Changelog

0.8.6.dev8+gb82465a (development)

0.8.5 (2021-08-09)

Improvements

  • Migrate to the new pycalphad internal APIs for the minimizer and calculate utilities (@bocklund - issue 201 and issue 206)

  • Improve AICc formulation to have more consistent behavior when the number of data points is small (@bocklund - issue 205)

  • Enable specifying custom pycalphad Model classes in MCMC simulations via the phase models data file (@bocklund - issue 202)

0.8.4 (2021-06-06)

Improvements

  • Migrate to pycalphad’s new minimizer (@bocklund - issue 196)

  • Fix a memory issue in large sublattice models by using the new minimizer to implement constrained driving forces (@bocklund - issue 196)

  • Fix a regression where plot_interaction and plot_endmember re-used reference labels and markers (@bocklund - issue 187)

  • Parameter selection now adds and fits only phases which in the phase models and are active (@bocklund - issue 188)

  • Fix a bug where plot_interaction and plot_endmember would raise an error when axes were not passed explicitly (@bocklund - issue 191)

  • Fix a bug where reference keys were assumed to be present in dataplot, plot_interaction and plot_endmember (@bocklund - issue 191)

  • Documentation: Rewrite phase diagram datasets section, switch paper references to RST citations, reorganize sections into how-to/reference material appropriately (@bocklund - issue 192)

  • Documentation: Switch from sphinx_rtd_theme to furo theme (@bocklund - issue 193)

Deprecations

  • pycalphad versions lower than 0.9.0 are no longer supported.

0.8.3 (2021-05-08)

Improvements

  • Fix a bug where excluded model contributions could be double counted (@bocklund - issue 181)

  • Support internal API changes for pycalphad 0.8.5 (@bocklund - issue 183)

  • Fix a regression for ZPF error calculations introduced in issue 181 where prescribed phase compositions of stoichiometric phases that used to work no longer work because the phase composition of a stoichiometric phase may be unsatisfiable (@bocklund - issue 185).

  • Fix a bug in ZPF error calculations where stoichiometric phases could give incorrect energies for exact equilibrium when prescribed mass balance conditions could not be satisfied. The fix now computes the driving force exactly in all cases for stoichiometric compounds. (@bocklund - issue 185)

0.8.2 (2021-05-05)

Improvements

Deprecations

  • plot_parameters is deprecated in favor of plot_interaction and plot_endmember (@bocklund - issue 177)

0.8.1 (2021-04-22)

This is a minor release that fixes a performance regression and retires unused utility code.

  • Fixes a performance regression in _sample_solution_constitution that could cause getting ZPF data for MCMC to be extremely slow. (@bocklund - issue 174)

  • The flexible_open_string and add_bibtex_to_bib_database utilities were removed. Both were unusued in ESPEI. ESPEI no longer depends on bibtexparser. (@bocklund - issue 171)

0.8 (2021-04-19)

This is a major release with bug fixes and a backward compatible public API, but breaking changes in the behavior of parameter selection and MCMC parameter estimation. Some internal functions were deprecated.

Improvements

  • Revamped internal logging. For users, ESPEI now has namespaced logging and filters out all non-ESPEI logs (e.g. dask and matplotlib). This change also fixed a bug where changing the verbosity in Jupyter was not taking effect. (@bocklund - issue 165)

  • Fixed a bug where scalar weights of non-equilibrium thermochemical datasets were not being broadcasted correctly and raised errors. (@bocklund - issue 154)

  • Fixed a bug where non-equilibrium thermochemical datasets using broadcasted temperatures and compositions were broadcasted against the values incorrectly. (@bocklund - issue 154)

  • Allow disabling datasets semantically using disabled: true in JSON datasets. (@bocklund - issue 153)

  • Users can now pass custom SER reference data to override SER phases, mass, H298, and S298 for existing elements or new elements. Includes better warnings for common errors when the SER data is incompatible with the phases being fit. (@bocklund - issue 158)

  • Fixed a bug in computing activity error in MCMC where species were not correctly generated from the pure comopnents. (@bocklund - issue 152)

Breaking changes

  • Driving forces in ZPF error are now computed from local minimum solutions rather than global minimum solutions. This change significantly improves the convergence for any phases with stable or metastable miscibility gaps. It also prevents users from prescribing phase composition conditions that cannot be satisfied. See the linked GitHub issue for a detailed description of the rationale and implementation of this change. (@bocklund - issue 151)

  • Removed automatically added ideal exclusions, which was deprecated in ESPEI 0.7. Non-equilibrium thermochemical data should use the excluded_model_contributions key to exclude idmix, mag or other model contributions. (@bocklund - issue 168)

  • Remove deprecated mcmc.py (@bocklund - issue 164)

Deprecations

  • Setting mcmc.scheduler to the string "None" to get a serial scheduler is deprecated. Users should use null in YAML/JSON or None in Python.

  • Deprecated multiplot and eqdataplot in favor of having users compose binplot and dataplot. pycalphad’s binplot is much faster than multiplot. The extra functional call added is worth removing the maintenance burden and allows users to understand more explictly the difference between plotting data and plotting the calculated phase diagram. The documentation was updated to reflect this change and no longer uses multiplot. (@bocklund - issue 162)

0.7.12 (2021-03-16)

This is a minor bugfix release that updates the SGTE reference state data for carbon and more strictly specifies dependences. No changes to the code were made since 0.7.11.

0.7.11 (2021-03-12)

This is a minor bugfix release with backwards compatible changes.

  • Fix numpy v1.20 deprecations (@bocklund - issue 147)

  • Add dataplot tie-line flag (@bocklund - issue 145)

  • Add corner package to dependencies so the recipes now work without installing extra packages

0.7.10 (2020-11-14)

This is a minor bugfix release that addresses a potential inconsistency with hyphen/underscore usage in dask configuration files (@bocklund - issue 136).

0.7.9 (2020-11-12)

This is a minor maintenance release that automatically disables work stealing (users are no longer required to configure this themselves) (@bocklund - issue 134).

0.7.8 (2020-11-10)

This is a bug fix release with backwards compatible changes.

  • Fix a bug triggered by pycalphad 0.8.4 where the new parameter extraction behavior could break the MCMC sampler (@bocklund - issue 132)

  • Fix a bug where some feature matrices had incorrect shape, stemming from using SymPy.Matrix to symbolically manipulate the data (@bocklund - issue 130)

  • Migrate to tinydb v4+ (@bocklund - issue 126)

0.7.7 (2020-04-11)

This is a minor feature and bug fix release with backwards compatible changes.

  • Preliminary support for thermochemical error for arbitrary properties (@bocklund - issue 124)

  • Update the preferred method for disabling tracefile, probfile, logfile, and no scheduler in YAML to use null instead of "None" (@bocklund - issue 125)

  • Fix a bug in truncate_arrays and optimal_parameters to allow some zeros (@bocklund - issue 122)

  • Enable custom unary reference states for parameter generation with entry_points plugin system (@bocklund - issue 121)

0.7.6 (2020-03-27)

This is a minor bug fix release.

  • Fixes a bug introduced in 0.7.5 for calculating likelihood for phase boundary data under equilibrium failures (@bocklund - issue 120)

  • Since Python 2 was dropped, six has been removed as a dependency (@bocklund - issue 119)

0.7.5 (2020-03-09)

This release includes performance optimizations, bug fixes and new features for MCMC simulations.

  • This version of ESPEI now requires pycalphad 0.8.2 or later for the features below.

  • Fitting subsystems of a large database is explicitly supported and tested for all implemented MCMC data types. Fixes a bug in ZPF error and activity error where having phases in the database that are inactive in the subsystem would raise errors (@bocklund - issue 118).

  • Computing thermochemical error and phase boundary (ZPF) error are now optimized to reduce overhead time in dependencies (@bocklund - issue 117)

  • A new feature for calculating approximate driving force for phase boundary data is implemented, which can give performance improvements of 3x-10x, depending on the system (@bocklund - issue 115)

0.7.4 (2019-12-09)

This release includes small fixes for parameter generation.

  • Excluded model contributions are fixed for models with different sublattice site ratios and for data that are not endmembers (@bocklund - issue 113)

0.7.3 (2019-12-02)

This change includes several new features and performance improvements.

  • Drop Python 2 support (Python 2 is no longer supported on January 1, 2020).

  • Update dask and distributed support to versions >=2. (@bocklund)

  • Users can tweak the AICc penalty factor for each phase to nudge parameter selection towards adding more or fewer parameters based on user modeling intuition. (@bocklund)

  • Allow for tracefile and probfile to be set to None. (@jwsiegel2510)

  • Weighting individual datasets in single phase fitting is now implemented via scikit-learn. (@bocklund)

  • Performance improvements by reducing overhead. (@bocklund)

  • Increased solver accuracy by using pycalphad’s exact Hessian solver. (@bocklund)

  • Support writing SER reference state information to the ELEMENT keyword in TDBs based on the SGTE unary 5 database. (@bocklund)

  • MCMC now calculates the likelihood of the initial parameter set so the starting point can be reasonably compared. (@bocklund)

  • Fixed a bug where mis-aligned configurations and site occupancies in single phase datasets passed the dataset checker (@bocklund)

0.7.2 (2019-06-12)

This is a small bugfix release that fixes the inability to provide the EmceeOptimizer a restart_trace.

0.7.1 (2019-06-03)

This is a significant update reflecting many internal improvements, new features, and bug fixes. Users using the YAML input or the run_espei Python API should see entirely backwards compatible changes with ESPEI 0.6.2.

pycalphad 0.8, which introduced many key features for these changes is now required. This should almost completely eliminate the time to build phases due to the symengine backend (phases will likely build in less time than to call the MCMC objective function). Users can expect a slight performance improvement for MCMC fitting.

Improvements

  • Priors can now be specified and are documented online.

  • Weights for different datasets are added and are supported by a "weight" key at the top level of any dataset.

  • Weights for different types of data are added. These are controlled via the input YAML and are documented there.

  • A new internal API is introduced for generic fitting of parameters to datasets in the OptimizerBase class. The MCMC optimizer in emcee was migrated to this API (the mcmc_fit function is now deprecated, but still works until the next major version of ESPEI). A simple SciPy-based optimizer was implemented using this API.

  • Parameter selection can now be passed initial databases with parameters (e.g. for adding magnetic or other parameters manually).

  • pycalphad’s reference state support can now be used to properly reference out different types of model contributions (ideal mixing, magnetic, etc.). This is especially useful for DFT thermochemical data which does not include model contributions from ideal mixing or magnetic heat capacity. Useful for experimental data which does include ideal mixing (previously ESPEI assumed all data

  • Datasets and input YAML files now have a tag system where tags that are specified in the input YAML can override any keys/values in the JSON datasets at runtime. This is useful for tagging data with different weights/model contribution exclusions (e.g. DFT tags may get lower weights and can be set to exclude model contributions). If no tags are applied, removing ideal mixing from all thermochemical data is applied automatically for backwards compatibility. This backwards compatibility feature will be removed in the next major version of ESPEI (all model contributions will be included by default and exclusions must be specified manually).

Bug fixes

  • Bug fixed where asymmetric ternary parameters were not properly replaced in SymPy

  • Fixed error where ZPF error was considering the chemical potentials of stoichiometric phases in the target hyperplane (they are meaningless)

  • Report the actual file paths when dask’s work-stealing is set to false.

  • Errors in the ZPF error function are no longer swallowed with -np.inf error. Any errors should be reported as bugs.

  • Fix bug where subsets of symbols to fit are not built properly for thermochemical data

Other

  • Documentation recipe added for plot_parameters

  • [Developer] ZPF and thermochemical datasets now have an function to get all the data up front in a dictionary that can be used in the functions for separation of concerns and calculation efficiency by not recalculating the same thing every iteration.

  • [Developer] a function to generate the a context dict to pass to lnprob now exists. It gets the datasets automatically using the above.

  • [Developer] transition to pycalphad’s new build_callables function, taking care of the v.N state variable.

  • [Developer] Load all YAML safely, silencing warnings.

0.6.2 (2018-11-27)

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.

  • [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.

0.6.1 (2018-08-28)

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 that contains some Python code for common utility operations.

  • Add documentation for running custom distributed schedulers in ESPEI

0.6 (2018-07-02)

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 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!)

0.5.2 (2018-04-28)

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.

0.5.1 (2018-04-17)

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.

0.5 (2018-04-03)

  • 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 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.

0.4.1 (2018-02-05)

  • Enable plotting of isothermal sections with data using dataplot (and multiplot, etc.)

  • Tielines are now plotted in dataplot for isothermal sections and T-x phase diagrams

  • Add a useful ravel_conditions method to unpack conditions from datasets

0.4 (2017-12-29)

  • MCMC is now deterministic by default (can be toggled off with the mcmc.deterministic setting).

  • Added support for having no scheduler (running with no parallelism) with the mcmc.scheduler option set to None. This may be useful for debugging.

  • Logging improvements

    • Extraneous warnings that may be confusing for users and dirty the log are silenced.

    • A warning is added for when there are no datasets found.

    • Fixed a bug where logging was silenced with the dask scheduler

  • Add optimal_parameters utility function as a helper to get optimal parameter sets for analysis

  • Several improvements to plotting

    • Users can now plot phase diagram data alone with dataplot, useful for checking datasets visually. This changes the API for dataplot to no longer infer the conditions from an equilibrium Dataset (from pycalphad). That functionality is preserved in eqdataplot.

    • Experimental data points are now plotted with unique symbols depending on the reference key in the dataset. This is for both phase diagram and single phase parameter plots.

    • Options to control plotting parameters (e.g. symbol size) and take user supplied Axes and Figures in the plotting functions. The symbol size is now smaller by default.

  • Documentation improvements for API and separation of theory from the Cu-Mg example

  • Fixes a bug where elements with single character names would not find the correct reference state (which are typically named GHSERCC for the example of C).

  • [Developer] All MCMC code is moved from the paramselect module to the mcmc module to separate these tasks

  • [Developer] Support for arbitrary user reference states (so long as the reference state is in the refdata module and follows the same format as SGTE91)

0.3.1.post2 (2017-10-31)

  • Propagate the new entry point to setup.py

0.3.1.post1 (2017-10-31)

  • Fix for module name/function conflict in entry point

0.3.1 (2017-10-31)

  • ESPEI is much easier to run interactively in Python and in Jupyter Notebooks

  • Reference data is now included in ESPEI instead of in pycalphad

  • Several reference data fixes including support for single character elements (‘V’, ‘B’, ‘C’, …)

  • Support for using multiprocessing to parallelize MCMC runs, used by default (@olivia-higgins)

  • Improved documentation for installing and developing ESPEI

0.3.post2 (2017-09-20)

  • Add input-schema.yaml file to installer

0.3.post1 (2017-09-20)

  • Add LICENSE to manifest

0.3 (2017-09-20)

  • ESPEI input is now described by a file. This change is breaking. Old command line arguments are not supported. See Writing input files for a full description of all the inputs.

  • New input options are supported, including modifying the number of chains and standard deviation from the mean

  • ESPEI is now available on conda-forge

  • TinyDB 2 support is dropped in favor of TinyDB 3 for conda-forge deployment

  • Allow for restarting previous mcmc calculations with a trace file

  • Add Cu-Mg example to documentation

0.2.1 (2017-08-17)

Fixes to the 0.2 release plotting interface

  • multiplot is renamed from multi_plot, as in docs.

  • Fixed an issue where phases in datasets, but not in equilibrium were not plotted by dataplot and raised an error.

0.2 (2017-08-15)

  • New multiplot interface for convenient plotting of phase diagrams + data. dataplot function underlies key data plotting features and can be used with eqplot. See their API docs for examples. Will break existing code using multiplot.

  • MPI support for local/HPC runs. Only single node runs are explicitly supported currently. Use --scheduler='MPIPool' command line option. Requires mpi4py.

  • Default debug reporting of acceptance ratios

  • Option (and default) to output the log probability array matching the trace. Use --probfile option to control.

  • Optimal parameters are now chosen based on lowest error in chain.

  • Bug fixes including

    • py2/3 compatibility

    • Unicode datasets

    • handling of singular matrix errors from pycalphad’s equilibrium

    • reporting of failed conditions

0.1.5 (2017-08-02)

  • Significant error checking of JSON inputs.

  • Add new --check-datasets option to check the datasets at path. It should be run before you run ESPEI fittings. All errors must be resolved before you run.

  • Move the espei script module from fit.py to run_espei.py.

  • Better docs building with mocking

  • Google docstrings are now NumPy docstrings

0.1.4 (2017-07-24)

  • Documentation improvements for usage and API docs

  • Fail fast on JSON errors

0.1.3 (2017-06-23)

  • Fix bad version pinning in setup.py

  • Explicitly support Python 2.7

0.1.2 (2017-06-23)

  • Fix dask incompatibility due to new API usage

0.1.1 (2017-06-23)

  • Fix a bug that caused logging to raise if bokeh isn’t installed

0.1 (2017-06-23)

ESPEI is now a package! New features include

  • Fork https://github.com/richardotis/pycalphad-fitting

  • Use emcee for MCMC fitting rather than pymc

  • Support single-phase only fitting

  • More control options for running ESPEI from the command line

  • Better support for incremental saving of the chain

  • Control over output with logging over printing

  • Significant code cleanup

  • Better usage documentation