pybids

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Expanding derivatives' configuration to validate existing BIDS-apps

10

Under the assumption that the main goal of this configuration file is to be able to query BIDS-apps' outputs, I think it would be great to validate the correspondence between...

GalKepler

alexisthual

There're some entities missing in both the derivatives' entities configuration and the corresponding default_path_patterns. It would be beneficial to expand this configuration to hold for more BIDS apps' outputs. For...

GalKepler

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...

pvandyken

[WIP] introduce BIDSLayoutV2

12

In agreement with @gkiar, the following approach allows for a better migration to pybids-core: - introduce a new interface BIDSLayoutV2 which uses ancpBIDS to mimic functionality from the BIDSLayout legacy...

erdalkaraca

Remove reports module in favor of pybids-reports namespace package

2

Closes #801. This PR removes everything related to the `reports` module, since we will move to using a namespace package called [`pybids-reports`](https://github.com/bids-standard/pybids-reports). This will remain a draft until I've addressed...

tsalo

This would allow auto_model to be run without downloading the full images

adelavega

Support for microscopy samples.tsv

2

I was wondering if it would be possible to add the `samples.tsv` file to the `get_collections `function at the "dataset" level At the moment, the "dataset" level seems to only...

Remi-Gau

`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...

pvandyken

variables: Add sparse/dense mode for to to_df, and add alternative design matrix API to access sparse variables

3

https://github.com/bids-standard/pybids/blob/f4bf70cccaf85dc65f2b610f448d141c014562d9/bids/variables/collections.py#L610-L620

adelavega