Fwdpy11

Fix for wheel building action. c31420aede4180becfe2a28936469ed471c6ea41

Same as previous 0.13.x releases otherwise.

Same as 0.13.0, but includes 682 to attempt to fix various deployment issues we had with the previous release.
See 680 and 681.

Copy/paste from the change log:

API changes

* The `demesizes` keyword is no longer accepted to initialize instances of {class}`fwdpy11.DiploidPopulation`.
{pr}`676`
* {meth}`fwdpy11.TreeIterator.nodes` no longer takes an argument.
{pr}`678`
* The type of {attr}`fwdpy11.Mutation.g` changed from an unsigned integer to a signed integer.
This change has no practical consequence to user code written in Python.
{pr}`656`
{pr}`670`

New features

* The dominance of a mutation may now be specified by a function.
See {ref}`mutationdominance_vignette`.
{pr}`590`
{pr}`629`
{pr}`630`
* Add {meth}`fwdpy11.TableCollection.build_indexes`.
{pr}`651`

Improved IDE and editor integration

* Several key classes and functions were reimplemented.
They are now Python layers on top of the C++.
These changes allow better type hinting and make the docstrings more easily discoverable, resulting in `jedi`, etc., being better able to use them for auto completion and other tasks.
{pr}`676`
{pr}`677`
{pr}`678`

Packaging changes

* The build system is now PEP 517/518 compliant.
{commit}`cfd95f57e97d0fff6d4d87d06bd280d2f58ea545`
* `setup.py` no longer imports `pybind11`.
{pr}`634`

Bug fixes

* Fixed bugs in experimental features involving simulating neutral mutations during simulations recording ancient samples.
These fixes make these features less experimental and part of the API now.
{pr}`643`
{pr}`647`
{pr}`650`
* Improved input parameter validation for {func}`fwdpy11.evolvets`.
{pr}`649`
* Fixed a bug where mutations on branches generated by `msprime` had invalid origin times, leading to exceptions when calling {meth}`fwdpy11.DiploidPopulation.dump_tables_to_tskit`.
{pr}`656`
{pr}`670`

Deployment changes

* Pushes to `main` and new releases now trigger updates to a Docker image.
See {ref}`sec_deployment`.
{pr}`652`
{pr}`663`
{pr}`671`
{pr}`672`
* Binary wheels are automatically deployed for macOS and Linux for new releases.
{pr}`669`

Documentation changes

* The manual is now built with [jupyter book](https://www.jupyterbook.org). {pr}`653`.
* The manual is now longer hosted on Read The Docs.
It has been moved [here](https://molpopgen.github.io/fwdpy11) and is automatically deployed by GitHub actions.
{pr}`654`.

API breakage:

* Simulation without tree sequence recording is no longer supported. 607

Bug fixes:

This release fixes two bugs.
Neither bug would affect results.
Rather, they affect the behavior of some advanced features.

* Explicit initialization of a data structure used for simplification is now always done. 626 627
* Simplification is now allowed to occur after a single generation. 624 627

New features:

* Recombination breakpoints can be restricted to integer positions. 612
* Improved methods for decoding `tskit` meta data. 609

.. note:

The meta data decoding is still a moving target/work in progress.
We anticipate further changes as we get a better idea of what works well/is most useful.

This release also includes several updates to dependencies, documentation, and CI testing.
These changes are collected under the `0.12.0` milestone on `GitHub`.

Point release.

Behavior changes:

* The events passed to :class:`fwdpy11.DiscreteDemography` are now sorted stably
by time. 598

Documentation changes:

* Fixed documentation for :class:`fwdpy11.SetMigrationRates`. 603

Back end changes:

* Cleanup some parts of the code base. 604
* Make the C++ back-end of :class:`fwdpy11.MassMigration` have the same initialization
semantics as other demographic events. 605

Point release.

Bug fixes:

* Fix some errors in :class:`fwdpy11.DemographyDebugger`. 594

Testing changes:

* We now use GitHub actions instead of Travis. 593

Documentation changes:

* We now use ``jupyter-sphinx`` to execute code in the manual. 597