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Feature (un)wrap enhancement

16

Changes made in this Pull Request: - Optimizes unwrapping by pre-screening AG fragments that span more than half the box vectors; - Extends the universe-validated cache mechanism to avoid re-calculating...

mnmelo

Implement context aware guesser

10

## Is your feature request related to a problem? The current `Guesser` class used by the users or inside parsers hava a downside of being generic, which makes it doesn't...

aya9aladdin

Multiprecision in core, NumPy dtypes and Cythonization

12

## Is your feature request related to a problem? ## With the ongoing work on Cythonising Core as part of the CZI performance track (see #3683), we need to start...

hmacdope

Inconsistent copyright/citation in file calc_distances.h

1

## Expected behavior ## Code files should all have the same copyright header and list the same copyright year/citations. ## Actual behavior ## In `calc_distances.h` the copyright year is listed...

hmacdope

Using OpenMP parallelization on Windows 10

3

Hi, I am using MDAnalysis on my Windows 10 laptop and was trying to run a clustering method on 4 cores as shown below. However, it only runs on a...

tanoury1

Add copy method to AuxReader

4

A copy method needs to be added to `MDAnalysis.auxiliary.base.AuxReader` which should work similarly to the ReaderBase copy method. This should then be extended to include the [XVGReader](https://github.com/MDAnalysis/mdanalysis/blob/develop/package/MDAnalysis/auxiliary/XVG.py).

richardjgowers

H5PY 3.4.0 causes H5MD writer tests fail with PermissionError on Windows (investigate temporary pin)

6

## Expected behavior ## All tests pass. ## Actual behavior ## For the Windows runners TestH5MDWriterWithRealTrajectory.test_write_with_drivers[core] fails due to a permission error in writing the H5MD file. ## Code to...

IAlibay

Adding Type Hints for MDAnalysis

3

## Is your feature request related to a problem? ## MDAnalysis library currently lacks type hints which would help in providing better documentation and help catch errors easily . ##...

umak1106

Passing dt explicitly to readers has a different default behaviour

1

## Expected behavior ## For readers which can derive their own `dt` values, passing a value for `dt` to the reader should yield the same behaviour across all readers. ##...

IAlibay

Multi-precision and dtypes

1

Discussion around #3544 and #3500 has raised some interesting points about floating point precision and dtypes. The current strategy in MDA is to squash down to an `np.float32` on box...

hmacdope