add codecov reports (#73)

* add codecov reports

* add codecov reports changelog

* add codecov fix token

* readme and new tests

* Updated coverage.svg

* add cov test

* fish test

* Updated coverage.svg

* Merge branch 'main' into codecov

.github/workflows/ci.yml

@@ -17,6 +17,10 @@ jobs:
       - name: Run tests
         run: |
           pytest
+      - name: Upload to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
       - name: coverage.py badge
         uses: tj-actions/coverage-badge-py@v2.0.3
       - name: Verify Changed files

CHANGELOG.md

@@ -28,5 +28,5 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 1.1.0 : Implemented symbolic as a new boltzmann solver class. Fixes of feedback prints. More docstrings.
 1.1.1 : Resolved gcsp bias bug, new test suite. 
 1.1.2 : Coverage badge
-
-1.1.3 : New split up demonstration notebooks 
+1.1.3 : New split up demonstration notebooks
+1.1.4 : Coverage reports with Codecov

README.md

@@ -1,7 +1,7 @@
 # cosmicfishpie
 
 [![Documentation Status](https://readthedocs.org/projects/cosmicfishpie/badge/?version=latest)](https://cosmicfishpie.readthedocs.io/en/latest/?badge=latest)
-![Coverage](./coverage.svg)
+![Coverage](./coverage.svg) [![codecov](https://codecov.io/github/santiagocasas/cosmicfishpie/graph/badge.svg?token=BXTVDPXPUO)](https://codecov.io/github/santiagocasas/cosmicfishpie)
 
 <div align="center">
   <img src="https://github.com/santiagocasas/cosmicfishpie/assets/6987716/1816b3b7-0920-4a2c-aafd-9c4ba1dc3e2b" width="280">

tests/cosmicfish_test.py

@@ -1,3 +1,4 @@
+from cosmicfishpie.analysis.fisher_operations import marginalise_over
 from cosmicfishpie.utilities.utils import printing as cpr
 
 
@@ -13,3 +14,13 @@ def test_FisherMatrix(spectro_fisher_matrix):
     assert hasattr(fish, "fisher_matrix")
     assert hasattr(fish, "fisher_matrix_inv")
     assert hasattr(fish, "get_confidence_bounds")
+
+
+def test_marginalise_over(spectro_fisher_matrix):
+    fish = spectro_fisher_matrix.compute(max_z_bins=1)
+    marginalized_fish = marginalise_over(fish, ["h"])
+    assert hasattr(marginalized_fish, "fisher_matrix")
+    assert hasattr(marginalized_fish, "fisher_matrix_inv")
+    assert hasattr(marginalized_fish, "get_confidence_bounds")
+    assert hasattr(marginalized_fish, "get_param_names")
+    assert len(marginalized_fish.get_param_names()) == (1 + 2)

tests/photo_cov_test.py

@@ -0,0 +1,35 @@
+from cosmicfishpie.LSSsurvey.photo_cov import PhotoCov
+
+# You might need to add more imports depending on what you're testing
+
+
+def test_photo_cov_initialization(photo_fisher_matrix):
+    cosmopars = {"Omegam": 0.3, "h": 0.7}  # Add more parameters as needed
+    cosmoFM = photo_fisher_matrix
+    photo_cov = PhotoCov(cosmopars, cosmoFM.photopars, cosmoFM.IApars, cosmoFM.biaspars)
+    assert isinstance(photo_cov, PhotoCov)
+    assert photo_cov.cosmopars == cosmopars
+
+
+def test_get_cls(photo_fisher_matrix):
+    cosmoFM = photo_fisher_matrix
+    cosmopars = {"Omegam": 0.3, "h": 0.7}  # Add more parameters as needed
+    photo_cov = PhotoCov(cosmopars, cosmoFM.photopars, cosmoFM.IApars, cosmoFM.biaspars)
+    allparsfid = dict()
+    allparsfid.update(cosmopars)
+    allparsfid.update(cosmoFM.IApars)
+    allparsfid.update(cosmoFM.biaspars)
+    allparsfid.update(cosmoFM.photopars)
+    cls = photo_cov.getcls(allparsfid)
+    assert isinstance(cls, dict)
+    # Add more specific assertions based on what you expect in the result
+
+
+def test_get_cls_noise(photo_fisher_matrix):
+    cosmoFM = photo_fisher_matrix
+    cosmopars = {"Omegam": 0.3, "h": 0.7}  # Add more parameters as needed
+    photo_cov = PhotoCov(cosmopars, cosmoFM.photopars, cosmoFM.IApars, cosmoFM.biaspars)
+    cls = photo_cov.getcls(photo_cov.allparsfid)
+    noisy_cls = photo_cov.getclsnoise(cls)
+    assert isinstance(noisy_cls, dict)
+    # Add more specific assertions based on what you expect in the result