From 8e83525da57a088a7ca9cfcce38fd54457d40b69 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Wed, 20 Sep 2023 20:42:53 -0300
Subject: [PATCH 1/4] * New attribure for Updatables: parameter_prefix. * Added
 the necessary calls to make the current Updatable implementation to pass
 sacc_tracer as the default parameter_prefix.

---
 .../statistic/cluster_number_counts.py        | 16 ++--
 .../statistic/source/number_counts.py         | 88 ++++++++++---------
 .../gauss_family/statistic/source/source.py   |  9 ++
 .../statistic/source/weak_lensing.py          | 70 +++++++--------
 .../gauss_family/statistic/statistic.py       |  4 +-
 .../gauss_family/statistic/supernova.py       |  2 +-
 firecrown/updatable.py                        | 20 +++--
 .../statistic/source/test_source.py           |  4 +-
 8 files changed, 113 insertions(+), 100 deletions(-)

diff --git a/firecrown/likelihood/gauss_family/statistic/cluster_number_counts.py b/firecrown/likelihood/gauss_family/statistic/cluster_number_counts.py
index 0f3246cbc..a7d41b3fc 100644
--- a/firecrown/likelihood/gauss_family/statistic/cluster_number_counts.py
+++ b/firecrown/likelihood/gauss_family/statistic/cluster_number_counts.py
@@ -46,8 +46,8 @@ def __init__(
         :param systematics: A list of the statistics-level systematics to apply to
             the statistic. The default of `None` implies no systematics.
         """
-        super().__init__()
-        self.sacc_tracer = survey_tracer
+        super().__init__(parameter_prefix=survey_tracer)
+        self.survey_tracer = survey_tracer
         self.systematics = systematics or []
         self.data_vector: Optional[DataVector] = None
         self.theory_vector: Optional[TheoryVector] = None
@@ -84,13 +84,13 @@ def _read_data_type(self, sacc_data, data_type):
 
         cluster_survey_tracers = tracers_combinations[:, 0]
 
-        if self.sacc_tracer not in cluster_survey_tracers:
+        if self.survey_tracer not in cluster_survey_tracers:
             raise ValueError(
-                f"The SACC tracer {self.sacc_tracer} is not "
+                f"The SACC tracer {self.survey_tracer} is not "
                 f"present in the SACC file."
             )
 
-        survey_selection = cluster_survey_tracers == self.sacc_tracer
+        survey_selection = cluster_survey_tracers == self.survey_tracer
 
         z_tracers = np.unique(tracers_combinations[survey_selection, 1])
         logM_tracers = np.unique(tracers_combinations[survey_selection, 2])
@@ -133,15 +133,15 @@ def read(self, sacc_data: sacc.Sacc):
         """
 
         try:
-            survey_tracer: SurveyTracer = sacc_data.get_tracer(self.sacc_tracer)
+            survey_tracer: SurveyTracer = sacc_data.get_tracer(self.survey_tracer)
         except KeyError as exc:
             raise ValueError(
                 f"The SACC file does not contain the SurveyTracer "
-                f"{self.sacc_tracer}."
+                f"{self.survey_tracer}."
             ) from exc
         if not isinstance(survey_tracer, SurveyTracer):
             raise ValueError(
-                f"The SACC tracer {self.sacc_tracer} is not a SurveyTracer."
+                f"The SACC tracer {self.survey_tracer} is not a SurveyTracer."
             )
 
         self.cluster_abundance.sky_area = survey_tracer.sky_area
diff --git a/firecrown/likelihood/gauss_family/statistic/source/number_counts.py b/firecrown/likelihood/gauss_family/statistic/source/number_counts.py
index 4c1fa69c4..1649ac700 100644
--- a/firecrown/likelihood/gauss_family/statistic/source/number_counts.py
+++ b/firecrown/likelihood/gauss_family/statistic/source/number_counts.py
@@ -58,25 +58,20 @@ class LinearBiasSystematic(NumberCountsSystematic):
 
     This systematic adds a linear bias model which varies with redshift and
     the growth function.
-
-    Parameters
-    ----------
-    alphaz : str
-        The name of redshift dependence parameter of the linear bias.
-    alphag : str
-        The name of the growth dependence parameter of the linear bias.
-    z_piv : str
-        The name of the pivot redshift parameter for the linear bias.
-
     """
 
     def __init__(self, sacc_tracer: str):
-        super().__init__()
+        """Initialize the LinearBiasSystematic.
+
+        :param sacc_tracer: the name of the tracer in the SACC file. This is used
+            as a prefix for its parameters.
+
+        """
+        super().__init__(parameter_prefix=sacc_tracer)
 
         self.alphaz = parameters.create()
         self.alphag = parameters.create()
         self.z_piv = parameters.create()
-        self.sacc_tracer = sacc_tracer
 
     def apply(
         self, tools: ModelingTools, tracer_arg: NumberCountsArgs
@@ -113,19 +108,20 @@ class PTNonLinearBiasSystematic(NumberCountsSystematic):
     """Non-linear bias systematic.
 
     This systematic adds a linear bias model which varies with redshift and
-
-    Parameters
-    ----------
-    b_2: float
-    b_s: float
+    the growth function.
     """
 
     def __init__(self, sacc_tracer: str):
-        super().__init__()
+        """Initialize the PTNonLinearBiasSystematic.
+
+        :param sacc_tracer: the name of the tracer in the SACC file. This is used
+            as a prefix for its parameters.
+
+        """
+        super().__init__(parameter_prefix=sacc_tracer)
 
         self.b_2 = parameters.create()
         self.b_s = parameters.create()
-        self.sacc_tracer = sacc_tracer
 
     def apply(
         self, tools: ModelingTools, tracer_arg: NumberCountsArgs
@@ -147,22 +143,15 @@ class MagnificationBiasSystematic(NumberCountsSystematic):
 
     This systematic adds a magnification bias model for galaxy number contrast
     following Joachimi & Bridle (2010), arXiv:0911.2454.
-
-    Parameters
-    ----------
-    r_lim : float
-        The name of the limiting magnitude in r band filter.
-    sig_c, eta, z_c, z_m : float
-        The name of the fitting parameters in Joachimi & Bridle (2010) equation
-        (C.1).
-
-    Methods
-    -------
-    apply : apply the systematic to a source
     """
 
     def __init__(self, sacc_tracer: str):
-        super().__init__()
+        """Initialize the MagnificationBiasSystematic.
+
+        :param sacc_tracer: the name of the tracer in the SACC file. This is used
+            as a prefix for its parameters.
+        """
+        super().__init__(parameter_prefix=sacc_tracer)
 
         self.r_lim = parameters.create()
         self.sig_c = parameters.create()
@@ -170,8 +159,6 @@ def __init__(self, sacc_tracer: str):
         self.z_c = parameters.create()
         self.z_m = parameters.create()
 
-        self.sacc_tracer = sacc_tracer
-
     def apply(
         self, tools: ModelingTools, tracer_arg: NumberCountsArgs
     ) -> NumberCountsArgs:
@@ -207,16 +194,19 @@ def apply(
 class ConstantMagnificationBiasSystematic(NumberCountsSystematic):
     """Simple constant magnification bias systematic.
 
-    Methods
-    -------
-    apply : apply the systematic to a source
+    This systematic adds a constant magnification bias model for galaxy number
+    contrast.
     """
 
     def __init__(self, sacc_tracer: str):
-        super().__init__()
+        """Initialize the ConstantMagnificationBiasSystematic.
+
+        :param sacc_tracer: the name of the tracer in the SACC file. This is used
+            as a prefix for its parameters.
+        """
+        super().__init__(parameter_prefix=sacc_tracer)
 
         self.mag_bias = parameters.create()
-        self.sacc_tracer = sacc_tracer
 
     def apply(
         self, tools: ModelingTools, tracer_arg: NumberCountsArgs
@@ -234,10 +224,14 @@ class PhotoZShift(NumberCountsSystematic):
     """
 
     def __init__(self, sacc_tracer: str):
-        super().__init__()
+        """Create a PhotoZShift object, using the specified tracer name.
+
+        :param sacc_tracer: the name of the tracer in the SACC file. This is used
+            as a prefix for its parameters.
+        """
+        super().__init__(parameter_prefix=sacc_tracer)
 
         self.delta_z = parameters.create()
-        self.sacc_tracer = sacc_tracer
 
     def apply(self, tools: ModelingTools, tracer_arg: NumberCountsArgs):
         """Apply a shift to the photo-z distribution of a source."""
@@ -268,7 +262,17 @@ def __init__(
         scale: float = 1.0,
         systematics: Optional[List[NumberCountsSystematic]] = None,
     ):
-        super().__init__()
+        """Initialize the NumberCounts object.
+
+        :param sacc_tracer: the name of the tracer in the SACC file. This is used
+            as a prefix for its parameters.
+        :param has_rsd: whether to include RSD in the tracer.
+        :param derived_scale: whether to include a derived parameter for the scale
+            of the tracer.
+        :param scale: the initial scale of the tracer.
+        :param systematics: a list of systematics to apply to the tracer.
+        """
+        super().__init__(sacc_tracer)
 
         self.sacc_tracer = sacc_tracer
         self.has_rsd = has_rsd
diff --git a/firecrown/likelihood/gauss_family/statistic/source/source.py b/firecrown/likelihood/gauss_family/statistic/source/source.py
index 1225a0cb2..10fc81b66 100644
--- a/firecrown/likelihood/gauss_family/statistic/source/source.py
+++ b/firecrown/likelihood/gauss_family/statistic/source/source.py
@@ -40,6 +40,15 @@ class Source(Updatable):
     cosmo_hash: Optional[int]
     tracers: Sequence[Tracer]
 
+    def __init__(self, sacc_tracer: str) -> None:
+        """Create a Source object that uses the named tracer.
+
+        :param sacc_tracer: the name of the tracer in the SACC file. This is used
+            as a prefix for its parameters.
+        """
+        super().__init__(parameter_prefix=sacc_tracer)
+        self.sacc_tracer = sacc_tracer
+
     @final
     def read(self, sacc_data: sacc.Sacc):
         """Read the data for this source from the SACC file."""
diff --git a/firecrown/likelihood/gauss_family/statistic/source/weak_lensing.py b/firecrown/likelihood/gauss_family/statistic/source/weak_lensing.py
index bbe0f09c0..6e3fe6491 100644
--- a/firecrown/likelihood/gauss_family/statistic/source/weak_lensing.py
+++ b/firecrown/likelihood/gauss_family/statistic/source/weak_lensing.py
@@ -56,19 +56,17 @@ class MultiplicativeShearBias(WeakLensingSystematic):
     """Multiplicative shear bias systematic.
 
     This systematic adjusts the `scale_` of a source by `(1 + m)`.
-
     """
 
     def __init__(self, sacc_tracer: str) -> None:
         """Create a MultiplicativeShearBias object that uses the named tracer.
-        Parameters
-        ----------
-        sacc_tracer : The name of the multiplicative bias parameter.
+
+        :param sacc_tracer: the name of the tracer in the SACC file. This is used
+            as a prefix for its parameters.
         """
-        super().__init__()
+        super().__init__(parameter_prefix=sacc_tracer)
 
         self.mult_bias = parameters.create()
-        self.sacc_tracer = sacc_tracer
 
     def apply(
         self, tools: ModelingTools, tracer_arg: WeakLensingArgs
@@ -93,36 +91,23 @@ class LinearAlignmentSystematic(WeakLensingSystematic):
 
     This systematic adds a linear intrinsic alignment model systematic
     which varies with redshift and the growth function.
-
-    Methods
-    -------
-    apply : apply the systematic to a source
     """
 
     def __init__(self, sacc_tracer: Optional[str] = None, alphag=1.0):
         """Create a LinearAlignmentSystematic object, using the specified
         tracer name.
 
-        Instance data are:
-
-        alphaz : The redshift dependence parameter of the intrinsic alignment
-        signal.
-
-        alphag : The growth dependence parameter of the intrinsic alignment
-        signal.
+        :param sacc_tracer: the name of the tracer in the SACC file. This is used
+            as a prefix for its parameters.
 
-        z_piv : The pivot redshift parameter for the intrinsic alignment
-        parameter.
         """
-        super().__init__()
+        super().__init__(parameter_prefix=sacc_tracer)
 
         self.ia_bias = parameters.create()
         self.alphaz = parameters.create()
         self.alphag = parameters.create(alphag)
         self.z_piv = parameters.create()
 
-        self.sacc_tracer = sacc_tracer
-
     def apply(
         self, tools: ModelingTools, tracer_arg: WeakLensingArgs
     ) -> WeakLensingArgs:
@@ -148,26 +133,20 @@ class TattAlignmentSystematic(WeakLensingSystematic):
     """TATT alignment systematic.
 
     This systematic adds a TATT (nonlinear) intrinsic alignment model systematic.
-
-    Parameters
-    ----------
-    ia_a_1: float
-    ia_a_2: float
-    ia_a_d: float
-
-    Methods
-    -------
-    apply : apply the systematic to a source
     """
 
     def __init__(self, sacc_tracer: Optional[str] = None):
-        super().__init__()
+        """Create a TattAlignmentSystematic object, using the specified
+        tracer name.
+
+        :param sacc_tracer: the name of the tracer in the SACC file. This is used
+            as a prefix for its parameters.
+        """
+        super().__init__(parameter_prefix=sacc_tracer)
         self.ia_a_1 = parameters.create()
         self.ia_a_2 = parameters.create()
         self.ia_a_d = parameters.create()
 
-        self.sacc_tracer = sacc_tracer
-
     def apply(
         self, tools: ModelingTools, tracer_arg: WeakLensingArgs
     ) -> WeakLensingArgs:
@@ -201,10 +180,14 @@ class PhotoZShift(WeakLensingSystematic):
     """
 
     def __init__(self, sacc_tracer: str):
-        super().__init__()
+        """Create a PhotoZShift object, using the specified tracer name.
+
+        :param sacc_tracer: the name of the tracer in the SACC file. This is used
+            as a prefix for its parameters.
+        """
+        super().__init__(parameter_prefix=sacc_tracer)
 
         self.delta_z = parameters.create()
-        self.sacc_tracer = sacc_tracer
 
     def apply(self, tools: ModelingTools, tracer_arg: WeakLensingArgs):
         """Apply a shift to the photo-z distribution of a source."""
@@ -233,8 +216,17 @@ def __init__(
         scale: float = 1.0,
         systematics: Optional[List[WeakLensingSystematic]] = None,
     ):
-        """Initialize the WeakLensing object."""
-        super().__init__()
+        """Initialize the WeakLensing object.
+
+        :param sacc_tracer: the name of the tracer in the SACC file. This is used
+            as a prefix for its parameters.
+        :param scale: the scale of the source. This is used to scale the shear
+            power spectrum.
+        :param systematics: a list of WeakLensingSystematic objects to apply to
+            this source.
+
+        """
+        super().__init__(sacc_tracer)
 
         self.sacc_tracer = sacc_tracer
         self.scale = scale
diff --git a/firecrown/likelihood/gauss_family/statistic/statistic.py b/firecrown/likelihood/gauss_family/statistic/statistic.py
index 111be335b..92b20c844 100644
--- a/firecrown/likelihood/gauss_family/statistic/statistic.py
+++ b/firecrown/likelihood/gauss_family/statistic/statistic.py
@@ -116,8 +116,8 @@ class Statistic(Updatable):
     Statistics represent things like two-point functions and mass functions.
     """
 
-    def __init__(self):
-        super().__init__()
+    def __init__(self, parameter_prefix: Optional[str] = None):
+        super().__init__(parameter_prefix=parameter_prefix)
         self.sacc_indices: Optional[npt.NDArray[np.int64]]
         self.ready = False
 
diff --git a/firecrown/likelihood/gauss_family/statistic/supernova.py b/firecrown/likelihood/gauss_family/statistic/supernova.py
index 9fcf06744..b6c894f7c 100644
--- a/firecrown/likelihood/gauss_family/statistic/supernova.py
+++ b/firecrown/likelihood/gauss_family/statistic/supernova.py
@@ -22,7 +22,7 @@ class Supernova(Statistic):
 
     def __init__(self, sacc_tracer) -> None:
         """Initialize this statistic."""
-        super().__init__()
+        super().__init__(parameter_prefix=sacc_tracer)
 
         self.sacc_tracer = sacc_tracer
         self.data_vector: Optional[DataVector] = None
diff --git a/firecrown/updatable.py b/firecrown/updatable.py
index e117cb1be..42e46a138 100644
--- a/firecrown/updatable.py
+++ b/firecrown/updatable.py
@@ -57,14 +57,22 @@ class Updatable(ABC):
 
     """
 
-    def __init__(self) -> None:
-        """Updatable initialization."""
+    def __init__(self, parameter_prefix: Optional[str] = None) -> None:
+        """Updatable initialization.
+
+        :param prefix: prefix for all parameters in this Updatable
+
+        Parameters created by firecrown.parameters.create will have a prefix
+        that is given by the prefix argument to the Updatable constructor. This
+        prefix is used to create the full name of the parameter. If `parameter_prefix`
+        is None, then the parameter will have no prefix.
+        """
         self._updated: bool = False
         self._returned_derived: bool = False
         self._sampler_parameters: Dict[str, SamplerParameter] = {}
         self._internal_parameters: Dict[str, InternalParameter] = {}
-        self.sacc_tracer: Optional[str] = None
         self._updatables: List[GeneralUpdatable] = []
+        self.parameter_prefix: Optional[str] = parameter_prefix
 
     def __setattr__(self, key: str, value: Any) -> None:
         """Set the attribute named :python:`key` to the supplied :python:`value`.
@@ -145,10 +153,10 @@ def update(self, params: ParamsMap) -> None:
 
         for parameter in self._sampler_parameters:
             try:
-                value = params.get_from_prefix_param(self.sacc_tracer, parameter)
+                value = params.get_from_prefix_param(self.parameter_prefix, parameter)
             except KeyError as exc:
                 raise MissingSamplerParameterError(
-                    parameter_get_full_name(self.sacc_tracer, parameter)
+                    parameter_get_full_name(self.parameter_prefix, parameter)
                 ) from exc
             setattr(self, parameter, value)
 
@@ -224,7 +232,7 @@ def required_parameters(self) -> RequiredParameters:  # pragma: no cover
 
         sampler_parameters = RequiredParameters(
             [
-                parameter_get_full_name(self.sacc_tracer, parameter)
+                parameter_get_full_name(self.parameter_prefix, parameter)
                 for parameter in self._sampler_parameters
             ]
         )
diff --git a/tests/likelihood/gauss_family/statistic/source/test_source.py b/tests/likelihood/gauss_family/statistic/source/test_source.py
index 1d156fcd8..4f4284d3e 100644
--- a/tests/likelihood/gauss_family/statistic/source/test_source.py
+++ b/tests/likelihood/gauss_family/statistic/source/test_source.py
@@ -49,7 +49,7 @@ def test_tracer_construction_with_name(empty_pyccl_tracer):
 def test_linear_bias_systematic():
     a = nc.LinearBiasSystematic("xxx")
     assert isinstance(a, nc.LinearBiasSystematic)
-    assert a.sacc_tracer == "xxx"
+    assert a.parameter_prefix == "xxx"
     assert a.alphag is None
     assert a.alphaz is None
     assert a.z_piv is None
@@ -63,7 +63,7 @@ def test_linear_bias_systematic():
 
     a.reset()
     assert not a.is_updated()
-    assert a.sacc_tracer == "xxx"
+    assert a.parameter_prefix == "xxx"
     assert a.alphag is None
     assert a.alphaz is None
     assert a.z_piv is None

From c6772cf033a8afbfea88b482d412d455684606cd Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Wed, 20 Sep 2023 20:55:38 -0300
Subject: [PATCH 2/4] Updated tests to parameter_prefix instead of sacc_tracer.

---
 firecrown/likelihood/likelihood.py              | 4 ++--
 tests/connector/cobaya/test_model_likelihood.py | 4 ++--
 tests/likelihood/lkdir/lk_sampler_parameter.py  | 2 +-
 tests/likelihood/lkdir/lkmodule.py              | 5 ++---
 4 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/firecrown/likelihood/likelihood.py b/firecrown/likelihood/likelihood.py
index 0945174f3..7b466f77c 100644
--- a/firecrown/likelihood/likelihood.py
+++ b/firecrown/likelihood/likelihood.py
@@ -36,9 +36,9 @@ class Likelihood(Updatable):
     these methods, and provide other abstract methods for their subclasses to implement.
     """
 
-    def __init__(self) -> None:
+    def __init__(self, parameter_prefix: Optional[str] = None) -> None:
         """Default initialization for a base Likelihood object."""
-        super().__init__()
+        super().__init__(parameter_prefix=parameter_prefix)
 
         self.predicted_data_vector: Optional[npt.NDArray[np.double]] = None
         self.measured_data_vector: Optional[npt.NDArray[np.double]] = None
diff --git a/tests/connector/cobaya/test_model_likelihood.py b/tests/connector/cobaya/test_model_likelihood.py
index 7c50a928a..c6446544d 100644
--- a/tests/connector/cobaya/test_model_likelihood.py
+++ b/tests/connector/cobaya/test_model_likelihood.py
@@ -214,7 +214,7 @@ def test_sampler_parameter_likelihood_missing(fiducial_params):
             "lk_connector": {
                 "external": LikelihoodConnector,
                 "firecrownIni": "tests/likelihood/lkdir/lk_sampler_parameter.py",
-                "build_parameters": NamedParameters({"sacc_tracer": "my_prefix"}),
+                "build_parameters": NamedParameters({"parameter_prefix": "my_prefix"}),
             }
         },
         "theory": {
@@ -235,7 +235,7 @@ def test_sampler_parameter_likelihood(fiducial_params):
             "lk_connector": {
                 "external": LikelihoodConnector,
                 "firecrownIni": "tests/likelihood/lkdir/lk_sampler_parameter.py",
-                "build_parameters": NamedParameters({"sacc_tracer": "my_prefix"}),
+                "build_parameters": NamedParameters({"parameter_prefix": "my_prefix"}),
             }
         },
         "theory": {
diff --git a/tests/likelihood/lkdir/lk_sampler_parameter.py b/tests/likelihood/lkdir/lk_sampler_parameter.py
index 5bc943c9b..32a3772b9 100644
--- a/tests/likelihood/lkdir/lk_sampler_parameter.py
+++ b/tests/likelihood/lkdir/lk_sampler_parameter.py
@@ -1,6 +1,6 @@
 """
 Provides a trivial likelihood factory function for testing purposes.
-The likelihood created requires a string parameter named "sacc_tracer"
+The likelihood created requires a string parameter named "parameter_prefix"
 and has a sampler parameter named "sampler_param0".
 """
 from firecrown.likelihood.likelihood import NamedParameters
diff --git a/tests/likelihood/lkdir/lkmodule.py b/tests/likelihood/lkdir/lkmodule.py
index d18a46f34..76d46a195 100644
--- a/tests/likelihood/lkdir/lkmodule.py
+++ b/tests/likelihood/lkdir/lkmodule.py
@@ -54,10 +54,9 @@ class SamplerParameterLikelihood(Likelihood):
 
     def __init__(self, params: NamedParameters):
         """Initialize the SamplerParameterLikelihood by reading the specificed
-        sacc_tracer value and creates a sampler parameter called "sampler_param0".
+        parameter_prefix value and creates a sampler parameter called "sampler_param0".
         """
-        super().__init__()
-        self.sacc_tracer = params.get_string("sacc_tracer")
+        super().__init__(parameter_prefix=params.get_string("parameter_prefix"))
         self.sampler_param0 = parameters.create()
 
     def read(self, sacc_data: sacc.Sacc) -> None:

From b1d666e263f9622456e5e8978f223755dfc3b7d9 Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Wed, 20 Sep 2023 21:07:13 -0300
Subject: [PATCH 3/4] Test documenting Updatable attributes.

---
 .../statistic/source/number_counts.py         | 36 +++++++++++++++++++
 .../statistic/source/weak_lensing.py          | 26 ++++++++++++++
 firecrown/models/cluster_mass_rich_proxy.py   | 12 ++++++-
 3 files changed, 73 insertions(+), 1 deletion(-)

diff --git a/firecrown/likelihood/gauss_family/statistic/source/number_counts.py b/firecrown/likelihood/gauss_family/statistic/source/number_counts.py
index 1649ac700..41ada58be 100644
--- a/firecrown/likelihood/gauss_family/statistic/source/number_counts.py
+++ b/firecrown/likelihood/gauss_family/statistic/source/number_counts.py
@@ -58,6 +58,14 @@ class LinearBiasSystematic(NumberCountsSystematic):
 
     This systematic adds a linear bias model which varies with redshift and
     the growth function.
+
+    The following parameters are special Updatable parameters, which means that
+    they can be updated by the sampler, sacc_tracer is going to be used as a
+    prefix for the parameters:
+    :ivar alphaz: the redshift exponent of the bias.
+    :ivar alphag: the growth function exponent of the bias.
+    :ivar z_piv: the pivot redshift of the bias.
+
     """
 
     def __init__(self, sacc_tracer: str):
@@ -109,6 +117,12 @@ class PTNonLinearBiasSystematic(NumberCountsSystematic):
 
     This systematic adds a linear bias model which varies with redshift and
     the growth function.
+
+    The following parameters are special Updatable parameters, which means that
+    they can be updated by the sampler, sacc_tracer is going to be used as a
+    prefix for the parameters:
+    :ivar b_2: the quadratic bias.
+    :ivar b_s: the stochastic bias.
     """
 
     def __init__(self, sacc_tracer: str):
@@ -143,6 +157,16 @@ class MagnificationBiasSystematic(NumberCountsSystematic):
 
     This systematic adds a magnification bias model for galaxy number contrast
     following Joachimi & Bridle (2010), arXiv:0911.2454.
+
+    The following parameters are special Updatable parameters, which means that
+    they can be updated by the sampler, sacc_tracer is going to be used as a
+    prefix for the parameters:
+    :ivar r_lim: the limiting magnitude.
+    :ivar sig_c: the intrinsic dispersion of the source redshift distribution.
+    :ivar eta: the slope of the luminosity function.
+    :ivar z_c: the characteristic redshift of the source distribution.
+    :ivar z_m: the slope of the source redshift distribution.
+
     """
 
     def __init__(self, sacc_tracer: str):
@@ -196,6 +220,12 @@ class ConstantMagnificationBiasSystematic(NumberCountsSystematic):
 
     This systematic adds a constant magnification bias model for galaxy number
     contrast.
+
+    The following parameters are special Updatable parameters, which means that
+    they can be updated by the sampler, sacc_tracer is going to be used as a
+    prefix for the parameters:
+    :ivar mag_bias: the magnification bias.
+
     """
 
     def __init__(self, sacc_tracer: str):
@@ -221,6 +251,12 @@ class PhotoZShift(NumberCountsSystematic):
     """A photo-z shift bias.
 
     This systematic shifts the photo-z distribution by some ammount `delta_z`.
+
+    The following parameters are special Updatable parameters, which means that
+    they can be updated by the sampler, sacc_tracer is going to be used as a
+    prefix for the parameters:
+    :ivar delta_z: the photo-z shift.
+
     """
 
     def __init__(self, sacc_tracer: str):
diff --git a/firecrown/likelihood/gauss_family/statistic/source/weak_lensing.py b/firecrown/likelihood/gauss_family/statistic/source/weak_lensing.py
index 6e3fe6491..8e70e8922 100644
--- a/firecrown/likelihood/gauss_family/statistic/source/weak_lensing.py
+++ b/firecrown/likelihood/gauss_family/statistic/source/weak_lensing.py
@@ -56,6 +56,11 @@ class MultiplicativeShearBias(WeakLensingSystematic):
     """Multiplicative shear bias systematic.
 
     This systematic adjusts the `scale_` of a source by `(1 + m)`.
+
+    The following parameters are special Updatable parameters, which means that
+    they can be updated by the sampler, sacc_tracer is going to be used as a
+    prefix for the parameters:
+    :ivar mult_bias: the multiplicative shear bias parameter.
     """
 
     def __init__(self, sacc_tracer: str) -> None:
@@ -91,6 +96,14 @@ class LinearAlignmentSystematic(WeakLensingSystematic):
 
     This systematic adds a linear intrinsic alignment model systematic
     which varies with redshift and the growth function.
+
+    The following parameters are special Updatable parameters, which means that
+    they can be updated by the sampler, sacc_tracer is going to be used as a
+    prefix for the parameters:
+    :ivar ia_bias: the intrinsic alignment bias parameter.
+    :ivar alphaz: the redshift dependence of the intrinsic alignment bias.
+    :ivar alphag: the growth function dependence of the intrinsic alignment bias.
+    :ivar z_piv: the pivot redshift for the intrinsic alignment bias.
     """
 
     def __init__(self, sacc_tracer: Optional[str] = None, alphag=1.0):
@@ -133,6 +146,14 @@ class TattAlignmentSystematic(WeakLensingSystematic):
     """TATT alignment systematic.
 
     This systematic adds a TATT (nonlinear) intrinsic alignment model systematic.
+
+    The following parameters are special Updatable parameters, which means that
+    they can be updated by the sampler, sacc_tracer is going to be used as a
+    prefix for the parameters:
+    :ivar ia_a_1: the amplitude of the linear alignment model.
+    :ivar ia_a_2: the amplitude of the quadratic alignment model.
+    :ivar ia_a_d: the amplitude of the density-dependent alignment model.
+
     """
 
     def __init__(self, sacc_tracer: Optional[str] = None):
@@ -177,6 +198,11 @@ class PhotoZShift(WeakLensingSystematic):
     """A photo-z shift bias.
 
     This systematic shifts the photo-z distribution by some amount `delta_z`.
+
+    The following parameters are special Updatable parameters, which means that
+    they can be updated by the sampler, sacc_tracer is going to be used as a
+    prefix for the parameters:
+    :ivar delta_z: the photo-z shift.
     """
 
     def __init__(self, sacc_tracer: str):
diff --git a/firecrown/models/cluster_mass_rich_proxy.py b/firecrown/models/cluster_mass_rich_proxy.py
index fee42b428..2138472e9 100644
--- a/firecrown/models/cluster_mass_rich_proxy.py
+++ b/firecrown/models/cluster_mass_rich_proxy.py
@@ -16,7 +16,17 @@
 
 
 class ClusterMassRich(ClusterMass):
-    """Cluster Mass Richness proxy."""
+    """Cluster Mass Richness proxy.
+
+    The following parameters are special Updatable parameters, which means that
+    they can be updated by the sampler.
+    :ivar mu_p0: mu parameter 0
+    :ivar mu_p1: mu parameter 1
+    :ivar mu_p2: mu parameter 2
+    :ivar sigma_p0: sigma parameter 0
+    :ivar sigma_p1: sigma parameter 1
+    :ivar sigma_p2: sigma parameter 2
+    """
 
     def __init__(
         self, pivot_mass, pivot_redshift, logMl: float = 13.0, logMu: float = 16.0

From c8d6fc062b7aa431fa5bc08599e691fd09ed9e3b Mon Sep 17 00:00:00 2001
From: Sandro Dias Pinto Vitenti <vitenti@uel.br>
Date: Wed, 20 Sep 2023 22:23:49 -0300
Subject: [PATCH 4/4] Adding missing empty line in docs.

---
 .../gauss_family/statistic/source/number_counts.py       | 9 +++++----
 .../gauss_family/statistic/source/weak_lensing.py        | 5 ++++-
 firecrown/models/cluster_mass_rich_proxy.py              | 3 ++-
 3 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/firecrown/likelihood/gauss_family/statistic/source/number_counts.py b/firecrown/likelihood/gauss_family/statistic/source/number_counts.py
index 41ada58be..6bd010301 100644
--- a/firecrown/likelihood/gauss_family/statistic/source/number_counts.py
+++ b/firecrown/likelihood/gauss_family/statistic/source/number_counts.py
@@ -62,10 +62,10 @@ class LinearBiasSystematic(NumberCountsSystematic):
     The following parameters are special Updatable parameters, which means that
     they can be updated by the sampler, sacc_tracer is going to be used as a
     prefix for the parameters:
+
     :ivar alphaz: the redshift exponent of the bias.
     :ivar alphag: the growth function exponent of the bias.
     :ivar z_piv: the pivot redshift of the bias.
-
     """
 
     def __init__(self, sacc_tracer: str):
@@ -121,6 +121,7 @@ class PTNonLinearBiasSystematic(NumberCountsSystematic):
     The following parameters are special Updatable parameters, which means that
     they can be updated by the sampler, sacc_tracer is going to be used as a
     prefix for the parameters:
+
     :ivar b_2: the quadratic bias.
     :ivar b_s: the stochastic bias.
     """
@@ -161,12 +162,12 @@ class MagnificationBiasSystematic(NumberCountsSystematic):
     The following parameters are special Updatable parameters, which means that
     they can be updated by the sampler, sacc_tracer is going to be used as a
     prefix for the parameters:
+
     :ivar r_lim: the limiting magnitude.
     :ivar sig_c: the intrinsic dispersion of the source redshift distribution.
     :ivar eta: the slope of the luminosity function.
     :ivar z_c: the characteristic redshift of the source distribution.
     :ivar z_m: the slope of the source redshift distribution.
-
     """
 
     def __init__(self, sacc_tracer: str):
@@ -224,8 +225,8 @@ class ConstantMagnificationBiasSystematic(NumberCountsSystematic):
     The following parameters are special Updatable parameters, which means that
     they can be updated by the sampler, sacc_tracer is going to be used as a
     prefix for the parameters:
-    :ivar mag_bias: the magnification bias.
 
+    :ivar mag_bias: the magnification bias.
     """
 
     def __init__(self, sacc_tracer: str):
@@ -255,8 +256,8 @@ class PhotoZShift(NumberCountsSystematic):
     The following parameters are special Updatable parameters, which means that
     they can be updated by the sampler, sacc_tracer is going to be used as a
     prefix for the parameters:
-    :ivar delta_z: the photo-z shift.
 
+    :ivar delta_z: the photo-z shift.
     """
 
     def __init__(self, sacc_tracer: str):
diff --git a/firecrown/likelihood/gauss_family/statistic/source/weak_lensing.py b/firecrown/likelihood/gauss_family/statistic/source/weak_lensing.py
index 8e70e8922..305bbc7ad 100644
--- a/firecrown/likelihood/gauss_family/statistic/source/weak_lensing.py
+++ b/firecrown/likelihood/gauss_family/statistic/source/weak_lensing.py
@@ -60,6 +60,7 @@ class MultiplicativeShearBias(WeakLensingSystematic):
     The following parameters are special Updatable parameters, which means that
     they can be updated by the sampler, sacc_tracer is going to be used as a
     prefix for the parameters:
+
     :ivar mult_bias: the multiplicative shear bias parameter.
     """
 
@@ -100,6 +101,7 @@ class LinearAlignmentSystematic(WeakLensingSystematic):
     The following parameters are special Updatable parameters, which means that
     they can be updated by the sampler, sacc_tracer is going to be used as a
     prefix for the parameters:
+
     :ivar ia_bias: the intrinsic alignment bias parameter.
     :ivar alphaz: the redshift dependence of the intrinsic alignment bias.
     :ivar alphag: the growth function dependence of the intrinsic alignment bias.
@@ -150,10 +152,10 @@ class TattAlignmentSystematic(WeakLensingSystematic):
     The following parameters are special Updatable parameters, which means that
     they can be updated by the sampler, sacc_tracer is going to be used as a
     prefix for the parameters:
+
     :ivar ia_a_1: the amplitude of the linear alignment model.
     :ivar ia_a_2: the amplitude of the quadratic alignment model.
     :ivar ia_a_d: the amplitude of the density-dependent alignment model.
-
     """
 
     def __init__(self, sacc_tracer: Optional[str] = None):
@@ -202,6 +204,7 @@ class PhotoZShift(WeakLensingSystematic):
     The following parameters are special Updatable parameters, which means that
     they can be updated by the sampler, sacc_tracer is going to be used as a
     prefix for the parameters:
+
     :ivar delta_z: the photo-z shift.
     """
 
diff --git a/firecrown/models/cluster_mass_rich_proxy.py b/firecrown/models/cluster_mass_rich_proxy.py
index 2138472e9..2b499b2cf 100644
--- a/firecrown/models/cluster_mass_rich_proxy.py
+++ b/firecrown/models/cluster_mass_rich_proxy.py
@@ -19,7 +19,8 @@ class ClusterMassRich(ClusterMass):
     """Cluster Mass Richness proxy.
 
     The following parameters are special Updatable parameters, which means that
-    they can be updated by the sampler.
+    they can be updated by the sampler:
+
     :ivar mu_p0: mu parameter 0
     :ivar mu_p1: mu parameter 1
     :ivar mu_p2: mu parameter 2