Hugo MacDermott-Opeskin

Add a reader for TNG files using pytng

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Fixes #3237 and partially addresses #865 (reading TNG) This PR adds functionality for reading TNG files using pytng (finally). :smile: The limitations of reading a TNG file using pytng are...

Remove use of `trajectory.timeseries` from `ENCORE`

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## Expected behavior ## The `ENCORE` module should work with all kinds of readers. As revealed by the use of the DUMPReader in [this](https://groups.google.com/g/mdnalysis-discussion/c/PEqfPk_aVvo ) mailing list question this is...

Add optional dtype argument to box routines

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Fixes #3500 Changes made in this Pull Request: - Add an optional dtype argument to the box routines. As we don't guarantee the input is an `ndarray` we can't pass...

Use of NumPy 1.21 style `npt.NDArray` typing hints

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## Problem With the merge of #3737 NumPy 1.20 is now our minimum supported NumPy version as per [NEP29](https://numpy.org/neps/nep-0029-deprecation_policy.html). However some open PRs (eg @hmacdope #3730 and @umak1106 #3746) are...

Expose public facing Cython in libmda layer

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## Is your feature request related to a problem? ## As part of #3683, the `libmda` folder with its own `__init__.pxd` was introduced to provide a single place to expose...

Investigate making Bonds use a C++ unordered map datastructure and Cython

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## Is your feature request related to a problem? ## As far as I can tell the `Bonds` datastructures and topology attributes currently use an `N*M` matrix to store Bond...

[HOLD] Re-implement distance_array using a batched algorithm and add compiled iterator layer [Core, WIP]

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Fixes #3708 UPDATE ------------ This PR is currently on hold pending decisions around batched distance arrays. **Aim:** - Add a batched distance array algorithm for efficient memory use. - Allow...

Multiprecision in core, NumPy dtypes and Cythonization

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## 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...

Inconsistent copyright/citation in file calc_distances.h

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## 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...

Multi-precision and dtypes

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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...