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Recent Releases of aimsim

aimsim - AIMSim v2.2.0

AIMSim Minor Release 2.2.0

A new pypi-only, developer-friendly version of aimsim called aimsim_core has been released, which follows the same version numbers as aimsim but does not include the visualization capabilities. This makes it easier to re-use the core functions for distance metrics and featurization.

This minor release also removes support for clustering via kmedoids because the underlying package that supports it has been abandoned and is no longer compatible with Python 3.12

What's Changed

  • Build a minimal dependency, core-only package by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/268
  • Drop k-medioids Clustering by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/269

Full Changelog: https://github.com/VlachosGroup/AIMSim/compare/v2.1.3...v2.2.0

- Python
Published by JacksonBurns almost 2 years ago

aimsim - AIMSim v2.1.3

AIMSim Patch Release 2.1.3

This patch release fixes a small bug in dataset visualization (missing import).

What's Changed

  • Fix Missing import of warnings Inside visualize_dataset.py by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/267

Full Changelog: https://github.com/VlachosGroup/AIMSim/compare/v2.1.2...v2.1.3

- Python
Published by JacksonBurns about 2 years ago

aimsim - AIMSim v2.1.2

AIMSim Patch Release 2.1.2

This patch release fixes compatibility with the latest versions of sklearn.

What's Changed

  • small patches to demo notebook by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/263
  • Update clustering.py for compatibility with latest sklearn by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/265

Full Changelog: https://github.com/VlachosGroup/AIMSim/compare/v2.1.1...v2.1.2

- Python
Published by JacksonBurns about 2 years ago

aimsim - AIMSim v2.1.1

AIMSim Patch Release 2.1.1

This patch release adds support for Python 3.12!

What's Changed

  • Update requirements.txt to avoid pyyaml 3.12 incompatible versions by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/261

Full Changelog: https://github.com/VlachosGroup/AIMSim/compare/v2.1.0...v2.1.1

- Python
Published by JacksonBurns over 2 years ago

aimsim - AIMSim v2.1.0

AIMSim Minor Release 2.1.0

This minor release of AIMSim adds a number of small patches and a new feature: - fixed packaging for compatibility with conda, and now a conda package - added mordredcommunity to support the mordred set of descriptors - refactored SimilarityMeasure to eliminate code duplication - new feature: @ramirandaq's MultipleComparisons Extended Similarity Indices are now supported in AIMSim through the GUI and the configuraiton file. Calculate them with get_extended_similarity_indices in the tasks list.

Changelog

  • AIMSim v2.1.0 by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/260

Full Changelog: https://github.com/VlachosGroup/AIMSim/compare/v2.0.3...v2.1.0

- Python
Published by JacksonBurns over 2 years ago

aimsim - AIMSim v2.0.3

AIMSim Patch Release v2.0.3

This release contains a few small patches, including decreasing the default amount of output when using the verbose=1 option, adding a citation file, adding the MinHash fingerprint, and fixing an issue with Cython 3/PyYaml compatibility.

What's Changed

  • Molecule set verbose fix by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/253
  • add citation file by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/254
  • add the minhash fingerprint by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/255
  • Fix PyYaml Cython 3 Incompatibility Issue by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/258

Full Changelog: https://github.com/VlachosGroup/AIMSim/compare/v2.0.2...v2.0.3

- Python
Published by JacksonBurns over 2 years ago

aimsim - AIMSim v2.0.2

Patch Release: AIMSim v2.0.2

This release clarifies in the documentation and README about usage of mordred and fixes an issue where environments which had mordred installed properly would still face issues running (due to an improper function decorator and missing dependency).

What's Changed

  • Optional mordred Install Cleanup and Documentation by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/252

Full Changelog: https://github.com/VlachosGroup/AIMSim/compare/v2.0.1...v2.0.2

- Python
Published by JacksonBurns about 3 years ago

aimsim - AIMSim v2.0.1

Major Release - AIMSim v2.0

This release of AIMSim includes significant changes to the distribution and packaging. The requirements for the dependencies have been simplified enormously, which should allow AIMSim to be installed in the same virtual environment as a variety of other dependencies.

We recommend creating a new virtual environment and running pip install aimsim to try out the latest version today!

Direct support for mordred has been changed to optional -- to use it, you must be running Python 3.7 and then use the command pip install aimsim[mordred]. We have had significant issues in the past few weeks as mordred falls further into disrepair, and we may drop support for it in the coming months.

Other minor bug fixes: - attempting to search for a fingerprint, but not a similarity measure, no longer raises an exception due to a missing configuration parameter. - windows measure search logfile generation was fixed - fixed an integer overflow error in the calculation of the pearson-morgan descriptor on windows platforms

Changelog

  • fix issue #244 by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/250
  • Loosen Dependency Requirements for Python Compatibility by Dropping Mordred by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/241

Full Changelog: https://github.com/VlachosGroup/AIMSim/compare/v1.1.2...v2.0.1

- Python
Published by JacksonBurns about 3 years ago

aimsim - AIMSim v1.1.2

This patch specifies an additional constraint on the requirements.txt to prevent use of a buggy update of the external dependency customtkinter.

What's Changed

  • do not use latest buggy ctk update by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/239

Full Changelog: https://github.com/VlachosGroup/AIMSim/compare/v1.1.1...v1.1.2

- Python
Published by JacksonBurns about 3 years ago

aimsim - AIMSim v1.1.1

New descriptors have been added, as well as small bug fixes in the user interface: * 232 pairwise similarity with numeric semtem characterization thermodynamic quantities catalyst and solvent descriptors by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/234 * Create test_ToolTip.py by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/236

Full Changelog: https://github.com/VlachosGroup/AIMSim/compare/v1.1.0...v1.1.1

- Python
Published by JacksonBurns about 3 years ago

aimsim - AIMSim v1.1.0

This release of AIMSim contains a number of QOL updates for the repository, some minor bug fixes and updates in the core functionality, and a complete overhaul of the GUI and accompanying tutorial notebook.

Changelog

  • move doc generation to separate branch by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/221
  • add explicit CI for python versions by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/222
  • use lru_cache for speedup and compatibility by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/223
  • Figures not displaying correctly fix by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/225
  • Add file browser using filedialog by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/226
  • GUI Upgrade by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/229
  • Update tutorial notebook to reflect new GUI design by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/231

Full Changelog: https://github.com/VlachosGroup/AIMSim/compare/v1.0.3...v1.1.0

- Python
Published by JacksonBurns over 3 years ago

aimsim - AIMSim v1.0.3

Bug fixes and more examples added.

What's Changed

  • Add conda env file for macOS by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/210
  • Change default cluster colors from cmap to hex by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/211
  • Fix error thrown if no params passed for lower dimensional embedding by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/212
  • Update tasks with docstring by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/213
  • Update references from AIMSim to aimsim for imports by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/214
  • Add new tutorial on using Tasks in Python by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/215
  • Add example by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/216
  • Add example by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/217
  • Update max specification config by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/218

Full Changelog: https://github.com/VlachosGroup/AIMSim/compare/v1.0.2...v1.0.3

- Python
Published by JacksonBurns almost 4 years ago

aimsim - AIMSim v1.0.2

This minor update contains a bug fix for smiles imports, as well as changes capitalization of the Python package to conform with PEP8 standards.

What's Changed

  • Fix bug init form excel throws error if no smiles by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/208
  • Rename AIMSim to aimsim on PyPI to Simplify imports and Conform with PEP8 by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/209

Full Changelog: https://github.com/VlachosGroup/AIMSim/compare/v1.0.1...v1.0.2

- Python
Published by JacksonBurns almost 4 years ago

aimsim - AIMSim v1.0.1

This minor version includes understandably minor tweaks, namely changing to ordering of the UI elements so they fit regardless of operating system and making fonts more readable.

What's Changed

  • Change plotting fontsizes by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/203
  • Update gitignore by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/204
  • Update docstring by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/205
  • Fix overlapping GUI elements on Mac while maintaining Windows Functionality by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/207

Full Changelog: https://github.com/VlachosGroup/AIMSim/compare/v1.0.0...v1.0.1

- Python
Published by JacksonBurns almost 4 years ago

aimsim - AIMSim v1.0.0

This is the initial stable release of AIMSim to coincide with submission.

What's Changed

  • Update documentation by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/189
  • PEP8 compliance by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/191
  • PEP8 formatting changes by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/192
  • Update documentation by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/193
  • Change docstring for MoleculeSet class by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/194
  • Change docstring for MoleculeSet class by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/195
  • Change docstring for MoleculeSet class by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/196
  • Solve empty handles passed for legends by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/198
  • Add interactive scatter plots for scatter plots by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/200
  • Reformat spaces by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/202

Full Changelog: https://github.com/VlachosGroup/AIMSim/compare/v1.0.0-rc.3...v1.0.0

- Python
Published by JacksonBurns about 4 years ago

aimsim - AIMSim v1.0.0-rc.3

This release includes a bugfix in the error-prevention of descriptor, as well as substantial speedup improvements (as discussed in #188). Still in pre-release, which will be changed to full release along with the manuscript.

What's Changed

  • Reducing Execution Time by @JacksonBurns in https://github.com/VlachosGroup/AIMSim/pull/188

Full Changelog: https://github.com/VlachosGroup/AIMSim/compare/v1.0.0-rc.2...v1.0.0-rc.3

- Python
Published by JacksonBurns about 4 years ago

aimsim - AIMSim v1.0.0-rc.2

Follow up to release candidate 1 including additional testing and some new dimensionality reduction algorithms.

What's Changed

  • Add new dimensionality reduction methods by @himaghna in https://github.com/VlachosGroup/AIMSim/pull/187
  • Add additional tests for experimental descriptors (test coverage now 90%) by @JacksonBurns in e7643fcfba031b4bb709335c7602fd21e20ff838

Full Changelog: https://github.com/VlachosGroup/AIMSim/compare/v1.0.0-rc.1...v1.0.0-rc.2

- Python
Published by JacksonBurns about 4 years ago

aimsim - AIMSim v1.0.0-rc.1

This is the initial release (release candidate 1) coinciding with submission for review on the corresponding manuscript.

- Python
Published by JacksonBurns about 4 years ago