Mike Lin

Repro: ``` docker run --rm -it -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp condaforge/miniforge3 \ bash -c 'conda install -y python=3.13 && conda install -y miniwdl=1.13 && miniwdl run_self_test' ``` (as miniforge3 is...

While it's concerning that bullet is apparently unmaintained, it's pure-python and unlikely to have a real problem with python3.13. Maintenance of the downstream conda-forge feedstock is the likely blocker right...

@adamnovak I think the cleanest way to do this is using the cgroups resource counters that are usually available inside each container. There is an [old example for this](https://github.com/chanzuckerberg/miniwdl/blob/main/examples/plugin_log_task_usage/miniwdl_log_task_usage.py), however,...

cgroups v2 does have counters for the block I/O devices! My hope with this approach is that it should work on any docker host (including AWS etc.) that doesn't go...

@adamnovak Mixed update on this, I updated https://github.com/chanzuckerberg/miniwdl/tree/main/examples/plugin_log_task_usage to work with cgroup v1 and v2. It only logs CPU memory usage, but it works both locally and on AWS Batch,...

@corneliusroemer Thanks for raising this, indeed in the first couple years of Apple Silicon, I don't think anyone had much expectations for Docker-based bioinformatics workflows to work on that platform,...

I've updated the miniwdl documentation to link instructions on setting up conda-forge properly, instead of trying to get away with the `conda install -c conda-forge ...` shortcut, which I think...

@TedBrookings I think `miniwdl run -i in.json --json` will do this, albeit it's very poorly named (the meaning of `--json` was to produce a combined+validated JSON from the command-line inputs...

Context: the "new shape feature" in [tiledbsoma 1.15](https://github.com/single-cell-data/TileDB-SOMA/releases/tag/1.15.0) has the dimension domains set to ~2^63 and uses the "current domain" for the desired shape. So TileDB-Vector-Search reads `dimensions` as ~2^63...

TODO: indeed support Expr as hint_value