mdanalysis

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CHARMM Velocity reader

4

Currently, there is no possibility to read in CHARMM velocity files. These are binaries, very similar to CHARMM dcds, just with a slightly different header, and the data block contains...

hesther

Cleanup and restructure of AnalysisBase classes docstrings

21

Fixes #919 Fixes #3651 Changes made in this Pull Request: * Deprecate `verbose` parameter in `AnalysisBase.__init__` (follows issue #3651) * Moved all docstrings from `__init__` function to class docstring (follows...

PicoCentauri

Setting attributes should have dtype checks

20

Our Topology system is statically typed, each `TopologyAttr` ([found here](https://github.com/MDAnalysis/mdanalysis/blob/develop/package/MDAnalysis/core/topologyattrs.py)) should only accept one data type, e.g. atom names ([here](https://github.com/MDAnalysis/mdanalysis/blob/develop/package/MDAnalysis/core/topologyattrs.py#L769)) should always be strings, resids should always be ints. Currently...

richardjgowers

add simple atomic distance analysis to analysis.distances

6

## Is your feature request related to a problem? ## We have many analysis tools for complicated problems, all using the consistent AnalysisBase approach. However, there's no functionality for fairly...

orbeckst

Deprecate `verbose` option in initialization of `AnalysisBase`

9

## Is your feature request related to a problem? ## The verbose option for Analysis classes appears in the `init` function and as well in the `run` method. The first...

PicoCentauri

Issue 2764 Setting attributes should have dtype checks

3

Changes made in this Pull Request: --------------------------------------- - Enforced strict adherence to the data types for `TopologyAttr` values This pull request attempts to address issue #2764 PR Checklist ------------ -...

fortune-max

LinearDensity should have more reliable tests

9

## Is your feature request related to a problem? ## Currently, some of the tests in test_lineardensity.py are basically tautologies because the expected values the tests check against were obtained...

BFedder

Enable Pylint warnings

8

This is a list of good sounding pylint warnings we might want to enable - [ ] arguments-differ, - [ ] assignment-from-none, - [ ] bad-builtin, - [ ] bad-indentation,...

kain88-de

Failed doc examples in align.py

3

## Expected behavior ## Sub-issue of #760 Doc examples work. ## Actual behavior ## This is after changing a `>>>` in the rotation matrix example to `...` ``` ================================================== FAILURES...

lilyminium

Mismatch in groupselections for RMSD between target and reference

8

## Expected behavior ## If I pass an atomgroup to RMSD, `groupselections` are taken only from that AtomGroup ## Actual behavior ## This does not happen for one of the...

lilyminium