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asv: remove distances.DistancesBench.time_contact_matrix_sparse 10,000 benchmark

1

## Expected behavior ## All ASV benchmarks for the latest develop run (see [benchmarks.benchmarks](https://github.com/MDAnalysis/mdanalysis/tree/develop/benchmarks/benchmarks) for the code and the [MDAnalysis/benchmarks](https://github.com/MDAnalysis/benchmarks) repo + the [benchmarks wiki](https://github.com/MDAnalysis/benchmarks/wiki) for more details.) ## Actual...

orbeckst

asv: fix GeoSelectionBench.time_geometric_selections

5

## Expected behavior ## All ASV benchmarks for the latest develop run (see [benchmarks.benchmarks](https://github.com/MDAnalysis/mdanalysis/tree/develop/benchmarks/benchmarks) for the code and the [MDAnalysis/benchmarks](https://github.com/MDAnalysis/benchmarks) repo + the [benchmarks wiki](https://github.com/MDAnalysis/benchmarks/wiki) for more details.) ## Actual...

orbeckst

## Expected behavior ## All ASV benchmarks for the latest develop run (see [benchmarks.benchmarks](https://github.com/MDAnalysis/mdanalysis/tree/develop/benchmarks/benchmarks) for the code and the [MDAnalysis/benchmarks](https://github.com/MDAnalysis/benchmarks) repo + the [benchmarks wiki](https://github.com/MDAnalysis/benchmarks/wiki) for more details.) ## Actual...

orbeckst

Follow-up on PR #1695, which included initial tests for distance based calculations. The comments noted a few issues * use of core.flags https://github.com/MDAnalysis/mdanalysis/pull/1695#discussion_r148338963 * clear separation of tests with and...

orbeckst

performance benchmarks

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It might be worth considering the use of simple performance benchmarks for the project over time -- I know that [airspeed velocity](https://github.com/spacetelescope/asv/) is commonly used for large python projects and...

tylerjereddy

Implementation of SugarSelection

3

Fixes #4563 Changes made in this Pull Request: - Creation of the `SugarSelection` class that allows the selection of sugars through the access of known PDB, CHARMM and GLYCAM abbreviations...

talagayev

Make the `AnalysisBase` compatible with live simulation streams

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## Is your feature request related to a problem? ## Related to #4827: for MDAnalysis to function with live simulation streams, the `AnalysisBase` must be modified to account for a...

ljwoods2

Implement fancy guessers (e.g., force-field aware)

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So with #363 we removed guessing of various things in Parsers (ie whilst reading the files) and deferred this guessing to be after Universe init. The guessing now needs to...

richardjgowers

Feature proposal: Adding a ResidenceTime Analysis Routine

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#### Summary Dear MDAnalysis community, I would like to propose a new analysis routine that I have developed, `ResidenceTime`, for MDAnalysis. The routine would allow to analyze how long specific...

mattiafelice-palermo

Support for numpy.dtypes.StringDType in AtomGroup containers?

1

In numpy 2.0+, the new dtype for strings in numpy are StringDType(). However, I don't believe MDAnalysis support this at all? Consider the following code: ``` import MDAnalysis as mda...

jauy123