Stefan Appelhoff

numpy convention --> colon spacing should be verified for parameters and return sections

1

The following is an example of a numpy convention parameter documentation: ```Python """ Parameters ---------- a : int The value of a. """ ``` The numpy docs say the following...

Add a "reject_by_annotation" parameter for finding bad channels

1

I think the functions to find noisy channels could benefit from a `reject_by_annotation` parameter, [as used in MNE-Python](https://mne.tools/dev/auto_tutorials/preprocessing/20_rejecting_bad_data.html#the-reject-by-annotation-parameter). It would mean that before working on the continuous raw data, `raw.annotations`...

Split "full PREP example" into two: 1) show how to use, 2) show validation against matlab

1

Currently the full PREP example does both, showing *how* it can be used, and *validating* the results against the Matlab results. https://pyprep.readthedocs.io/en/latest/auto_examples/index.html I think we should rather have two examples:...

Compare RANSAC in pyprep and autoreject

23

both the pyprep and the autoreject package have an implementation of RANSAC. We should make a comparison to: 1. see whether they provide the same results 1. potentially find bugs...

pyprep needs to be split into smaller, testable chunks

4

we need to refactor much of the code to be in smaller chunks (functions, preferably) that can be properly tested with pytest. that'd make everyone more comfortable when we change...

Came up in https://github.com/mne-tools/mne-bids/pull/831#issuecomment-879789206 We had problems across platforms: On POSIX, `BIDSPath.root` has forward slashes when printed (`__str__`), on Windows, it has backslashes. That's undesirable for testing, because BIDS wants...

Reduce code duplication in tests, test functions in correct test modules

1

Currently, we are testing `read_raw_bids` in `test_write.py`--> it SHOULD be tested in `test_read.py` ... but to avoid code duplication, it is being tested in `test_write.py` Furthermore, we are having some...

read_raw_bids should read digitization files

3

This is currently not implemented. Our `_read_raw` function does accept the respective arguments to read a digitized montage: https://github.com/mne-tools/mne-bids/blob/0fa987edeef36fed8dfc04f04c50224900158f8f/mne_bids/read.py#L38-L41 and while `_read_raw` gets called in `read_raw_bids`, that function does NOT...

[came up on discourse](https://mne.discourse.group/t/error-in-bidspath-while-reading-openneuro-bids/4098) `EEGLAB` and `EEGLAB-HJ` are [supported in BIDS](https://bids-specification.readthedocs.io/en/latest/99-appendices/08-coordinate-systems.html#eeg-specific-coordinate-systems), and [EEGLAB-BIDS will soon write data this way](https://github.com/sccn/bids-matlab-tools/blob/7ec2968e4a31b459b1f3f720e701954f4b08506b/bids_export.m#L1085-L1090). Should be done here: https://github.com/mne-tools/mne-bids/blob/4c0755c6eb567c7840d70acf06f22201c5e75c65/mne_bids/config.py#L196-L197 ... perhaps with a little utility...

Bipolar electrode recordings and "electrodes.tsv"

14

When working on the impedances PR, I was working with data that included EOG and ECG *channels*. (see electrode vs channel disambiguation [in the entry paragraph of the BIDS EEG...