Ali Khan
Ali Khan
The _check_path_matches_patterns function was failing for cloud (e.g. s3, gc3) URIs (added in #1074): 1) the path.relative_to() function doesn't work for cloud URIs (it just returns the original). 2) combining...
With #435 is merged in, we now have ~0p3 (18k), ~0p5mm (8k) and ~1mm (2k) surfaces. However, our previous set of surfaces were 0p5mm (14,266 verts), 1mm (3,870 verts), and...
I haven't been looking for this recently, but I recall it was an issue when we moved to new surface generation (e.g. I think the surface normals can point in...
With hippunfold installed via conda, we now don't get the dev dependencies (e.g. snakefmt, isort, black) for linting and code quality.. What I've been doing now is using both conda...
Once things have finalized a bit more, we should start the process to put the hippunfold surface template(s) on templateflow. This would be a natural home for them since they...
We talked about GIN/datalad for hosting larger resources and Mackenzie had tried it out -- would make running the create_atlas workflow much easier (e.g. datalad install, then run hippunfold) The...
I have an idea of doing this in an elegant way with a params function (for python scripts that create/modify gifti)..
Now that we have #351, we can update our docker build to use [--containerize](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#containerization-of-conda-based-workflows) @Dhananjhay maybe you could explore this? (I haven't tried it out yet myself)..
A reminder here that we need to update the resources: - templates should include dentate src/sink labels (otherwise they should be left out of v2.0.0) - surface-templates should be based...
Currently we have zip files for each, and so snakemake tracks the folder that contains the files. This led to some awkward workarounds (defining the atlas dir as an input,...