Peter Van Dyken

fix: Stop checking for unneeded temp files from groups

6

When I run group jobs on a cluster, I'll often write temporary files to the node-specific local scratch folder. I'll label them `temp(...)` and the sub-snakemake instance will dutifully delete...

Refactor add derivatives

1

Here's an example of the reformatting I alluded to in #805. Most of the code was written just in my playing around with solutions: there's no tests yet, and just...

`layout.get(scope=...)` still uses `PipelineDescription`

2

## Problem The scope parameter of `BIDSLayout.get()` is supposed to take a pipeline name, causing `get` to return only files generated by that particular pipeline. In the latest version of...

I'd like the ability to wrap deprecation warnings within another sphinx admonition such as `info` or `warning`. My idea is to have an `admonition` argument in `deprecated()` which defaults to...

`nargs` default for optional regular fields

10

**Describe the bug** Not exactly a bug, more of a behavioural question: For optional arguments such as in the reproduction section below, the default behaviour is to allow passing `--arg`...

Use trailing undescore to disambiguate entity names from python keywords

4

Currently, the `from` entity, not yet officially part of BIDS spec afaik but still found withing the `derivatives` config in pybids, overlaps with the python keyword `from`, as in `from...

This came to my attention via the following error: ``` File /local/scratch/BrainStat/brainstat/stats/SLM.py:325, in SLM._surfstat_to_brainstat_rft(self) 323 yeo_names, _ = fetch_yeo_networks_metadata(7) 324 yeo_names.insert(0, "Undefined") --> 325 yeo7_index = yeo7[self.P["peak"]["vertid"][i]] 326 if "yeo7"...

BUG: Nonrigid transform causes type error

3

## Problem When running a nonrigid transform using `wm_register_to_atlas_new.py`, it crashes as soon as it tries to save the results of its first iteration with the error: `TypeError: 'float' object...

**Describe the bug** In pyright 1.1.358, the generated `__init__` types for attrs-wrapped classes no longer respect functions or constructors provided to the `converter` argument of `attrs.field`. The now-expected type seems...

I was working with an atlas (Brainnetome) that interleaves nodes from each hemisphere (e.g. `1=L, 2=R, 3=L, 4=R, ...`). `find_parcel_centroids` separates the two hemispheres in its return, such that all...