pz-rail-astro-tools 1.0.1__tar.gz → 1.0.3__tar.gz

{pz_rail_astro_tools-1.0.1 → pz_rail_astro_tools-1.0.3}/.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier
-_commit: v0.3.2
+_commit: v0.3.3
 _src_path: gh:LSSTDESC/RAIL-project-template
 author_email: lsst-desc-rail-admin@slac.stanford.edu
 author_name: LSST Dark Energy Science Collaboration (DESC)

{pz_rail_astro_tools-1.0.1 → pz_rail_astro_tools-1.0.3}/.github/workflows/testing-and-coverage.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.10', '3.11']
 
     steps:
     - uses: actions/checkout@v3
@@ -35,4 +35,6 @@ jobs:
       run: |
         python -m pytest tests --cov=astro_tools --cov-report=xml
     - name: Upload coverage report to codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}

{pz_rail_astro_tools-1.0.1 → pz_rail_astro_tools-1.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pz-rail-astro-tools
-Version: 1.0.1
+Version: 1.0.3
 Author-email: "LSST Dark Energy Science Collaboration (DESC)" <lsst-desc-rail-admin@slac.stanford.edu>
 License: MIT License
         
@@ -34,7 +34,9 @@ Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: deprecated
-Requires-Dist: pz-rail-base
+Requires-Dist: pz-rail-base>=1.0.3
+Requires-Dist: numpy
+Requires-Dist: pandas>=2.2.2
 Requires-Dist: astropy
 Requires-Dist: healpy
 Requires-Dist: photerr

{pz_rail_astro_tools-1.0.1 → pz_rail_astro_tools-1.0.3}/pyproject.toml

@@ -17,7 +17,9 @@ classifiers = [
 dynamic = ["version"]
 dependencies = [
     "deprecated",
-    "pz-rail-base",
+    "pz-rail-base>=1.0.3",
+    "numpy",
+    "pandas>=2.2.2",
     "astropy",
     "healpy",
     "photerr",

{pz_rail_astro_tools-1.0.1 → pz_rail_astro_tools-1.0.3}/src/pz_rail_astro_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pz-rail-astro-tools
-Version: 1.0.1
+Version: 1.0.3
 Author-email: "LSST Dark Energy Science Collaboration (DESC)" <lsst-desc-rail-admin@slac.stanford.edu>
 License: MIT License
         
@@ -34,7 +34,9 @@ Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: deprecated
-Requires-Dist: pz-rail-base
+Requires-Dist: pz-rail-base>=1.0.3
+Requires-Dist: numpy
+Requires-Dist: pandas>=2.2.2
 Requires-Dist: astropy
 Requires-Dist: healpy
 Requires-Dist: photerr

{pz_rail_astro_tools-1.0.1 → pz_rail_astro_tools-1.0.3}/src/pz_rail_astro_tools.egg-info/requires.txt

@@ -1,5 +1,7 @@
 deprecated
-pz-rail-base
+pz-rail-base>=1.0.3
+numpy
+pandas>=2.2.2
 astropy
 healpy
 photerr

{pz_rail_astro_tools-1.0.1 → pz_rail_astro_tools-1.0.3}/src/rail/astro_tools/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '1.0.1'
-__version_tuple__ = version_tuple = (1, 0, 1)
+__version__ = version = '1.0.3'
+__version_tuple__ = version_tuple = (1, 0, 3)

{pz_rail_astro_tools-1.0.1 → pz_rail_astro_tools-1.0.3}/src/rail/creation/degraders/grid_selection.py

@@ -57,9 +57,9 @@ class GridSelection(Selector):
                           random_seed=Param(int, 12345, msg="random seed for reproducibility"),
                           scaling_factor=Param(float, 1.588, msg="multiplicative factor for ratios to adjust number of galaxies kept"))
 
-    def __init__(self, args, comm=None):
+    def __init__(self, args, **kwargs):
 
-        Selector.__init__(self, args, comm=comm)
+        super().__init__(args, **kwargs)
 
         if self.config.redshift_cut < 0:
             raise ValueError("redshift cut must be positive")

{pz_rail_astro_tools-1.0.1 → pz_rail_astro_tools-1.0.3}/src/rail/creation/degraders/lsst_error_model.py

@@ -38,13 +38,13 @@ class LSSTErrorModel(Degrader):
             required=False,
         )
 
-    def __init__(self, args, comm=None):
+    def __init__(self, args, **kwargs):
         """
         Constructor
 
         Does standard Degrader initialization and sets up the error model.
         """
-        Degrader.__init__(self, args, comm=comm)
+        super().__init__(args, **kwargs)
         self.error_model = PhotErrErrorModel(
             **{key: self.config[key] for key in self._photerr_params}
         )

{pz_rail_astro_tools-1.0.1 → pz_rail_astro_tools-1.0.3}/src/rail/creation/degraders/observing_condition_degrader.py

@@ -116,8 +116,8 @@ class ObsCondition(Noisifier):
         }
     
 
-    def __init__(self, args, comm=None):
-        Noisifier.__init__(self, args, comm=comm)
+    def __init__(self, args, **kwargs):
+        super().__init__(args, **kwargs)
 
         # store a list of keys relevant for
         # survey conditions;

{pz_rail_astro_tools-1.0.1 → pz_rail_astro_tools-1.0.3}/src/rail/creation/degraders/photometric_errors.py

@@ -53,14 +53,6 @@ class PhotoErrorModel(Noisifier):
                 required=False,
             )
         
-    def __init__(self, args, comm=None):
-        """
-        Constructor
-
-        Does standard Degrader initialization and sets up the error model.
-        """
-        Noisifier.__init__(self, args, comm=comm)
-        
     def _initNoiseModel(self):
         """
         Initialize the noise model by the peNoiseModel
@@ -93,9 +85,9 @@ class LSSTErrorModel(PhotoErrorModel):
     
     name = "LSSTErrorModel"
     
-    def __init__(self, args, comm=None):
+    def __init__(self, args, **kwargs):
 
-        PhotoErrorModel.__init__(self, args, comm=comm)
+        super().__init__(args, **kwargs)
         
         self.set_params(peLsstErrorParams)   
         self.peNoiseModel = peLsstErrorModel
@@ -111,9 +103,9 @@ class RomanErrorModel(PhotoErrorModel):
     
     name = "RomanErrorModel"
     
-    def __init__(self, args, comm=None):
+    def __init__(self, args, **kwargs):
 
-        PhotoErrorModel.__init__(self, args, comm=comm)
+        super().__init__(args, **kwargs)
         
         self.set_params(peRomanErrorParams)    
         self.peNoiseModel = peRomanErrorModel
@@ -128,9 +120,9 @@ class EuclidErrorModel(PhotoErrorModel):
     
     name = "EuclidErrorModel"
     
-    def __init__(self, args, comm=None):
+    def __init__(self, args, **kwargs):
 
-        PhotoErrorModel.__init__(self, args, comm=comm)
+        super().__init__(args, **kwargs)
         
         self.set_params(peEuclidErrorParams)    
         self.peNoiseModel = peEuclidErrorModel

{pz_rail_astro_tools-1.0.1 → pz_rail_astro_tools-1.0.3}/src/rail/creation/degraders/spectroscopic_degraders.py

@@ -44,10 +44,10 @@ class LineConfusion(Noisifier):
                           wrong_wavelen=float,
                           frac_wrong=float)
 
-    def __init__(self, args, comm=None):
+    def __init__(self, args, **kwargs):
         """
         """
-        Noisifier.__init__(self, args, comm=comm)
+        super().__init__(args, **kwargs)
         # validate parameters
         if self.config.true_wavelen < 0:
             raise ValueError("true_wavelen must be positive, not {self.config.true_wavelen}")
@@ -115,10 +115,10 @@ class InvRedshiftIncompleteness(Selector):
     config_options = Selector.config_options.copy()
     config_options.update(pivot_redshift=float)
 
-    def __init__(self, args, comm=None):
+    def __init__(self, args, **kwargs):
         """
         """
-        Selector.__init__(self, args, comm=comm)
+        super().__init__(args, **kwargs)
         if self.config.pivot_redshift < 0:
             raise ValueError("pivot redshift must be positive, not {self.config.pivot_redshift}")
 

{pz_rail_astro_tools-1.0.1 → pz_rail_astro_tools-1.0.3}/src/rail/creation/degraders/spectroscopic_selections.py

@@ -67,8 +67,8 @@ class SpecSelection(Selector):
         random_seed=Param(int, 42, msg="random seed for reproducibility"),
     )
 
-    def __init__(self, args, comm=None):
-        Selector.__init__(self, args, comm=comm)
+    def __init__(self, args, **kwargs):
+        super().__init__(args, **kwargs)
         self._validate_settings()
         self.mask = None
         self.rng = None
@@ -155,7 +155,7 @@ class SpecSelection(Selector):
         # get the bands and bandNames present in the data
         data = self.get_data("input", allow_missing=True)
         self.validate_colnames(data)
-        self.mask = np.product(~np.isnan(data.to_numpy()), axis=1)
+        self.mask = np.prod(~np.isnan(data.to_numpy()), axis=1)
         self.invalid_cut(data)
         self.selection(data)
         if self.config.downsample is True:

{pz_rail_astro_tools-1.0.1 → pz_rail_astro_tools-1.0.3}/src/rail/creation/engines/gcr_engine.py

@@ -52,8 +52,8 @@ class GCRCreator(Creator):
         ),
     )
 
-    def __init__(self, args, comm=None):
-        Creator.__init__(self, args, comm=comm)
+    def __init__(self, args, **kwargs):
+        super().__init__(args, **kwargs)
 
         # Provides override for unit test
         self._catalog_override = None

{pz_rail_astro_tools-1.0.1 → pz_rail_astro_tools-1.0.3}/src/rail/tools/photometry_tools.py

@@ -13,6 +13,7 @@ from ceci.config import StageParameter as Param
 from rail.core.data import PqHandle
 from rail.core.stage import RailStage
 from rail.core.data import PqHandle, Hdf5Handle
+from rail.core.common_params import SHARED_PARAMS
 
 import hyperbolic  # https://github.com/jlvdb/hyperbolic
 
@@ -94,8 +95,8 @@ class PhotometryManipulator(RailStage, ABC):
     inputs = [('input', PqHandle)]
     outputs = [('output', PqHandle)]
 
-    def __init__(self, args, comm=None):
-        super().__init__(args, comm)
+    def __init__(self, args, **kwargs):
+        super().__init__(args, **kwargs)
         self._check_config()
         # convenience remapping of parameters
         self.value_columns = self.config.value_columns
@@ -331,7 +332,7 @@ class HyperbolicMagnitudes(PhotometryManipulator):
             Input table with photometry (magnitudes or flux columns and their respective
             uncertainties) as defined by the configuration.
         parameters : `PqHandle`
-            Table with smoothing parameters per photometric band, determined by
+            Table witdh smoothing parameters per photometric band, determined by
             `HyperbolicSmoothing`.
 
         Returns
@@ -370,9 +371,6 @@ class LSSTFluxToMagConverter(RailStage):
     inputs = [('input', PqHandle)]
     outputs = [('output', Hdf5Handle)]
 
-    def __init__(self, args, comm=None):
-        RailStage.__init__(self, args, comm=comm)
-
     def _flux_to_mag(self, flux_vals):
         return -2.5*np.log10(flux_vals) + self.config.mag_offset
 
@@ -420,6 +418,8 @@ class DustMapBase(RailStage):
 
     config_options = RailStage.config_options.copy()
     config_options.update(bands='ugrizy')
+    config_options.update(ra_name='ra')
+    config_options.update(dec_name='dec')
     config_options.update(mag_name="mag_{band}_lsst")
     config_options.update(band_a_env=[4.81,3.64,2.70,2.06,1.58,1.31])
     config_options.update(dustmap_name='sfd')
@@ -449,14 +449,11 @@ class DustMapBase(RailStage):
         fetch_func = dust_map_submod.fetch
         fetch_func()
         
-            
-    def __init__(self, args, comm=None):
-        RailStage.__init__(self, args, comm=comm)
 
     def run(self):
         data = self.get_data('input', allow_missing=True)
         out_data = {}
-        coords = SkyCoord(data['ra'], data['dec'], unit = 'deg',frame='fk5')
+        coords = SkyCoord(data[self.config.ra_name], data[self.config.dec_name], unit = 'deg',frame='fk5')
         dust_map_dict = dict(sfd=dustmaps_sfd.SFDQuery)
         try:
             dust_map_class = dust_map_dict[self.config.dustmap_name]

{pz_rail_astro_tools-1.0.1 → pz_rail_astro_tools-1.0.3}/tests/astro_tools/test_degraders.py

@@ -90,6 +90,26 @@ def test_InvRedshiftIncompleteness_returns_correct_shape(data):
     assert degraded_data.shape[1] == data.data.shape[1]
     os.remove(degrader.get_output(degrader.get_aliased_tag("output"), final_name=True))
 
+    
+def test_LineConfusion_returns_correct_shape(data):
+    """Make sure returns same number of columns, fewer rows"""
+    OII = 3727
+    OIII = 5007
+
+    lc_2p_0II_0III = LineConfusion.make_stage(
+        name="lc_2p_0II_0III", true_wavelen=OII, wrong_wavelen=OIII, frac_wrong=0.02
+    )
+    lc_1p_0III_0II = LineConfusion.make_stage(
+        name="lc_1p_0III_0II", true_wavelen=OIII, wrong_wavelen=OII, frac_wrong=0.01
+    )
+    degraded_data = lc_1p_0III_0II(
+        lc_2p_0II_0III(data)
+    ).data
+    assert degraded_data.shape[0] <= data.data.shape[0]
+    assert degraded_data.shape[1] == data.data.shape[1]
+    os.remove(lc_2p_0II_0III.get_output(lc_2p_0II_0III.get_aliased_tag("output"), final_name=True))
+    os.remove(lc_1p_0III_0II.get_output(lc_1p_0III_0II.get_aliased_tag("output"), final_name=True))
+    
 
 @pytest.mark.parametrize(
     "percentile_cut,redshift_cut,errortype",