Merge branch 'main' into issue/13/create-cosmos-example

.github/workflows/testing-and-coverage.yml

@@ -34,4 +34,6 @@ jobs:
       run: |
         python -m pytest tests -m "not slow" --cov=lephare --cov-report=xml
     - name: Upload coverage report to codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}

README.md

@@ -1,7 +1,7 @@
 # pz-rail-lephare
 
 [![Template](https://img.shields.io/badge/Template-LINCC%20Frameworks%20Python%20Project%20Template-brightgreen)](https://lincc-ppt.readthedocs.io/en/latest/)
-[![codecov](https://codecov.io/gh/LSSTDESC/pz-rail-lephare/branch/main/graph/badge.svg)](https://codecov.io/gh/LSSTDESC/pz-rail-lephare)
+[![codecov](https://codecov.io/gh/LSSTDESC/rail_lephare/graph/badge.svg?token=I597zffkaM)](https://codecov.io/gh/LSSTDESC/rail_lephare)
 [![PyPI](https://img.shields.io/pypi/v/pz-rail-lephare?color=blue&logo=pypi&logoColor=white)](https://pypi.org/project/pz-rail-lephare/)
 
 ## RAIL LePHARE

src/rail/estimation/algos/lephare.py

@@ -261,7 +261,7 @@ def _rail_to_lephare_input(data, mag_cols, mag_err_cols):
 
 
     """
-    ng = data["redshift"].shape[0]
+    ng = data[mag_cols[0]].shape[0]
     # Make input catalogue in standard lephare format
     input = Table()
     try:
@@ -280,12 +280,15 @@ def _rail_to_lephare_input(data, mag_cols, mag_err_cols):
         mask &= input[mag_err_cols[n]] > 0
         mask &= ~np.isnan(input[mag_err_cols[n]])
         context += mask * 2**n
-    # Set context to data value or excluding all negative and nan values
+    # Set context to data value if set or else exclude all negative and nan values
     try:
         input["context"] = data["context"]
     except KeyError:
         input["context"] = context
-    input["zspec"] = data["redshift"]
+    try:
+        input["zspec"] = data["redshift"]
+    except KeyError:
+        input["zspec"] = np.full(ng,-99.)
     input["string_data"] = " "
     return input