Merge pull request #46 from LSSTDESC/fix_numpy_error

Fix error with new numpy version

.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

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",

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")

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}
         )

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;

src/rail/creation/degraders/photometric_errors.py

@@ -53,14 +53,6 @@ def set_params(self, peparams):
                 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

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}")
 

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 @@ def _select(self):
         # 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:

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

src/rail/tools/photometry_tools.py

@@ -95,8 +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
@@ -371,9 +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
 
@@ -452,9 +449,6 @@ def fetch_map(self):
         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)

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",