From 934a6e191e3834adb4d0fb3c7d065bc6ef2007f1 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Mon, 28 Oct 2024 07:19:03 -0300
Subject: [PATCH 01/25] Turning tests into a package to allow importing.

---
 tests/__init__.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 tests/__init__.py

diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 000000000..e69de29bb

From f51762b233819a7f4f173cd6e7749c90b407f6d5 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Mon, 28 Oct 2024 07:25:19 -0300
Subject: [PATCH 02/25] Introducing CCL creation modes. Adapating code from PR
 #458 to allow CCL MG models.

---
 firecrown/ccl_factory.py                   | 120 ++++++++++++++++++++-
 firecrown/connector/cobaya/likelihood.py   |  52 +++++----
 firecrown/connector/cosmosis/likelihood.py |   7 +-
 firecrown/likelihood/factories.py          |   4 +-
 4 files changed, 158 insertions(+), 25 deletions(-)

diff --git a/firecrown/ccl_factory.py b/firecrown/ccl_factory.py
index 14f03e003..9f59de1be 100644
--- a/firecrown/ccl_factory.py
+++ b/firecrown/ccl_factory.py
@@ -25,6 +25,7 @@
 
 import pyccl
 from pyccl.neutrinos import NeutrinoMassSplits
+from pyccl.modified_gravity import MuSigmaMG
 
 from firecrown.updatable import Updatable
 from firecrown.parameters import register_new_updatable_parameter
@@ -96,6 +97,79 @@ def _validate_neutrino_mass_splits(value):
     return value
 
 
+class CCLCreationMode(YAMLSerializable, str, Enum):
+    """This class defines the CCL instance creation mode.
+
+    The DEFAULT mode represents the current CCL behavior. It will use CCL's calculator
+    mode if `prepare` is called with a `CCLCalculatorArgs` object. Otherwise, it will
+    use the default CCL mode.
+
+    The MU_SIGMA_ISITGR mode enables the mu-sigma modified gravity model with the ISiTGR
+    transfer function, it is not compatible with the Calculator mode.
+
+    The PURE_CCL_MODE mode will create a CCL instance with the default parameters. It is
+    not compatible with the Calculator mode.
+    """
+
+    @staticmethod
+    def _generate_next_value_(name, _start, _count, _last_values):
+        return name.lower()
+
+    DEFAULT = auto()
+    MU_SIGMA_ISITGR = auto()
+    PURE_CCL_MODE = auto()
+
+
+def _validate_ccl_creation_mode(value):
+    if isinstance(value, str):
+        try:
+            return CCLCreationMode(value.lower())  # Convert from string to Enum
+        except ValueError as exc:
+            raise ValueError(f"Invalid value for CCLCreationMode: {value}") from exc
+    return value
+
+
+class MuSigmaModel(Updatable):
+    """Model for the mu-sigma modified gravity model."""
+
+    def __init__(self):
+        """Initialize the MuSigmaModel object."""
+        super().__init__(parameter_prefix="mu_sigma")
+
+        self.mu = register_new_updatable_parameter(default_value=1.0)
+        self.sigma = register_new_updatable_parameter(default_value=0.0)
+        self.c1 = register_new_updatable_parameter(default_value=1.0)
+        self.c2 = register_new_updatable_parameter(default_value=1.0)
+        self.lambda_mg = register_new_updatable_parameter(default_value=0.0)
+
+    def create(self) -> MuSigmaMG:
+        """Create a `pyccl.modified_gravity.MuSigmaMG` object."""
+        if not self.is_updated():
+            raise ValueError("Parameters have not been updated yet.")
+
+        return MuSigmaMG(self.mu, self.sigma, self.c1, self.c2, self.lambda_mg)
+
+
+class CAMBExtraParams(BaseModel):
+    """Extra parameters for CAMB."""
+
+    model_config = ConfigDict(extra="forbid")
+
+    halofit_version: Annotated[str | None, Field(frozen=True)] = None
+    HMCode_A_baryon: Annotated[float | None, Field(frozen=True)] = None
+    HMCode_eta_baryon: Annotated[float | None, Field(frozen=True)] = None
+    HMCode_logT_AGN: Annotated[float | None, Field(frozen=True)] = None
+    kmax: Annotated[float | None, Field(frozen=True)] = None
+    lmax: Annotated[int | None, Field(frozen=True)] = None
+    dark_energy_model: Annotated[str | None, Field(frozen=True)] = None
+
+    def get_dict(self) -> dict:
+        """Return the extra parameters as a dictionary."""
+        return {
+            key: value for key, value in self.model_dump().items() if value is not None
+        }
+
+
 class CCLFactory(Updatable, BaseModel):
     """Factory class for creating instances of the `pyccl.Cosmology` class."""
 
@@ -111,6 +185,12 @@ class CCLFactory(Updatable, BaseModel):
         BeforeValidator(_validate_neutrino_mass_splits),
         Field(frozen=True),
     ] = NeutrinoMassSplits.NORMAL
+    creation_mode: Annotated[
+        CCLCreationMode,
+        BeforeValidator(_validate_ccl_creation_mode),
+        Field(frozen=True),
+    ] = CCLCreationMode.DEFAULT
+    camb_extra_params: Annotated[CAMBExtraParams | None, Field(frozen=True)] = None
 
     def __init__(self, **data):
         """Initialize the CCLFactory object."""
@@ -149,6 +229,11 @@ def __init__(self, **data):
                     default_value=ccl_cosmo["sigma8"]
                 )
 
+        self.mu_sigma_model: None | MuSigmaModel = None
+        match self.creation_mode:
+            case CCLCreationMode.MU_SIGMA_ISITGR:
+                self.mu_sigma_model = MuSigmaModel()
+
     @model_serializer(mode="wrap")
     def serialize_model(self, nxt: SerializerFunctionWrapHandler, _: SerializationInfo):
         """Serialize the CCLFactory object."""
@@ -171,6 +256,12 @@ def serialize_mass_split(cls, value: NeutrinoMassSplits) -> str:
         """Serialize the mass split parameter."""
         return value.name
 
+    @field_serializer("creation_mode")
+    @classmethod
+    def serialize_creation_mode(cls, value: CCLCreationMode) -> str:
+        """Serialize the creation mode parameter."""
+        return value.name
+
     def model_post_init(self, __context) -> None:
         """Initialize the WeakLensingFactory object."""
 
@@ -214,11 +305,38 @@ def create(
             else:
                 ccl_args["nonlinear_model"] = None
 
-            return pyccl.CosmologyCalculator(**ccl_args)
+            if (self.creation_mode != CCLCreationMode.DEFAULT) or (
+                self.camb_extra_params is not None
+            ):
+                raise ValueError(
+                    "Calculator Mode can only be used with the DEFAULT creation "
+                    "mode and no CAMB extra parameters."
+                )
+
+            self._ccl_cosmo = pyccl.CosmologyCalculator(**ccl_args)
+            return self._ccl_cosmo
 
         if self.require_nonlinear_pk:
             ccl_args["matter_power_spectrum"] = "halofit"
 
+        if self.camb_extra_params is not None:
+            ccl_args["extra_parameters"] = {"camb": self.camb_extra_params.get_dict()}
+
+        match self.creation_mode:
+            case CCLCreationMode.DEFAULT:
+                pass
+            case CCLCreationMode.MU_SIGMA_ISITGR:
+                assert self.mu_sigma_model is not None
+                ccl_args.update(
+                    mg_parametrization=self.mu_sigma_model.create(),
+                    matter_power_spectrum="linear",
+                    transfer_function="boltzmann_isitgr",
+                )
+            case CCLCreationMode.PURE_CCL_MODE:
+                pass
+            case _:
+                raise ValueError(f"Invalid creation mode: {self.creation_mode}")
+
         self._ccl_cosmo = pyccl.Cosmology(**ccl_args)
         return self._ccl_cosmo
 
diff --git a/firecrown/connector/cobaya/likelihood.py b/firecrown/connector/cobaya/likelihood.py
index 54dcc3042..3607f8435 100644
--- a/firecrown/connector/cobaya/likelihood.py
+++ b/firecrown/connector/cobaya/likelihood.py
@@ -11,14 +11,15 @@
 from cobaya.likelihood import Likelihood
 
 from firecrown.likelihood.likelihood import load_likelihood, NamedParameters
+from firecrown.likelihood.likelihood import Likelihood as FirecrownLikelihood
 from firecrown.parameters import ParamsMap
-from firecrown.ccl_factory import PoweSpecAmplitudeParameter
+from firecrown.ccl_factory import PoweSpecAmplitudeParameter, CCLCreationMode
 
 
 class LikelihoodConnector(Likelihood):
     """A class implementing cobaya.likelihood.Likelihood."""
 
-    likelihood: Likelihood
+    likelihood: FirecrownLikelihood
     firecrownIni: str
     derived_parameters: list[str] = []
     build_parameters: NamedParameters
@@ -87,24 +88,27 @@ def get_requirements(
         Required by Cobaya.
         :return: a dictionary
         """
-        likelihood_requires: dict[
-            str, None | dict[str, npt.NDArray[np.float64]] | dict[str, object]
-        ] = {"pyccl_args": None, "pyccl_params": None}
         required_params = (
             self.likelihood.required_parameters() + self.tools.required_parameters()
         )
-        # Cosmological parameters differ from Cobaya's, so we need to remove them.
-        required_params -= self.tools.ccl_factory.required_parameters()
+
+        likelihood_requires: dict[
+            str, None | dict[str, npt.NDArray[np.float64]] | dict[str, object]
+        ] = {}
+        if self.tools.ccl_factory.creation_mode == CCLCreationMode.DEFAULT:
+            likelihood_requires.update(pyccl_args=None, pyccl_params=None)
+            # Cosmological parameters differ from Cobaya's boltzmann interface, so we
+            # need to remove them when using Calculator mode.
+            required_params -= self.tools.ccl_factory.required_parameters()
+            if (
+                self.tools.ccl_factory.amplitude_parameter
+                == PoweSpecAmplitudeParameter.SIGMA8
+            ):
+                likelihood_requires["sigma8"] = None
 
         for param_name in required_params.get_params_names():
             likelihood_requires[param_name] = None
 
-        if (
-            self.tools.ccl_factory.amplitude_parameter
-            == PoweSpecAmplitudeParameter.SIGMA8
-        ):
-            likelihood_requires["sigma8"] = None
-
         return likelihood_requires
 
     def must_provide(self, **requirements) -> None:
@@ -119,14 +123,20 @@ def logp(self, **params_values) -> float:
         Required by Cobaya.
         :params values: The values of the parameters to use.
         """
-        pyccl_args = self.provider.get_pyccl_args()
-        pyccl_params = self.provider.get_pyccl_params()
-
-        derived = params_values.pop("_derived", {})
-        params = ParamsMap(params_values | pyccl_params)
-        self.likelihood.update(params)
-        self.tools.update(params)
-        self.tools.prepare(calculator_args=pyccl_args)
+        if self.tools.ccl_factory.creation_mode == CCLCreationMode.DEFAULT:
+            pyccl_args = self.provider.get_pyccl_args()
+            pyccl_params = self.provider.get_pyccl_params()
+            derived = params_values.pop("_derived", {})
+            params = ParamsMap(params_values | pyccl_params)
+            self.likelihood.update(params)
+            self.tools.update(params)
+            self.tools.prepare(calculator_args=pyccl_args)
+        else:
+            derived = params_values.pop("_derived", {})
+            params = ParamsMap(params_values)
+            self.likelihood.update(params)
+            self.tools.update(params)
+            self.tools.prepare()
 
         loglike = self.likelihood.compute_loglike(self.tools)
 
diff --git a/firecrown/connector/cosmosis/likelihood.py b/firecrown/connector/cosmosis/likelihood.py
index 9163ceafa..916f1fb8b 100644
--- a/firecrown/connector/cosmosis/likelihood.py
+++ b/firecrown/connector/cosmosis/likelihood.py
@@ -16,6 +16,7 @@
 from firecrown.likelihood.gaussfamily import GaussFamily
 from firecrown.likelihood.two_point import TwoPoint
 from firecrown.likelihood.likelihood import load_likelihood, Likelihood, NamedParameters
+from firecrown.ccl_factory import CCLCreationMode
 from firecrown.parameters import ParamsMap
 from firecrown.updatable import MissingSamplerParameterError
 
@@ -109,7 +110,6 @@ def execute(self, sample: cosmosis.datablock) -> int:
             sample, "cosmological_parameters"
         )
         self.map.set_params_from_cosmosis(cosmological_params)
-        ccl_args = self.map.calculate_ccl_args(sample)
 
         # TODO: Future development will need to capture elements that get put into the
         # datablock. This probably will be in a different "physics module" and not in
@@ -121,7 +121,10 @@ def execute(self, sample: cosmosis.datablock) -> int:
         firecrown_params.use_lower_case_keys(True)
         self.update_likelihood_and_tools(firecrown_params)
 
-        self.tools.prepare(calculator_args=ccl_args)
+        if self.tools.ccl_factory.creation_mode == CCLCreationMode.DEFAULT:
+            self.tools.prepare(calculator_args=self.map.calculate_ccl_args(sample))
+        else:
+            self.tools.prepare()
         loglike = self.likelihood.compute_loglike(self.tools)
 
         derived_params_collection = self.likelihood.get_derived_parameters()
diff --git a/firecrown/likelihood/factories.py b/firecrown/likelihood/factories.py
index a00510a9a..d96349fbd 100644
--- a/firecrown/likelihood/factories.py
+++ b/firecrown/likelihood/factories.py
@@ -35,6 +35,7 @@
     check_two_point_consistence_harmonic,
 )
 from firecrown.modeling_tools import ModelingTools
+from firecrown.ccl_factory import CCLFactory
 from firecrown.utils import YAMLSerializable
 
 
@@ -101,6 +102,7 @@ class TwoPointExperiment(BaseModel):
 
     two_point_factory: TwoPointFactory
     data_source: DataSourceSacc
+    ccl_factory: CCLFactory | None = None
 
     def model_post_init(self, __context) -> None:
         """Initialize the TwoPointExperiment object."""
@@ -131,7 +133,7 @@ def build_two_point_likelihood(
         raise ValueError("No likelihood config found.")
 
     exp = TwoPointExperiment.model_validate(likelihood_config, strict=True)
-    modeling_tools = ModelingTools()
+    modeling_tools = ModelingTools(ccl_factory=exp.ccl_factory)
 
     # Load the SACC file
     sacc_data = exp.data_source.get_sacc_data()

From 78129222cf9daa7125451f7a1695174c06772868 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Mon, 28 Oct 2024 10:38:30 -0300
Subject: [PATCH 03/25] Reorganized cobaya example in subdiretorie.

---
 .../evaluate.yaml}                            |   4 +-
 .../evaluate_PT.yaml}                         |   4 +-
 .../cobaya/evaluate_pure_ccl.yaml             | 162 +++++++++++++++++
 examples/des_y1_3x2pt/cobaya/mcmc.yaml        | 168 ++++++++++++++++++
 examples/des_y1_3x2pt/cobaya_mcmc.yaml        |  40 -----
 5 files changed, 334 insertions(+), 44 deletions(-)
 rename examples/des_y1_3x2pt/{cobaya_evaluate.yaml => cobaya/evaluate.yaml} (98%)
 rename examples/des_y1_3x2pt/{cobaya_evaluate_PT.yaml => cobaya/evaluate_PT.yaml} (95%)
 create mode 100644 examples/des_y1_3x2pt/cobaya/evaluate_pure_ccl.yaml
 create mode 100644 examples/des_y1_3x2pt/cobaya/mcmc.yaml
 delete mode 100644 examples/des_y1_3x2pt/cobaya_mcmc.yaml

diff --git a/examples/des_y1_3x2pt/cobaya_evaluate.yaml b/examples/des_y1_3x2pt/cobaya/evaluate.yaml
similarity index 98%
rename from examples/des_y1_3x2pt/cobaya_evaluate.yaml
rename to examples/des_y1_3x2pt/cobaya/evaluate.yaml
index d4dbaa58b..1a7cab405 100644
--- a/examples/des_y1_3x2pt/cobaya_evaluate.yaml
+++ b/examples/des_y1_3x2pt/cobaya/evaluate.yaml
@@ -10,7 +10,7 @@ theory:
 likelihood:
   des_y1_3x2pt:
     external: !!python/name:firecrown.connector.cobaya.likelihood.LikelihoodConnector ''
-    firecrownIni: des_y1_3x2pt.py
+    firecrownIni: ../des_y1_3x2pt.py
     derived_parameters: 
     - TwoPoint__NumberCountsScale_lens0
     - TwoPoint__NumberCountsScale_lens1
@@ -182,7 +182,7 @@ params:
 sampler:
   evaluate: null
 stop_at_error: true
-output: cobaya_evaluate_output
+output: output
 packages_path: null
 test: false
 debug: false
diff --git a/examples/des_y1_3x2pt/cobaya_evaluate_PT.yaml b/examples/des_y1_3x2pt/cobaya/evaluate_PT.yaml
similarity index 95%
rename from examples/des_y1_3x2pt/cobaya_evaluate_PT.yaml
rename to examples/des_y1_3x2pt/cobaya/evaluate_PT.yaml
index 05335bf89..ab4e763d9 100644
--- a/examples/des_y1_3x2pt/cobaya_evaluate_PT.yaml
+++ b/examples/des_y1_3x2pt/cobaya/evaluate_PT.yaml
@@ -10,7 +10,7 @@ theory:
 likelihood:
   des_y1_3x2pt:
     external: !!python/name:firecrown.connector.cobaya.likelihood.LikelihoodConnector ''
-    firecrownIni: des_y1_3x2pt_PT.py
+    firecrownIni: ../des_y1_3x2pt_PT.py
 params:
   As:
     prior:
@@ -96,7 +96,7 @@ params:
 sampler:
   evaluate: null
 stop_at_error: true
-output: cobaya_evaluate_output_PT
+output: output_PT
 packages_path: null
 test: false
 debug: false
diff --git a/examples/des_y1_3x2pt/cobaya/evaluate_pure_ccl.yaml b/examples/des_y1_3x2pt/cobaya/evaluate_pure_ccl.yaml
new file mode 100644
index 000000000..4fd5789ac
--- /dev/null
+++ b/examples/des_y1_3x2pt/cobaya/evaluate_pure_ccl.yaml
@@ -0,0 +1,162 @@
+likelihood:
+  des_y1_3x2pt:
+    external: !!python/name:firecrown.connector.cobaya.likelihood.LikelihoodConnector ''
+    firecrownIni: firecrown.likelihood.factories.build_two_point_likelihood
+    build_parameters:
+      likelihood_config: ../des_y1_3x2pt_pure_ccl_experiment.yaml
+params:
+  sigma8:
+    prior:
+      min: 0.6
+      max: 1.0
+    ref: 0.8
+    proposal: 0.01
+  Omega_b: 0.05
+  Omega_c:
+    prior:
+      min: 0.05
+      max: 0.35
+    ref: 0.25
+    proposal: 0.01
+  Omega_k: 0.0
+  h: 0.682
+  Neff: 3.046
+  m_nu: 0.06
+  n_s: 0.971
+  w0: -1.0
+  wa: 0.0
+  T_CMB: 2.7255
+  
+#   Likelihood params
+#   - IA model
+  ia_bias:
+     ref: 0.5
+     prior:
+        min: -5.0
+        max: +5.0
+  alphaz:
+     ref: 0.0
+     prior:
+        min: -5.0
+        max: +5.0
+
+#   - these parameters are fixed
+  z_piv: 0.62
+
+#   - linear bias for lenses
+  lens0_bias: 
+     ref: 1.4
+     prior:
+        min: 0.8
+        max: 3.0
+  lens1_bias: 
+     ref: 1.6
+     prior:
+        min: 0.8
+        max: 3.0
+  lens2_bias: 
+     ref: 1.6
+     prior:
+        min: 0.8
+        max: 3.0
+  lens3_bias: 
+     ref: 1.9
+     prior:
+        min: 0.8
+        max: 3.0
+  lens4_bias: 
+     ref: 2.0
+     prior:
+        min: 0.8
+        max: 3.0
+
+#   - photoz shifts for the lensing sources
+  src0_delta_z: 
+     ref: -0.001
+     prior:
+        dist: norm
+        loc: -0.001
+        scale: 0.016
+  src1_delta_z: 
+     ref: -0.019
+     prior:
+        dist: norm
+        loc: -0.019
+        scale: 0.013
+  src2_delta_z: 
+     ref: +0.009
+     prior:
+        dist: norm
+        loc: 0.009
+        scale: 0.011
+  src3_delta_z: 
+     ref: -0.018
+     prior:
+        dist: norm
+        loc: -0.018
+        scale: 0.022
+
+#   - photoz shifts for the lenses
+  lens0_delta_z:
+     ref: 0.001
+     prior:
+        dist: norm
+        loc: 0.001
+        scale: 0.008
+  lens1_delta_z: 
+     ref: 0.002
+     prior:
+        dist: norm
+        loc: 0.002
+        scale: 0.007
+  lens2_delta_z: 
+     ref: 0.001
+     prior:
+        dist: norm
+        loc: 0.001
+        scale: 0.007
+  lens3_delta_z: 
+     ref: 0.003
+     prior:
+        dist: norm
+        loc: 0.003
+        scale: 0.01
+  lens4_delta_z: 
+     ref: 0.0
+     prior:
+        dist: norm
+        loc: 0.0
+        scale: 0.01
+
+#   - shear errors
+  src0_mult_bias: 
+     ref: 0.0
+     prior:
+        dist: norm
+        loc: 0.012
+        scale: 0.023
+  src1_mult_bias: 
+     ref: 0.0
+     prior:
+        dist: norm
+        loc: 0.012
+        scale: 0.023
+  src2_mult_bias: 
+     ref: 0.0
+     prior:
+        dist: norm
+        loc: 0.012
+        scale: 0.023
+  src3_mult_bias: 
+     ref: 0.0
+     prior:
+        dist: norm
+        loc: 0.012
+        scale: 0.023
+sampler:
+  evaluate: null
+stop_at_error: true
+output: output_pure_ccl
+packages_path: null
+test: false
+debug: false
diff --git a/examples/des_y1_3x2pt/cobaya/mcmc.yaml b/examples/des_y1_3x2pt/cobaya/mcmc.yaml
new file mode 100644
index 000000000..41f45042a
--- /dev/null
+++ b/examples/des_y1_3x2pt/cobaya/mcmc.yaml
@@ -0,0 +1,168 @@
+theory:
+  camb:
+    stop_at_error: true
+    extra_args:
+      num_massive_neutrinos: 1
+      halofit_version: mead
+  fcc_ccl:
+    external: !!python/name:firecrown.connector.cobaya.ccl.CCLConnector ''
+    input_style: CAMB
+likelihood:
+  des_y1_3x2pt:
+    external: !!python/name:firecrown.connector.cobaya.likelihood.LikelihoodConnector ''
+    firecrownIni: ../des_y1_3x2pt.py
+params:
+  As:
+    prior:
+      min: 5.0e-10
+      max: 8.0e-09
+    ref: 2.0e-09
+    proposal: 1.0e-10
+  ombh2: 0.02242
+  omch2:
+    prior:
+      min: 0.05
+      max: 0.2
+    ref: 0.11933
+    proposal: 0.01
+  H0: 67.66
+  tau: 0.0561
+  mnu: 0.06
+  nnu: 3.046
+  ns: 0.9665
+  YHe: 0.2454
+
+#   Likelihood params
+#   - IA model
+  ia_bias:
+     ref: 0.5
+     prior:
+        min: -5.0
+        max: +5.0
+  alphaz:
+     ref: 0.0
+     prior:
+        min: -5.0
+        max: +5.0
+
+#   - these parameters are fixed
+  z_piv: 0.62
+
+#   - linear bias for lenses
+  lens0_bias: 
+     ref: 1.4
+     prior:
+        min: 0.8
+        max: 3.0
+  lens1_bias: 
+     ref: 1.6
+     prior:
+        min: 0.8
+        max: 3.0
+  lens2_bias: 
+     ref: 1.6
+     prior:
+        min: 0.8
+        max: 3.0
+  lens3_bias: 
+     ref: 1.9
+     prior:
+        min: 0.8
+        max: 3.0
+  lens4_bias: 
+     ref: 2.0
+     prior:
+        min: 0.8
+        max: 3.0
+
+#   - photoz shifts for the lensing sources
+  src0_delta_z: 
+     ref: -0.001
+     prior:
+        dist: norm
+        loc: -0.001
+        scale: 0.016
+  src1_delta_z: 
+     ref: -0.019
+     prior:
+        dist: norm
+        loc: -0.019
+        scale: 0.013
+  src2_delta_z: 
+     ref: +0.009
+     prior:
+        dist: norm
+        loc: 0.009
+        scale: 0.011
+  src3_delta_z: 
+     ref: -0.018
+     prior:
+        dist: norm
+        loc: -0.018
+        scale: 0.022
+
+#   - photoz shifts for the lenses
+  lens0_delta_z:
+     ref: 0.001
+     prior:
+        dist: norm
+        loc: 0.001
+        scale: 0.008
+  lens1_delta_z: 
+     ref: 0.002
+     prior:
+        dist: norm
+        loc: 0.002
+        scale: 0.007
+  lens2_delta_z: 
+     ref: 0.001
+     prior:
+        dist: norm
+        loc: 0.001
+        scale: 0.007
+  lens3_delta_z: 
+     ref: 0.003
+     prior:
+        dist: norm
+        loc: 0.003
+        scale: 0.01
+  lens4_delta_z: 
+     ref: 0.0
+     prior:
+        dist: norm
+        loc: 0.0
+        scale: 0.01
+
+#   - shear errors
+  src0_mult_bias: 
+     ref: 0.0
+     prior:
+        dist: norm
+        loc: 0.012
+        scale: 0.023
+  src1_mult_bias: 
+     ref: 0.0
+     prior:
+        dist: norm
+        loc: 0.012
+        scale: 0.023
+  src2_mult_bias: 
+     ref: 0.0
+     prior:
+        dist: norm
+        loc: 0.012
+        scale: 0.023
+  src3_mult_bias: 
+     ref: 0.0
+     prior:
+        dist: norm
+        loc: 0.012
+        scale: 0.023
+
+sampler:
+  mcmc:
+    Rminus1_stop: 0.01
+    max_tries: 1000
+stop_at_error: true
+output: output_mcmc
+resume: True
diff --git a/examples/des_y1_3x2pt/cobaya_mcmc.yaml b/examples/des_y1_3x2pt/cobaya_mcmc.yaml
deleted file mode 100644
index f5c9f56dc..000000000
--- a/examples/des_y1_3x2pt/cobaya_mcmc.yaml
+++ /dev/null
@@ -1,40 +0,0 @@
-theory:
-  camb:
-    stop_at_error: true
-    extra_args:
-      num_massive_neutrinos: 1
-      halofit_version: mead
-  fcc_ccl:
-    external: !!python/name:firecrown.connector.cobaya.ccl.CCLConnector ''
-    input_style: CAMB
-likelihood:
-  des_y1_3x2pt:
-    external: !!python/name:firecrown.connector.cobaya.likelihood.LikelihoodConnector ''
-    firecrownIni: des_y1_3x2pt.yaml
-params:
-  As:
-    prior:
-      min: 5.0e-10
-      max: 8.0e-09
-    ref: 2.0e-09
-    proposal: 1.0e-10
-  ombh2: 0.02242
-  omch2:
-    prior:
-      min: 0.05
-      max: 0.2
-    ref: 0.11933
-    proposal: 0.01
-  H0: 67.66
-  tau: 0.0561
-  mnu: 0.06
-  nnu: 3.046
-  ns: 0.9665
-  YHe: 0.2454
-sampler:
-  mcmc:
-    Rminus1_stop: 0.01
-    max_tries: 1000
-stop_at_error: true
-output: cobaya_mcmc_output_mpi2
-resume: True

From cfe4eeb32bff1dbf41ea70805947c807436efa90 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Mon, 28 Oct 2024 10:39:20 -0300
Subject: [PATCH 04/25] Handling experiment loading directories.

---
 firecrown/likelihood/factories.py | 48 ++++++++++++++++++++++---------
 1 file changed, 34 insertions(+), 14 deletions(-)

diff --git a/firecrown/likelihood/factories.py b/firecrown/likelihood/factories.py
index d96349fbd..6523eb174 100644
--- a/firecrown/likelihood/factories.py
+++ b/firecrown/likelihood/factories.py
@@ -85,16 +85,28 @@ class DataSourceSacc(BaseModel):
     """Model for the data source in a likelihood configuration."""
 
     sacc_data_file: str
+    _path: Path | None = None
 
-    def model_post_init(self, __context) -> None:
-        """Initialize the DataSourceSacc object."""
-        sacc_data_file = Path(self.sacc_data_file)
-        if not sacc_data_file.exists():
-            raise FileNotFoundError(f"File {sacc_data_file} does not exist")
+    def set_path(self, path: Path) -> None:
+        """Set the path for the data source."""
+        self._path = path
 
     def get_sacc_data(self) -> sacc.Sacc:
         """Load the SACC data file."""
-        return sacc.Sacc.load_fits(self.sacc_data_file)
+        sacc_data_path = Path(self.sacc_data_file)
+        # If sacc_data_file is absolute, use it directly
+        if sacc_data_path.is_absolute():
+            return sacc.Sacc.load_fits(self.sacc_data_file)
+        # If path is set, use it to find the file
+        if self._path is not None:
+            full_sacc_data_path = self._path / sacc_data_path
+            if full_sacc_data_path.exists():
+                return sacc.Sacc.load_fits(full_sacc_data_path)
+        # If path is not set, use the current directory
+        if sacc_data_path.exists():
+            return sacc.Sacc.load_fits(sacc_data_path)
+        # If the file does not exist, raise an error
+        raise FileNotFoundError(f"File {sacc_data_path} does not exist")
 
 
 class TwoPointExperiment(BaseModel):
@@ -107,6 +119,21 @@ class TwoPointExperiment(BaseModel):
     def model_post_init(self, __context) -> None:
         """Initialize the TwoPointExperiment object."""
 
+    @classmethod
+    def load_from_yaml(cls, file: str | Path) -> "TwoPointExperiment":
+        """Load a TwoPointExperiment object from a YAML file."""
+        if isinstance(file, str):
+            file = Path(file)
+
+        # Determine file directory
+        file_dir = file.parent
+        with open(file, "r", encoding="utf-8") as f:
+            config = yaml.safe_load(f)
+            tpe = cls.model_validate(config, strict=True)
+
+        tpe.data_source.set_path(file_dir)
+        return tpe
+
 
 def build_two_point_likelihood(
     build_parameters: NamedParameters,
@@ -125,14 +152,7 @@ def build_two_point_likelihood(
         - statistic_factories: A YAML file containing the statistic factories to use.
     """
     likelihood_config_file = build_parameters.get_string("likelihood_config")
-
-    with open(likelihood_config_file, "r", encoding="utf-8") as f:
-        likelihood_config = yaml.safe_load(f)
-
-    if likelihood_config is None:
-        raise ValueError("No likelihood config found.")
-
-    exp = TwoPointExperiment.model_validate(likelihood_config, strict=True)
+    exp = TwoPointExperiment.load_from_yaml(likelihood_config_file)
     modeling_tools = ModelingTools(ccl_factory=exp.ccl_factory)
 
     # Load the SACC file

From 8a38848768ab3491800023a0e29b74f8c04932a5 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Mon, 28 Oct 2024 10:52:35 -0300
Subject: [PATCH 05/25] Reorganized cosmosis example subdir.

---
 .../default_factory.ini}                      |  4 +-
 .../factory.ini}                              |  4 +-
 .../factory_PT.ini}                           |  4 +-
 .../cosmosis/pure_ccl_default_factory.ini     | 46 +++++++++++++++++++
 .../values.ini}                               |  0
 .../values_PT.ini}                            |  0
 .../des_y1_3x2pt_pure_ccl_experiment.yaml     | 32 +++++++++++++
 7 files changed, 84 insertions(+), 6 deletions(-)
 rename examples/des_y1_3x2pt/{des_y1_3x2pt_default_factory.ini => cosmosis/default_factory.ini} (92%)
 rename examples/des_y1_3x2pt/{des_y1_3x2pt.ini => cosmosis/factory.ini} (92%)
 rename examples/des_y1_3x2pt/{des_y1_3x2pt_PT.ini => cosmosis/factory_PT.ini} (91%)
 create mode 100644 examples/des_y1_3x2pt/cosmosis/pure_ccl_default_factory.ini
 rename examples/des_y1_3x2pt/{des_y1_3x2pt_values.ini => cosmosis/values.ini} (100%)
 rename examples/des_y1_3x2pt/{des_y1_3x2pt_PT_values.ini => cosmosis/values_PT.ini} (100%)
 create mode 100644 examples/des_y1_3x2pt/des_y1_3x2pt_pure_ccl_experiment.yaml

diff --git a/examples/des_y1_3x2pt/des_y1_3x2pt_default_factory.ini b/examples/des_y1_3x2pt/cosmosis/default_factory.ini
similarity index 92%
rename from examples/des_y1_3x2pt/des_y1_3x2pt_default_factory.ini
rename to examples/des_y1_3x2pt/cosmosis/default_factory.ini
index 8f6a211c1..a1eb169e7 100644
--- a/examples/des_y1_3x2pt/des_y1_3x2pt_default_factory.ini
+++ b/examples/des_y1_3x2pt/cosmosis/default_factory.ini
@@ -12,7 +12,7 @@ verbosity = 0
 
 [pipeline]
 modules = consistency camb firecrown_likelihood
-values = ${FIRECROWN_DIR}/examples/des_y1_3x2pt/des_y1_3x2pt_values.ini
+values = ${FIRECROWN_DIR}/examples/des_y1_3x2pt/cosmosis/values.ini
 likelihoods = firecrown
 quiet = T
 debug = T
@@ -48,7 +48,7 @@ sampling_parameters_sections = firecrown_two_point
 
 [test]
 fatal_errors = T
-save_dir = des_y1_3x2pt_output
+save_dir = output_default_factory
 
 [metropolis]
 samples = 1000
diff --git a/examples/des_y1_3x2pt/des_y1_3x2pt.ini b/examples/des_y1_3x2pt/cosmosis/factory.ini
similarity index 92%
rename from examples/des_y1_3x2pt/des_y1_3x2pt.ini
rename to examples/des_y1_3x2pt/cosmosis/factory.ini
index ea10dca2c..6c57aac24 100644
--- a/examples/des_y1_3x2pt/des_y1_3x2pt.ini
+++ b/examples/des_y1_3x2pt/cosmosis/factory.ini
@@ -12,7 +12,7 @@ verbosity = 0
 
 [pipeline]
 modules = consistency camb firecrown_likelihood
-values = ${FIRECROWN_DIR}/examples/des_y1_3x2pt/des_y1_3x2pt_values.ini
+values = ${FIRECROWN_DIR}/examples/des_y1_3x2pt/cosmosis/values.ini
 likelihoods = firecrown
 quiet = T
 debug = T
@@ -46,7 +46,7 @@ sampling_parameters_sections = firecrown_two_point
 
 [test]
 fatal_errors = T
-save_dir = des_y1_3x2pt_output
+save_dir = output_factory
 
 [metropolis]
 samples = 1000
diff --git a/examples/des_y1_3x2pt/des_y1_3x2pt_PT.ini b/examples/des_y1_3x2pt/cosmosis/factory_PT.ini
similarity index 91%
rename from examples/des_y1_3x2pt/des_y1_3x2pt_PT.ini
rename to examples/des_y1_3x2pt/cosmosis/factory_PT.ini
index aa786bc36..5b75b3233 100644
--- a/examples/des_y1_3x2pt/des_y1_3x2pt_PT.ini
+++ b/examples/des_y1_3x2pt/cosmosis/factory_PT.ini
@@ -12,7 +12,7 @@ verbosity = 0
 
 [pipeline]
 modules = consistency camb firecrown_likelihood
-values = ${FIRECROWN_DIR}/examples/des_y1_3x2pt/des_y1_3x2pt_PT_values.ini
+values = ${FIRECROWN_DIR}/examples/des_y1_3x2pt/cosmosis/values_PT.ini
 likelihoods = firecrown
 quiet = T
 debug = T
@@ -45,7 +45,7 @@ sampling_parameters_sections = firecrown_two_point
 
 [test]
 fatal_errors = T
-save_dir = des_y1_3x2pt_output
+save_dir = output_factory_PT
 
 [metropolis]
 samples = 1000
diff --git a/examples/des_y1_3x2pt/cosmosis/pure_ccl_default_factory.ini b/examples/des_y1_3x2pt/cosmosis/pure_ccl_default_factory.ini
new file mode 100644
index 000000000..f7bc10867
--- /dev/null
+++ b/examples/des_y1_3x2pt/cosmosis/pure_ccl_default_factory.ini
@@ -0,0 +1,46 @@
+[runtime]
+sampler = test
+root = ${PWD}
+
+[DEFAULT]
+fatal_errors = T
+
+[output]
+filename = output/des_y1_3x2pt_samples.txt
+format = text
+verbosity = 0
+
+[pipeline]
+modules = consistency firecrown_likelihood
+values = ${FIRECROWN_DIR}/examples/des_y1_3x2pt/cosmosis/values.ini
+likelihoods = firecrown
+quiet = T
+debug = T
+timing = T
+
+[consistency]
+file = ${CSL_DIR}/utility/consistency/consistency_interface.py
+
+[firecrown_likelihood]
+;; Fix this to use an environment variable to find the files.
+;; Set FIRECROWN_DIR to the base of the firecrown installation (or build, if you haven't
+;; installed it)
+file = ${FIRECROWN_DIR}/firecrown/connector/cosmosis/likelihood.py
+likelihood_source = firecrown.likelihood.factories.build_two_point_likelihood
+likelihood_config = ${FIRECROWN_DIR}/examples/des_y1_3x2pt/des_y1_3x2pt_pure_ccl_experiment.yaml
+;; Connector settings
+require_nonlinear_pk = True
+sampling_parameters_sections = firecrown_two_point
+
+[test]
+fatal_errors = T
+save_dir = output_pure_ccl
+
+[metropolis]
+samples = 1000
+nsteps = 1
+
+[emcee]
+walkers = 64
+samples = 400
+nsteps = 10
diff --git a/examples/des_y1_3x2pt/des_y1_3x2pt_values.ini b/examples/des_y1_3x2pt/cosmosis/values.ini
similarity index 100%
rename from examples/des_y1_3x2pt/des_y1_3x2pt_values.ini
rename to examples/des_y1_3x2pt/cosmosis/values.ini
diff --git a/examples/des_y1_3x2pt/des_y1_3x2pt_PT_values.ini b/examples/des_y1_3x2pt/cosmosis/values_PT.ini
similarity index 100%
rename from examples/des_y1_3x2pt/des_y1_3x2pt_PT_values.ini
rename to examples/des_y1_3x2pt/cosmosis/values_PT.ini
diff --git a/examples/des_y1_3x2pt/des_y1_3x2pt_pure_ccl_experiment.yaml b/examples/des_y1_3x2pt/des_y1_3x2pt_pure_ccl_experiment.yaml
new file mode 100644
index 000000000..b5a580856
--- /dev/null
+++ b/examples/des_y1_3x2pt/des_y1_3x2pt_pure_ccl_experiment.yaml
@@ -0,0 +1,32 @@
+---
+
+# This file contains all information about the DES Y1 3x2pt experiment.
+
+# The 'data_source:' field points to the SACC file containing the DES Y1 3x2pt data vector 
+# and covariance matrix, which is used for analysis.
+
+# The 'two_point_factory:' field points to the factory that will create the TwoPoint 
+# objects. These objects represent the chosen theoretical models for each data point 
+# found in the SACC file.
+
+data_source:
+  sacc_data_file: des_y1_3x2pt_sacc_data.fits
+
+# The two point statistics are defined by the TwoPoint objects. The TwoPoint statistics
+# are created using the factories defined in this file.
+two_point_factory:
+  correlation_space: real
+  number_counts_factory:
+    global_systematics: []
+    per_bin_systematics:
+      - type: PhotoZShiftFactory
+  weak_lensing_factory:
+    global_systematics:
+      - alphag: 1
+        type: LinearAlignmentSystematicFactory
+    per_bin_systematics:
+      - type: MultiplicativeShearBiasFactory
+      - type: PhotoZShiftFactory
+
+ccl_factory:
+  creation_mode: 'pure_ccl_mode'

From c1a9f90c5649704c7645f5a330d18cdb5a173c08 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Mon, 28 Oct 2024 11:04:39 -0300
Subject: [PATCH 06/25] Renaming example files.

---
 examples/des_y1_3x2pt/cobaya/evaluate.yaml                    | 2 +-
 examples/des_y1_3x2pt/cobaya/evaluate_PT.yaml                 | 2 +-
 examples/des_y1_3x2pt/cobaya/evaluate_pure_ccl.yaml           | 2 +-
 examples/des_y1_3x2pt/cobaya/mcmc.yaml                        | 2 +-
 examples/des_y1_3x2pt/cosmosis/default_factory.ini            | 2 +-
 examples/des_y1_3x2pt/cosmosis/factory.ini                    | 2 +-
 examples/des_y1_3x2pt/cosmosis/factory_PT.ini                 | 2 +-
 examples/des_y1_3x2pt/cosmosis/pure_ccl_default_factory.ini   | 2 +-
 .../{des_y1_3x2pt_experiment.yaml => experiment.yaml}         | 2 +-
 examples/des_y1_3x2pt/{des_y1_3x2pt.py => factory.py}         | 4 +---
 examples/des_y1_3x2pt/{des_y1_3x2pt_PT.py => factory_PT.py}   | 4 +---
 ...x2pt_pure_ccl_experiment.yaml => pure_ccl_experiment.yaml} | 2 +-
 .../{des_y1_3x2pt_sacc_data.fits => sacc_data.fits}           | 0
 13 files changed, 12 insertions(+), 16 deletions(-)
 rename examples/des_y1_3x2pt/{des_y1_3x2pt_experiment.yaml => experiment.yaml} (95%)
 rename examples/des_y1_3x2pt/{des_y1_3x2pt.py => factory.py} (97%)
 mode change 100755 => 100644
 rename examples/des_y1_3x2pt/{des_y1_3x2pt_PT.py => factory_PT.py} (99%)
 mode change 100755 => 100644
 rename examples/des_y1_3x2pt/{des_y1_3x2pt_pure_ccl_experiment.yaml => pure_ccl_experiment.yaml} (95%)
 rename examples/des_y1_3x2pt/{des_y1_3x2pt_sacc_data.fits => sacc_data.fits} (100%)

diff --git a/examples/des_y1_3x2pt/cobaya/evaluate.yaml b/examples/des_y1_3x2pt/cobaya/evaluate.yaml
index 1a7cab405..58e68c1fe 100644
--- a/examples/des_y1_3x2pt/cobaya/evaluate.yaml
+++ b/examples/des_y1_3x2pt/cobaya/evaluate.yaml
@@ -10,7 +10,7 @@ theory:
 likelihood:
   des_y1_3x2pt:
     external: !!python/name:firecrown.connector.cobaya.likelihood.LikelihoodConnector ''
-    firecrownIni: ../des_y1_3x2pt.py
+    firecrownIni: ../factory.py
     derived_parameters: 
     - TwoPoint__NumberCountsScale_lens0
     - TwoPoint__NumberCountsScale_lens1
diff --git a/examples/des_y1_3x2pt/cobaya/evaluate_PT.yaml b/examples/des_y1_3x2pt/cobaya/evaluate_PT.yaml
index ab4e763d9..b19f92334 100644
--- a/examples/des_y1_3x2pt/cobaya/evaluate_PT.yaml
+++ b/examples/des_y1_3x2pt/cobaya/evaluate_PT.yaml
@@ -10,7 +10,7 @@ theory:
 likelihood:
   des_y1_3x2pt:
     external: !!python/name:firecrown.connector.cobaya.likelihood.LikelihoodConnector ''
-    firecrownIni: ../des_y1_3x2pt_PT.py
+    firecrownIni: ../factory_PT.py
 params:
   As:
     prior:
diff --git a/examples/des_y1_3x2pt/cobaya/evaluate_pure_ccl.yaml b/examples/des_y1_3x2pt/cobaya/evaluate_pure_ccl.yaml
index 4fd5789ac..1eb3bf9e0 100644
--- a/examples/des_y1_3x2pt/cobaya/evaluate_pure_ccl.yaml
+++ b/examples/des_y1_3x2pt/cobaya/evaluate_pure_ccl.yaml
@@ -3,7 +3,7 @@ likelihood:
     external: !!python/name:firecrown.connector.cobaya.likelihood.LikelihoodConnector ''
     firecrownIni: firecrown.likelihood.factories.build_two_point_likelihood
     build_parameters:
-      likelihood_config: ../des_y1_3x2pt_pure_ccl_experiment.yaml
+      likelihood_config: ../pure_ccl_experiment.yaml
 params:
   sigma8:
     prior:
diff --git a/examples/des_y1_3x2pt/cobaya/mcmc.yaml b/examples/des_y1_3x2pt/cobaya/mcmc.yaml
index 41f45042a..3a064dab5 100644
--- a/examples/des_y1_3x2pt/cobaya/mcmc.yaml
+++ b/examples/des_y1_3x2pt/cobaya/mcmc.yaml
@@ -10,7 +10,7 @@ theory:
 likelihood:
   des_y1_3x2pt:
     external: !!python/name:firecrown.connector.cobaya.likelihood.LikelihoodConnector ''
-    firecrownIni: ../des_y1_3x2pt.py
+    firecrownIni: ../factory.py
 params:
   As:
     prior:
diff --git a/examples/des_y1_3x2pt/cosmosis/default_factory.ini b/examples/des_y1_3x2pt/cosmosis/default_factory.ini
index a1eb169e7..055beccd7 100644
--- a/examples/des_y1_3x2pt/cosmosis/default_factory.ini
+++ b/examples/des_y1_3x2pt/cosmosis/default_factory.ini
@@ -41,7 +41,7 @@ nk = 1000
 ;; installed it)
 file = ${FIRECROWN_DIR}/firecrown/connector/cosmosis/likelihood.py
 likelihood_source = firecrown.likelihood.factories.build_two_point_likelihood
-likelihood_config = ${FIRECROWN_DIR}/examples/des_y1_3x2pt/des_y1_3x2pt_experiment.yaml
+likelihood_config = ${FIRECROWN_DIR}/examples/des_y1_3x2pt/experiment.yaml
 ;; Connector settings
 require_nonlinear_pk = True
 sampling_parameters_sections = firecrown_two_point
diff --git a/examples/des_y1_3x2pt/cosmosis/factory.ini b/examples/des_y1_3x2pt/cosmosis/factory.ini
index 6c57aac24..271cb35aa 100644
--- a/examples/des_y1_3x2pt/cosmosis/factory.ini
+++ b/examples/des_y1_3x2pt/cosmosis/factory.ini
@@ -40,7 +40,7 @@ nk = 1000
 ;; Set FIRECROWN_DIR to the base of the firecrown installation (or build, if you haven't
 ;; installed it)
 file = ${FIRECROWN_DIR}/firecrown/connector/cosmosis/likelihood.py
-likelihood_source = ${FIRECROWN_DIR}/examples/des_y1_3x2pt/des_y1_3x2pt.py
+likelihood_source = ${FIRECROWN_DIR}/examples/des_y1_3x2pt/factory.py
 require_nonlinear_pk = True
 sampling_parameters_sections = firecrown_two_point
 
diff --git a/examples/des_y1_3x2pt/cosmosis/factory_PT.ini b/examples/des_y1_3x2pt/cosmosis/factory_PT.ini
index 5b75b3233..6dde09546 100644
--- a/examples/des_y1_3x2pt/cosmosis/factory_PT.ini
+++ b/examples/des_y1_3x2pt/cosmosis/factory_PT.ini
@@ -39,7 +39,7 @@ nk = 1000
 ;; Set FIRECROWN_DIR to the base of the firecrown installation (or build, if you haven't
 ;; installed it)
 file = ${FIRECROWN_DIR}/firecrown/connector/cosmosis/likelihood.py
-likelihood_source = ${FIRECROWN_DIR}/examples/des_y1_3x2pt/des_y1_3x2pt_PT.py
+likelihood_source = ${FIRECROWN_DIR}/examples/des_y1_3x2pt/factory_PT.py
 require_nonlinear_pk = True
 sampling_parameters_sections = firecrown_two_point
 
diff --git a/examples/des_y1_3x2pt/cosmosis/pure_ccl_default_factory.ini b/examples/des_y1_3x2pt/cosmosis/pure_ccl_default_factory.ini
index f7bc10867..1f5e3c64f 100644
--- a/examples/des_y1_3x2pt/cosmosis/pure_ccl_default_factory.ini
+++ b/examples/des_y1_3x2pt/cosmosis/pure_ccl_default_factory.ini
@@ -27,7 +27,7 @@ file = ${CSL_DIR}/utility/consistency/consistency_interface.py
 ;; installed it)
 file = ${FIRECROWN_DIR}/firecrown/connector/cosmosis/likelihood.py
 likelihood_source = firecrown.likelihood.factories.build_two_point_likelihood
-likelihood_config = ${FIRECROWN_DIR}/examples/des_y1_3x2pt/des_y1_3x2pt_pure_ccl_experiment.yaml
+likelihood_config = ${FIRECROWN_DIR}/examples/des_y1_3x2pt/pure_ccl_experiment.yaml
 ;; Connector settings
 require_nonlinear_pk = True
 sampling_parameters_sections = firecrown_two_point
diff --git a/examples/des_y1_3x2pt/des_y1_3x2pt_experiment.yaml b/examples/des_y1_3x2pt/experiment.yaml
similarity index 95%
rename from examples/des_y1_3x2pt/des_y1_3x2pt_experiment.yaml
rename to examples/des_y1_3x2pt/experiment.yaml
index 298317a39..218b9b239 100644
--- a/examples/des_y1_3x2pt/des_y1_3x2pt_experiment.yaml
+++ b/examples/des_y1_3x2pt/experiment.yaml
@@ -10,7 +10,7 @@
 # found in the SACC file.
 
 data_source:
-  sacc_data_file: des_y1_3x2pt_sacc_data.fits
+  sacc_data_file: sacc_data.fits
 
 # The two point statistics are defined by the TwoPoint objects. The TwoPoint statistics
 # are created using the factories defined in this file.
diff --git a/examples/des_y1_3x2pt/des_y1_3x2pt.py b/examples/des_y1_3x2pt/factory.py
old mode 100755
new mode 100644
similarity index 97%
rename from examples/des_y1_3x2pt/des_y1_3x2pt.py
rename to examples/des_y1_3x2pt/factory.py
index fb10ffa43..5e2428546
--- a/examples/des_y1_3x2pt/des_y1_3x2pt.py
+++ b/examples/des_y1_3x2pt/factory.py
@@ -102,9 +102,7 @@ def build_likelihood(_):
 
     # We load the correct SACC file.
     saccfile = os.path.expanduser(
-        os.path.expandvars(
-            "${FIRECROWN_DIR}/examples/des_y1_3x2pt/des_y1_3x2pt_sacc_data.fits"
-        )
+        os.path.expandvars("${FIRECROWN_DIR}/examples/des_y1_3x2pt/sacc_data.fits")
     )
     sacc_data = sacc.Sacc.load_fits(saccfile)
 
diff --git a/examples/des_y1_3x2pt/des_y1_3x2pt_PT.py b/examples/des_y1_3x2pt/factory_PT.py
old mode 100755
new mode 100644
similarity index 99%
rename from examples/des_y1_3x2pt/des_y1_3x2pt_PT.py
rename to examples/des_y1_3x2pt/factory_PT.py
index 9431b9886..32890f0eb
--- a/examples/des_y1_3x2pt/des_y1_3x2pt_PT.py
+++ b/examples/des_y1_3x2pt/factory_PT.py
@@ -25,9 +25,7 @@
 
 
 saccfile = os.path.expanduser(
-    os.path.expandvars(
-        "${FIRECROWN_DIR}/examples/des_y1_3x2pt/des_y1_3x2pt_sacc_data.fits"
-    )
+    os.path.expandvars("${FIRECROWN_DIR}/examples/des_y1_3x2pt/sacc_data.fits")
 )
 
 
diff --git a/examples/des_y1_3x2pt/des_y1_3x2pt_pure_ccl_experiment.yaml b/examples/des_y1_3x2pt/pure_ccl_experiment.yaml
similarity index 95%
rename from examples/des_y1_3x2pt/des_y1_3x2pt_pure_ccl_experiment.yaml
rename to examples/des_y1_3x2pt/pure_ccl_experiment.yaml
index b5a580856..af4bd33d8 100644
--- a/examples/des_y1_3x2pt/des_y1_3x2pt_pure_ccl_experiment.yaml
+++ b/examples/des_y1_3x2pt/pure_ccl_experiment.yaml
@@ -10,7 +10,7 @@
 # found in the SACC file.
 
 data_source:
-  sacc_data_file: des_y1_3x2pt_sacc_data.fits
+  sacc_data_file: sacc_data.fits
 
 # The two point statistics are defined by the TwoPoint objects. The TwoPoint statistics
 # are created using the factories defined in this file.
diff --git a/examples/des_y1_3x2pt/des_y1_3x2pt_sacc_data.fits b/examples/des_y1_3x2pt/sacc_data.fits
similarity index 100%
rename from examples/des_y1_3x2pt/des_y1_3x2pt_sacc_data.fits
rename to examples/des_y1_3x2pt/sacc_data.fits

From 7f8180779c5cf0870462db2d1ae9c81b46ccdf7d Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Mon, 28 Oct 2024 11:15:26 -0300
Subject: [PATCH 07/25] Better path specification for cobaya.

---
 examples/des_y1_3x2pt/cobaya/evaluate.yaml          | 2 +-
 examples/des_y1_3x2pt/cobaya/evaluate_PT.yaml       | 2 +-
 examples/des_y1_3x2pt/cobaya/evaluate_pure_ccl.yaml | 2 +-
 examples/des_y1_3x2pt/cobaya/mcmc.yaml              | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/examples/des_y1_3x2pt/cobaya/evaluate.yaml b/examples/des_y1_3x2pt/cobaya/evaluate.yaml
index 58e68c1fe..52c4fcf20 100644
--- a/examples/des_y1_3x2pt/cobaya/evaluate.yaml
+++ b/examples/des_y1_3x2pt/cobaya/evaluate.yaml
@@ -10,7 +10,7 @@ theory:
 likelihood:
   des_y1_3x2pt:
     external: !!python/name:firecrown.connector.cobaya.likelihood.LikelihoodConnector ''
-    firecrownIni: ../factory.py
+    firecrownIni: ${FIRECROWN_DIR}/examples/des_y1_3x2pt/factory.py
     derived_parameters: 
     - TwoPoint__NumberCountsScale_lens0
     - TwoPoint__NumberCountsScale_lens1
diff --git a/examples/des_y1_3x2pt/cobaya/evaluate_PT.yaml b/examples/des_y1_3x2pt/cobaya/evaluate_PT.yaml
index b19f92334..da48e5d23 100644
--- a/examples/des_y1_3x2pt/cobaya/evaluate_PT.yaml
+++ b/examples/des_y1_3x2pt/cobaya/evaluate_PT.yaml
@@ -10,7 +10,7 @@ theory:
 likelihood:
   des_y1_3x2pt:
     external: !!python/name:firecrown.connector.cobaya.likelihood.LikelihoodConnector ''
-    firecrownIni: ../factory_PT.py
+    firecrownIni: ${FIRECROWN_DIR}/examples/des_y1_3x2pt/factory_PT.py
 params:
   As:
     prior:
diff --git a/examples/des_y1_3x2pt/cobaya/evaluate_pure_ccl.yaml b/examples/des_y1_3x2pt/cobaya/evaluate_pure_ccl.yaml
index 1eb3bf9e0..3ab2867fd 100644
--- a/examples/des_y1_3x2pt/cobaya/evaluate_pure_ccl.yaml
+++ b/examples/des_y1_3x2pt/cobaya/evaluate_pure_ccl.yaml
@@ -3,7 +3,7 @@ likelihood:
     external: !!python/name:firecrown.connector.cobaya.likelihood.LikelihoodConnector ''
     firecrownIni: firecrown.likelihood.factories.build_two_point_likelihood
     build_parameters:
-      likelihood_config: ../pure_ccl_experiment.yaml
+      likelihood_config: ${FIRECROWN_DIR}/examples/des_y1_3x2pt/pure_ccl_experiment.yaml
 params:
   sigma8:
     prior:
diff --git a/examples/des_y1_3x2pt/cobaya/mcmc.yaml b/examples/des_y1_3x2pt/cobaya/mcmc.yaml
index 3a064dab5..1f374f988 100644
--- a/examples/des_y1_3x2pt/cobaya/mcmc.yaml
+++ b/examples/des_y1_3x2pt/cobaya/mcmc.yaml
@@ -10,7 +10,7 @@ theory:
 likelihood:
   des_y1_3x2pt:
     external: !!python/name:firecrown.connector.cobaya.likelihood.LikelihoodConnector ''
-    firecrownIni: ../factory.py
+    firecrownIni: ${FIRECROWN_DIR}/examples/des_y1_3x2pt/factory.py
 params:
   As:
     prior:

From 90a2a43e9044a0cf48ab1b045779d2756495a213 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Mon, 28 Oct 2024 11:24:44 -0300
Subject: [PATCH 08/25] Adding support for pure_ccl in numcosmo connector.

---
 firecrown/connector/numcosmo/numcosmo.py | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/firecrown/connector/numcosmo/numcosmo.py b/firecrown/connector/numcosmo/numcosmo.py
index 0e39f934e..ebdd087e4 100644
--- a/firecrown/connector/numcosmo/numcosmo.py
+++ b/firecrown/connector/numcosmo/numcosmo.py
@@ -22,6 +22,7 @@
     PowerSpec,
     CCLFactory,
     PoweSpecAmplitudeParameter,
+    CCLCreationMode,
 )
 
 
@@ -568,12 +569,16 @@ def do_prepare(  # pylint: disable-msg=arguments-differ
         self.tools.reset()
 
         self._nc_mapping.set_params_from_numcosmo(mset, self.tools.ccl_factory)
-        ccl_args = self._nc_mapping.calculate_ccl_args(mset)
         params_map = self._nc_mapping.create_params_map(self.model_list, mset)
 
         self.likelihood.update(params_map)
         self.tools.update(params_map)
-        self.tools.prepare(calculator_args=ccl_args)
+        if self.tools.ccl_factory.creation_mode == CCLCreationMode.DEFAULT:
+            self.tools.prepare(
+                calculator_args=self._nc_mapping.calculate_ccl_args(mset)
+            )
+        else:
+            self.tools.prepare()
 
     def do_m2lnL_val(self, _) -> float:  # pylint: disable-msg=arguments-differ
         """Implements the virtual method `m2lnL`.
@@ -840,12 +845,16 @@ def do_prepare(  # pylint: disable-msg=arguments-differ
         self.tools.reset()
 
         self._nc_mapping.set_params_from_numcosmo(mset, self.tools.ccl_factory)
-        ccl_args = self._nc_mapping.calculate_ccl_args(mset)
         params_map = self._nc_mapping.create_params_map(self._model_list, mset)
 
         self.likelihood.update(params_map)
         self.tools.update(params_map)
-        self.tools.prepare(calculator_args=ccl_args)
+        if self.tools.ccl_factory.creation_mode == CCLCreationMode.DEFAULT:
+            self.tools.prepare(
+                calculator_args=self._nc_mapping.calculate_ccl_args(mset)
+            )
+        else:
+            self.tools.prepare()
 
     # pylint: disable-next=arguments-differ
     def do_mean_func(self, _, vp) -> None:

From f2cc227fc5a620b020cabfe31829ae7f34316723 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Mon, 28 Oct 2024 11:42:31 -0300
Subject: [PATCH 09/25] Updated tests.

---
 tests/integration/test_des_y1_3x2pt.py | 36 +++++++++++++++++++-------
 tests/likelihood/test_factories.py     |  9 ++++---
 tests/test_pt_systematics.py           |  2 +-
 3 files changed, 33 insertions(+), 14 deletions(-)

diff --git a/tests/integration/test_des_y1_3x2pt.py b/tests/integration/test_des_y1_3x2pt.py
index 99fee1ab3..1d45cfd7a 100644
--- a/tests/integration/test_des_y1_3x2pt.py
+++ b/tests/integration/test_des_y1_3x2pt.py
@@ -13,9 +13,10 @@ def test_des_y1_3x2pt_cosmosis():
             """
                 set -e
                 cd examples/des_y1_3x2pt
-                cosmosis des_y1_3x2pt.ini
-                cosmosis des_y1_3x2pt_PT.ini
-                cosmosis des_y1_3x2pt_default_factory.ini
+                cosmosis cosmosis/factory.ini
+                cosmosis cosmosis/factory_PT.ini
+                cosmosis cosmosis/default_factory.ini
+                cosmosis cosmosis/pure_ccl_default_factory.ini
             """,
         ],
         capture_output=True,
@@ -36,12 +37,28 @@ def test_des_y1_3x2pt_numcosmo():
             """
                 set -e
                 cd examples/des_y1_3x2pt
-                numcosmo from-cosmosis des_y1_3x2pt.ini --matter-ps eisenstein_hu\\
+                mkdir -p numcosmo
+                cd numcosmo
+
+                numcosmo from-cosmosis ../cosmosis/factory.ini \\
+                    --matter-ps eisenstein_hu \\
+                    --nonlin-matter-ps halofit
+                numcosmo run test factory.yaml
+
+                numcosmo from-cosmosis ../cosmosis/factory_PT.ini \\
+                    --matter-ps eisenstein_hu \\
                     --nonlin-matter-ps halofit
-                numcosmo run test des_y1_3x2pt.yaml
-                numcosmo from-cosmosis des_y1_3x2pt_PT.ini --matter-ps eisenstein_hu\\
+                numcosmo run test factory_PT.yaml
+
+                numcosmo from-cosmosis ../cosmosis/default_factory.ini \\
+                    --matter-ps eisenstein_hu \\
+                    --nonlin-matter-ps halofit
+                numcosmo run test default_factory.yaml
+
+                numcosmo from-cosmosis ../cosmosis/pure_ccl_default_factory.ini \\
+                    --matter-ps eisenstein_hu \\
                     --nonlin-matter-ps halofit
-                numcosmo run test des_y1_3x2pt_PT.yaml
+                numcosmo run test pure_ccl_default_factory.yaml
             """,
         ],
         capture_output=True,
@@ -62,8 +79,9 @@ def test_des_y1_3x2pt_cobaya():
             """
                 set -e
                 cd examples/des_y1_3x2pt
-                cobaya-run cobaya_evaluate.yaml
-                cobaya-run cobaya_evaluate_PT.yaml
+                cobaya-run cobaya/evaluate.yaml
+                cobaya-run cobaya/evaluate_PT.yaml
+                cobaya-run cobaya/evaluate_pure_ccl.yaml
             """,
         ],
         capture_output=True,
diff --git a/tests/likelihood/test_factories.py b/tests/likelihood/test_factories.py
index 45c15da1c..df71df960 100644
--- a/tests/likelihood/test_factories.py
+++ b/tests/likelihood/test_factories.py
@@ -99,10 +99,11 @@ def test_data_source_sacc_direct() -> None:
 
 def test_data_source_sacc_invalid_file() -> None:
     data_source_sacc_dict = {"sacc_data_file": "tests/file_not_found.sacc.gz"}
+    data_source = DataSourceSacc.model_validate(data_source_sacc_dict)
     with pytest.raises(
         FileNotFoundError, match=".*File tests/file_not_found.sacc.gz does not exist.*"
     ):
-        DataSourceSacc.model_validate(data_source_sacc_dict)
+        _ = data_source.get_sacc_data()
 
 
 def test_data_source_sacc_get_sacc_data() -> None:
@@ -209,7 +210,7 @@ def test_build_two_point_likelihood_real(tmp_path: Path) -> None:
     per_bin_systematics: []
     global_systematics: []
 data_source:
-    sacc_data_file: examples/des_y1_3x2pt/des_y1_3x2pt_sacc_data.fits
+    sacc_data_file: examples/des_y1_3x2pt/sacc_data.fits
 """
     )
 
@@ -282,7 +283,7 @@ def test_build_two_point_likelihood_harmonic_no_harmonic_data(tmp_path: Path) ->
         per_bin_systematics: []
         global_systematics: []
 data_source:
-    sacc_data_file: examples/des_y1_3x2pt/des_y1_3x2pt_sacc_data.fits
+    sacc_data_file: examples/des_y1_3x2pt/sacc_data.fits
 """
     )
 
@@ -302,7 +303,7 @@ def test_build_two_point_likelihood_empty_likelihood_config(tmp_path: Path) -> N
     tmp_experiment_file.write_text("")
 
     build_parameters = NamedParameters({"likelihood_config": str(tmp_experiment_file)})
-    with pytest.raises(ValueError, match="No likelihood config found."):
+    with pytest.raises(ValueError, match="validation error for TwoPointExperiment"):
         _ = build_two_point_likelihood(build_parameters)
 
 
diff --git a/tests/test_pt_systematics.py b/tests/test_pt_systematics.py
index 11a4d1fe5..4a9d90dad 100644
--- a/tests/test_pt_systematics.py
+++ b/tests/test_pt_systematics.py
@@ -48,7 +48,7 @@ def fixture_sacc_data():
     # This shouldn't be necessary, since we only use the n(z) from the sacc file
     saccfile = os.path.join(
         os.path.split(__file__)[0],
-        "../examples/des_y1_3x2pt/des_y1_3x2pt_sacc_data.fits",
+        "../examples/des_y1_3x2pt/sacc_data.fits",
     )
     return sacc.Sacc.load_fits(saccfile)
 

From fba1ef7cd8245c7676eeb8fefc84bb0cf4479f63 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Mon, 28 Oct 2024 18:46:46 -0300
Subject: [PATCH 10/25] Updated file names.

---
 environment.yml                               |  1 +
 examples/des_y1_3x2pt/README.md               | 40 ++++++++++++++++++-
 ...e_ccl_default_factory.ini => pure_ccl.ini} |  0
 .../des_y1_3x2pt/des_y1_cosmic_shear_TATT.py  |  4 +-
 .../des_y1_cosmic_shear_pk_modifier.py        |  4 +-
 examples/des_y1_3x2pt/generate_des_data.py    |  2 +-
 examples/des_y1_3x2pt/plot_des_chain.ipynb    |  2 +-
 .../des_y1_3x2pt/plot_des_data_model.ipynb    |  2 +-
 firecrown/ccl_factory.py                      |  9 +++--
 tests/integration/test_des_y1_3x2pt.py        | 13 ++++--
 tutorial/two_point_factories.qmd              |  2 +-
 11 files changed, 60 insertions(+), 19 deletions(-)
 rename examples/des_y1_3x2pt/cosmosis/{pure_ccl_default_factory.ini => pure_ccl.ini} (100%)

diff --git a/environment.yml b/environment.yml
index 697a25c9b..b497bd969 100644
--- a/environment.yml
+++ b/environment.yml
@@ -18,6 +18,7 @@ dependencies:
   - getdist
   - glib
   - idna
+  - isitgr
   - matplotlib-base
   - more-itertools
   - mypy
diff --git a/examples/des_y1_3x2pt/README.md b/examples/des_y1_3x2pt/README.md
index ae6f39950..bc33bbaaf 100644
--- a/examples/des_y1_3x2pt/README.md
+++ b/examples/des_y1_3x2pt/README.md
@@ -1,6 +1,42 @@
 # DES Y1 3x2pt Analysis
 
-The code here will run a test sample for a Flat LCDM cosmology using either Cobaya or CosmoSIS. 
+The DES Y1 3x2pt analysis is a joint analysis of the DES Y1 cosmic shear, galaxy-galaxy
+lensing, and galaxy clustering data. In this example, we show how to use the DES Y1
+3x2pt data products to calculate the likelihood using `Cobaya`, `CosmoSIS`, and
+`NumCosmo`.
+
+## Likelihood factories
+
+Firecrown likelihood can be constructed through user defined factories. In this example:
+
+  - `factory.py`: The FireCrown factory file for the DES Y1 3x2pt analysis.
+  - `factory_PT.py`: The FireCrown factory file for the DES Y1 3x2pt analysis with
+    perturbation theory.
+
+Firecrown default factories can also be used, in this case they are configure through the
+experiment configuration file:
+
+  - `experiment.yaml`: The FireCrown experiment configuration file for the DES Y1 3x2pt
+    analysis.
+  - `pure_ccl_experiment.yaml`: The FireCrown experiment configuration file for the DES Y1
+    3x2pt analysis using the `pure_ccl` mode.
+  - `mu_sigma_experiment.yaml`: The FireCrown experiment configuration file for the DES Y1
+    3x2pt analysis using the `mu_sigma_isitgr` mode.
+
+
+## Running cosmosis
+
+For each of the likelihood factories, we provide a CosmoSIS pipeline configuration file:
+
+  - `cosmosis/factory.ini`: The CosmoSIS pipeline configuration file for the DES Y1 3x2pt
+    analysis.
+  - `cosmosis/factory_PT.ini`: The CosmoSIS pipeline configuration file for the DES Y1 3x2pt
+    analysis with perturbation theory.
+  - `cosmosis/pure_ccl.ini`: The CosmoSIS pipeline configuration file for the DES Y1 3x2pt
+    analysis using the `pure_ccl` mode.
+  - `cosmosis/mu_sigma.ini`: The CosmoSIS pipeline configuration file for the DES Y1 3x2pt
+
+
 
 ## Running Cobaya
 
@@ -29,7 +65,7 @@ It also creates the directory `des_y1_3x2pt_output` which is populated with the
 ## Generating the `firecrown` Inputs
 
 Note, this code below only has to be run if you want to generate the firecrown input from the DES Y1 3x2pt data products.
-This file is stored at `examples/des_y1_3x2pt/des_y1_3x2pt_sacc_data.fits`.
+This file is stored at `examples/des_y1_3x2pt/sacc_data.fits`.
 You do not have to make it yourself.
 
 To generate the `firecrown` inputs, first download the DES Y1 3x2pt data products [here](http://desdr-server.ncsa.illinois.edu/despublic/y1a1_files/chains/2pt_NG_mcal_1110.fits).
diff --git a/examples/des_y1_3x2pt/cosmosis/pure_ccl_default_factory.ini b/examples/des_y1_3x2pt/cosmosis/pure_ccl.ini
similarity index 100%
rename from examples/des_y1_3x2pt/cosmosis/pure_ccl_default_factory.ini
rename to examples/des_y1_3x2pt/cosmosis/pure_ccl.ini
diff --git a/examples/des_y1_3x2pt/des_y1_cosmic_shear_TATT.py b/examples/des_y1_3x2pt/des_y1_cosmic_shear_TATT.py
index 647268bdc..0b410b684 100644
--- a/examples/des_y1_3x2pt/des_y1_cosmic_shear_TATT.py
+++ b/examples/des_y1_3x2pt/des_y1_cosmic_shear_TATT.py
@@ -16,9 +16,7 @@
 from firecrown.metadata_types import TracerNames, TRACER_NAMES_TOTAL
 
 SACCFILE = os.path.expanduser(
-    os.path.expandvars(
-        "${FIRECROWN_DIR}/examples/des_y1_3x2pt/des_y1_3x2pt_sacc_data.fits"
-    )
+    os.path.expandvars("${FIRECROWN_DIR}/examples/des_y1_3x2pt/sacc_data.fits")
 )
 
 
diff --git a/examples/des_y1_3x2pt/des_y1_cosmic_shear_pk_modifier.py b/examples/des_y1_3x2pt/des_y1_cosmic_shear_pk_modifier.py
index 40620eb6e..80ba10353 100644
--- a/examples/des_y1_3x2pt/des_y1_cosmic_shear_pk_modifier.py
+++ b/examples/des_y1_3x2pt/des_y1_cosmic_shear_pk_modifier.py
@@ -20,9 +20,7 @@
 from firecrown.metadata_types import TracerNames
 
 SACCFILE = os.path.expanduser(
-    os.path.expandvars(
-        "${FIRECROWN_DIR}/examples/des_y1_3x2pt/des_y1_3x2pt_sacc_data.fits"
-    )
+    os.path.expandvars("${FIRECROWN_DIR}/examples/des_y1_3x2pt/sacc_data.fits")
 )
 
 
diff --git a/examples/des_y1_3x2pt/generate_des_data.py b/examples/des_y1_3x2pt/generate_des_data.py
index 74be2086a..0f7ff53fd 100644
--- a/examples/des_y1_3x2pt/generate_des_data.py
+++ b/examples/des_y1_3x2pt/generate_des_data.py
@@ -225,4 +225,4 @@
 
     sacc_data.add_covariance(new_cov)
 
-sacc_data.save_fits("des_y1_3x2pt_sacc_data.fits", overwrite=True)
+sacc_data.save_fits("sacc_data.fits", overwrite=True)
diff --git a/examples/des_y1_3x2pt/plot_des_chain.ipynb b/examples/des_y1_3x2pt/plot_des_chain.ipynb
index af7550f0d..55cf7687d 100644
--- a/examples/des_y1_3x2pt/plot_des_chain.ipynb
+++ b/examples/des_y1_3x2pt/plot_des_chain.ipynb
@@ -56,7 +56,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "des_data = sacc.Sacc.load_fits(\"des_y1_3x2pt_sacc_data.fits\")\n",
+    "des_data = sacc.Sacc.load_fits(\"sacc_data.fits\")\n",
     "fc_data = sacc.Sacc.load_fits(\n",
     "    \"output_%s/statistics/two_point/sacc_predicted.fits\" % ANALYSIS_ID\n",
     ")"
diff --git a/examples/des_y1_3x2pt/plot_des_data_model.ipynb b/examples/des_y1_3x2pt/plot_des_data_model.ipynb
index 45b1c4e3c..266365595 100644
--- a/examples/des_y1_3x2pt/plot_des_data_model.ipynb
+++ b/examples/des_y1_3x2pt/plot_des_data_model.ipynb
@@ -54,7 +54,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "des_data = sacc.Sacc.load_fits(\"des_y1_3x2pt_sacc_data.fits\")\n",
+    "des_data = sacc.Sacc.load_fits(\"sacc_data.fits\")\n",
     "fc_meas_data = sacc.Sacc.load_fits(\n",
     "    \"output_%s/statistics/two_point/sacc_measured.fits\" % ANALYSIS_ID\n",
     ")\n",
diff --git a/firecrown/ccl_factory.py b/firecrown/ccl_factory.py
index 9f59de1be..adc351625 100644
--- a/firecrown/ccl_factory.py
+++ b/firecrown/ccl_factory.py
@@ -134,20 +134,21 @@ class MuSigmaModel(Updatable):
 
     def __init__(self):
         """Initialize the MuSigmaModel object."""
-        super().__init__(parameter_prefix="mu_sigma")
+        super().__init__(parameter_prefix="mg_musigma")
 
         self.mu = register_new_updatable_parameter(default_value=1.0)
-        self.sigma = register_new_updatable_parameter(default_value=0.0)
+        self.sigma = register_new_updatable_parameter(default_value=1.0)
         self.c1 = register_new_updatable_parameter(default_value=1.0)
         self.c2 = register_new_updatable_parameter(default_value=1.0)
-        self.lambda_mg = register_new_updatable_parameter(default_value=0.0)
+        # We cannot clash with the lambda keyword
+        self.lambda0 = register_new_updatable_parameter(default_value=1.0)
 
     def create(self) -> MuSigmaMG:
         """Create a `pyccl.modified_gravity.MuSigmaMG` object."""
         if not self.is_updated():
             raise ValueError("Parameters have not been updated yet.")
 
-        return MuSigmaMG(self.mu, self.sigma, self.c1, self.c2, self.lambda_mg)
+        return MuSigmaMG(self.mu, self.sigma, self.c1, self.c2, self.lambda0)
 
 
 class CAMBExtraParams(BaseModel):
diff --git a/tests/integration/test_des_y1_3x2pt.py b/tests/integration/test_des_y1_3x2pt.py
index 1d45cfd7a..328696683 100644
--- a/tests/integration/test_des_y1_3x2pt.py
+++ b/tests/integration/test_des_y1_3x2pt.py
@@ -16,7 +16,8 @@ def test_des_y1_3x2pt_cosmosis():
                 cosmosis cosmosis/factory.ini
                 cosmosis cosmosis/factory_PT.ini
                 cosmosis cosmosis/default_factory.ini
-                cosmosis cosmosis/pure_ccl_default_factory.ini
+                cosmosis cosmosis/pure_ccl.ini
+                cosmosis cosmosis/mu_sigma.ini
             """,
         ],
         capture_output=True,
@@ -55,10 +56,15 @@ def test_des_y1_3x2pt_numcosmo():
                     --nonlin-matter-ps halofit
                 numcosmo run test default_factory.yaml
 
-                numcosmo from-cosmosis ../cosmosis/pure_ccl_default_factory.ini \\
+                numcosmo from-cosmosis ../cosmosis/pure_ccl.ini \\
                     --matter-ps eisenstein_hu \\
                     --nonlin-matter-ps halofit
-                numcosmo run test pure_ccl_default_factory.yaml
+                numcosmo run test pure_ccl.yaml
+
+                numcosmo from-cosmosis ../cosmosis/mu_sigma.ini \\
+                    --matter-ps eisenstein_hu \\
+                    --nonlin-matter-ps halofit
+                numcosmo run test mu_sigma.yaml
             """,
         ],
         capture_output=True,
@@ -82,6 +88,7 @@ def test_des_y1_3x2pt_cobaya():
                 cobaya-run cobaya/evaluate.yaml
                 cobaya-run cobaya/evaluate_PT.yaml
                 cobaya-run cobaya/evaluate_pure_ccl.yaml
+                cobaya-run cobaya/evaluate_mu_sigma.yaml
             """,
         ],
         capture_output=True,
diff --git a/tutorial/two_point_factories.qmd b/tutorial/two_point_factories.qmd
index ef3b6c90a..fb1fa7009 100644
--- a/tutorial/two_point_factories.qmd
+++ b/tutorial/two_point_factories.qmd
@@ -32,7 +32,7 @@ In the code below we extract the metadata indices from the `examples/des_y1_3x2p
 from firecrown.metadata_functions import extract_all_real_metadata_indices
 import sacc
 
-sacc_data = sacc.Sacc.load_fits("../examples/des_y1_3x2pt/des_y1_3x2pt_sacc_data.fits")
+sacc_data = sacc.Sacc.load_fits("../examples/des_y1_3x2pt/sacc_data.fits")
 
 all_meta = extract_all_real_metadata_indices(sacc_data)
 ```

From 181e2074ef95612414e5a45de6d8f6eca92c2566 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Mon, 28 Oct 2024 18:47:13 -0300
Subject: [PATCH 11/25] Adding support for mu_sigma experiments.

---
 .../cobaya/evaluate_mu_sigma.yaml             | 176 ++++++++++++++++++
 examples/des_y1_3x2pt/cosmosis/mu_sigma.ini   |  46 +++++
 .../des_y1_3x2pt/cosmosis/mu_sigma_values.ini |  51 +++++
 .../des_y1_3x2pt/mu_sigma_experiment.yaml     |  32 ++++
 4 files changed, 305 insertions(+)
 create mode 100644 examples/des_y1_3x2pt/cobaya/evaluate_mu_sigma.yaml
 create mode 100644 examples/des_y1_3x2pt/cosmosis/mu_sigma.ini
 create mode 100644 examples/des_y1_3x2pt/cosmosis/mu_sigma_values.ini
 create mode 100644 examples/des_y1_3x2pt/mu_sigma_experiment.yaml

diff --git a/examples/des_y1_3x2pt/cobaya/evaluate_mu_sigma.yaml b/examples/des_y1_3x2pt/cobaya/evaluate_mu_sigma.yaml
new file mode 100644
index 000000000..d05309515
--- /dev/null
+++ b/examples/des_y1_3x2pt/cobaya/evaluate_mu_sigma.yaml
@@ -0,0 +1,176 @@
+likelihood:
+  des_y1_3x2pt:
+    external: !!python/name:firecrown.connector.cobaya.likelihood.LikelihoodConnector ''
+    firecrownIni: firecrown.likelihood.factories.build_two_point_likelihood
+    build_parameters:
+      likelihood_config: ${FIRECROWN_DIR}/examples/des_y1_3x2pt/mu_sigma_experiment.yaml
+params:
+  sigma8:
+    prior:
+      min: 0.6
+      max: 1.0
+    ref: 0.8
+    proposal: 0.01
+  Omega_b: 0.05
+  Omega_c:
+    prior:
+      min: 0.05
+      max: 0.35
+    ref: 0.25
+    proposal: 0.01
+  Omega_k: 0.0
+  h: 0.682
+  Neff: 3.046
+  m_nu: 0.06
+  n_s: 0.971
+  w0: -1.0
+  wa: 0.0
+  T_CMB: 2.7255
+
+#   - MG Model
+  mg_musigma_mu: 
+     ref: 1.0
+     prior:
+        min: 0.8
+        max: 1.2
+  mg_musigma_sigma:
+       ref: 1.0
+       prior:
+         min: 0.8
+         max: 1.2
+  mg_musigma_c1: 1.0
+  mg_musigma_c2: 1.0
+  mg_musigma_lambda0: 1.0
+#   Likelihood params
+#   - IA model
+  ia_bias:
+     ref: 0.5
+     prior:
+        min: -5.0
+        max: +5.0
+  alphaz:
+     ref: 0.0
+     prior:
+        min: -5.0
+        max: +5.0
+
+#   - these parameters are fixed
+  z_piv: 0.62
+
+#   - linear bias for lenses
+  lens0_bias: 
+     ref: 1.4
+     prior:
+        min: 0.8
+        max: 3.0
+  lens1_bias: 
+     ref: 1.6
+     prior:
+        min: 0.8
+        max: 3.0
+  lens2_bias: 
+     ref: 1.6
+     prior:
+        min: 0.8
+        max: 3.0
+  lens3_bias: 
+     ref: 1.9
+     prior:
+        min: 0.8
+        max: 3.0
+  lens4_bias: 
+     ref: 2.0
+     prior:
+        min: 0.8
+        max: 3.0
+
+#   - photoz shifts for the lensing sources
+  src0_delta_z: 
+     ref: -0.001
+     prior:
+        dist: norm
+        loc: -0.001
+        scale: 0.016
+  src1_delta_z: 
+     ref: -0.019
+     prior:
+        dist: norm
+        loc: -0.019
+        scale: 0.013
+  src2_delta_z: 
+     ref: +0.009
+     prior:
+        dist: norm
+        loc: 0.009
+        scale: 0.011
+  src3_delta_z: 
+     ref: -0.018
+     prior:
+        dist: norm
+        loc: -0.018
+        scale: 0.022
+
+#   - photoz shifts for the lenses
+  lens0_delta_z:
+     ref: 0.001
+     prior:
+        dist: norm
+        loc: 0.001
+        scale: 0.008
+  lens1_delta_z: 
+     ref: 0.002
+     prior:
+        dist: norm
+        loc: 0.002
+        scale: 0.007
+  lens2_delta_z: 
+     ref: 0.001
+     prior:
+        dist: norm
+        loc: 0.001
+        scale: 0.007
+  lens3_delta_z: 
+     ref: 0.003
+     prior:
+        dist: norm
+        loc: 0.003
+        scale: 0.01
+  lens4_delta_z: 
+     ref: 0.0
+     prior:
+        dist: norm
+        loc: 0.0
+        scale: 0.01
+
+#   - shear errors
+  src0_mult_bias: 
+     ref: 0.0
+     prior:
+        dist: norm
+        loc: 0.012
+        scale: 0.023
+  src1_mult_bias: 
+     ref: 0.0
+     prior:
+        dist: norm
+        loc: 0.012
+        scale: 0.023
+  src2_mult_bias: 
+     ref: 0.0
+     prior:
+        dist: norm
+        loc: 0.012
+        scale: 0.023
+  src3_mult_bias: 
+     ref: 0.0
+     prior:
+        dist: norm
+        loc: 0.012
+        scale: 0.023
+sampler:
+  evaluate: null
+stop_at_error: true
+output: output_mu_sigma
+packages_path: null
+test: false
+debug: false
diff --git a/examples/des_y1_3x2pt/cosmosis/mu_sigma.ini b/examples/des_y1_3x2pt/cosmosis/mu_sigma.ini
new file mode 100644
index 000000000..c0edc1dcd
--- /dev/null
+++ b/examples/des_y1_3x2pt/cosmosis/mu_sigma.ini
@@ -0,0 +1,46 @@
+[runtime]
+sampler = test
+root = ${PWD}
+
+[DEFAULT]
+fatal_errors = T
+
+[output]
+filename = output/des_y1_3x2pt_samples.txt
+format = text
+verbosity = 0
+
+[pipeline]
+modules = consistency firecrown_likelihood
+values = ${FIRECROWN_DIR}/examples/des_y1_3x2pt/cosmosis/mu_sigma_values.ini
+likelihoods = firecrown
+quiet = T
+debug = T
+timing = T
+
+[consistency]
+file = ${CSL_DIR}/utility/consistency/consistency_interface.py
+
+[firecrown_likelihood]
+;; Fix this to use an environment variable to find the files.
+;; Set FIRECROWN_DIR to the base of the firecrown installation (or build, if you haven't
+;; installed it)
+file = ${FIRECROWN_DIR}/firecrown/connector/cosmosis/likelihood.py
+likelihood_source = firecrown.likelihood.factories.build_two_point_likelihood
+likelihood_config = ${FIRECROWN_DIR}/examples/des_y1_3x2pt/mu_sigma_experiment.yaml
+;; Connector settings
+require_nonlinear_pk = True
+sampling_parameters_sections = firecrown_two_point
+
+[test]
+fatal_errors = T
+save_dir = output_pure_ccl
+
+[metropolis]
+samples = 1000
+nsteps = 1
+
+[emcee]
+walkers = 64
+samples = 400
+nsteps = 10
diff --git a/examples/des_y1_3x2pt/cosmosis/mu_sigma_values.ini b/examples/des_y1_3x2pt/cosmosis/mu_sigma_values.ini
new file mode 100644
index 000000000..1d242f644
--- /dev/null
+++ b/examples/des_y1_3x2pt/cosmosis/mu_sigma_values.ini
@@ -0,0 +1,51 @@
+; Parameters and data in CosmoSIS are organized into sections
+; so we can easily see what they mean.
+; There is only one section in this case, called cosmological_parameters
+[cosmological_parameters]
+
+; These are the only parameters being varied.
+omega_c = 0.06 0.26 0.46
+omega_b = 0.03 0.04 0.07
+
+; The following parameters are set, but not varied.
+omega_k = 0.0
+tau = 0.08
+n_s = 0.971
+sigma_8 = 0.801
+h0 = 0.682
+w = -1.0
+wa = 0.0
+
+
+[firecrown_two_point]
+
+mg_musigma_mu = 0.8 1.0 1.2
+mg_musigma_sigma = 0.8 1.0 1.2
+mg_musigma_c1 = 1.0
+mg_musigma_c2 = 1.0
+mg_musigma_lambda0 = 1.0
+
+ia_bias = -5.0 0.5 +5.0
+alphaz = -5.0 0.0 +5.0
+z_piv = 0.62
+lens0_bias = 0.8 1.4 3.0
+lens1_bias = 0.8 1.6 3.0
+lens2_bias = 0.8 1.6 3.0 
+lens3_bias = 0.8 1.9 3.0
+lens4_bias = 0.8 2.0 3.0
+
+src0_delta_z = -0.05 -0.001 0.05
+src1_delta_z = -0.05 -0.019 0.05
+src2_delta_z = -0.05  0.009 0.05
+src3_delta_z = -0.05 -0.018 0.05
+
+lens0_delta_z = -0.05 0.001 0.05
+lens1_delta_z = -0.05 0.002 0.05
+lens2_delta_z = -0.05 0.001 0.05
+lens3_delta_z = -0.05 0.003 0.05
+lens4_delta_z = -0.05 0.000 0.05
+
+src0_mult_bias = 0.001 0.012 0.1
+src1_mult_bias = 0.001 0.012 0.1
+src2_mult_bias = 0.001 0.012 0.1
+src3_mult_bias = 0.001 0.012 0.1
diff --git a/examples/des_y1_3x2pt/mu_sigma_experiment.yaml b/examples/des_y1_3x2pt/mu_sigma_experiment.yaml
new file mode 100644
index 000000000..b1bac85df
--- /dev/null
+++ b/examples/des_y1_3x2pt/mu_sigma_experiment.yaml
@@ -0,0 +1,32 @@
+---
+
+# This file contains all information about the DES Y1 3x2pt experiment.
+
+# The 'data_source:' field points to the SACC file containing the DES Y1 3x2pt data vector 
+# and covariance matrix, which is used for analysis.
+
+# The 'two_point_factory:' field points to the factory that will create the TwoPoint 
+# objects. These objects represent the chosen theoretical models for each data point 
+# found in the SACC file.
+
+data_source:
+  sacc_data_file: sacc_data.fits
+
+# The two point statistics are defined by the TwoPoint objects. The TwoPoint statistics
+# are created using the factories defined in this file.
+two_point_factory:
+  correlation_space: real
+  number_counts_factory:
+    global_systematics: []
+    per_bin_systematics:
+      - type: PhotoZShiftFactory
+  weak_lensing_factory:
+    global_systematics:
+      - alphag: 1
+        type: LinearAlignmentSystematicFactory
+    per_bin_systematics:
+      - type: MultiplicativeShearBiasFactory
+      - type: PhotoZShiftFactory
+
+ccl_factory:
+  creation_mode: 'mu_sigma_isitgr'

From 1ba6fea326ed1442e294eae86eac2939cab290fc Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Mon, 28 Oct 2024 20:53:18 -0300
Subject: [PATCH 12/25] Updated README.md

---
 examples/des_y1_3x2pt/README.md | 84 ++++++++++++++++-----------------
 1 file changed, 41 insertions(+), 43 deletions(-)

diff --git a/examples/des_y1_3x2pt/README.md b/examples/des_y1_3x2pt/README.md
index bc33bbaaf..9e14cf2a6 100644
--- a/examples/des_y1_3x2pt/README.md
+++ b/examples/des_y1_3x2pt/README.md
@@ -1,66 +1,64 @@
 # DES Y1 3x2pt Analysis
 
-The DES Y1 3x2pt analysis is a joint analysis of the DES Y1 cosmic shear, galaxy-galaxy
-lensing, and galaxy clustering data. In this example, we show how to use the DES Y1
-3x2pt data products to calculate the likelihood using `Cobaya`, `CosmoSIS`, and
-`NumCosmo`.
+The DES Y1 3x2pt analysis of the Dark Energy Survey (DES) Year 1 (Y1) data, focusing on
+**cosmic shear**, **galaxy-galaxy lensing**, and **galaxy clustering**. This repository
+demonstrates how to use the DES Y1 3x2pt data products to compute the likelihood with
+the following tools:
 
-## Likelihood factories
+- **Cobaya**  
+- **CosmoSIS**  
+- **NumCosmo**  
 
-Firecrown likelihood can be constructed through user defined factories. In this example:
+## Likelihood Factories
 
-  - `factory.py`: The FireCrown factory file for the DES Y1 3x2pt analysis.
-  - `factory_PT.py`: The FireCrown factory file for the DES Y1 3x2pt analysis with
-    perturbation theory.
+The **Firecrown** likelihoods can be customized through user-defined factories. In this
+example, the following factory files are provided:
 
-Firecrown default factories can also be used, in this case they are configure through the
-experiment configuration file:
+- `factory.py`: Factory for the DES Y1 3x2pt analysis.
+- `factory_PT.py`: Factory for the DES Y1 3x2pt analysis using perturbation theory.
 
-  - `experiment.yaml`: The FireCrown experiment configuration file for the DES Y1 3x2pt
-    analysis.
-  - `pure_ccl_experiment.yaml`: The FireCrown experiment configuration file for the DES Y1
-    3x2pt analysis using the `pure_ccl` mode.
-  - `mu_sigma_experiment.yaml`: The FireCrown experiment configuration file for the DES Y1
-    3x2pt analysis using the `mu_sigma_isitgr` mode.
+Alternatively, Firecrown’s **default factories** can be configured using experiment
+configuration files:
 
+- `experiment.yaml`: Standard configuration for the DES Y1 3x2pt analysis.
+- `pure_ccl_experiment.yaml`: Configuration for the DES Y1 3x2pt analysis in
+  **pure_ccl** mode.
+- `mu_sigma_experiment.yaml`: Configuration for **mu_sigma_isitgr** mode.
 
-## Running cosmosis
-
-For each of the likelihood factories, we provide a CosmoSIS pipeline configuration file:
+## Running CosmoSIS
 
-  - `cosmosis/factory.ini`: The CosmoSIS pipeline configuration file for the DES Y1 3x2pt
-    analysis.
-  - `cosmosis/factory_PT.ini`: The CosmoSIS pipeline configuration file for the DES Y1 3x2pt
-    analysis with perturbation theory.
-  - `cosmosis/pure_ccl.ini`: The CosmoSIS pipeline configuration file for the DES Y1 3x2pt
-    analysis using the `pure_ccl` mode.
-  - `cosmosis/mu_sigma.ini`: The CosmoSIS pipeline configuration file for the DES Y1 3x2pt
+For each likelihood factory, a corresponding **CosmoSIS** pipeline configuration file is
+provided:
 
+- `cosmosis/factory.ini`: Pipeline for the standard DES Y1 3x2pt analysis.
+- `cosmosis/factory_PT.ini`: Pipeline for the analysis with perturbation theory.
+- `cosmosis/pure_ccl.ini`: Pipeline for the analysis in **pure CCL** mode.
+- `cosmosis/mu_sigma.ini`: Pipeline for the analysis in **mu_sigma_isitgr** mode.
 
+### Example Command
 
-## Running Cobaya
+To run the CosmoSIS pipeline, use the following command:
 
-The Cobaya file `cobaya_evaluate.yaml` configures Cobaya to use the `des_y1_3x2pt.py` likelihood.
-Run it using:
-
-    cobaya-run cobaya_evaluate.yaml
+```bash
+cosmosis cosmosis/factory.ini
+```
 
-This will produce the output files:
+## Running Cobaya
 
-    cobaya_evaluate_output.input.yaml
-    cobaya_evaluate_output.updated.yaml
-    cobaya_evaluate_output.updated.dill_pickle
-    cobaya_evaluate_output.1.txt
+For Cobaya, the pipeline configuration files are:
 
-## Running CosmoSIS
+- `cobaya/evaluate.yaml`: Pipeline for the standard DES Y1 3x2pt analysis.
+- `cobaya/evaluate_PT.yaml`: Pipeline for the analysis with perturbation theory.
+- `cobaya/evaluate_pure_ccl.yaml`: Pipeline for the analysis in **pure CCL** mode.
+- `cobaya/evaluate_mu_sigma.yaml`: Pipeline for the analysis in **mu_sigma_isitgr** mode.
 
-The pipeline configuration file `des_y1_3x2pt.ini` and the related `des_y1_3x2pt_values.ini` configure CosmoSIS to use the `des_y1_3x2pt.py` likelihood.
-Run this using:
+### Example Command
 
-    cosmosis des_y1_3x2pt.ini
+To run the Cobaya pipeline, use the following command:
 
-This will produce the output to the screen, showing the calculated likelihood.
-It also creates the directory `des_y1_3x2pt_output` which is populated with the CosmoSIS datablock contents for the generated sample.
+```bash
+cobaya-run cobaya/factory.yaml
+```
 
 ## Generating the `firecrown` Inputs
 

From 1c0b139c52eeba2016ce8364c7c5235830e06a89 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Mon, 28 Oct 2024 20:55:06 -0300
Subject: [PATCH 13/25] Updated README.md

---
 examples/des_y1_3x2pt/README.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/examples/des_y1_3x2pt/README.md b/examples/des_y1_3x2pt/README.md
index 9e14cf2a6..e7becbfac 100644
--- a/examples/des_y1_3x2pt/README.md
+++ b/examples/des_y1_3x2pt/README.md
@@ -62,11 +62,11 @@ cobaya-run cobaya/factory.yaml
 
 ## Generating the `firecrown` Inputs
 
-Note, this code below only has to be run if you want to generate the firecrown input from the DES Y1 3x2pt data products.
-This file is stored at `examples/des_y1_3x2pt/sacc_data.fits`.
-You do not have to make it yourself.
-
-To generate the `firecrown` inputs, first download the DES Y1 3x2pt data products [here](http://desdr-server.ncsa.illinois.edu/despublic/y1a1_files/chains/2pt_NG_mcal_1110.fits).
+There is already a `sacc_data.fits` file in this directory that contains the DES Y1
+3x2pt data products. If you want to regenerate the `firecrown` inputs, you can run
+`generate_des_data.py`. To generate the `firecrown` inputs, first download the DES Y1
+3x2pt data products
+[here](http://desdr-server.ncsa.illinois.edu/despublic/y1a1_files/chains/2pt_NG_mcal_1110.fits).
 
 Then run the script
 

From 65b53c9d937b0ac756fd01fec19452c8c3b9a412 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Mon, 28 Oct 2024 22:55:45 -0300
Subject: [PATCH 14/25] Improving integration tests. Making mu_sigma tests run
 only if isitgr is available. Updating documentation.

---
 .github/workflows/ci.yml               |  4 +-
 environment.yml                        |  1 -
 examples/des_y1_3x2pt/README.md        |  4 ++
 tests/integration/test_des_y1_3x2pt.py | 86 +++++++++++++++-----------
 4 files changed, 56 insertions(+), 39 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index adb1a716e..760d293f7 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -100,7 +100,9 @@ jobs:
         run: python -m pytest -vv --runslow --cov firecrown --cov-report xml
       - name: Running integration tests
         shell: bash -l {0}
-        run: python -m pytest -vv -s --integration tests/integration 
+        run: |
+          pip install isitgr
+          python -m pytest -vv -s --integration tests/integration 
       - name: Upload coverage reports to Codecov
         if: ${{ (matrix.os == 'ubuntu') && (matrix.python-version == '3.11') }}
         uses: codecov/codecov-action@v4
diff --git a/environment.yml b/environment.yml
index b497bd969..697a25c9b 100644
--- a/environment.yml
+++ b/environment.yml
@@ -18,7 +18,6 @@ dependencies:
   - getdist
   - glib
   - idna
-  - isitgr
   - matplotlib-base
   - more-itertools
   - mypy
diff --git a/examples/des_y1_3x2pt/README.md b/examples/des_y1_3x2pt/README.md
index e7becbfac..aa8b3012a 100644
--- a/examples/des_y1_3x2pt/README.md
+++ b/examples/des_y1_3x2pt/README.md
@@ -25,6 +25,10 @@ configuration files:
   **pure_ccl** mode.
 - `mu_sigma_experiment.yaml`: Configuration for **mu_sigma_isitgr** mode.
 
+Note that `mu_sigma_experiment.yaml` requires the
+[`isitgr`](https://github.com/mishakb/ISiTGR) package to be installed. This package is
+not installed by default in the Firecrown environment.
+
 ## Running CosmoSIS
 
 For each likelihood factory, a corresponding **CosmoSIS** pipeline configuration file is
diff --git a/tests/integration/test_des_y1_3x2pt.py b/tests/integration/test_des_y1_3x2pt.py
index 328696683..716cdcd43 100644
--- a/tests/integration/test_des_y1_3x2pt.py
+++ b/tests/integration/test_des_y1_3x2pt.py
@@ -4,20 +4,55 @@
 import pytest
 
 
+HAS_ISITGR = False
+try:
+    import isitgr
+
+    if isitgr is not None:
+        HAS_ISITGR = True
+except ImportError:
+    HAS_ISITGR = False
+
+INI_FILES = [
+    "factory.ini",
+    "factory_PT.ini",
+    "default_factory.ini",
+    "pure_ccl.ini",
+]
+if HAS_ISITGR:
+    INI_FILES.append("mu_sigma.ini")
+
+COBAYA_YAML_FILES = [
+    "evaluate.yaml",
+    "evaluate_PT.yaml",
+    "evaluate_pure_ccl.yaml",
+]
+if HAS_ISITGR:
+    COBAYA_YAML_FILES.append("evaluate_mu_sigma.yaml")
+
+
+@pytest.fixture(name="ini_file", params=INI_FILES)
+def fixture_ini_file(request) -> str:
+    """Fixture to provide the ini files for the DES Y1 3x2pt analysis."""
+    return request.param
+
+
+@pytest.fixture(name="cobaya_yaml_file", params=COBAYA_YAML_FILES)
+def fixture_cobaya_yaml_file(request) -> str:
+    """Fixture to provide the cobaya yaml files for the DES Y1 3x2pt analysis."""
+    return request.param
+
+
 @pytest.mark.integration
-def test_des_y1_3x2pt_cosmosis():
+def test_des_y1_3x2pt_cosmosis(ini_file: str):
     result = subprocess.run(
         [
             "bash",
             "-c",
-            """
+            f"""
                 set -e
                 cd examples/des_y1_3x2pt
-                cosmosis cosmosis/factory.ini
-                cosmosis cosmosis/factory_PT.ini
-                cosmosis cosmosis/default_factory.ini
-                cosmosis cosmosis/pure_ccl.ini
-                cosmosis cosmosis/mu_sigma.ini
+                cosmosis cosmosis/{ini_file}
             """,
         ],
         capture_output=True,
@@ -30,41 +65,21 @@ def test_des_y1_3x2pt_cosmosis():
 
 
 @pytest.mark.integration
-def test_des_y1_3x2pt_numcosmo():
+def test_des_y1_3x2pt_numcosmo(ini_file: str):
     result = subprocess.run(
         [
             "bash",
             "-c",
-            """
+            f"""
                 set -e
                 cd examples/des_y1_3x2pt
                 mkdir -p numcosmo
                 cd numcosmo
 
-                numcosmo from-cosmosis ../cosmosis/factory.ini \\
-                    --matter-ps eisenstein_hu \\
-                    --nonlin-matter-ps halofit
-                numcosmo run test factory.yaml
-
-                numcosmo from-cosmosis ../cosmosis/factory_PT.ini \\
-                    --matter-ps eisenstein_hu \\
-                    --nonlin-matter-ps halofit
-                numcosmo run test factory_PT.yaml
-
-                numcosmo from-cosmosis ../cosmosis/default_factory.ini \\
-                    --matter-ps eisenstein_hu \\
-                    --nonlin-matter-ps halofit
-                numcosmo run test default_factory.yaml
-
-                numcosmo from-cosmosis ../cosmosis/pure_ccl.ini \\
-                    --matter-ps eisenstein_hu \\
-                    --nonlin-matter-ps halofit
-                numcosmo run test pure_ccl.yaml
-
-                numcosmo from-cosmosis ../cosmosis/mu_sigma.ini \\
+                numcosmo from-cosmosis ../cosmosis/{ini_file} \\
                     --matter-ps eisenstein_hu \\
                     --nonlin-matter-ps halofit
-                numcosmo run test mu_sigma.yaml
+                numcosmo run test {ini_file.replace('.ini', '.yaml')}
             """,
         ],
         capture_output=True,
@@ -77,18 +92,15 @@ def test_des_y1_3x2pt_numcosmo():
 
 
 @pytest.mark.integration
-def test_des_y1_3x2pt_cobaya():
+def test_des_y1_3x2pt_cobaya(cobaya_yaml_file: str):
     result = subprocess.run(
         [
             "bash",
             "-c",
-            """
+            f"""
                 set -e
                 cd examples/des_y1_3x2pt
-                cobaya-run cobaya/evaluate.yaml
-                cobaya-run cobaya/evaluate_PT.yaml
-                cobaya-run cobaya/evaluate_pure_ccl.yaml
-                cobaya-run cobaya/evaluate_mu_sigma.yaml
+                cobaya-run cobaya/{cobaya_yaml_file}
             """,
         ],
         capture_output=True,

From 6adedff11ae56eeab3954ac3fd971ad3a787aff8 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Mon, 28 Oct 2024 23:12:33 -0300
Subject: [PATCH 15/25] Removing mu_sigma test from NumCosmo list.

---
 tests/integration/test_des_y1_3x2pt.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/integration/test_des_y1_3x2pt.py b/tests/integration/test_des_y1_3x2pt.py
index 716cdcd43..16e1ad864 100644
--- a/tests/integration/test_des_y1_3x2pt.py
+++ b/tests/integration/test_des_y1_3x2pt.py
@@ -66,6 +66,10 @@ def test_des_y1_3x2pt_cosmosis(ini_file: str):
 
 @pytest.mark.integration
 def test_des_y1_3x2pt_numcosmo(ini_file: str):
+    # FIXME: New NumCosmo 0.23.0 on will support the mu_sigma.ini. Update the following
+    # line to remove the skip when the new version is released.
+    if "mu_sigma" in ini_file:
+        pytest.skip("numcosmo does not support mu_sigma.ini")
     result = subprocess.run(
         [
             "bash",

From 659360baadaba306a16cc83bdbf759cea97c585f Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Tue, 29 Oct 2024 10:43:20 -0300
Subject: [PATCH 16/25] Testing new camb_extra_parameters.

---
 firecrown/ccl_factory.py  |   2 +-
 tests/test_ccl_factory.py | 114 +++++++++++++++++++++++++++++++++++++-
 2 files changed, 114 insertions(+), 2 deletions(-)

diff --git a/firecrown/ccl_factory.py b/firecrown/ccl_factory.py
index adc351625..c406b1221 100644
--- a/firecrown/ccl_factory.py
+++ b/firecrown/ccl_factory.py
@@ -322,6 +322,7 @@ def create(
 
         if self.camb_extra_params is not None:
             ccl_args["extra_parameters"] = {"camb": self.camb_extra_params.get_dict()}
+            ccl_args["matter_power_spectrum"] = "camb"
 
         match self.creation_mode:
             case CCLCreationMode.DEFAULT:
@@ -337,7 +338,6 @@ def create(
                 pass
             case _:
                 raise ValueError(f"Invalid creation mode: {self.creation_mode}")
-
         self._ccl_cosmo = pyccl.Cosmology(**ccl_args)
         return self._ccl_cosmo
 
diff --git a/tests/test_ccl_factory.py b/tests/test_ccl_factory.py
index 3e12d6140..dc833c8bb 100644
--- a/tests/test_ccl_factory.py
+++ b/tests/test_ccl_factory.py
@@ -3,12 +3,16 @@
 import numpy as np
 import pytest
 import pyccl
+import pyccl.modified_gravity
 from pyccl.neutrinos import NeutrinoMassSplits
 
 from firecrown.ccl_factory import (
+    CAMBExtraParams,
+    CCLCalculatorArgs,
+    CCLCreationMode,
     CCLFactory,
+    MuSigmaModel,
     PoweSpecAmplitudeParameter,
-    CCLCalculatorArgs,
 )
 from firecrown.updatable import get_default_params_map
 from firecrown.parameters import ParamsMap
@@ -34,6 +38,38 @@ def fixture_require_nonlinear_pk(request):
     return request.param
 
 
+@pytest.fixture(
+    name="ccl_creation_mode",
+    params=[
+        CCLCreationMode.DEFAULT,
+        CCLCreationMode.PURE_CCL_MODE,
+        CCLCreationMode.MU_SIGMA_ISITGR,
+    ],
+    ids=["default", "pure_ccl_mode", "mu_sigma_isitgr"],
+)
+def fixture_ccl_creation_mode(request):
+    return request.param
+
+
+@pytest.fixture(
+    name="camb_extra_params",
+    params=[
+        None,
+        {"halofit_version": "mead"},
+        {"halofit_version": "mead", "kmax": 0.1},
+        {"halofit_version": "mead", "kmax": 0.1, "lmax": 100},
+        {"dark_energy_model": "ppf"},
+    ],
+    ids=["default", "mead", "mead_kmax", "mead_kmax_lmax", "ppf"],
+)
+def fixture_camb_extra_params(request) -> CAMBExtraParams | None:
+    return (
+        CAMBExtraParams.model_validate(request.param)
+        if request.param is not None
+        else None
+    )
+
+
 Z_ARRAY = np.linspace(0.0, 5.0, 100)
 A_ARRAY = 1.0 / (1.0 + np.flip(Z_ARRAY))
 K_ARRAY = np.geomspace(1.0e-5, 10.0, 100)
@@ -79,11 +115,15 @@ def test_ccl_factory_simple(
     amplitude_parameter: PoweSpecAmplitudeParameter,
     neutrino_mass_splits: NeutrinoMassSplits,
     require_nonlinear_pk: bool,
+    ccl_creation_mode: CCLCreationMode,
+    camb_extra_params: CAMBExtraParams | None,
 ) -> None:
     ccl_factory = CCLFactory(
         amplitude_parameter=amplitude_parameter,
         mass_split=neutrino_mass_splits,
         require_nonlinear_pk=require_nonlinear_pk,
+        creation_mode=ccl_creation_mode,
+        camb_extra_params=camb_extra_params,
     )
 
     assert ccl_factory is not None
@@ -194,6 +234,24 @@ def test_ccl_factory_neutrino_mass_splits(
     assert isinstance(cosmo, pyccl.Cosmology)
 
 
+def test_ccl_factory_ccl_creation_mode(
+    ccl_creation_mode: CCLCreationMode,
+) -> None:
+    ccl_factory = CCLFactory(creation_mode=ccl_creation_mode)
+
+    assert ccl_factory is not None
+    assert ccl_factory.creation_mode == CCLCreationMode(ccl_creation_mode)
+
+    default_params = get_default_params_map(ccl_factory)
+
+    ccl_factory.update(default_params)
+
+    cosmo = ccl_factory.create()
+
+    assert cosmo is not None
+    assert isinstance(cosmo, pyccl.Cosmology)
+
+
 def test_ccl_factory_get() -> None:
     ccl_factory = CCLFactory()
 
@@ -338,6 +396,14 @@ def test_ccl_factory_invalid_mass_splits() -> None:
         CCLFactory(mass_split="Im not a valid value")
 
 
+def test_ccl_factory_invalid_creation_mode() -> None:
+    with pytest.raises(
+        ValueError,
+        match=".*Invalid value for CCLCreationMode: Im not a valid value.*",
+    ):
+        CCLFactory(creation_mode="Im not a valid value")
+
+
 def test_ccl_factory_from_dict() -> None:
     ccl_factory_dict = {
         "amplitude_parameter": PoweSpecAmplitudeParameter.SIGMA8,
@@ -365,3 +431,49 @@ def test_ccl_factory_from_dict_wrong_type() -> None:
         match=".*Input should be.*",
     ):
         CCLFactory.model_validate(ccl_factory_dict)
+
+
+def test_ccl_factory_camb_extra_params_invalid() -> None:
+    with pytest.raises(
+        ValueError,
+        match=".*validation error for CCLFactory*",
+    ):
+        CCLFactory(camb_extra_params="Im not a valid value")
+
+
+def test_ccl_factory_camb_extra_params_invalid_model() -> None:
+    ccl_factory = CCLFactory(
+        camb_extra_params={"dark_energy_model": "Im not a valid value"}
+    )
+    params = get_default_params_map(ccl_factory)
+    ccl_factory.update(params)
+    ccl_cosmo = ccl_factory.create()
+    with pytest.raises(
+        ValueError,
+        match="The only dark energy models CCL supports with CAMB are fluid and ppf.",
+    ):
+        ccl_cosmo.compute_linear_power()
+
+
+def test_mu_sigma_model() -> None:
+    mu_sigma_model = MuSigmaModel()
+
+    assert mu_sigma_model is not None
+
+    default_params = get_default_params_map(mu_sigma_model)
+
+    mu_sigma_model.update(default_params)
+
+    musigma = mu_sigma_model.create()
+
+    assert musigma is not None
+    assert isinstance(musigma, pyccl.modified_gravity.MuSigmaMG)
+
+
+def test_mu_sigma_create_not_updated() -> None:
+    mu_sigma_model = MuSigmaModel()
+
+    assert mu_sigma_model is not None
+
+    with pytest.raises(ValueError, match="Parameters have not been updated yet."):
+        mu_sigma_model.create()

From 51b1bf277f38cdb39b19ec4f80db1977d3fa34f4 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Tue, 29 Oct 2024 11:34:25 -0300
Subject: [PATCH 17/25] Testing Cobaya connector with ccl_pure mode.

---
 firecrown/ccl_factory.py                      | 13 +++--
 .../connector/cobaya/test_model_likelihood.py | 54 +++++++++++++++++++
 tests/test_ccl_factory.py                     | 12 ++++-
 3 files changed, 74 insertions(+), 5 deletions(-)

diff --git a/firecrown/ccl_factory.py b/firecrown/ccl_factory.py
index c406b1221..8632d2ebb 100644
--- a/firecrown/ccl_factory.py
+++ b/firecrown/ccl_factory.py
@@ -199,6 +199,11 @@ def __init__(self, **data):
         BaseModel.__init__(self, **data)
         Updatable.__init__(self, parameter_prefix=parameter_prefix)
 
+        if set(data) - set(self.model_fields.keys()):
+            raise ValueError(
+                f"Invalid parameters: {set(data) - set(self.model_fields.keys())}"
+            )
+
         self._ccl_cosmo: None | pyccl.Cosmology = None
 
         ccl_cosmo = pyccl.CosmologyVanillaLCDM()
@@ -230,10 +235,10 @@ def __init__(self, **data):
                     default_value=ccl_cosmo["sigma8"]
                 )
 
-        self.mu_sigma_model: None | MuSigmaModel = None
+        self._mu_sigma_model: None | MuSigmaModel = None
         match self.creation_mode:
             case CCLCreationMode.MU_SIGMA_ISITGR:
-                self.mu_sigma_model = MuSigmaModel()
+                self._mu_sigma_model = MuSigmaModel()
 
     @model_serializer(mode="wrap")
     def serialize_model(self, nxt: SerializerFunctionWrapHandler, _: SerializationInfo):
@@ -328,9 +333,9 @@ def create(
             case CCLCreationMode.DEFAULT:
                 pass
             case CCLCreationMode.MU_SIGMA_ISITGR:
-                assert self.mu_sigma_model is not None
+                assert self._mu_sigma_model is not None
                 ccl_args.update(
-                    mg_parametrization=self.mu_sigma_model.create(),
+                    mg_parametrization=self._mu_sigma_model.create(),
                     matter_power_spectrum="linear",
                     transfer_function="boltzmann_isitgr",
                 )
diff --git a/tests/connector/cobaya/test_model_likelihood.py b/tests/connector/cobaya/test_model_likelihood.py
index 609add67e..c5107e8ec 100644
--- a/tests/connector/cobaya/test_model_likelihood.py
+++ b/tests/connector/cobaya/test_model_likelihood.py
@@ -1,6 +1,7 @@
 """Unit tests for the cobaya Mapping connector."""
 
 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
@@ -271,3 +272,56 @@ def test_derived_parameter_likelihood(fiducial_params):
     logpost = model_fiducial.logposterior({})
     assert logpost.logpost == -3.14
     assert logpost.derived[0] == 1.0
+
+
+def test_default_factory():
+    fiducial_params = {
+        "ia_bias": 1.0,
+        "sigma8": 0.8,
+        "alphaz": 1.0,
+        "h": 0.7,
+        "lens0_bias": 1.0,
+        "lens0_delta_z": 0.1,
+        "lens1_bias": 1.0,
+        "lens1_delta_z": 0.1,
+        "lens2_bias": 1.0,
+        "lens2_delta_z": 0.1,
+        "lens3_bias": 1.0,
+        "lens3_delta_z": 0.1,
+        "lens4_delta_z": 0.1,
+        "lens4_bias": 1.0,
+        "m_nu": 0.06,
+        "n_s": 0.96,
+        "Neff": 3.046,
+        "Omega_b": 0.048,
+        "Omega_c": 0.26,
+        "Omega_k": 0.0,
+        "src0_delta_z": 0.1,
+        "src0_mult_bias": 1.0,
+        "src1_delta_z": 0.1,
+        "src1_mult_bias": 1.0,
+        "src2_delta_z": 0.1,
+        "src2_mult_bias": 1.0,
+        "src3_delta_z": 0.1,
+        "src3_mult_bias": 1.0,
+        "w0": -1.0,
+        "wa": 0.0,
+        "z_piv": 0.3,
+        "T_CMB": 2.7255,
+    }
+    info_fiducial = {
+        "params": fiducial_params,
+        "likelihood": {
+            "lk_connector": {
+                "external": LikelihoodConnector,
+                "firecrownIni": "firecrown.likelihood.factories.build_two_point_likelihood",
+                "build_parameters": {
+                    "likelihood_config": "examples/des_y1_3x2pt/pure_ccl_experiment.yaml"
+                },
+            },
+        },
+    }
+    model_fiducial = get_model(info_fiducial)
+    assert isinstance(model_fiducial, Model)
+    logpost = model_fiducial.logposterior({})
+    assert np.isfinite(logpost.logpost)
diff --git a/tests/test_ccl_factory.py b/tests/test_ccl_factory.py
index dc833c8bb..c359ec6f6 100644
--- a/tests/test_ccl_factory.py
+++ b/tests/test_ccl_factory.py
@@ -1,5 +1,6 @@
 """Test the CCLFactory object."""
 
+import re
 import numpy as np
 import pytest
 import pyccl
@@ -220,7 +221,7 @@ def test_ccl_factory_amplitude_parameter(
 def test_ccl_factory_neutrino_mass_splits(
     neutrino_mass_splits: NeutrinoMassSplits,
 ) -> None:
-    ccl_factory = CCLFactory(neutrino_mass_splits=neutrino_mass_splits)
+    ccl_factory = CCLFactory(mass_split=neutrino_mass_splits)
 
     assert ccl_factory is not None
 
@@ -409,6 +410,7 @@ def test_ccl_factory_from_dict() -> None:
         "amplitude_parameter": PoweSpecAmplitudeParameter.SIGMA8,
         "mass_split": NeutrinoMassSplits.EQUAL,
         "require_nonlinear_pk": True,
+        "creation_mode": CCLCreationMode.DEFAULT,
     }
 
     ccl_factory = CCLFactory.model_validate(ccl_factory_dict)
@@ -455,6 +457,14 @@ def test_ccl_factory_camb_extra_params_invalid_model() -> None:
         ccl_cosmo.compute_linear_power()
 
 
+def test_ccl_factory_invalid_extra_params() -> None:
+    with pytest.raises(
+        ValueError,
+        match=re.escape("Invalid parameters: {'not_a_valid_param'}"),
+    ):
+        CCLFactory(not_a_valid_param="Im not a valid value")
+
+
 def test_mu_sigma_model() -> None:
     mu_sigma_model = MuSigmaModel()
 

From d02513e36498cb45f9b7e016cd781cf15ae89806 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Tue, 29 Oct 2024 11:41:58 -0300
Subject: [PATCH 18/25] Fixed long lines.

---
 tests/connector/cobaya/test_model_likelihood.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/connector/cobaya/test_model_likelihood.py b/tests/connector/cobaya/test_model_likelihood.py
index c5107e8ec..3020e49de 100644
--- a/tests/connector/cobaya/test_model_likelihood.py
+++ b/tests/connector/cobaya/test_model_likelihood.py
@@ -309,15 +309,15 @@ def test_default_factory():
         "z_piv": 0.3,
         "T_CMB": 2.7255,
     }
+    default_factory = "firecrown.likelihood.factories.build_two_point_likelihood"
+    likelihood_config = "examples/des_y1_3x2pt/pure_ccl_experiment.yaml"
     info_fiducial = {
         "params": fiducial_params,
         "likelihood": {
             "lk_connector": {
                 "external": LikelihoodConnector,
-                "firecrownIni": "firecrown.likelihood.factories.build_two_point_likelihood",
-                "build_parameters": {
-                    "likelihood_config": "examples/des_y1_3x2pt/pure_ccl_experiment.yaml"
-                },
+                "firecrownIni": default_factory,
+                "build_parameters": {"likelihood_config": likelihood_config},
             },
         },
     }

From a44a6a08b9858ce9189de701c63c50472fc108a0 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Tue, 29 Oct 2024 12:23:37 -0300
Subject: [PATCH 19/25] More testing for CCLFactory.

---
 firecrown/ccl_factory.py  | 18 ++++++------------
 tests/test_ccl_factory.py | 20 ++++++++++++++++++++
 2 files changed, 26 insertions(+), 12 deletions(-)

diff --git a/firecrown/ccl_factory.py b/firecrown/ccl_factory.py
index 8632d2ebb..88b0bf0fc 100644
--- a/firecrown/ccl_factory.py
+++ b/firecrown/ccl_factory.py
@@ -121,12 +121,11 @@ def _generate_next_value_(name, _start, _count, _last_values):
 
 
 def _validate_ccl_creation_mode(value):
-    if isinstance(value, str):
-        try:
-            return CCLCreationMode(value.lower())  # Convert from string to Enum
-        except ValueError as exc:
-            raise ValueError(f"Invalid value for CCLCreationMode: {value}") from exc
-    return value
+    assert isinstance(value, str)
+    try:
+        return CCLCreationMode(value.lower())  # Convert from string to Enum
+    except ValueError as exc:
+        raise ValueError(f"Invalid value for CCLCreationMode: {value}") from exc
 
 
 class MuSigmaModel(Updatable):
@@ -329,9 +328,8 @@ def create(
             ccl_args["extra_parameters"] = {"camb": self.camb_extra_params.get_dict()}
             ccl_args["matter_power_spectrum"] = "camb"
 
+        assert self.creation_mode in CCLCreationMode
         match self.creation_mode:
-            case CCLCreationMode.DEFAULT:
-                pass
             case CCLCreationMode.MU_SIGMA_ISITGR:
                 assert self._mu_sigma_model is not None
                 ccl_args.update(
@@ -339,10 +337,6 @@ def create(
                     matter_power_spectrum="linear",
                     transfer_function="boltzmann_isitgr",
                 )
-            case CCLCreationMode.PURE_CCL_MODE:
-                pass
-            case _:
-                raise ValueError(f"Invalid creation mode: {self.creation_mode}")
         self._ccl_cosmo = pyccl.Cosmology(**ccl_args)
         return self._ccl_cosmo
 
diff --git a/tests/test_ccl_factory.py b/tests/test_ccl_factory.py
index c359ec6f6..9a9684b11 100644
--- a/tests/test_ccl_factory.py
+++ b/tests/test_ccl_factory.py
@@ -465,6 +465,26 @@ def test_ccl_factory_invalid_extra_params() -> None:
         CCLFactory(not_a_valid_param="Im not a valid value")
 
 
+def test_validate_creation_mode_incompatible():
+    ccl_factory = CCLFactory(creation_mode=CCLCreationMode.PURE_CCL_MODE)
+    params = get_default_params_map(ccl_factory)
+    ccl_factory.update(params)
+    with pytest.raises(
+        ValueError,
+        match="Calculator Mode can only be used with the DEFAULT "
+        "creation mode and no CAMB extra parameters.",
+    ):
+        ccl_factory.create(
+            calculator_args=CCLCalculatorArgs(
+                background={
+                    "a": A_ARRAY,
+                    "chi": CHI_ARRAY,
+                    "h_over_h0": H_OVER_H0_ARRAY,
+                }
+            )
+        )
+
+
 def test_mu_sigma_model() -> None:
     mu_sigma_model = MuSigmaModel()
 

From 304199e6cd497e398862213c4e8fabd9792d535a Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Tue, 29 Oct 2024 16:55:47 -0300
Subject: [PATCH 20/25] Testing NumCosmo connector.

---
 environment.yml                               |   1 +
 firecrown/connector/numcosmo/numcosmo.py      |   2 +-
 .../numcosmo/test_numcosmo_connector.py       | 112 +++++++++++++++++-
 3 files changed, 112 insertions(+), 3 deletions(-)

diff --git a/environment.yml b/environment.yml
index 697a25c9b..a0236c9f6 100644
--- a/environment.yml
+++ b/environment.yml
@@ -27,6 +27,7 @@ dependencies:
   - pip:
     - autoclasstoc
     - cobaya
+    - isitgr
     - pygobject-stubs
   - portalocker
   - pybobyqa
diff --git a/firecrown/connector/numcosmo/numcosmo.py b/firecrown/connector/numcosmo/numcosmo.py
index ebdd087e4..71cb88821 100644
--- a/firecrown/connector/numcosmo/numcosmo.py
+++ b/firecrown/connector/numcosmo/numcosmo.py
@@ -923,7 +923,7 @@ def __init__(
                 build_parameters,
             )
 
-    def get_data(self) -> Ncm.Data:
+    def get_data(self) -> NumCosmoGaussCov | NumCosmoData:
         """This method return the appropriate Ncm.Data class to be used by NumCosmo.
 
         :return: the data used by NumCosmo
diff --git a/tests/connector/numcosmo/test_numcosmo_connector.py b/tests/connector/numcosmo/test_numcosmo_connector.py
index eae4a4e0d..3fea53dc6 100644
--- a/tests/connector/numcosmo/test_numcosmo_connector.py
+++ b/tests/connector/numcosmo/test_numcosmo_connector.py
@@ -1,7 +1,7 @@
 """Unit tests for the numcosmo connector."""
 
 import pytest
-from numcosmo_py import Ncm, Nc
+from numcosmo_py import Ncm, Nc, GObject
 
 from firecrown.connector.numcosmo.numcosmo import (
     NumCosmoFactory,
@@ -10,7 +10,9 @@
     NumCosmoGaussCov,
 )
 
-from firecrown.likelihood.likelihood import NamedParameters, Likelihood
+from firecrown.likelihood.likelihood import NamedParameters, Likelihood, load_likelihood
+from firecrown.likelihood.gaussian import ConstGaussian
+from firecrown.updatable import get_default_params
 
 Ncm.cfg_init()
 
@@ -260,3 +262,109 @@ def test_empty_gauss_cov_data():
     nc_data = NumCosmoGaussCov()
     assert nc_data.likelihood_source is None
     assert nc_data.likelihood_build_parameters is None
+
+
+def test_default_factory_const_gauss():
+    """Test the NumCosmo connector."""
+    map_cosmo = MappingNumCosmo(
+        dist=Nc.Distance.new(6.0),
+        p_ml=Nc.PowspecMLTransfer.new(Nc.TransferFuncEH.new()),
+    )
+    build_parameters = NamedParameters(
+        {"likelihood_config": "examples/des_y1_3x2pt/pure_ccl_experiment.yaml"}
+    )
+    model_name = "firecrown_model_gauss"
+
+    likelihood_source = "firecrown.likelihood.factories.build_two_point_likelihood"
+    likelihood, tools = load_likelihood(likelihood_source, build_parameters)
+    assert isinstance(likelihood, ConstGaussian)
+    data = NumCosmoGaussCov.new_from_likelihood(
+        likelihood,
+        [model_name],
+        tools,
+        map_cosmo,
+        likelihood_source,
+        build_parameters,
+    )
+
+    run_likelihood(model_name, data)
+
+
+def test_default_factory_plain():
+    """Test the NumCosmo connector."""
+    map_cosmo = MappingNumCosmo(
+        dist=Nc.Distance.new(6.0),
+        p_ml=Nc.PowspecMLTransfer.new(Nc.TransferFuncEH.new()),
+    )
+    build_parameters = NamedParameters(
+        {"likelihood_config": "examples/des_y1_3x2pt/pure_ccl_experiment.yaml"}
+    )
+    model_name = "firecrown_model_plain"
+
+    likelihood_source = "firecrown.likelihood.factories.build_two_point_likelihood"
+    likelihood, tools = load_likelihood(likelihood_source, build_parameters)
+    assert isinstance(likelihood, ConstGaussian)
+    data = NumCosmoData.new_from_likelihood(
+        likelihood,
+        [model_name],
+        tools,
+        map_cosmo,
+        likelihood_source,
+        build_parameters,
+    )
+
+    run_likelihood(model_name, data)
+
+
+def run_likelihood(model_name, data):
+    """Run the likelihood."""
+    default_parameters = get_default_params(data.likelihood, data.tools)
+    model_builder = Ncm.ModelBuilder.new(
+        Ncm.Model,
+        model_name,
+        f"Test model {model_name}",
+    )
+    mapping_dict = [
+        "h",
+        "m_nu",
+        "n_s",
+        "Neff",
+        "Omega_b",
+        "Omega_c",
+        "Omega_k",
+        "sigma8",
+        "T_CMB",
+        "w0",
+        "wa",
+    ]
+    for param, value in default_parameters.items():
+        if param not in mapping_dict:
+            model_builder.add_sparam(
+                param,
+                param,
+                -1.0e10,
+                1.0e10,
+                1.0e-2,
+                0.0,
+                value,
+                Ncm.ParamType.FIXED,
+            )
+
+    FirecrownModel = model_builder.create()  # pylint: disable=invalid-name
+    GObject.new(FirecrownModel)
+    NcmFirecrownModel = FirecrownModel.pytype  # pylint: disable=invalid-name
+    GObject.type_register(NcmFirecrownModel)
+
+    model: Ncm.Model = NcmFirecrownModel()
+    model.params_set_default_ftype()
+
+    assert data is not None
+    assert isinstance(data, Ncm.Data)
+    cosmo = Nc.HICosmoDEXcdm()
+    cosmo.add_submodel(Nc.HIPrimPowerLaw.new())
+    cosmo.add_submodel(Nc.HIReionCamb.new())
+    mset = Ncm.MSet()
+    mset.set(cosmo)
+    mset.set(model)
+    mset.prepare_fparam_map()
+    data.prepare(mset)

From 2399c58d6a9f919dd733e5f412cd1138b4a0ce81 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Tue, 29 Oct 2024 17:06:42 -0300
Subject: [PATCH 21/25] Removing the conditional testing.

---
 tests/integration/test_des_y1_3x2pt.py | 16 ++--------------
 1 file changed, 2 insertions(+), 14 deletions(-)

diff --git a/tests/integration/test_des_y1_3x2pt.py b/tests/integration/test_des_y1_3x2pt.py
index 16e1ad864..d181237cc 100644
--- a/tests/integration/test_des_y1_3x2pt.py
+++ b/tests/integration/test_des_y1_3x2pt.py
@@ -3,32 +3,20 @@
 import subprocess
 import pytest
 
-
-HAS_ISITGR = False
-try:
-    import isitgr
-
-    if isitgr is not None:
-        HAS_ISITGR = True
-except ImportError:
-    HAS_ISITGR = False
-
 INI_FILES = [
     "factory.ini",
     "factory_PT.ini",
     "default_factory.ini",
     "pure_ccl.ini",
+    "mu_sigma.ini",
 ]
-if HAS_ISITGR:
-    INI_FILES.append("mu_sigma.ini")
 
 COBAYA_YAML_FILES = [
     "evaluate.yaml",
     "evaluate_PT.yaml",
     "evaluate_pure_ccl.yaml",
+    "evaluate_mu_sigma.yaml",
 ]
-if HAS_ISITGR:
-    COBAYA_YAML_FILES.append("evaluate_mu_sigma.yaml")
 
 
 @pytest.fixture(name="ini_file", params=INI_FILES)

From ce94a1b6171665fe90c24b506c7313388cff50e9 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Tue, 29 Oct 2024 17:13:43 -0300
Subject: [PATCH 22/25] Testing absolute path in DataSource.

---
 tests/likelihood/test_factories.py | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/tests/likelihood/test_factories.py b/tests/likelihood/test_factories.py
index df71df960..9f9fee60c 100644
--- a/tests/likelihood/test_factories.py
+++ b/tests/likelihood/test_factories.py
@@ -90,11 +90,37 @@ def test_data_source_sacc_dict() -> None:
     data_source_sacc = DataSourceSacc.model_validate(data_source_sacc_dict)
     assert isinstance(data_source_sacc, DataSourceSacc)
     assert data_source_sacc.sacc_data_file == "tests/bug_398.sacc.gz"
+    sacc_data = data_source_sacc.get_sacc_data()
+    assert sacc_data is not None
+    assert isinstance(sacc_data, sacc.Sacc)
+
+
+def test_data_source_sacc_dict_absolute() -> None:
+    sacc_file = Path("tests/bug_398.sacc.gz").absolute()
+    data_source_sacc_dict = {"sacc_data_file": sacc_file.as_posix()}
+    data_source_sacc = DataSourceSacc.model_validate(data_source_sacc_dict)
+    assert isinstance(data_source_sacc, DataSourceSacc)
+    assert data_source_sacc.sacc_data_file == sacc_file.as_posix()
+    sacc_data = data_source_sacc.get_sacc_data()
+    assert sacc_data is not None
+    assert isinstance(sacc_data, sacc.Sacc)
 
 
 def test_data_source_sacc_direct() -> None:
     data_source_sacc = DataSourceSacc(sacc_data_file="tests/bug_398.sacc.gz")
     assert data_source_sacc.sacc_data_file == "tests/bug_398.sacc.gz"
+    sacc_data = data_source_sacc.get_sacc_data()
+    assert sacc_data is not None
+    assert isinstance(sacc_data, sacc.Sacc)
+
+
+def test_data_source_sacc_direct_absolute() -> None:
+    sacc_file = Path("tests/bug_398.sacc.gz").absolute()
+    data_source_sacc = DataSourceSacc(sacc_data_file=sacc_file.as_posix())
+    assert data_source_sacc.sacc_data_file == sacc_file.as_posix()
+    sacc_data = data_source_sacc.get_sacc_data()
+    assert sacc_data is not None
+    assert isinstance(sacc_data, sacc.Sacc)
 
 
 def test_data_source_sacc_invalid_file() -> None:

From 72002e6a6e86b1715d020a1d6c560674f2167a13 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Tue, 29 Oct 2024 17:35:54 -0300
Subject: [PATCH 23/25] Testing cosmosis connector with pure ccl.

---
 .../cosmosis/test_cosmosis_module.py          | 19 ++++--
 .../lkscript_two_point_pure_ccl.py            | 59 +++++++++++++++++++
 2 files changed, 73 insertions(+), 5 deletions(-)
 create mode 100644 tests/likelihood/gauss_family/lkscript_two_point_pure_ccl.py

diff --git a/tests/connector/cosmosis/test_cosmosis_module.py b/tests/connector/cosmosis/test_cosmosis_module.py
index dc4394b05..6a286db86 100644
--- a/tests/connector/cosmosis/test_cosmosis_module.py
+++ b/tests/connector/cosmosis/test_cosmosis_module.py
@@ -105,15 +105,24 @@ def fixture_config_with_two_point_real() -> DataBlock:
     return result
 
 
-@pytest.fixture(name="config_with_two_point_harmonic")
-def fixture_config_with_two_point_harmonic() -> DataBlock:
+@pytest.fixture(name="config_with_two_point_harmonic", params=["default", "pure_ccl"])
+def fixture_config_with_two_point_harmonic(request) -> DataBlock:
     result = DataBlock()
+    likelihood_file = ""
+    if request.param == "default":
+        likelihood_file = (
+            "${FIRECROWN_DIR}/tests/likelihood/gauss_family/lkscript_two_point.py"
+        )
+    elif request.param == "pure_ccl":
+        likelihood_file = (
+            "${FIRECROWN_DIR}/tests/likelihood/"
+            "gauss_family/lkscript_two_point_pure_ccl.py"
+        )
+
     result.put_string(
         option_section,
         "Likelihood_source",
-        expandvars(
-            "${FIRECROWN_DIR}/tests/likelihood/gauss_family/lkscript_two_point.py"
-        ),
+        expandvars(likelihood_file),
     )
     result.put_string(
         option_section,
diff --git a/tests/likelihood/gauss_family/lkscript_two_point_pure_ccl.py b/tests/likelihood/gauss_family/lkscript_two_point_pure_ccl.py
new file mode 100644
index 000000000..64e64a7ac
--- /dev/null
+++ b/tests/likelihood/gauss_family/lkscript_two_point_pure_ccl.py
@@ -0,0 +1,59 @@
+"""
+Provides a trivial likelihood factory function for a ConstGaussian
+for testing purposes.
+"""
+
+import numpy as np
+import sacc
+
+from firecrown.likelihood.likelihood import NamedParameters
+from firecrown.likelihood.gaussian import ConstGaussian
+from firecrown.likelihood.two_point import TwoPoint
+from firecrown.likelihood.number_counts import (
+    NumberCounts,
+)
+from firecrown.modeling_tools import ModelingTools
+from firecrown.ccl_factory import (
+    CCLFactory,
+    PoweSpecAmplitudeParameter,
+    CCLCreationMode,
+)
+
+
+def build_likelihood(params: NamedParameters):
+    """Return a ConstGaussian (likelihood) object."""
+    sacc_data = sacc.Sacc()
+
+    src0 = NumberCounts(sacc_tracer="lens0")
+    z = np.linspace(0, 0.8, 50) + 0.05
+    dndz = np.exp(-0.5 * (z - 0.4) ** 2 / 0.02 / 0.02)
+    sacc_data.add_tracer("NZ", "lens0", z, dndz)
+
+    if params.get_string("projection") == "harmonic":
+        two_point = TwoPoint("galaxy_density_cl", source0=src0, source1=src0)
+        ells = np.unique(np.logspace(1, 3, 10).astype(np.int64))
+        Cells = np.random.normal(size=ells.shape[0])
+        sacc_data.add_ell_cl("galaxy_density_cl", "lens0", "lens0", ells, Cells)
+        cov = np.diag(np.ones_like(Cells) * 0.01)
+        sacc_data.add_covariance(cov)
+    elif params.get_string("projection") == "real":
+        two_point = TwoPoint("galaxy_density_xi", source0=src0, source1=src0)
+        thetas = np.linspace(0.0, np.pi, 10)
+        xis = np.random.normal(size=thetas.shape[0])
+        sacc_data.add_theta_xi("galaxy_density_xi", "lens0", "lens0", thetas, xis)
+        cov = np.diag(np.ones_like(xis) * 0.01)
+        sacc_data.add_covariance(cov)
+    else:
+        raise ValueError("Invalid projection")
+
+    likelihood = ConstGaussian(statistics=[two_point])
+    likelihood.read(sacc_data)
+
+    tools = ModelingTools(
+        ccl_factory=CCLFactory(
+            amplitude_parameter=PoweSpecAmplitudeParameter.SIGMA8,
+            creation_mode=CCLCreationMode.PURE_CCL_MODE,
+        )
+    )
+
+    return likelihood, tools

From ae8e911ebd63cd6f8e1d98fe530a15eb4f8c3c05 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Tue, 29 Oct 2024 18:15:04 -0300
Subject: [PATCH 24/25] Adding missing mass_split test check.

---
 tests/test_ccl_factory.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/test_ccl_factory.py b/tests/test_ccl_factory.py
index 9a9684b11..fb736bb6e 100644
--- a/tests/test_ccl_factory.py
+++ b/tests/test_ccl_factory.py
@@ -224,6 +224,7 @@ def test_ccl_factory_neutrino_mass_splits(
     ccl_factory = CCLFactory(mass_split=neutrino_mass_splits)
 
     assert ccl_factory is not None
+    assert ccl_factory.mass_split == neutrino_mass_splits
 
     default_params = get_default_params_map(ccl_factory)
 

From 33213a4f1a79009c55aaf57a23b1dea4148e79de Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Tue, 29 Oct 2024 18:35:48 -0300
Subject: [PATCH 25/25] Removing unnecessary pip install of isitgr.

---
 .github/workflows/ci.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 760d293f7..adb1a716e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -100,9 +100,7 @@ jobs:
         run: python -m pytest -vv --runslow --cov firecrown --cov-report xml
       - name: Running integration tests
         shell: bash -l {0}
-        run: |
-          pip install isitgr
-          python -m pytest -vv -s --integration tests/integration 
+        run: python -m pytest -vv -s --integration tests/integration 
       - name: Upload coverage reports to Codecov
         if: ${{ (matrix.os == 'ubuntu') && (matrix.python-version == '3.11') }}
         uses: codecov/codecov-action@v4