CHANGES.rst

What's New

0.5.2 (2017-08-10)

This is a minor release with a new feature, bug fixes and performance improvements.

• ENH: Add ternary isothermal phase diagram plotting. ( 98 ).
• FIX: sympy 1.1 compatibility ( 108 ).
• ENH/FIX: Make equilibrium Datasets serializable to netCDF ( 111 ).
• FIX: Raise an error if invalid keyword arguments are passed to Database.write ( 117 ).
• ENH/DOC: Remove log.py module ( 104 ).
• FIX: Mistake in the Cementite Analysis example ( 91 ).

0.5.1 (2017-05-12)

This is a minor release with bug fixes.

• FIX: Custom Models involving certain mathematical constants will compile. Fixes 91.
• FIX: Undefined symbols in CompiledModel are automatically set to zero. Fixes 90.

0.5 (2017-05-04)

This is a major release with bug fixes and performance improvements.

• Python 3.6 is now supported. Python 3.3 support has been dropped.
• The equilibrium solver is now significantly faster and more robust. A new Cython-based implementation of the Model class, CompiledModel, has virtually eliminated cold-start calculation time.
• Cython is now a run-time and build-time dependency. Obsolete dependencies have been removed. Windows is still supported with the caveat that users will need to install the Microsoft Visual C++ Build Tools to get a working C compiler.
• The [pycalphad paper](http://doi.org/10.5334/jors.140) has been published.
• The progress bar has been removed along with the dependency on tqdm.
• ENH: Raise warning if unused kwargs are passed to equilibrium
• ENH: TDB compatibility: All characters after command delimiters should be ignored.
• FIX: Fix solver when sum of compositions > 1
• DOC: calculate: Add default pdens value to docstring. Fixes 85.
• FIX: Indexing errors ( 63 ).
• FIX: eqsolver: Handle component index correctly when VA is not last component in alphabetical order. Fixes 62.
• ENH: calculate/equilibrium: Add parameters kwarg to allow users to override Database FUNCTIONs.
• DOC: Add Getting Help section to readme and docs.
• FIX: binplot: Fix ordering of phase labels and colors.
• tdb: Make ELEMENT grammar more strict to catch typos easier. Fixes 57.
• ENH: Caching rewrite and performance increase. Database objects are now hashable.
• ENH: calculate: Performance enhancements via profiling.
• ENH: equilibrium: Break computation up into parallelizable pieces using dask.

0.4.2 (2016-08-26)

This is a minor feature release with one breaking change. * There is now support for the Xiong magnetic model (Xiong et al, Calphad, 2012), two-state liquid-amorphous model, and Einstein model in the Model class. TDB support has been extended where necessary. * ENH/BRK: Model: Add 'contributions' class attribute to make it easier for users to define custom energetic contributions. The API for custom contributions has changed; the old method will no longer work. * FIX: equilibrium: Correctly use custom models during property calculation with output keyword argument.

0.4.1 (2016-08-08)

This is a minor bug fix release.

• Python 3.3 support has been dropped. See 46.
• Documentation has been transitioned to a new domain, [https://pycalphad.org](https://pycalphad.org). See 47.
• BLD: Exclude xarray 0.8 from dependencies since it has a regression. (Newer versions are fine.)
• DOC: Automated project documentation building and deployment via Travis CI.

0.4 (2016-08-03)

This is a major release with bug fixes and performance improvements.

• The equilibrium solver core has been rewritten, resulting in a significant increase in robustness and accuracy, particularly for chemical potential calculation with miscibility gaps. See 43.
• For performance, dask-powered multiprocessing is now used to parallelize equilibrium calculations. Because of this, dask and dill are now dependencies.
• Database and Model objects can now be pickled on all supported platforms, fixing a multiprocessing issue.

0.3.6 (2016-06-01)

This is a minor release with bug fixes and performance improvements.

• Fix installation problem on Windows when using Anaconda.
• Add new compiled backend for phase models. This new backend provides a significant performance improvement.
• Experimental support for the numba library has been removed.

0.3.5 (2016-05-14)

This is a minor bug fix release.

• tdb: Fix TDB parsing errors on recent (>=2.1) versions of pyparsing.
• equilibrium: Improve convergence and numerical stability of solver. Fix potential sign error in Hessian matrix. Support mapping over two composition variables at once. An error is now raised if a calculation specifies components not in the Database.

0.3.4 (2016-04-28)

This is a minor bug fix release.

• Model: Support the use of the absolute value function in the energy function.

0.3.3 (2016-04-21)

This is a minor release with bug fixes and performance improvements.

• equilibrium: Significant improvements to the speed and accuracy of the solver. There is still some work to do for step and map calculations, planned for 0.4.
• Model: Numerical accuracy improvement for the magnetic model 40.
• Database: Improvements to TDB writing, particularly for order-disorder models.
• Database: Support for reading diffusion mobility databases. Kinetic simulations are not on the roadmap, but this makes it easier to manipulate diffusion data. Pull requests improving pycalphad's support for kinetic calculations are welcome.

0.3.2 (2016-02-22)

This is a minor bug fix release.

• equilibrium: Fix a bug causing calculations at multiple temperatures to fail in multi-component systems. Thanks to Ali for reporting.
• equilibrium: More numerical robustness improvements. (Global search now satisfies the strong Wolfe conditions on every iteration.) Further performance improvements will come to this soon.
• pycalphad now depends on pyparsing<2.1.0 pending resolution of 38.

0.3.1 (2016-02-18)

This is a minor bug fix release.

• Model: Make the curie_temperature attribute work when dealing with the order-disorder model.
• equilibrium: Fix a bug involving the output keyword argument in multi-phase calculations.

0.3 (2016-02-17)

This is a major release with new features and fixes. It is very likely that if you will need to update code to be compatible with this version.

• Breaking change: Removed residuals module and the deprecated energy_surf routine.
• Breaking change: Removed ternary isotherm plotting for now, pending a rewrite.
• Breaking change: The refstates module has been renamed to refdata.
• Breaking change in Database: Removed typedefs member.
• binplot: Completely rewritten to use the new equilibrium engine. See also the new companion function eqplot. Breaking change: The API for calling binplot has also been completely changed.
• Database: to_file learned a groupby keyword argument for changing how PARAMETERs are sorted. Loading a TDB will now raise ValueError if the file contains duplicate FUNCTIONs. The TDB writer now generates output more conformant with Thermo-Calc.
• equilibrium: Substantively rewritten for robustness and accuracy. Users will notice a difference, especially for dilute calculations. Unfortunately it's still a bit slow; fixing that will be a focus of the 0.3.x cycle. See 37. Learned a output keyword argument for specifying additional equilibrium properties to compute.
• The tqdm library is now a dependency. It adds progress bar support to equilibrium.
• Model: Added constituents, phase_name and site_ratios attributes, in analogy with Phase objects. This makes it easier to interact with the sublattice model without having to keep Database objects around. Added a degree_of_ordering (abbreviation DOO) property. Only has meaning for phases with sublattice ordering. Added a curie_temperature (abbreviation TC) property. Only nonzero for phases with magnetic ordering.
• calculate: Learned a broadcast boolean keyword argument for turning broadcasting off. This is useful for computing many different system configurations in a pointwise fashion, when there's no obvious way of expressing the calculation as a traditional "step" or "map".
• The xray dependency was renamed to xarray. The change should be transparent to users when updating.

0.2.5 (2015-12-22)

This is a minor release with new features and bug fixes.

• Breaking change in Model: All mixing attributes have been renamed from MIX_{attr} to {attr}_MIX.
• Early support for reference states has been added to the refstates module. The reference molar Gibbs energies of the pure elements according to the 1991 SGTE standard can be found in pycalphad.refstates.SGTE91.
• Database now has file import/export support with to_file, from_file, from_string and to_string. Currently TDB is the only supported format, but more can now easily be added in the future. The function for extending pycalphad with new formats is Database.register_format. Loading databases with the default constructor, i.e., Database('file.tdb'), will continue to work.
• Equivalence comparison support for Database and Model. For example, if dbf is a Database, dbf == Database.from_string(dbf.to_string(fmt='tdb'), fmt='tdb'). Equivalent Database objects should always produce equivalent Model objects. We have tests for this, but if you find a case where this isn't true, it's a bug and can be reported on the issue tracker.
• A new sampling algorithm for equilibrium calculation, based on the scrambled Halton sequence, has been implemented. It should improve performance for multi-component systems once some other improvements have been finalized. For now, users will probably not notice a difference.
• Model: Added CPM_MIX attribute for molar isobaric heat capacity of mixing.
• Many unit tests have been cleaned up and streamlined, with test coverage back up above 80%.

0.2.4 (2015-11-18)

This is a minor release with bug fixes and performance improvements.

• Optional, experimental support for numba has been added to calculate. If numba>=0.22 is installed and calculate is directly called without the mode keyword argument, a numba-optimized function will be generated for the calculation. You can force the old behavior with mode='numpy'. equilibrium does not currently use this code path regardless.
• A performance improvement to how lower_convex_hull computes driving force gives a nice speedup when calling equilibrium. There's still a lot of room for improvement, especially for step/map calculations.
• Piecewise-defined functions are now lazily-evaluated, meaning only the values necessary for the given conditions will be computed. Before, all values were always computed. Users will notice the biggest difference when calculating phases with the magnetic model.
• Fix a small but serious bug when running tinydb v3 with pycalphad ( 30 ).
• Fix a platform-dependent crash bug when using binplot ( 31 ).
• Support for numexpr has been removed.
• The documentation on ReadTheDocs should be building properly again ( 26 ).

0.2.3 (2015-11-08)

This is a minor release with bug fixes and performance improvements.

• Autograd is now a required dependency. It should be automatically installed on upgrade.
• The magnetic contribution to the energy has been improved in performance. For some users (mainly Fe or Ni systems), the difference will be dramatic.
• Numerical stability improvements to the energy minimizer ( 23 ). The minimizer now solves using exact Hessians and is generally more robust. pycalphad.core.equilibrium.MIN_STEP_LENGTH has been removed. There are still issues computing dilute compositions; these will continue to be addressed. Please report these numerical issues if you run into them because they are difficult to find through automated testing.
• Automated testing is now enabled for Mac OSX and Windows, as well as Linux (previously enabled). This should help to find tricky bugs more quickly. (Note that this runs entirely on separate infrastructure and is not collecting information from users.)

0.2.2 (2015-10-17)

This is a minor bugfix release.

• Numerical stability improvements to the energy minimizer ( 23 ). If you're still getting singular matrix errors occasionally, you can try adjusting the value of pycalphad.core.equilibrium.MIN_STEP_LENGTH as discussed in the issue above. Please report these numerical issues if you run into them because they are difficult to find through automated testing.
• Fixes for the minimizer sometimes giving type conversion errors on numpy 1.10 ( 24 ).

0.2.1 (2015-09-10)

This is a minor bugfix release.

• Composition conditions are correctly constructed when the dependent component does not come last in alphabetical order ( 21 ).

0.2 (2015-08-23)

This is a big release and is largely incompatible with 0.1.x. This was necessary for the move to the new equilibrium engine. 0.2.x will be the last "alpha" version of pycalphad where APIs are broken without notice. 0.3 will begin the "beta" cycle where API stability will be enforced.

• pycalphad now depends on numpy>=1.9 and xray
• New unified equilibrium computation interface with equilibrium function. Features point, step and map calculation for multi-phase, multi-component problems. Time performance is a known issue. A typical calculation will take 3-5 minutes until it's fixed.
• Ellipsis or ... can be used in the phases argument of equilibrium to mean "all phases in a Database".
• pycalphad.eq is renamed to pycalphad.core
• energy_surf is now deprecated in favor of the new xray-based calculate. It's possible to convert xray Datasets to pandas DataFrames with the .to_dataframe() function.
• The Equilibrium class has been removed without deprecation. The old engine worked unreliably. Use the new equilibrium routine instead.
• The Model class has been streamlined. It's now much easier to modify a Model by accessing the Model.models member dict. Changes to models will be reflected in Model.ast, Model.energy, etc.
• Adding a property attribute to a subclass of Model automatically makes it available to use in the output keyword argument of calculate. This is useful for computing properties not yet defined in Model.
• Experimental support for model parameter fitting is available in the residuals module. It requires the unlisted dependency lmfit to import.
• BUG: tdb: Sanitize sympify input and clean up pyparsing tracebacks inside parser actions.
• BUG: Always alphabetically sort components listed in interaction parameters ( 17 ).
• ENH: V0 TDB parameter support
• ENH: Model: Symbol replacement performance improvement during initialization.
• TST: Test coverage above 80%

0.1.1.post1 (2015-04-10)

• Fixes for automated test coverage
• Add funding acknowledgment

0.1.1 (2015-04-09)

• Single-source version support with Versioneer

0.1 (2015-04-09)

• Initial public release