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update change log and conf.py (#527)
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molpopgen authored Jun 11, 2020
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1 change: 1 addition & 0 deletions doc/conf.py
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"sparse": ("https://sparse.pydata.org/en/latest/", None),
"tskit": ("https://tskit.readthedocs.io/en/stable", None),
"msprime": ("https://msprime.readthedocs.io/en/stable", None),
"attrs": ("https://www.attrs.org/en/stable", None),
}

# 'breathe']
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71 changes: 69 additions & 2 deletions doc/misc/changelog.rst
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Changelog
====================================================================================

Major changes are listed below. Each release likely contains fiddling with back-end code, updates to latest fwdpp
version, etc.
Major changes are listed below. Each release likely contains fiddling with back-end code,
updates to latest `fwdpp` version, etc.

0.8.0a0
++++++++++++++++++++++++++++++++++++++++

This is the first alpha release of 0.8.0.

In addition to what is below, this release contains
a smattering of build system changes, documentation changes,
etc., that are collected under the 0.8.0 milestone on `Github`.

`API`/`UI` changes:

This release brings Python classes that have been reimplemented using `attrs <https://www.attrs.org>`_. These changes have a lot of benefits:

* A lot of C++ code got removed (yay!) because we can use `attrs` for the pickling
machinery, `__repr__`, etc..
* We now get *much* nicer `__repr__` for all of the types that get sent into
instances of :class:`fwdpy11.ModelParams`.

However, these changes required some simplification to the `__init__` methods,
which meant some `API` breakage. See the :ref:`upgrade guide <upgrade_path>`
for details.

This release also removes features deprecated in previous releases. :pr:`482`

Performance improvements:

* Sorting edge tables prior to tree sequence simplification has been replaced
by an efficient buffering algorithm. :pr:`526`.

New demographic models:

* The [Tennessen2012]_ model is added via :func:`fwdpy11.demographic_models.human.tennessen`.
:pr:`479`

Improved behavior:

* Improved warnings about demographic events scheduled to happen
before the population's current generation. :pr:`495`
* Built-in demographic models now return instances of
:class:`fwdpy11.demographic_models.DemographicModelDetails`.
Such instances can be passed as the `demography` keyword argument
to initialize :class:`fwdpy11.ModelParams`.
:pr:`509`.
* The "individual" column of a node table is now populated
when exporting to a :class:`tskit.TableCollection`. :pr:`488`

Changes to implementation of Python classes

* :class:`fwdpy11.ModelParams` has been reimplemented
using `attrs <https://www.attrs.org>`_. :pr:`484`, :pr:`486`, :pr:`487`.
* Demographic model types are now implemented using `attrs <https://www.attrs.org>`_ and
inherit from the C++ back-end class. :pr:`492`
* Region types are now implemented using `attrs <https://www.attrs.org>`_ and
inherit from the C++ back-end class. :pr:`497`
* Genetic value types are now implemented using `attrs <https://www.attrs.org>`_ and
inherit from the C++ back-end class. :pr:`504`
* Genetic map unit types are now implemented using `attrs <https://www.attrs.org>`_ and
inherit from the C++ back-end class. :pr:`506`

C++ back end changes:

* The default C++ language standard is now C++14. :pr:`517`.
* Custom exceptions now have default symbol visibility. :pr:`519`.
* The back-end code for discrete demography got cleaned up. :pr:`521`.
* The `fwdpp` submodule was updated a few times.
:pr:`489` :pr:`523` :pr:`525`

0.7.1
++++++++++++++++++++++++++++++++++++++++
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