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malramsay64 / statdyn-analysis

Collection of tools for the statistical dynamics analysis of Molecular Dynamics trajectories.
MIT License
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chore(deps): bump freud-analysis from 1.0.0 to 1.2.0 #89

Closed dependabot-preview[bot] closed 5 years ago

dependabot-preview[bot] commented 5 years ago

Bumps freud-analysis from 1.0.0 to 1.2.0.

Changelog *Sourced from [freud-analysis's changelog](https://github.com/glotzerlab/freud/blob/master/ChangeLog.md).* > ## v1.2.0 - 2019-06-27 > > ### Added > * Added `.plot()` method and IPython/Jupyter PNG representations for many classes. > * `AttributeError` is raised when one tries to access an attribute that has not yet been computed. > * Added `freud.parallel.getNumThreads()` method. > * New examples for integration with simulation and visualization workflows. > > ### Changed > * Removed extra C++ includes to speed up builds. > * The C++ style is now based on clang-format. > * Refactored C++ handling of thread-local storage. > * SolLiq order parameter computations are parallelized with TBB. > * Optimized performance of Voronoi. > * Several Box properties are now given as NumPy arrays instead of tuples. > * Box methods handling multiple vectors are parallelized with TBB. > * Eigen is now used for all matrix diagonalizations. > > ### Fixed > * Calling setNumThreads works correctly even if a parallel compute method has already been called. > * Fixed segfault with chained calls to NeighborQuery API. > * Correct `exclude_ii` logic. > > ### Removed > * Removed outdated `computeNList` function from `LocalDescriptors`. > > ## v1.1.0 - 2019-05-23 > > ### Added > * New neighbor querying API to enable reuse of query data structures. > * AABBQuery (AABB tree-based neighbor finding) added to public API. > * Ability to dynamically select query method based on struct of arguments. > * All compute objects have `__repr__` and `__str__` methods defined. > * NeighborLists can be accessed as arrays of particle indices via `__getitem__`. > * ParticleBuffer supports different buffer sizes in x, y, z. > * Box makeCoordinates, makeFraction, getImage now support 2D arrays with multiple points. > > ### Changed > * Use constant memoryviews to prevent errors with read-only inputs. > * LocalQl is now parallelized with TBB. > * Optimized performance of RotationalAutocorrelation. > * NematicOrderParameter uses SelfAdjointEigenSolver for improved stability. > * Added build flags for Cython debugging. > * LinkCell computes cell neighbors on-demand and caches the results for significant speedup. > > ### Fixed > * Corrected type of `y_max` argument to PMFTXY2D from int to float. > * Reduce logging verbosity about array conversion. > * Fixed number of threads set upon exiting the NumThreads context manager. > * Corrected quaternion array sizes and added missing defaults in the documentation. > ... (truncated)
Commits - [`2d58545`](https://github.com/glotzerlab/freud/commit/2d585454caa00a3e0e5ec2c7a7bdeaf973acbe00) Bump up to version 1.2.0. - [`4c14f6e`](https://github.com/glotzerlab/freud/commit/4c14f6e712a52201e728327ec71c72f57da01ae4) Re-cythonize. - [`b9811fa`](https://github.com/glotzerlab/freud/commit/b9811faf5054c93708bfcb5a874ed989f543fd7d) clang-format - [`4e56490`](https://github.com/glotzerlab/freud/commit/4e5649067ef13b7bce3f544c1b0319eaeda65848) Update mailmap. - [`c8e1507`](https://github.com/glotzerlab/freud/commit/c8e150716fbf490f2fcb38279d2bf77bfbde2c79) Update changelog. - [`2bb8816`](https://github.com/glotzerlab/freud/commit/2bb88164c06c9a52de82627e61677c62901b874f) Merge pull request [#321](https://github-redirect.dependabot.com/glotzerlab/freud/issues/321) from glotzerlab/feature/parallelize-sol-liq - [`264bbd2`](https://github.com/glotzerlab/freud/commit/264bbd249585dd4ba7b8d97a524be7f0a174bd78) Merge pull request [#329](https://github-redirect.dependabot.com/glotzerlab/freud/issues/329) from glotzerlab/fix/cubatic-remove-saru - [`13822c2`](https://github.com/glotzerlab/freud/commit/13822c28c5a49924645644405db2f49b8689ea77) Merge branch 'master' into feature/parallelize-sol-liq - [`3136378`](https://github.com/glotzerlab/freud/commit/31363785c5274a2bc3acfab1c1e9e884b6bdcb57) Merge pull request [#300](https://github-redirect.dependabot.com/glotzerlab/freud/issues/300) from glotzerlab/refactor/ndhistogram - [`2ec61a5`](https://github.com/glotzerlab/freud/commit/2ec61a504920b70c974d96a2cc65e053c9c57ff7) Merge pull request [#318](https://github-redirect.dependabot.com/glotzerlab/freud/issues/318) from glotzerlab/feature/repr_png_more - Additional commits viewable in [compare view](https://github.com/glotzerlab/freud/compare/v1.0.0...v1.2.0)


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dependabot-preview[bot] commented 5 years ago

Superseded by #93.