Yuxuan Zhuang

No need to redirect to the original frame explicitly during deserialization

17

Fixes #3723 Partial fix: #3721 Changes made in this Pull Request: - no redirection to the original frame (explicitly) during deserialization - TextIOPicklable serializes the raw class instance instead of...

## Expected behavior ## All readers can be double serialized (i.e. serialize the newly deserialized Reader) ## Code to reproduce the behavior ## ``` python import MDAnalysis as mda import...

## Current Writer API ## ```python # option 1 AtomGroup.write(filename,..., **kwargs) # option 2 with mda.Writer(filename, n_atoms) as w: for ts in Universe.trajectory: w.write(AtomGroup) ``` ## New API (`append=False` in...

It seems to be a recurring question (related #1576 #1553 #1582 and maybe more). And I know you guys will replace the implementation of it in a future version of...

Adding Appending Functionality method to WriterBase

1

Fixes #3861 Changes made in this Pull Request: - add new SingleFrameWriterBase - add new flag `append` for appending trajectory to WriterBase - add a check for the number of...

Limit threads usage in numpy during test to avoid time-out

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fix #4209 Changes made in this Pull Request: - make numpy only use one thread during test - reduce pytest worker - make tests lighter Similar to https://github.com/MDAnalysis/mdanalysis/pull/2950, allowing numpy...

PSFParser reads and converts string-Like residue number to the leading number

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Fixes #2053 #4189 Changes made in this Pull Request: - Updated PSFParser to convert string-like residue numbers to their leading number. If the conversion fails, the residue number defaults to...

Unifying _single_frame() of AnalysisBase and ParallelAnalysisBase

5

Note this only works after https://github.com/MDAnalysis/mdanalysis/pull/2723 is merged to MDAnalysis The key idea is not to break user's current codes and apply multiprocessing to AnalysisBase-based methods in MDAnalysis. i.e. a...

Refactor pmda after universe can be serialized

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Fixes #133 Changes made in this Pull Request: - refactor each part of pmda (test passed) - [x] parallel.py - [x] custom.py - [x] rmsd - [x] rmsf - [x]...

Bad Performance of Parallelization with On-the-fly Transformation

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### Expected behaviour Analysis of a `Universe` with on-the-fly transformation scales good (reasonable). ### Actual behaviour The scaling performance is really bad even with two cores. ### Code ```python import...