Elmar Pruesse

Great! The devil will be in the details and corner cases I'm afraid. To stay pythonic and keep the code lean, it might actually be necessary to implement this only...

From https://github.com/bioconda/bioconda-utils/blob/613aadb1c042fc81b8e1add17fa632e69b30006f/bioconda_utils/cli.py#L46-L61 ```python def enable_logging(default_loglevel='info'): """Adds the parameter ``--loglevel`` and sets up logging Args: default_loglevel: loglevel used when --loglevel is not passed """ def decorator(func): @arg('--loglevel', help="Set logging level (debug,...

Since `argh` inspects the argspec, transparently adding common things to some of the defined comands needs keeping the argspec intact.

I know - it's a little easier to do this with `click`, but in that use case, switching CLI libs wasn't really on my list.

BTW: there seems to be an issue wrapping callables that have type annotations. I got errors while compiling the new stub. Using the quoted style (`def x(arg: "MyType"):`) fixed it.

I've got this for now, in the main server function: ```R server_env = environment() lapply( list.files(path = "R", pattern = ".*\\.R$", full.names = TRUE), source, local = server_env ) ```...

Yes, that's what I meant. Though I was thinking less about nested loops in client code that are known to the user and easily configured with `plan(list(...))`, but about the...

See https://github.com/bioconda/bioconda-recipes/pull/24094 - just need to work out why the package is failing its build there and it'll update in Bioconda.

No clue... what does the option do? @annahake You could try running `gdb --args phyml....` and then `run` in the prompt `gdb` opens and then after a while press Ctrl-C...

Can you reproduce it?