Oliver Beckstein

Note issue #336 regarding JAX issues.

With https://github.com/conda-forge/alchemlyb-feedstock/pull/25 we will have conda-forge packages *alchemlyb* (includes pymbar and thus jax) and *alchemlyb-core* (depends on pymbar-core and no jax). We will just need to **document** these choices in...

Thanks for the explanation and clarification @xiki-tempula – I had only briefly skim-read the conda-forge PRs. We should still document the installation options with variants as they will solve the...

Of course, yes please. > On Aug 28, 2025, at 12:59, Zhiyi Wu ***@***.***> wrote: > > > xiki-tempula > left a comment > (alchemistry/alchemlyb#327) > > @orbeckst Are you...

First issue is that proka does not anymore understand `--quiet` in ```python mol = pk.single(pstream, optargs=['--quiet']) ```

Is the following a reasonable way to set up the develop environment? ```bash mamba create -n mda312dev python=3.12 mamba install -n mda312dev --only-deps mdanalysis mdanalysistests mamba activate mda312dev echo "Do...

You can add recipes/suggestions to the discussion post https://github.com/MDAnalysis/mdanalysis/discussions/4636

My read of the discussion here and https://github.com/MDAnalysis/mdanalysis/discussions/4636 is that we should start with a simple `develop_environment.yaml` file in the source tree (possibly removing/commenting out *hole2*, *distopia*, and *clustalw* (do...

We want to have updated installation instructions in time for the UGM so that we can have people work with develop during the hackathon. cc @yuxuanzhuang as the hackathon organizer

I raised https://github.com/MDAnalysis/mdanalysis/issues/4645 Btw, what is the env file [maintainer/conda/environment.yml](https://github.com/MDAnalysis/mdanalysis/blob/develop/maintainer/conda/environment.yml) good for? Can we just use that one?