Oliver Beckstein

Create a 1.0 release (we have a reasonably stable API). * This would be the last release that supports pymbar 3 (see #205 ). * Should contain the ABFE workflow....

[TST] avoid evaluating data loader functions in parametrized tests at set-up time

1

# Problem Our tests contain examples of parametrizing over different datasets by *calling* the data loader function in the `pytest.mark.parametrize` such as https://github.com/alchemistry/alchemlyb/blob/72622c99c16c74efd1f8517cb15ef21e16d6ebda/src/alchemlyb/tests/test_preprocessing.py#L66-L69 The data loader functions `gmx_benzene_dHdl()` and `gmx_benzene_u_nk()`...

Gromacs EDR reader

8

At the moment, the native Gromacs energy (EDR) files have to be converted to XVG files. Instead we should also offer a EDR parser. @jbarnoud wrote https://github.com/jbarnoud/panedr which reads a...

use logging

3

For debug and info output we do not want to use `print` but use the standard [logging](https://docs.python.org/3/howto/logging.html) facility.

JOSS paper

3

Write a short software paper on alchemlyb/alchemtest for [JOSS](http://joss.theoj.org/). - [Author instructions](https://joss.readthedocs.io/en/latest/submitting.html) – create a repo and then submit, ~1000 words, see examples - authors? - any contributor (name on...

list features to be moved from alchemical-analysis to alchemlyb

4

We would like to produce a [list of **highly desirable alchemical-analysis features in alchemlyb**](https://github.com/alchemistry/alchemlyb/wiki/alchemical-analysis-features). As expressed in the [Roadmap](https://github.com/alchemistry/alchemlyb/wiki/Roadmap#librarify-alchemical-analysis-functionality), the idea is to use little pieces from [alchemical-analysis](https://github.com/MobleyLab/alchemical-analysis) and re-implement...

use AtomGroup in place of selection strings

4

**Is your feature request related to a problem? Please describe.** Many analysis methods (`Contacts`, old and new H-bond analysis PR #2237, ...) require the user to provide _selection strings_ and...

performance benchmarks for dihedral analysis

4

With the merge of PR #2706 , the performance of the Ramachandran analysis tool improved markedly. It would be nice to see the improvements in the automatic [performance benchmarks](https://www.mdanalysis.org/benchmarks/) (see...

Replace `deprecated logger.warn()` with `logger.warning()` everywhere.

enable readers to work with non-seekable streams

2

## Is your feature request related to a problem? ## The coordinate readers cannot easily ingest generic streams (remote data) because they assume that any source is seekable to a...