skycatalog_root=None, verbose=False):
 
     at_slac = os.getenv('HOME').startswith('/sdf/home/')
     if not at_slac:
-        obj_types = {'star', 'galaxy', 'sncosmo', 'snana'}
+        # obj_types = {'star', 'galaxy', 'sncosmo', 'snana'}
+        obj_types = {'star', 'galaxy', 'snana'}
     else:
-        obj_types = {'star', 'galaxy', 'sncosmo', 'snana', 'gaia_star'}
+        # obj_types = {'star', 'galaxy', 'sncosmo', 'snana', 'gaia_star'}
+        obj_types = {'star', 'galaxy', 'snana', 'gaia_star'}
 
     print('Invoke get_objects_by_region with box region, no gaia')
     t0 = time.time()
     object_list = cat.get_objects_by_region(rgn,
-                                            obj_type_set={'star', 'galaxy',
-                                                          'sncosmo'},
+                                            obj_type_set={'star', 'galaxy'},
+                                            # obj_type_set={'star', 'galaxy',
+                                            #              'sncosmo'},
                                             mjd=63200.0)
     t_done = time.time()
     print('Took ', t_done - t0)
@@ -1000,10 +1004,10 @@ def open_catalog(config_file, mp=False, skycatalog_root=None, verbose=False):
                     print('For star magnorm: ', magnorm)
                     if magnorm < 1000:
                         print('Length of sed: ', len(sed.wave_list))
-            elif o.object_type == 'sncosmo':
-                print(o.get_instcat_entry())
-                for b in {'u', 'g', 'r', 'i', 'z', 'y'}:
-                    print(o.get_LSST_flux(b))
+            # elif o.object_type == 'sncosmo':
+            #     print(o.get_instcat_entry())
+            #     for b in {'u', 'g', 'r', 'i', 'z', 'y'}:
+            #         print(o.get_LSST_flux(b))
             elif o.object_type == 'galaxy':
                 for cmp in ['disk', 'bulge', 'knots']:
                     print(cmp)

skycatalogs/utils/__init__.py

@@ -4,6 +4,6 @@
 from .exceptions import *
 from .parquet_schema_utils import *
 from .sed_tools import *
-from .sn_tools import *
+# from .sn_tools import *
 from .shapes import *
 from .creator_utils import *

skycatalogs/utils/config_utils.py

@@ -284,7 +284,7 @@ def assemble_provenance(pkg_root, inputs={}, schema_version=None):
 # In config just keep track of models by object type. Information
 # about the parameters they require is internal to the code.
 _AGN_MODELS = ['agn_random_walk']
-_SNCOSMO_MODELS = ['sn_salt2_extended']
+# _SNCOSMO_MODELS = ['sn_salt2_extended']
 
 
 def assemble_variability_models(object_types):
@@ -305,7 +305,7 @@ def assemble_variability_models(object_types):
     models = dict()
     if 'agn' in object_types:
         models['agn'] = _AGN_MODELS
-    if 'sncosmo' in object_types:
-        models['sncosmo'] = _SNCOSMO_MODELS
+    # if 'sncosmo' in object_types:
+    #     models['sncosmo'] = _SNCOSMO_MODELS
 
     return models