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Again more docstrings #447

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merged 3 commits into from
Aug 20, 2024
Merged

Again more docstrings #447

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3b798a6
Update docstrings and type annotations
marcpaterno Aug 16, 2024
5dd87d6
Update docstrings
marcpaterno Aug 20, 2024
e9c8ed6
Update source.py
marcpaterno Aug 20, 2024
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2 changes: 1 addition & 1 deletion firecrown/likelihood/number_counts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -231,7 +231,7 @@ def apply(
) -> NumberCountsArgs:
"""Apply a magnification bias systematic.

:param tools: currently unused, by required by the interface
:param tools: currently unused, but required by the interface
:param tracer_arg: a NumberCountsArgs object with values to be updated

:return: an updated NumberCountsArgs object
Expand Down
107 changes: 80 additions & 27 deletions firecrown/likelihood/source.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,19 +29,15 @@ class SourceSystematic(Updatable):
the `apply` method of different subclasses are different.
"""

def read(self, sacc_data: sacc.Sacc):
"""Call to allow this object to read from the appropriate sacc data."""
def read(self, sacc_data: sacc.Sacc) -> None:
"""Call to allow this object to read from the appropriate sacc data.

:param sacc_data: The SACC data object to be read
"""

class Source(Updatable):
"""An abstract source class (e.g., a sample of lenses).

Parameters
----------
systematics : list of str, optional
A list of the source-level systematics to apply to the source. The
default of `None` implies no systematics.
"""
class Source(Updatable):
"""The abstract base class for all sources."""

systematics: Sequence[SourceSystematic]
cosmo_hash: None | int
Expand All @@ -57,22 +53,30 @@ def __init__(self, sacc_tracer: str) -> None:
self.sacc_tracer = sacc_tracer

@final
def read(self, sacc_data: sacc.Sacc):
"""Read the data for this source from the SACC file."""
def read(self, sacc_data: sacc.Sacc) -> None:
"""Read the data for this source from the SACC file.

:param sacc_data: The SACC data object to be read
"""
if hasattr(self, "systematics"):
for systematic in self.systematics:
systematic.read(sacc_data)
self._read(sacc_data)

@abstractmethod
def _read(self, sacc_data: sacc.Sacc):
"""Abstract method to read the data for this source from the SACC file."""
def _read(self, sacc_data: sacc.Sacc) -> None:
"""Abstract method to read the data for this source from the SACC file.

:param sacc_data: The SACC data object to be read
"""

def _update_source(self, params: ParamsMap):
def _update_source(self, params: ParamsMap) -> None:
"""Method to update the source from the given ParamsMap.

Any subclass that needs to do more than update its contained :class:`Updatable`
objects should implement this method.

:param params: the parameters to be used for the update
"""

@final
Expand All @@ -81,25 +85,36 @@ def _update(self, params: ParamsMap):

This clears the current hash and tracer, and calls the abstract method
`_update_source`, which must be implemented in all subclasses.

:param params: the parameters to be used for the update
"""
self.cosmo_hash = None
self.tracers = []
self._update_source(params)

@abstractmethod
def get_scale(self) -> float:
"""Abstract method to return the scales for this `Source`."""
"""Abstract method to return the scale for this `Source`.

:return: the scale
"""

@abstractmethod
def create_tracers(self, tools: ModelingTools):
"""Create tracers for this `Source`, for the given cosmology."""
"""Abstract method to create tracers for this Source.

:param tools: The modeling tools used for creating the tracers
"""

@final
def get_tracers(self, tools: ModelingTools) -> Sequence[Tracer]:
"""Return the tracer for the given cosmology.

This method caches its result, so if called a second time with the same
cosmology, no calculation needs to be done.

:param tools: The modeling tools used for creating the tracers
:return: the list of tracers
"""
ccl_cosmo = tools.get_ccl_cosmology()

Expand Down Expand Up @@ -128,6 +143,10 @@ def determine_field_name(field: None | str, tracer: None | str) -> str:

It is a static method only to keep it grouped with the class for which it is
defining the initialization policy.

:param field: the (stub) name of the field
:param tracer: the name of the tracer
:return: the full name of the field
"""
if field is not None:
return field
Expand All @@ -144,7 +163,7 @@ def __init__(
halo_profile: None | pyccl.halos.HaloProfile = None,
halo_2pt: None | pyccl.halos.Profile2pt = None,
):
"""Initialize a new Tracer based on the pyccl.Tracer which must not be None.
"""Initialize a new Tracer based on the provided tracer.

Note that the :class:`pyccl.Tracer` is not copied; we store a reference to the
original tracer. Be careful not to accidentally share :class:`pyccl.Tracer`s.
Expand All @@ -154,6 +173,13 @@ def __init__(

If no `field` is given, then the attribute :attr:`field` is set to either
(1) the tracer_name, if one was given, or (2) 'delta_matter'.

:param tracer: the pyccl.Tracer used as the basis for this Tracer.
:param tracer_name: optional name of the tracer.
:param field: optional name of the field associated with the tracer.
:param pt_tracer: optional non-linear perturbation theory tracer.
:param halo_profile: optional halo profile.
:param halo_2pt: optional halo profile 2-point object.
"""
assert tracer is not None
self.ccl_tracer = tracer
Expand All @@ -165,12 +191,18 @@ def __init__(

@property
def has_pt(self) -> bool:
"""Return True if we have a pt_tracer, and False if not."""
"""Answer whether we have a perturbation theory tracer.

:return: True if we have a pt_tracer, and False if not.
"""
return self.pt_tracer is not None

@property
def has_hm(self) -> bool:
"""Return True if we have a halo_profile, and False if not."""
"""Answer whether we have a halo profile.

:return: True if we have a halo_profile, and False if not.
"""
return self.halo_profile is not None


Expand All @@ -193,13 +225,19 @@ class SourceGalaxyArgs:


class SourceGalaxySystematic(SourceSystematic, Generic[_SourceGalaxyArgsT]):
"""Abstract base class for all galaxy based source systematics."""
"""Abstract base class for all galaxy-based source systematics."""

@abstractmethod
def apply(
self, tools: ModelingTools, tracer_arg: _SourceGalaxyArgsT
) -> _SourceGalaxyArgsT:
"""Apply method to include systematics in the tracer_arg."""
"""Apply method to include systematics in the tracer_arg.

:param tools: the modeling tools use to update the tracer arg
:param tracer_arg: the original source galaxy tracer arg to which we
apply the systematic.
:return: a new source galaxy tracer arg with the systematic applied
"""


_SourceGalaxySystematicT = TypeVar(
Expand Down Expand Up @@ -236,8 +274,16 @@ def __init__(self, sacc_tracer: str) -> None:
default_value=SOURCE_GALAXY_SYSTEMATIC_DEFAULT_DELTA_Z
)

def apply(self, tools: ModelingTools, tracer_arg: _SourceGalaxyArgsT):
"""Apply a shift to the photo-z distribution of a source."""
def apply(
self, tools: ModelingTools, tracer_arg: _SourceGalaxyArgsT
) -> _SourceGalaxyArgsT:
"""Apply a shift to the photo-z distribution of a source.

:param tools: the modeling tools use to update the tracer arg
:param tracer_arg: the original source galaxy tracer arg to which we
apply the systematic.
:return: a new source galaxy tracer arg with the systematic applied
"""
dndz_interp = Akima1DInterpolator(tracer_arg.z, tracer_arg.dndz)

dndz = dndz_interp(tracer_arg.z - self.delta_z, extrapolate=False)
Expand All @@ -263,15 +309,20 @@ def __init__(self, field: str = "delta_matter"):
"""Specify which 3D field should be used when computing angular power spectra.

:param field: the name of the 3D field that is associated to the tracer.
Default: `"delta_matter"`
"""
super().__init__()
self.field = field

def apply(
self, tools: ModelingTools, tracer_arg: _SourceGalaxyArgsT
) -> _SourceGalaxyArgsT:
"""Apply method to include systematics in the tracer_arg."""
"""Apply method to include systematics in the tracer_arg.

:param tools: the modeling tools used to update the tracer_arg
:param tracer_arg: the original source galaxy tracer arg to which we
apply the systematics.
:return: a new source galaxy tracer arg with the systematic applied
"""
return replace(tracer_arg, field=self.field)


Expand Down Expand Up @@ -299,11 +350,13 @@ def __init__(
)
self.tracer_args: _SourceGalaxyArgsT

def _read(self, sacc_data: sacc.Sacc):
def _read(self, sacc_data: sacc.Sacc) -> None:
"""Read the galaxy redshift distribution model from a sacc file.

All derived classes must call this method in their own `_read` method
after they have read their own data and initialized their tracer_args.

:param sacc_data: The SACC data object to be read
"""
try:
tracer_args = self.tracer_args
Expand Down
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