Releases | Open Source Science

Major Changes:

pySIPFENN can now handle ONNX models with vector outputs (e.g., multi-property/multi-taks/MTL models)! This was done by adjustment of the low-level makePredictions function, which now automatically populates predictedProperties list then used by result-outputting functions. This change does maintain backwards-compatibility, so no workflow based around single-property models needs to be adjusted. In a future release, the naming scheme will be possible to be automatically overridden from the level of models JSON / YAML definitions.

Minor Changes:

README and documentation updates; listing new information and pointing to the up-to-date scientific articles.
Small bugfix by @ricardonpa in https://github.com/PhasesResearchLab/pySIPFENN/pull/22
Official support for Intel MacOS has been dropped due to GitHub deprecating the test runners.

Full Changelog: https://github.com/PhasesResearchLab/pySIPFENN/compare/v0.16.2...v0.16.3

- Python
Published by amkrajewski 12 months ago

Minor Changes:

The OPTIMADEAdjuster model tuning class now includes more explicit provenance tracking through its references attribute, populated if the provider response includes "relations" to the references. As of now, many popular providers do not include these, but some, like alexandria, can be used and should populate references with a list of lists of DOI strings.
The KS2022_randomSolutions's optional metadata dictionary, returned when returnMeta=True is passed to generate_descriptor function, now includes a list of KS2022 featurizations of each supercell expansion (i.e., iteration) under the individualResults field, which can be used in addition to the converged global ensemble. Among several use cases, users can use these to run ML models over subsets of the global ensemble and look at the prediction distributions to gain additional insights. E.g.:
KS2022_randomSolutions implementation and code style have been generally improved.
Appropriate documentation and tests were added.

Full Changelog: https://github.com/PhasesResearchLab/pySIPFENN/compare/v0.16.1...v0.16.2

- Python
Published by amkrajewski over 1 year ago

Minor Changes:

Mitigate pymatgen's incompatibility (currently preventing installation) with numpy>=2 by setting the maximum version
Added a convenience function in misc for patching pymatgen's core/periodic_table.json for exotic elements like Livermorium of Hessium.
Added a simple cubic (SC) prototype of Po to the library.
Other minor updates.

Full Changelog: https://github.com/PhasesResearchLab/pySIPFENN/compare/v0.16.0...v0.16.1

- Python
Published by amkrajewski over 1 year ago

This version introduces 3 exciting changes! (1) The all new ModelAdjusters submodule automates tuning and can fetch data directly from OPTIMADE API; (2) A new manuscript detailing advantages of our featurization tools has been put on arXiv:2404.02849; and (3) the name of the software was updated to python toolset for Structure-Informed Property and Feature Engineering with Neural Networks to retain the pySIPFENN acronym but better reflect our strengths and development direction.

Major Changes:

Submodule of ModelAdjusters has been set up for all kinds of model adjusting efforts.
The LocalAdjuster implements local model tuning, plotting of results, and hyperparameter matrix search.
The OPTIMADEAdjuster class combines it with the powerful OPTIMADE API to automate data fetching. Now, you can quickly ```python from pysipfenn import Calculator, OPTIMADEAdjuster c = Calculator(autoLoad=False) c.loadModels("SIPFENNKrajewski2022NN30") ma = OPTIMADEAdjuster(c, model="SIPFENNKrajewski2022NN30",
provider="mp", targetPath=("attributes", "mpstability", "ggagga+u", "formationenergyperatom"), device="mps" # MPS is for Apple M-series GPU )

ma.fetchAndFeturize( 'elements HAS "Hf" AND elements HAS "Mo" AND NOT elements HAS ANY "O","C","F","Cl","S"', parallelWorkers=4) ma.adjust()

ma.plotStarting() # See the starting performance ma.plotAdjusted() # See the adjusted performance or to perform a hyperparameter search, replace the `ma.adjust()` with:python ma.matrixHyperParameterSearch() ma.adjust(learningRate=0.0001, optimizer='AdamW', weightDecay=1e-05, epochs=37) ``` - The new manuscript on Efficient Structure-Informed Featurization and Property Prediction of Ordered, Dilute, and Random Atomic Structures has been uploaded to arXiv:2404.02849 and will be submitted to journal in a couple days after comments from collaborators.

Minor Changes:

Added writeDescriptorsToNPY function to streamline persisting feature data into NumPy for our end-users. Appropriate tests were added. Thanks @rdamaral for making this contribution!
Improved numerous docstrings.
Random solution featurizer now exits gently on KeyboardInterrupt
The LocalAdjuster and OPTIMADEAdjuster were (optionally) connected to ClearML for neat tracking of ML training histories.
Minor bugfixes in several spots.

New Contributors

@rdamaral made their first contribution in https://github.com/PhasesResearchLab/pySIPFENN/pull/15

Full Changelog: https://github.com/PhasesResearchLab/pySIPFENN/compare/v0.15.1...v0.16.0

- Python
Published by amkrajewski almost 2 years ago

pysipfenn - v0.15.1

Major Changes:

The printout of Calculator initialization, model parsing, prototype parsing, etc., is now colorized (granted verbose=True) for quick and effortless reading of critical settings and information.
Model download is now handled by our in-house-maintained pysmartdl2, instead of pySmartDL. It allows us to better test CI with modern Python versions and ensure long term stability.

Minor Changes:

Requires pymatgen version 2024.2.20, which fixed a serious security issue in pymatgen.io.
Small bug fixes for two rare cases.
Workshop materials in examples updated to be compatible with the current pymatgen version.
Minor style improvements.

Full Changelog: https://github.com/PhasesResearchLab/pySIPFENN/compare/v0.15.0...v0.15.1

- Python
Published by amkrajewski almost 2 years ago

pysipfenn - v0.15.0

Welcome to pySIPFENN v0.15, which is our biggest singular jump since 2020 spanning 196 commits since v0.13.0 🎉 It covers improvements in nearly every place of the codebase, including new features, better performance and more convenient high-level API. Two key new features are (1) a neat prototype library (v0.14) simplifying the handling of atomic structures, and (2) random solid solution (RSS) featurizer / descriptor calculator (v0.15), which allows you to featurize chemical composition occupying a prototype structure.

Now, you can efficiently utilize pySIPFENN to, for instance, featurize high entropy alloys (HEAs) occupying BCC, FCC, C14, and C15 structures. Have a look below for details!

Major Changes:

Random Solid Solution Featurization

KS2022 Random Solution Featurization (KS2022_randomSolutions) added by @amkrajewski (mostly in https://github.com/PhasesResearchLab/pySIPFENN/pull/10), which allows users to quickly obtain KS2022 feature vector corresponding to a random solid solution with composition comp occupying arbitrary structure struct (including library BCC, FCC, HCP) through iterative expansion of ensemble of local chemical environments (LCEs) until all features, i.e., statistics over LCEs, and composition converge onto stable values.
- This method is philosophically similar to the SQS approach (10.1103/PhysRevLett.65.353), which one can generate with Alloy Theoretic Automated Toolkit (ATAT) (10.1016/j.calphad.2013.06.006) or approximate with sqsgenerator; however, here, we are not only encoding the correlations between anonymous species types but also (1) consider differences between them, thus, e.g., solutions of elements with similar electronic configurations will converge faster) and (2) allow arbitrary complexity of the chemical composition under a single methodology.
- It should also be better at capturing randomly occurring uncommon extreme-case events, which may not occur in low-correlation cases.
- We have tuned the default values of the method for complex cases of (a) high entropy alloys (HEAs) with 6+ components and (b) multicomponent steels with several minor alloying elements.
Added matching tests for all methods of KS2022_randomSolutions featurizer. Added documentation for all tests, so that they can serve as runnable examples.
Added complete API documentation of all methods and all parameters, with both meaning and motivation, for KS2022_randomSolutions.
Added top-level Calculator.calculate_KS2022_randomSolutions() and Calculator.runModels_randomSolutions() for conveniently calling everything on complex problems, even with mixed-type inputs like: python c.calculate_KS2022_randomSolutions( ['FCC', myDistortedBCC, 'BCC', 'HCP'], ['WMo', Composition.from_weight_dict({'Mo': 20, 'W': 70, 'Zr': 10}), 'FeNi', 'CrNi'], mode='parallel', max_workers=4)

Prototype Library:

The new prototype library functionality allows you to store commonly used structures in a consistent fashion and pleasant schema under misc/prototypeLibrary.yaml file in your pySIPFENN installation. It is initialized alongside every Calculator instance.
Parsing custom libraries is very easy and can be done from a file in your directory or from a remote repository like Zenodo! Simply use the parsePrototypeLibrary to fetch it. Or, to append your library with an external one and persist it your installation, use appendPrototypeLibrary. ```yaml
- name: BCC origin: https://www.oqmd.org/materials/prototype/A2_W POSCAR: | W 1.0 -1.58250 1.58250 1.58250 1.58250 -1.58250 1.58250 1.58250 1.58250 -1.58250 W 1 Direct 0.00000 0.00000 0.00000 ```
Added complete API documentation of all methods and all parameters, with both meaning and motivation, for everything prototypeLibrary-related.
Added matching tests for all new prototypeLibrary-related methods. Added documentation for all tests, so that they can serve as runnable examples.

General:

Complete overhaul of the documentation in terms of consistent styling, type-hinting, and extent of the content. Most functions can be well-understood just by looking at information displayed by IDE like PyCharm or VSCode.
The Calculator class now can self-destruct and deallocate by call to its destroy() function, allowing users to better manage memory used in calculations on low-power systems.
Performance improvements in chemical attributes calculation of all KS2022-calculating featurizers.
Performance improvements and minor fixes in KS2022_dilute featurizer.
Performance and feature improvements in the modelExporters, including imports optimization so that are now they only run when needed by given exporter class.
Optimized testing workflows in terms of events triggering them and general performance.
Improved testing clarity and platform compatibility, by splitting them into individual workflows.
Dependencies were analyzed for compatibility and set in a way to ensure long-term maintainability and near-future compatibility with Python 3.12.
Added instructions for contributing to pySIPFENN, explaining philosophy of the software and several design choices.

Minor Changes:

Improved printouts from Calculator initialization and current state reporting.
Improved verbosity handling in Calculator instances.
CITATION.cff added for clear citation guidance in the future.
Documentation now includes miscellaneous notes users may find useful.
.gitignore improvements as requested by users.
Added testing for several smaller functions like ward2ks2022, to increase coverage by 1%. Now it is over 95%.
Code style improvements.
Commenting improvements scattered throughout the codebase to make modifying our code easier.
And many more added on the way :)

Notices:

In the near future (likely next release), pySIPFENN will drop official support for Python 3.9, due to (1) noticeably lower performance, (2) deprecation of 3.9 on some platforms (MacOS14), and (3) next release using several pure-Python features added in Python 3.9.
In the near future (likely next release), pySIPFENN will add support for Python 3.12 to keep it up-to-date and take advantage of performance boost. Our codebase is ready for the switch. We are waiting for PyTorch support for it in its stable release.

Full Changelog: https://github.com/PhasesResearchLab/pySIPFENN/compare/v0.13.1...v0.15.0

- Python
Published by amkrajewski about 2 years ago

pysipfenn - v0.13.1

Major Changes

All tests are now documented under API pySIPFENN Tests page with hyperlinks to their sources, acting as minimalistic examples of using the software.

Minor Changes

Improvements to FAQ, docs index, and README.
Polishing of the documentation page and general maintenance.

Full Changelog: https://github.com/PhasesResearchLab/pySIPFENN/compare/v0.13.0...v0.13.1

- Python
Published by amkrajewski over 2 years ago

pysipfenn - v0.13.0

Major Changes:

Per [add] modelExporters by @amkrajewski, 3 model exporter classes have been added to pySIPFENN in the modelExporters module:
- ONNXExporter allowing (1) exporting back to ONNX after models were adjusted to new datasets or new properties (transfer learning), (2) automated simplification of model architecture for improved performance, and (3) adjusting model internal precision to FP16 to reduce its size by half with only minor performance impact.
- TorchExporter to export models to PyTorch which are used internally by pySIPFENN.
- CoreMLExporter to export models to Apple's CoreML format developed for use in their devices, where it provides the most seamless integration with existing apps and can harvest very efficient Neural Engine hardware acceleration. At the same time, it can be used on other platforms as well, such as Linux or Windows. Note that by default, models will be converted to FP16 precision, similar to one of the ONNXExporter options.

The above changes are a step in our effort to make advanced use of pySIPFENN easier for end-users. Next items on the roadmap include (1) automation of transfer learning on small datasets and (2) OPTIMADE integrations, which will make pySIPFENN API a one-stop solution for model fine-tuning.

Minor Changes:

Small improvements in the Calculator object printout with the verbose option (true by default) added to its initialization.
Matching tests were added to the CI pipelines.
dev extra dependencies have been established, alongside appropriate documentation, for all future dependencies that are not required for core pySIPFENN functionalities to keep it as light as possible while not limiting advanced users. One of the future directions will be to make core dependencies lighter.
Model exports and motivations were added to the documentation under Exporting pySIPFENN Models page.

Full Changelog: https://github.com/PhasesResearchLab/pySIPFENN/compare/v0.12.2...v0.13.0

- Python
Published by amkrajewski over 2 years ago

pysipfenn - v0.12.2

This is a minor release that changes the license to LGPLv3 in order to allow for integration with proprietary software developed by the CALPHAD community (shipping pySIPFENN and then calling it from closed-source tools will be allowed) while supporting the development of new pySIPFENN features for all users, as modifications to pySIPFENN (except for models, see below) itself need to be open.
This change does not affect the default pySIPFENN models which are distributed under Creative Commons 4.0 that already comes with no restrictions.
Many thanks to our colleagues from GTT-Technologies and other participants of 50th CALPHAD 2023 conference in Boston for fruitful discussions.

- Python
Published by amkrajewski over 2 years ago

pysipfenn - v0.12.1

Changes: - FIX: This update addresses network loading issues, affecting some SIPFENN models (with Dropout), caused by onnx2torch=1.5.7 recently introducing a new naming schema for the "insides" of ONNX neural networks translated to PyTorch. - Improved testing, including automated benchmarking of featurizer performance across Python versions and platforms.

Full Changelog: https://github.com/PhasesResearchLab/pySIPFENN/compare/v0.12.0...v0.12.1

- Python
Published by amkrajewski over 2 years ago

pysipfenn - v0.12.0

Major Changes:

Automated matrix-testing on Linux / Mac / Windows with Python 3.9 / 3.10 / 3.11 through GitHub Actions CLI. Core functions are tested across all of them, and badges in the README indicate test status after every code change
Automated test coverage analysis through GitHub Actions CI and reporting through Codecov service
Many improvements in the testing procedures and additional tests bringing the coverage up from 74% (in v0.11.0) to 86%.
(affects backward compatibility) The models download and run functions built around MxNet, which have been deprecated for a while since v0.9.0, have been removed.
(affects backward compatibility) Small change in the behavior of the runModelsdilute() function. Now it expects the _descriptor / feature vector input "KS2022" to run the "KS2022dilute" _descriptor calculator / featurizer. This change is due to a few new featurizers being in the works, including for approximating random solid solutions and quasicrystals, and all of them will use the "KS2022" descriptor, so this will make workflows much more clear.
Added official Python 3.11 support and tests using it.
Added small automated benchmarking on Linux using different Python versions so that users can select one that works best. Generally, Python 3.10 is the fastest. Across all 3 featurizers (KS2022, KS2022_dilute, and Ward2017), relative to the Python 3.9 baseline, 3.10 is around 35-40% faster, while 3.11 is 25-30% faster, based on the tests in GitHub Actions CI.

Minor Changes:

Minor bug fixes, mostly in tests, not the user code.
The wget dependency has been removed, as we moved to the multi-threaded pySmartDL package for model download.
Documentation updates.

Full Changelog: https://github.com/PhasesResearchLab/pySIPFENN/compare/v0.11.0...v0.12.0

- Python
Published by amkrajewski almost 3 years ago

pysipfenn - v0.11.0post1

Minor Changes:

Documentation and README updates.
Minor bug fixes.

- Python
Published by amkrajewski almost 3 years ago

pysipfenn - v0.11.0

Major Changes: - Model download from Zenodo is now multi-threaded. Users should see 15x faster speeds. - Added an FAQ page to the documentation. - KS2022 can filter out all structure-independent features to better compare polymorphs. - Printing Calculator object shows the models' location and relevant current state information.

Minor Changes: - Minor bug fixes. - It's now possible to load a single model with loadModels(); similar to downloadModels(). - Offline documentation available inside the package. - Documentation updates.

Full Changelog: https://github.com/PhasesResearchLab/pySIPFENN/compare/v0.10.3...v0.11.0

- Python
Published by amkrajewski almost 3 years ago

pysipfenn - v0.10.3

Changes in this version: - Some functionality upgrades related to handling models and files in environments with no write access to the pySIPFENN package directory, mostly dedicated towards High-Performance Computers (HPCs) users. - Updates to the documentation. The core of pysipfenn is entirely and extensively described. The descriptor calculators are mostly covered. - Final version of the workshop notebook (only minor changes) - Minor bugfixes

New Contributors * @shimanek made their first contribution in https://github.com/PhasesResearchLab/pySIPFENN/pull/3

Full Changelog: https://github.com/PhasesResearchLab/pySIPFENN/compare/v0.10.2...v0.10.3

- Python
Published by amkrajewski almost 3 years ago

pysipfenn - v0.10.2

This minor version release has no effect on the code functionalities, however it significantly expands the documentation for the package, which will now be hosted on Read The Docs page under:

It also significantly expands the code documentation and type hinting. Something that new users should find very helpful. The coverage will be completed in the near future within the planned 0.10.3 release.

Full Commit Changelog: https://github.com/PhasesResearchLab/pySIPFENN/compare/v0.10.1...v0.10.2

- Python
Published by amkrajewski about 3 years ago

pysipfenn - v0.10.1

This is the first version release created and tagged on GitHub, corresponding to a second PyPI release after v0.10.0; although the SIPFENN software has been developed since 2019 by researchers at Penn State. It had 8 internal releases followed by the public release of v0.9.0 along with 2022 paper titled Extensible Structure-Informed Prediction of Formation Energy with improved accuracy and usability employing neural networks published in Computational Materials Science (https://doi.org/10.1016/j.commatsci.2022.111254).

The v0.10.0 has brought many changes, including: - Translation of all code into pure Python, including structure featurization code. - PyPI packaging - New featurization code (KS2022) with up to x10 speed improvement; especially useful for ordered compounds. - New featurization code (KS2022_dilute) working only on dilute structures (both pure elements and compounds) with up to x50 speed improvement. - General improvements in the handling of models and data - Many more in 70+ commits (Full Changelog from v0.9 to 0.10: https://github.com/PhasesResearchLab/pySIPFENN/commits/v0.10.1)

These changes will be described in a journal article in near future, which will appear in the README.md after its publication.

- Python
Published by amkrajewski about 3 years ago

Recent Releases of pysipfenn

pysipfenn - v0.16.3

Major Changes:

Minor Changes:

pysipfenn - v0.16.2

Minor Changes:

pysipfenn - v0.16.1

Minor Changes:

pysipfenn - v0.16.0

Major Changes:

Minor Changes:

New Contributors

pysipfenn - v0.15.1

Major Changes:

Minor Changes:

pysipfenn - v0.15.0

Major Changes:

Random Solid Solution Featurization

Prototype Library:

General:

Minor Changes:

Notices:

pysipfenn - v0.13.1

Major Changes

Minor Changes

pysipfenn - v0.13.0

Major Changes:

Minor Changes:

pysipfenn - v0.12.2

pysipfenn - v0.12.1

pysipfenn - v0.12.0

Major Changes:

Minor Changes:

pysipfenn - v0.11.0post1

Minor Changes:

pysipfenn - v0.11.0

pysipfenn - v0.10.3

pysipfenn - v0.10.2

pysipfenn - v0.10.1