malramsay64 / statdyn-analysis

Collection of tools for the statistical dynamics analysis of Molecular Dynamics trajectories.
MIT License
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chore(deps): Update freud-analysis requirement from <1.3,>=1.0 to >=1.0,<2.1 #143

Closed dependabot-preview[bot] closed 4 years ago

dependabot-preview[bot] commented 4 years ago

Updates the requirements on freud-analysis to permit the latest version.

Changelog *Sourced from [freud-analysis's changelog](https://github.com/glotzerlab/freud/blob/master/ChangeLog.md).* > ## v2.0.0 - 2019-10-31 > > ### Added > * Ability to specify "system-like" objects that contain a box and set of points for most computes. > * NeighborLists and query arguments are now accepted on equal footing by compute methods that involve neighbor finding via the `neighbors=...` argument. > * Extensive new documentation including tutorial for new users and reference sections on crucial topics. > * Standard method for preprocessing arguments of pair computations. > * New internal ManagedArray object that allows data persistence and improves indexing in C++. > * Internal threaded storage uses the standard ManagedArray object. > * C++ Histogram class to standardize n-dimensional binning and simplify writing new methods. > * Upper bound r\_max option for number of neighbors queries. > * Lower bound r\_min option for all queries. > * Steinhardt now supports l = 0, 1. > * C++ BondHistogramCompute class encapsulates logic of histogram-based methods. > * 2D PMFTs accept quaternions as well as angles for their orientations. > * ClusterProperties computes radius of gyration from the gyration tensor for each cluster. > * `freud.data` module for generating example particle systems. > * Optional normalization for RDF, useful for small systems. > * `plot()` methods for `NeighborQuery` and `Box` objects. > * Added support for reading system data directly from MDAnalysis, garnett, gsd, HOOMD-blue, and OVITO. > * Various validation tests. > > ### Changed > * All compute objects that perform neighbor computations now use NeighborQuery internally. > * Neighbor-based compute methods now accept NeighborQuery (or "system-like") objects as the first argument. > * All compute objects that perform neighbor computations now loop over NeighborBond objects. > * Renamed (ref\_points, points) to (points, query\_points) to clarify their usage. > * Bond vector directionality is standardized for all computes that use it (always from query\_point to point). > * Standardized naming of various common parameters across freud such as the search distance r\_max. > * Accumulation is now performed with `compute(..., reset=False)`. > * Arrays returned to Python persist even after the compute object is destroyed or resizes its arrays. > * All class attributes are stored in the C++ members and accessed via getters wrapped as Python properties. > * Code in the freud.common has been moved to freud.util. > * NeighborQuery objects require z == 0 for all points if the box is 2D. > * Renamed several Box methods, box.ParticleBuffer is now locality.PeriodicBuffer. > * Cluster now finds connected components of the neighbor graph (the cluster cutoff distance is given through query arguments). > * Refactored and renamed attributes of Cluster and ClusterProperties modules. > * CorrelationFunction of complex inputs performs the necessary conjugation of the values before computing. > * Updated GaussianDensity constructor to accept tuples as width instead of having 2 distinct signatures. > * RDF bin centers are now strictly at the center of bins. > * RDF no longer performs parallel accumulation of cumulative counts (provided no performance gains and was substantially more complex code). > * MatchEnv has been split into separate classes for the different types of computations it is capable of performing, and these classes all use v2.0-style APIs. > * The Voronoi class was rewritten to use voro++ for vastly improved performance and correctness in edge cases. > * Improved Voronoi plotting code. > * Cubatic uses standard library random functions instead of Saru (which has been removed from the repo). > * APIs for several order parameters have been standardized. > * SolidLiquid order parameter has been completely rewritten, fixing several bugs and simplifying its C++ code. > * Steinhardt uses query arguments. > * PMFTXY2D has been renamed to PMFTXY. > * Removed unused orientations from PMFTXYZ and PMFTXY. > ... (truncated)
Commits - [`cd3faae`](https://github.com/glotzerlab/freud/commit/cd3faae00150613d46a6751e072fe43175f19170) Update citation info in README. - [`1ee28ff`](https://github.com/glotzerlab/freud/commit/1ee28fffb95a46007d885268112fe06df00e1291) Restrict builds to Python 3.5, 3.6, 3.7 (3.8 not yet supported by scipy). - [`0c16e0a`](https://github.com/glotzerlab/freud/commit/0c16e0aba81633034673315be424747d564f18cd) Use same Python versions for building and testing, make matplotlib version le... - [`332065f`](https://github.com/glotzerlab/freud/commit/332065f4b2083138fc931cd0abe063f743faeba5) Adjust scipy requirements, add other dependencies. - [`dd17844`](https://github.com/glotzerlab/freud/commit/dd17844177876200e304d71a53a9f6bcec0a3f4c) Fix supported Python versions. - [`e35c9ab`](https://github.com/glotzerlab/freud/commit/e35c9ab501ae1b12f691d2faf255b25654dfdb78) Remove set -u to allow checking if unbound variable CPATH is empty. - [`55428f7`](https://github.com/glotzerlab/freud/commit/55428f760c67ef10d6c1f2a7a1d121a768a006f2) Update fsph submodule. - [`42e3a48`](https://github.com/glotzerlab/freud/commit/42e3a485c2846076ae6ac3fe723985768e7bb4da) Try sourcing build scripts. - [`065b6ae`](https://github.com/glotzerlab/freud/commit/065b6ae17aab21876ac6f89684bb905d41ec763c) Remove working directory. - [`9ce9217`](https://github.com/glotzerlab/freud/commit/9ce9217e1e2fded1e03df67f994ef23e98fe22ce) Bump up to version 2.0.0. - Additional commits viewable in [compare view](https://github.com/glotzerlab/freud/compare/v1.0.0...v2.0.0)


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malramsay64 commented 4 years ago

This is very incompatible and requires significant changes. Putting this off for a while

dependabot-preview[bot] commented 4 years ago

OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting @dependabot ignore this major version or @dependabot ignore this minor version.

If you change your mind, just re-open this PR and I'll resolve any conflicts on it.

malramsay64 commented 4 years ago

@dependabot ignore this major version

dependabot-preview[bot] commented 4 years ago

OK, I won't notify you about version 2.x.x again, unless you re-open this PR or update to a 2.x.x release yourself.