Testing missing branches

.github/workflows/ci.yml

@@ -99,7 +99,7 @@ jobs:
           pylint --rcfile examples/pylintrc  examples
       - name: Running unit tests
         shell: bash -l {0}
-        run: python -m pytest -vv --runslow --cov firecrown --cov-report xml
+        run: python -m pytest -vv --runslow --cov firecrown --cov-report xml --cov-branch
       - name: Running integration tests
         shell: bash -l {0}
         run: python -m pytest -vv -s --integration tests/integration 

firecrown/__init__.py

@@ -1,5 +1,4 @@
-"""A package for the creation of DESC likelihoods.
-"""
+"""A package for the creation of DESC likelihoods."""
 
 from firecrown.version import __version__
 

firecrown/connector/numcosmo/helpers.py

@@ -23,7 +23,7 @@ def get_hiprim(hi_cosmo: Nc.HICosmo) -> Nc.HIPrimPowerLaw:
 
 
 def get_amplitude_parameters(
-    ccl_factory: fac.CCLFactory,
+    amplitude_parameter: fac.PoweSpecAmplitudeParameter,
     p_ml: None | Nc.PowspecML,
     hi_cosmo: Nc.HICosmo,
 ) -> tuple[float | None, float | None]:
@@ -39,7 +39,7 @@ def get_amplitude_parameters(
     sigma8: float | None = None
 
     # mypy verifies that the match statement below is exhaustive
-    match ccl_factory.amplitude_parameter:
+    match amplitude_parameter:
         case fac.PoweSpecAmplitudeParameter.SIGMA8:
             if p_ml is None:
                 raise ValueError("PowspecML object must be provided when using sigma8.")

firecrown/connector/numcosmo/numcosmo.py

@@ -19,8 +19,8 @@
 from firecrown.modeling_tools import ModelingTools
 from firecrown.ccl_factory import (
     CCLCalculatorArgs,
-    CCLFactory,
     CCLCreationMode,
+    PoweSpecAmplitudeParameter,
 )
 from firecrown.connector.numcosmo import helpers
 
@@ -175,7 +175,7 @@ def _set_dist(self, value: Nc.Distance) -> None:
     )
 
     def set_params_from_numcosmo(
-        self, mset: Ncm.MSet, ccl_factory: CCLFactory
+        self, mset: Ncm.MSet, amplitude_parameter: PoweSpecAmplitudeParameter
     ) -> None:  # pylint: disable-msg=too-many-locals
         """Set the parameters of the contained Mapping object.
 
@@ -209,9 +209,9 @@ def set_params_from_numcosmo(
             case _:
                 raise ValueError(f"NumCosmo object {type(hi_cosmo)} not supported.")
 
-        A_s, sigma8 = helpers.get_amplitude_parameters(ccl_factory, self.p_ml, hi_cosmo)
-
-        assert (A_s is not None) or (sigma8 is not None)
+        A_s, sigma8 = helpers.get_amplitude_parameters(
+            amplitude_parameter, self.p_ml, hi_cosmo
+        )
 
         # pylint: disable=duplicate-code
         self.mapping.set_params(
@@ -570,7 +570,9 @@ def do_prepare(  # pylint: disable-msg=arguments-differ
         self.likelihood.reset()
         self.tools.reset()
 
-        self._nc_mapping.set_params_from_numcosmo(mset, self.tools.ccl_factory)
+        self._nc_mapping.set_params_from_numcosmo(
+            mset, self.tools.ccl_factory.amplitude_parameter
+        )
         params_map = self._nc_mapping.create_params_map(self.model_list, mset)
 
         self.likelihood.update(params_map)
@@ -850,7 +852,9 @@ def do_prepare(  # pylint: disable-msg=arguments-differ
         self.likelihood.reset()
         self.tools.reset()
 
-        self._nc_mapping.set_params_from_numcosmo(mset, self.tools.ccl_factory)
+        self._nc_mapping.set_params_from_numcosmo(
+            mset, self.tools.ccl_factory.amplitude_parameter
+        )
         params_map = self._nc_mapping.create_params_map(self._model_list, mset)
 
         self.likelihood.update(params_map)

firecrown/generators/__init__.py

@@ -1,4 +1,3 @@
-"""Classes used to generate metadata for likelihoods and cosmological models.
-"""
+"""Classes used to generate metadata for likelihoods and cosmological models."""
 
 # flake8: noqa

firecrown/generators/inferred_galaxy_zdist.py

@@ -447,7 +447,7 @@ def generate(self) -> npt.NDArray:
 
 
 def make_measurements(
-    value: set[Measurement] | list[dict[str, Any]]
+    value: set[Measurement] | list[dict[str, Any]],
 ) -> set[Measurement]:
     """Create a Measurement object from a dictionary."""
     if isinstance(value, set) and all(

firecrown/likelihood/gauss_family/statistic/statistic.py

@@ -1,4 +1,4 @@
-""""Deprecated module with classes related to Statistic."""
+"""Deprecated module with classes related to Statistic."""
 
 # flake8: noqa
 

firecrown/models/__init__.py

@@ -1,5 +1,3 @@
-"""Classes used to define and implement the number density functions.
-
-"""
+"""Classes used to define and implement the number density functions."""
 
 # flake8: noqa

tests/connector/cobaya/test_model_likelihood.py

@@ -1,12 +1,18 @@
 """Unit tests for the cobaya Mapping connector."""
 
+import types
+import sys
 import pytest
 import numpy as np
 from cobaya.model import get_model, Model
 from cobaya.log import LoggedError
 from firecrown.connector.cobaya.ccl import CCLConnector
 from firecrown.connector.cobaya.likelihood import LikelihoodConnector
 from firecrown.likelihood.likelihood import NamedParameters
+from firecrown.likelihood.gaussian import ConstGaussian
+from firecrown.modeling_tools import ModelingTools
+import firecrown.likelihood.statistic as stat
+import firecrown.ccl_factory as ccl_factory
 
 
 def test_cobaya_ccl_initialize():
@@ -325,3 +331,36 @@ def test_default_factory():
     assert isinstance(model_fiducial, Model)
     logpost = model_fiducial.logposterior({})
     assert np.isfinite(logpost.logpost)
+
+
+def _factory_as(_: NamedParameters):
+    return ConstGaussian([stat.TrivialStatistic()]), ModelingTools(
+        ccl_factory=ccl_factory.CCLFactory(
+            amplitude_parameter=ccl_factory.PoweSpecAmplitudeParameter.AS
+        )
+    )
+
+
+def _factory_sigma8(_: NamedParameters):
+    return ConstGaussian([stat.TrivialStatistic()]), ModelingTools(
+        ccl_factory=ccl_factory.CCLFactory(
+            amplitude_parameter=ccl_factory.PoweSpecAmplitudeParameter.SIGMA8
+        )
+    )
+
+
+def test_likelihood_connector_from_module():
+    name = "my_dummy_likelihood_module"
+    factory_full = f"{name}.factory"
+    mod = types.ModuleType(factory_full)
+    mod.factory = _factory_as  # type: ignore
+    sys.modules[name] = mod
+
+    lk_connector = LikelihoodConnector(info={"firecrownIni": factory_full})
+    assert isinstance(lk_connector, LikelihoodConnector)
+    assert "sigma8" not in lk_connector.get_requirements()
+
+    mod.factory = _factory_sigma8  # type: ignore
+    lk_connector = LikelihoodConnector(info={"firecrownIni": factory_full})
+    assert isinstance(lk_connector, LikelihoodConnector)
+    assert "sigma8" in lk_connector.get_requirements()

tests/connector/numcosmo/test_numcosmo_mapping.py

@@ -16,7 +16,7 @@
     NumCosmoFactory,
     helpers,
 )
-from firecrown.ccl_factory import CCLFactory, PoweSpecAmplitudeParameter
+from firecrown.ccl_factory import PoweSpecAmplitudeParameter
 
 Ncm.cfg_init()
 
@@ -167,7 +167,7 @@ def test_numcosmo_mapping_unsupported(map_cosmo_dist: MappingNumCosmo):
     mset.set(cosmo)
 
     with pytest.raises(ValueError, match="NumCosmo object .* not supported."):
-        map_cosmo_dist.set_params_from_numcosmo(mset, CCLFactory())
+        map_cosmo_dist.set_params_from_numcosmo(mset, PoweSpecAmplitudeParameter.SIGMA8)
 
 
 def test_numcosmo_mapping_missing_hiprim(map_cosmo_dist: MappingNumCosmo):
@@ -181,9 +181,7 @@ def test_numcosmo_mapping_missing_hiprim(map_cosmo_dist: MappingNumCosmo):
     with pytest.raises(
         ValueError, match="NumCosmo object must include a HIPrim object."
     ):
-        map_cosmo_dist.set_params_from_numcosmo(
-            mset, CCLFactory(amplitude_parameter=PoweSpecAmplitudeParameter.AS)
-        )
+        map_cosmo_dist.set_params_from_numcosmo(mset, PoweSpecAmplitudeParameter.AS)
 
 
 def test_numcosmo_mapping_invalid_hiprim(map_cosmo_dist: MappingNumCosmo):
@@ -199,9 +197,7 @@ def test_numcosmo_mapping_invalid_hiprim(map_cosmo_dist: MappingNumCosmo):
     with pytest.raises(
         ValueError, match="NumCosmo HIPrim object type .* not supported."
     ):
-        map_cosmo_dist.set_params_from_numcosmo(
-            mset, CCLFactory(amplitude_parameter=PoweSpecAmplitudeParameter.AS)
-        )
+        map_cosmo_dist.set_params_from_numcosmo(mset, PoweSpecAmplitudeParameter.AS)
 
 
 @pytest.mark.parametrize(
@@ -221,7 +217,7 @@ def test_numcosmo_mapping(numcosmo_cosmo_fixture, request):
     mset = Ncm.MSet()
     mset.set(cosmo)
 
-    map_cosmo.set_params_from_numcosmo(mset, CCLFactory())
+    map_cosmo.set_params_from_numcosmo(mset, PoweSpecAmplitudeParameter.SIGMA8)
     ccl_args = map_cosmo.calculate_ccl_args(mset)
     ccl_cosmo = ccl.CosmologyCalculator(**map_cosmo.mapping.asdict(), **ccl_args)
 
@@ -257,8 +253,8 @@ def test_numcosmo_serialize_mapping(numcosmo_cosmo_fixture, request):
     mset = Ncm.MSet()
     mset.set(cosmo)
 
-    map_cosmo.set_params_from_numcosmo(mset, CCLFactory())
-    map_cosmo_dup.set_params_from_numcosmo(mset, CCLFactory())
+    map_cosmo.set_params_from_numcosmo(mset, PoweSpecAmplitudeParameter.SIGMA8)
+    map_cosmo_dup.set_params_from_numcosmo(mset, PoweSpecAmplitudeParameter.SIGMA8)
 
     if map_cosmo_dup.p_ml is None:
         assert map_cosmo_dup.p_ml is None
@@ -457,9 +453,7 @@ def test_numcosmo_mapping_sigma8_missing_pk(map_cosmo_dist: MappingNumCosmo):
     with pytest.raises(
         ValueError, match="PowspecML object must be provided when using sigma8."
     ):
-        map_cosmo_dist.set_params_from_numcosmo(
-            mset, CCLFactory(amplitude_parameter=PoweSpecAmplitudeParameter.SIGMA8)
-        )
+        map_cosmo_dist.set_params_from_numcosmo(mset, PoweSpecAmplitudeParameter.SIGMA8)
 
 
 @pytest.fixture(name="numcosmo_cosmo")
@@ -475,8 +469,9 @@ def test_get_amplitude_parameters_sigma8_no_powerspectrum(numcosmo_cosmo):
     with pytest.raises(
         ValueError, match="PowspecML object must be provided when using sigma8."
     ):
-        ccl_factory = CCLFactory(amplitude_parameter=PoweSpecAmplitudeParameter.SIGMA8)
-        _, _ = helpers.get_amplitude_parameters(ccl_factory, None, numcosmo_cosmo)
+        _, _ = helpers.get_amplitude_parameters(
+            PoweSpecAmplitudeParameter.SIGMA8, None, numcosmo_cosmo
+        )
 
 
 def test_accessors_with_no_powerspectrum():
@@ -491,26 +486,105 @@ def test_accessors_with_no_powerspectrum():
     linear = Nc.PowspecMLTransfer.new(Nc.TransferFuncEH.new())
     nonlinear = Nc.PowspecMNLHaloFit.new(linear, 3.0, 1.0e-5)
     mapping.p_mnl = nonlinear
-    assert mapping._p is None
+    assert mapping._p is None  # pylint: disable=protected-access
 
 
 def test_accessors_with_only_linear_powerspectrum():
     linear = Nc.PowspecMLTransfer.new(Nc.TransferFuncEH.new())
     mapping = MappingNumCosmo(p_ml=linear)
-    assert mapping._p is not None
+    assert mapping._p is not None  # pylint: disable=protected-access
     mapping.p_ml = linear
     assert mapping.p_mnl is None
 
     # Change to a different linear power spectrum
     other_linear = Nc.PowspecMLTransfer.new(Nc.TransferFuncBBKS.new())
     mapping.p_ml = other_linear
-    assert mapping._p is not None
+    assert mapping._p is not None  # pylint: disable=protected-access
     assert mapping.p_ml == other_linear
     assert mapping.p_mnl is None
 
     # Add a non-linear component
     nonlinear = Nc.PowspecMNLHaloFit.new(other_linear, 3.0, 1.0e-5)
     mapping.p_mnl = nonlinear
-    assert mapping._p is not None
+    assert mapping._p is not None  # pylint: disable=protected-access
     assert mapping.p_ml == other_linear
     assert mapping.p_mnl == nonlinear
+
+
+def test_mapping_ccl_args_bg_only():
+    """Test the MappingNumCosmo class with background only."""
+    mapping = MappingNumCosmo(dist=Nc.Distance.new(6.0))
+    assert mapping.p_ml is None
+    assert mapping.p_mnl is None
+
+    cosmo = Nc.HICosmoDEXcdm()
+    cosmo.add_submodel(Nc.HIPrimPowerLaw.new())
+    cosmo.add_submodel(Nc.HIReionCamb.new())
+
+    mset = Ncm.MSet.new_array([cosmo])
+    mset.prepare_fparam_map()
+
+    mapping.set_params_from_numcosmo(mset, PoweSpecAmplitudeParameter.AS)
+    ccl_args = mapping.calculate_ccl_args(mset)
+    assert "background" in ccl_args
+    assert "pk_linear" not in ccl_args
+    assert "pk_nonlin" not in ccl_args
+
+
+def test_mapping_ccl_args_bg_pk_ml():
+    """Test the MappingNumCosmo class with background and pk_ml."""
+    mapping = MappingNumCosmo(
+        dist=Nc.Distance.new(6.0),
+        p_ml=Nc.PowspecMLTransfer.new(Nc.TransferFuncEH.new()),
+    )
+    assert mapping.p_mnl is None
+
+    cosmo = Nc.HICosmoDEXcdm()
+    cosmo.add_submodel(Nc.HIPrimPowerLaw.new())
+    cosmo.add_submodel(Nc.HIReionCamb.new())
+
+    mset = Ncm.MSet.new_array([cosmo])
+    mset.prepare_fparam_map()
+
+    mapping.set_params_from_numcosmo(mset, PoweSpecAmplitudeParameter.AS)
+    ccl_args = mapping.calculate_ccl_args(mset)
+    assert "background" in ccl_args
+    assert "pk_linear" in ccl_args
+    assert "pk_nonlin" not in ccl_args
+
+
+def test_mapping_ccl_args_bg_pk_ml_pk_mnl():
+    """Test the MappingNumCosmo class with background, pk_ml and pk_mnl."""
+    p_ml = Nc.PowspecMLTransfer.new(Nc.TransferFuncEH.new())
+    mapping = MappingNumCosmo(
+        dist=Nc.Distance.new(6.0),
+        p_ml=p_ml,
+        p_mnl=Nc.PowspecMNLHaloFit.new(p_ml, 3.0, 1.0e-4),
+    )
+    assert mapping.p_ml is not None
+    assert mapping.p_mnl is not None
+
+    cosmo = Nc.HICosmoDEXcdm()
+    cosmo.add_submodel(Nc.HIPrimPowerLaw.new())
+    cosmo.add_submodel(Nc.HIReionCamb.new())
+
+    mset = Ncm.MSet.new_array([cosmo])
+    mset.prepare_fparam_map()
+
+    mapping.set_params_from_numcosmo(mset, PoweSpecAmplitudeParameter.AS)
+    ccl_args = mapping.calculate_ccl_args(mset)
+    assert "background" in ccl_args
+    assert "pk_linear" in ccl_args
+    assert "pk_nonlin" in ccl_args
+
+
+def test_mapping_ccl_args_bg_pk_mnl():
+    """Test the MappingNumCosmo class with background, pk_ml and pk_mnl."""
+    p_ml = Nc.PowspecMLTransfer.new(Nc.TransferFuncEH.new())
+    with pytest.raises(
+        AssertionError, match="PowspecML object must be provided when using PowspecMNL"
+    ):
+        _ = MappingNumCosmo(
+            dist=Nc.Distance.new(6.0),
+            p_mnl=Nc.PowspecMNLHaloFit.new(p_ml, 3.0, 1.0e-4),
+        )

tests/likelihood/gauss_family/statistic/test_supernova.py

@@ -1,5 +1,4 @@
-"""Tests for the Supernova statistic.
-"""
+"""Tests for the Supernova statistic."""
 
 import pytest
 

tests/likelihood/gauss_family/test_const_gaussian.py

@@ -1,5 +1,4 @@
-"""Unit testsing for ConstGaussian
-"""
+"""Unit testsing for ConstGaussian"""
 
 import re
 

tests/likelihood/gauss_family/test_student_t.py

@@ -1,5 +1,4 @@
-"""Unit testsing for Student-t distribution
-"""
+"""Unit testsing for Student-t distribution"""
 
 import pytest
 import numpy as np

tests/likelihood/test_factories.py

@@ -1,5 +1,4 @@
-"""Tests for the module firecrown.likelihood.factories.
-"""
+"""Tests for the module firecrown.likelihood.factories."""
 
 import re
 from pathlib import Path