Espei

==================

This backwards-compatible release includes several bug fixes and improvements.

* Updated branding to include the new ESPEI logo. See the logo in the ``docs/_static`` directory.
* Add support for fitting excess heat capacity.
* Bug fix for broken potassium unary.
* Documentation improvements for recipes
* pycalphad 0.7.1 fixes for dask, sympy, and gmpy2 should mean that ESPEI should not require package upgrade or downgrades. Please report any installations issues in `ESPEI's Gitter Channel <https://gitter.im/PhasesResearchLab/ESPEI>`_.
* [Developers] ESPEI's ``eq_callables_dict`` is now ``pycalphad.codegen.callables.build_callables``.
* [Developers] matplotlib plotting tests are removed because nose is no longer supported.

==================

This a major release with several important features and bug fixes.

* Enable use of ridge regression alpha for parameter selection via the ``parameter_generation.ridge_alpha`` input parameter.
* Add ternary parameter selection. Works by default, just add data.
* Set memory limit to zero to avoid dask killing workers near the dask memory limits.
* Remove ideal mixing from plotting models so that ``plot_parameters`` gives the correct entropy values.
* Add `recipes documentation <https://github.com/PhasesResearchLab/ESPEI/blob/master/docs/recipes.rst>`_ that contains some Python code for common utility operations.
* Add documentation for running custom distributed schedulers in ESPEI

================

This is a update including *breaking changes to the input files* and several minor improvements.

* Update input file schema and Python API to be more consistent so that the ``trace`` always refers to the collection of chains and ``chain`` refers to individual chains. Additionally removed some redundancy in the parameters nested under the ``mcmc`` heading, e.g. ``mcmc_steps`` is now ``iterations`` and ``mcmc_save_interval`` is now ``save_interval`` in the input file and Python API. See `Writing Input <http://espei.org/en/latest/writing_input.html>`_ documentation for all of the updates.
* The default save interval is now 1, which is more reasonable for most MCMC systems with significant numbers of phase equilibria.
* Bug fixes for plotting and some better plotting defaults for plotting input data
* Dataset parsing and cleaning improvements.
* Documentation improvements (see the `PDF <http://readthedocs.org/projects/espei/downloads/pdf/latest/>`_!)

==================

This is a major bugfix release for MCMC multi-phase fitting runs for single phase data.

* Fixed a major issue where single phase thermochemical data was always compared to Gibbs energy, giving incorrect errors in MCMC runs.
* Single phase errors in ESPEI incorrectly compared values with ideal mixing contributions to data, which is excess only.
* Fixed a bug where single phase thermochemical data with that are dependent on composition and pressure and/or temperature were not fit correctly.
* Added utilities for analyzing ESPEI results and add them to the Cu-Mg example docs.

==================

This is a minor bugfix release.

* Parameter generation for phases with vacancies would produce incorrect parameters because the vacancy site fractions were not being correctly removed from the contributions due to their treatment as ``Species`` objects in ``pycalphad >=0.7``.

================

* Parameter selection now uses the corrected AIC, which further prevents overparameterization where there is sparse training data.
* Activity and single phase thermochemical data can now be included in MCMC fitting runs. Including single phase data can help anchor metastable phases to DFT data when they are not on the stable phase diagram. See the `Gathering input data <http://espei.org/en/latest/input_data.html>`_ documentation for information on how to input activity data.
* Dataset checking has been improved. Now there are checks to make sure sublattice interactions are properly sorted and mole fractions sum to less than 1.0 in ZPF data.
* Support for fitting phases with arbitrary pycalphad Models in MCMC, including (charged and neutral) species and ionic liquids. There are several consequences of this:

- ESPEI requires support on ``pycalphad >=0.7``
- ESPEI now uses pycalphad ``Model`` objects directly. Using the JIT compiled Models has shown up to a *50% performance improvement* in MCMC runs.
- Using JIT compiled ``Model`` objects required the use of ``cloudpickle`` everywhere. Due to challenges in overriding ``pickle`` for upstream packages, we now rely solely on ``dask`` for scheduler tasks, including ``mpi`` via ``dask-mpi``. Note that users must turn off ``work-stealing`` in their ``~/.dask/config.yaml`` file.

* [Developers] Each method for calculating error in MCMC has been moved into a module for that method in an ``error_functions`` subpackage. One top level function from each module should be imported into the ``mcmc.py`` and used in ``lnprob``. Developers should then just customize ``lnprob``.
* [Developers] Significant internal docs improvements: all non-trivial functions have complete docstrings.