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Improve Python class implementation for editor/IDE integration #677

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Mar 1, 2021
Merged

Improve Python class implementation for editor/IDE integration #677

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62 changes: 30 additions & 32 deletions fwdpy11/discrete_demography.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,19 +28,17 @@
attr_class_to_from_dict,
attr_class_to_from_dict_no_recurse)

_common_attr_attribs = {"frozen": True, "auto_attribs": True, "repr_ns": "fwdpy11"}


@attr_add_asblack
@attr_class_pickle_with_super
@attr_class_to_from_dict
@attr.s(**_common_attr_attribs)
@attr.s(auto_attribs=True, frozen=True, repr_ns="fwdpy11")
class MassMigration(fwdpy11._fwdpy11._ll_MassMigration):
"""
Mass migration events.

This class has the following attributes, whose names
are also ``kwargs`` for intitialization. The attribute names
are also `kwargs` for intitialization. The attribute names
also determine the order of positional arguments:

:param when: When the mass migration happens
Expand All @@ -51,12 +49,12 @@ class MassMigration(fwdpy11._fwdpy11._ll_MassMigration):
:type destination: int
:param fraction: The fraction of `source` to move to `destination`.
:type fraction: float
:param move_individuals: If ``True``, the event moves individuals.
If ``False``, individuals are copied.
:param move_individuals: If `True`, the event moves individuals.
If `False`, individuals are copied.
:type move_individuals: bool
:param resets_growth_rate: (True) Whether or not to reset the
growth rates of `source` and `destination` to
:data:`fwdpy11.NOGROWTH`
growth rates of `source` and `destination` to
:data:`fwdpy11.NOGROWTH`
:type resets_growth_rate: bool

.. note::
Expand Down Expand Up @@ -107,8 +105,8 @@ def move_individuals(
:param fraction: The fraction of `source` to move to `destination`.
:type fraction: float
:param resets_growth_rate: (True) Whether or not to reset the
growth rates of `source` and `destination` to
:data:`fwdpy11.NOGROWTH`
growth rates of `source` and `destination` to
:data:`fwdpy11.NOGROWTH`
:type resets_growth_rate: bool

:rtype: :class:`fwdpy11.MassMigration`
Expand All @@ -133,8 +131,8 @@ def copy_individuals(
:param fraction: The fraction of `source` to copy to `destination`.
:type fraction: float
:param resets_growth_rate: (True) Whether or not to reset the
growth rates of `source` and `destination` to
:data:`fwdpy11.NOGROWTH`
growth rates of `source` and `destination` to
:data:`fwdpy11.NOGROWTH`
:type resets_growth_rate: bool

:rtype: :class:`fwdpy11.MassMigration`
Expand All @@ -145,13 +143,13 @@ def copy_individuals(
@attr_add_asblack
@attr_class_pickle_with_super
@attr_class_to_from_dict
@attr.s(**_common_attr_attribs)
@attr.s(auto_attribs=True, frozen=True, repr_ns="fwdpy11")
class SetDemeSize(fwdpy11._fwdpy11._ll_SetDemeSize):
"""
Set the size of a deme at a given time.

This class has the following attributes, whose names
are also ``kwargs`` for intitialization. The attribute names
are also `kwargs` for intitialization. The attribute names
also determine the order of positional arguments:

:param when: The generation when the event occurs
Expand All @@ -161,7 +159,7 @@ class SetDemeSize(fwdpy11._fwdpy11._ll_SetDemeSize):
:param new_size: The new size
:type new_size: int
:param resets_growth_rate: (True) If deme size change resets
growth rate to :data:`fwdpy11.NOGROWTH`
growth rate to :data:`fwdpy11.NOGROWTH`
:type resets_growth_rate: bool

.. versionadded:: 0.5.3
Expand All @@ -186,13 +184,13 @@ def __attrs_post_init__(self):
@attr_class_to_from_dict
@attr_add_asblack
@attr_class_pickle_with_super
@attr.s(**_common_attr_attribs)
@attr.s(auto_attribs=True, frozen=True, repr_ns="fwdpy11")
class SetExponentialGrowth(fwdpy11._fwdpy11._ll_SetExponentialGrowth):
"""
Set the growth rate of a deme at a given time.

This class has the following attributes, whose names
are also ``kwargs`` for intitialization. The attribute names
are also `kwargs` for intitialization. The attribute names
also determine the order of positional arguments:

:param when: The generation when the event occurs
Expand Down Expand Up @@ -221,13 +219,13 @@ def __attrs_post_init__(self):
@attr_add_asblack
@attr_class_pickle_with_super
@attr_class_to_from_dict
@attr.s(**_common_attr_attribs)
@attr.s(auto_attribs=True, frozen=True, repr_ns="fwdpy11")
class SetSelfingRate(fwdpy11._fwdpy11._ll_SetSelfingRate):
"""
Set the selfing probability within a deme at a given time.

This class has the following attributes, whose names
are also ``kwargs`` for intitialization. The attribute names
are also `kwargs` for intitialization. The attribute names
also determine the order of positional arguments:

:param when: The generation when the event occurs
Expand Down Expand Up @@ -263,19 +261,19 @@ def __setstate__(self, d):
@attr_add_asblack
@attr_class_pickle_with_super
@attr_class_to_from_dict
@attr.s(eq=False, **_common_attr_attribs)
@attr.s(eq=False, auto_attribs=True, frozen=True, repr_ns="fwdpy11")
class MigrationMatrix(fwdpy11._fwdpy11._ll_MigrationMatrix):
"""
The forward migration matrix for a simulation.

This class has the following attributes, whose names
are also ``kwargs`` for intitialization. The attribute names
are also `kwargs` for intitialization. The attribute names
also determine the order of positional arguments:

:param migmatrix: A square matrix of non-negative floats.
:type migmatrix: numpy.ndarray
:param scaled: (True) If entries in `migmatrix` will be
multiplied by deme sizes during simulation
multiplied by deme sizes during simulation
:type scaled: bool

.. versionadded:: 0.5.3
Expand Down Expand Up @@ -314,15 +312,15 @@ def _set_migration_rates_convert_deme(i: typing.Optional[int]) -> int:

@attr_add_asblack
@attr_class_to_from_dict
@attr.s(eq=False, **_common_attr_attribs)
@attr.s(eq=False, auto_attribs=True, frozen=True, repr_ns="fwdpy11")
class SetMigrationRates(fwdpy11._fwdpy11._ll_SetMigrationRates):
"""
Set the migration parameters of a simulation at a given time.
May be used to set either the migration rates from a given
deme or the entire migration matrix.

This class has the following attributes, whose names
are also ``kwargs`` for intitialization. The attribute names
are also `kwargs` for intitialization. The attribute names
also determine the order of positional arguments:

:param when: The generation when the event occurs
Expand All @@ -333,11 +331,11 @@ class SetMigrationRates(fwdpy11._fwdpy11._ll_SetMigrationRates):
:type migrates: list or numpy.ndarray

The migration rates are equivalent to the single-generation ancestry proportions
with respect to ``deme``.
with respect to `deme`.

In order to change the entire migration matrix, pass ``None`` (or -1)
to ``deme`` and a 2d ``numpy.ndarray`` for ``migrates``. A value of
``None`` will be converted to ``-1`` in this case.
In order to change the entire migration matrix, pass `None` (or -1)
to `deme` and a 2d `numpy.ndarray` for `migrates`. A value of
`None` will be converted to `-1` in this case.

.. versionadded:: 0.5.3

Expand Down Expand Up @@ -430,14 +428,14 @@ def _convert_migmatrix(o):

@attr_add_asblack
@attr_class_to_from_dict_no_recurse
@attr.s(**_common_attr_attribs)
@attr.s(auto_attribs=True, frozen=True, repr_ns="fwdpy11")
class DiscreteDemography(fwdpy11._fwdpy11._ll_DiscreteDemography):
"""
Representation of demographic events acting on
discrete demes (sub-populations).

This class has the following attributes, whose names
are also ``kwargs`` for intitialization. The attribute names
are also `kwargs` for intitialization. The attribute names
also determine the order of positional arguments:

:param mass_migrations: Instances of :class:`fwdpy11.MassMigration`
Expand All @@ -449,8 +447,8 @@ class DiscreteDemography(fwdpy11._fwdpy11._ll_DiscreteDemography):
:param set_selfing_rates: Instances of :class:`fwdpy11.SetSelfingRate`
:type set_selfing_rates: None or list[fwdpy11.SetSelfingRate]
:param migmatrix: A migraton matrix. See :ref:`migration`. If not
``None``, then input are converted into an
instance of :class:`fwdpy11.MigrationMatrix`.
`None`, then input are converted into an
instance of :class:`fwdpy11.MigrationMatrix`.
:type migmatrix: None or numpy.ndarray or fwdpy11.MigrationMatrix
:param set_migration_rates: Instances of :class:`fwdpy11.SetMigrationRates`
:type set_migration_rates: None or list[fwdpy11.SetMigrationRates]
Expand Down
52 changes: 25 additions & 27 deletions fwdpy11/genetic_map_unit.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,8 +27,6 @@
from .class_decorators import (attr_add_asblack, attr_class_pickle_with_super,
attr_class_to_from_dict)

_common_attr_attribs = {"frozen": True, "auto_attribs": True, "repr_ns": "fwdpy11"}


def _is_integer_if_discrete(self, attribute, value):
if self.discrete is True:
Expand All @@ -38,13 +36,13 @@ def _is_integer_if_discrete(self, attribute, value):
@attr_add_asblack
@attr_class_pickle_with_super
@attr_class_to_from_dict
@attr.s(**_common_attr_attribs)
@attr.s(auto_attribs=True, frozen=True, repr_ns="fwdpy11")
class PoissonInterval(fwdpy11._fwdpy11._ll_PoissonInterval):
"""
Generate poisson number of crossover breakpoints.

This class has the following attributes, whose names
are also ``kwargs`` for intitialization. The attribute names
are also `kwargs` for intitialization. The attribute names
also determine the order of positional arguments:

:param beg: The beginning of the region
Expand All @@ -53,8 +51,8 @@ class PoissonInterval(fwdpy11._fwdpy11._ll_PoissonInterval):
:type end: int or float
:param mean: The mean number of breakpoints per meiosis
:type mean: float
:param discrete: If ``False``, positions are continuous and uniform from ``[beg, end)``.
If ``True``, positions take integer values uniformly from ``[beg, end)``.
:param discrete: If `False`, positions are continuous and uniform from `[beg, end)`.
If `True`, positions take integer values uniformly from `[beg, end)`.
:type discrete: bool

.. versionadded:: 0.3.0
Expand All @@ -74,7 +72,7 @@ class PoissonInterval(fwdpy11._fwdpy11._ll_PoissonInterval):

.. versionchanged:: 0.12.0

Added ``discrete`` option to initializer.
Added `discrete` option to initializer.
"""

beg: typing.Union[int, float] = attr.ib(validator=_is_integer_if_discrete)
Expand All @@ -91,22 +89,22 @@ def __attrs_post_init__(self):
@attr_add_asblack
@attr_class_pickle_with_super
@attr_class_to_from_dict
@attr.s(**_common_attr_attribs)
@attr.s(auto_attribs=True, frozen=True, repr_ns="fwdpy11")
class PoissonPoint(fwdpy11._fwdpy11._ll_PoissonPoint):
"""
Generate a recombination breakpoint at a fixed position if the
number of crossover events is odd.

This class has the following attributes, whose names
are also ``kwargs`` for intitialization. The attribute names
are also `kwargs` for intitialization. The attribute names
also determine the order of positional arguments:

:param position: The position of the crossover
:type position: int or float
:param mean: The mean number of breakpoints per meiosis
:type mean: float
:param discrete: If ``False``, positions are continuous and uniform from ``[beg, end)``.
If ``True``, positions take integer values uniformly from ``[beg, end)``.
:param discrete: If `False`, positions are continuous and uniform from `[beg, end)`.
If `True`, positions take integer values uniformly from `[beg, end)`.
:type discrete: bool

.. versionadded:: 0.3.0
Expand All @@ -126,7 +124,7 @@ class PoissonPoint(fwdpy11._fwdpy11._ll_PoissonPoint):

.. versionchanged:: 0.12.0

Added ``discrete`` option to initializer.
Added `discrete` option to initializer.
"""

position: typing.Union[int, float] = attr.ib(validator=_is_integer_if_discrete)
Expand All @@ -148,13 +146,13 @@ def __setstate__(self, d):

@attr_class_pickle_with_super
@attr_class_to_from_dict
@attr.s(**_common_attr_attribs)
@attr.s(auto_attribs=True, frozen=True, repr_ns="fwdpy11")
class BinomialInterval(fwdpy11._fwdpy11._ll_BinomialInterval):
"""
Generate exactly one crossover with a given probability

This class has the following attributes, whose names
are also ``kwargs`` for intitialization. The attribute names
are also `kwargs` for intitialization. The attribute names
also determine the order of positional arguments:

:param beg: The beginning of the region
Expand All @@ -163,8 +161,8 @@ class BinomialInterval(fwdpy11._fwdpy11._ll_BinomialInterval):
:type end: int or float
:param probability: The probability of a recombination (per meiosis).
:type probability: float
:param discrete: If ``False``, positions are continuous and uniform from ``[beg, end)``.
If ``True``, positions take integer values uniformly from ``[beg, end)``.
:param discrete: If `False`, positions are continuous and uniform from `[beg, end)`.
If `True`, positions take integer values uniformly from `[beg, end)`.
:type discrete: bool

.. versionadded:: 0.5.2
Expand All @@ -180,7 +178,7 @@ class BinomialInterval(fwdpy11._fwdpy11._ll_BinomialInterval):

.. versionchanged:: 0.12.0

Added ``discrete`` option to initializer.
Added `discrete` option to initializer.
"""

beg: typing.Union[int, float] = attr.ib(validator=_is_integer_if_discrete)
Expand All @@ -200,23 +198,23 @@ def __attrs_post_init__(self):
@attr_add_asblack
@attr_class_pickle_with_super
@attr_class_to_from_dict
@attr.s(**_common_attr_attribs)
@attr.s(auto_attribs=True, frozen=True, repr_ns="fwdpy11")
class BinomialPoint(fwdpy11._fwdpy11._ll_BinomialPoint):
"""
Generate a crossover breakpoint at a fixed position with a
fixed probability. This class represents genetic distance
as centiMorgans/100.

This class has the following attributes, whose names
are also ``kwargs`` for intitialization. The attribute names
are also `kwargs` for intitialization. The attribute names
also determine the order of positional arguments:

:param position: The beginning of the region
:type position: int or float
:param probability: The probability of a recombination (per meiosis).
:type probability: float
:param discrete: If ``False``, positions are continuous and uniform from ``[beg, end)``.
If ``True``, positions take integer values uniformly from ``[beg, end)``.
:param discrete: If `False`, positions are continuous and uniform from `[beg, end)`.
If `True`, positions take integer values uniformly from `[beg, end)`.
:type discrete: bool

.. versionadded:: 0.3.0
Expand All @@ -236,7 +234,7 @@ class BinomialPoint(fwdpy11._fwdpy11._ll_BinomialPoint):

.. versionchanged:: 0.12.0

Added ``discrete`` option to initializer.
Added `discrete` option to initializer.
"""

position: typing.Union[int, float] = attr.ib(validator=_is_integer_if_discrete)
Expand All @@ -252,13 +250,13 @@ def __attrs_post_init__(self):
@attr_add_asblack
@attr_class_pickle_with_super
@attr_class_to_from_dict
@attr.s(**_common_attr_attribs)
@attr.s(auto_attribs=True, frozen=True, repr_ns="fwdpy11")
class FixedCrossovers(fwdpy11._fwdpy11._ll_FixedCrossovers):
"""
Generate a fixed number of crossover breakpoints.

This class has the following attributes, whose names
are also ``kwargs`` for intitialization. The attribute names
are also `kwargs` for intitialization. The attribute names
also determine the order of positional arguments:

:param beg: The beginning of the region
Expand All @@ -267,8 +265,8 @@ class FixedCrossovers(fwdpy11._fwdpy11._ll_FixedCrossovers):
:type end: int or float
:param num_xovers: The number of breakpoints per meiosis
:type num_xovers: float
:param discrete: If ``False``, positions are continuous and uniform from ``[beg, end)``.
If ``True``, positions take integer values uniformly from ``[beg, end)``.
:param discrete: If `False`, positions are continuous and uniform from `[beg, end)`.
If `True`, positions take integer values uniformly from `[beg, end)`.
:type discrete: bool

.. versionadded:: 0.3.0
Expand All @@ -288,7 +286,7 @@ class FixedCrossovers(fwdpy11._fwdpy11._ll_FixedCrossovers):

.. versionchanged:: 0.12.0

Added ``discrete`` option to initializer.
Added `discrete` option to initializer.
"""

beg: typing.Union[int, float] = attr.ib(validator=_is_integer_if_discrete)
Expand Down