snakebids

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The number of tests has changed since the last generated test-timings file. This PR contains an automatically regenerated file.

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If a wildcard is specified via the CLI (e.g. `--wildcards-COMP ...`), it is merely appended to the list of wildcards specified in the `config.yaml` without any deduplication. This creates a...

pvandyken

This issue picks up from #209. There's going to be a few steps involved in establishing the breaking `BidsDataset` API, so we can use this issue for tracking. - [x]...

pvandyken

Version plugin does not add CLI parameter

1

Currently it just resolves the app version and stores it in the config. It would be more useful if it also created a `--version` flag. Need to think a bit...

pvandyken

Add an option in generate_inputs to ignore files from pybids parsing?

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## The problem Would be useful to be able to ignore specific files when parsing a bids dataset. In my case, it is because I'm now parsing some datasets that...

akhanf

In my workflow, I tend to save my (usually very long) snakebids calls to an executable file. I leave a `$@` variable at the end of the call so I...

pvandyken

# Background Currently, `BidsComponentRow.filter` supports a position-only `spec` argument that takes directly the list of values to be kept. The idea is that since the row has only one entity,...

pvandyken

`export_sourcedir` plugin

2

This proposal will supersede #180 . The plugin will allow the copying or symlinking of directories in the app to the output dir. This will allow the snakemake app to...

pvandyken

In recent versions of `snakemake`, the app will start subinstances of snakemake under many different circumstances, including cluster submission, use of the `run` directive, use of `shadow`, and probably others....

pvandyken

Improve implementation of `get()` in `MultiSelectDict`

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I was confronted with a current limitation of our MultiSelectDicts: it is currently somewhat difficult to select only the keys that are contained inside the dict. You need something like...

pvandyken