[BUG]: `extMDN` coordinates are falsely registered as `extDMN` coordinates in `junifer` #251

Merged

synchon merged 2 commits from fix/emdn-docs into main

2023-10-05 09:38:32 +00:00

synchon commented

2023-10-05 08:51:05 +00:00

(Migrated from github.com)

Is there an existing issue for this?

I have searched the existing issues

Current Behavior

In this table the extended multiple-demand network is correctly listed as extMDN, but when using the following marker:

  - name: extMDN
    kind: SphereAggregation
    coords: extMDN
    radius: 5
    method: mean

one gets the following error:

ValueError: Coordinates extMDN not found.

Using the list_coordinates() function, it seems clear why:
The naming is incorrect in junifer (extDMN)

>>> from junifer.data.coordinates import list_coordinates
>>> list_coordinates()
['CogAC', 'CogAR', 'DMNBuckner', 'Dosenbach', 'Empathy', 'Motor', 'MultiTask', 'PhysioStress', 'Power', 'Rew', 'Somatosensory', 'ToM', 'VigAtt', 'WM', 'eMDN', 'eSAD', 'extDMN']

Expected Behavior

It should have the correct name and the marker should work.

Steps To Reproduce

described above

Environment

❱ junifer wtf                                                                                                                              130 !
junifer:
  version: 0.0.2
python:
  version: 3.11.4
  implementation: CPython
dependencies:
  click: 8.1.3
  numpy: 1.23.5
  datalad: 0.18.4
  pandas: 1.5.3
  nibabel: 4.0.2
  nilearn: 0.10.0
  sqlalchemy: 1.4.48
  yaml: '6.0'
system:
  platform: Linux-6.2.0-27-generic-x86_64-with-glibc2.37
environment:
  LC_CTYPE: en_US.UTF-8
  PATH: /home/leonard/.venvs/base/bin:/home/leonard/.local/bin/pypy3.9-v7.3.11-linux64/bin:/usr/local/MRIcroGL:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/local/games:/usr/games:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/leonard/.cargo/bin:/home/leonard/.local/bin/pypy3.9-v7.3.11-linux64/bin:/usr/local/MRIcroGL:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/local/games:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin



### Relevant log output

_No response_

### Anything else?

_No response_

### Is there an existing issue for this? - [X] I have searched the existing issues ### Current Behavior [In this table](https://juaml.github.io/junifer/main/builtin.html#id6) the extended multiple-demand network is correctly listed as `extMDN`, but when using the following marker: ``` - name: extMDN kind: SphereAggregation coords: extMDN radius: 5 method: mean ``` one gets the following error: ``` ValueError: Coordinates extMDN not found. ``` Using the `list_coordinates()` function, it seems clear why: The naming is incorrect in junifer (`extDMN`) ``` >>> from junifer.data.coordinates import list_coordinates >>> list_coordinates() ['CogAC', 'CogAR', 'DMNBuckner', 'Dosenbach', 'Empathy', 'Motor', 'MultiTask', 'PhysioStress', 'Power', 'Rew', 'Somatosensory', 'ToM', 'VigAtt', 'WM', 'eMDN', 'eSAD', 'extDMN'] ``` ### Expected Behavior It should have the correct name and the marker should work. ### Steps To Reproduce described above ### Environment ```markdown ❱ junifer wtf 130 ! junifer: version: 0.0.2 python: version: 3.11.4 implementation: CPython dependencies: click: 8.1.3 numpy: 1.23.5 datalad: 0.18.4 pandas: 1.5.3 nibabel: 4.0.2 nilearn: 0.10.0 sqlalchemy: 1.4.48 yaml: '6.0' system: platform: Linux-6.2.0-27-generic-x86_64-with-glibc2.37 environment: LC_CTYPE: en_US.UTF-8 PATH: /home/leonard/.venvs/base/bin:/home/leonard/.local/bin/pypy3.9-v7.3.11-linux64/bin:/usr/local/MRIcroGL:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/local/games:/usr/games:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/leonard/.cargo/bin:/home/leonard/.local/bin/pypy3.9-v7.3.11-linux64/bin:/usr/local/MRIcroGL:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/local/games:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin ``` ``` ### Relevant log output _No response_ ### Anything else? _No response_

fraimondo commented

2023-10-04 10:30:48 +00:00

(Migrated from github.com)

Bug in the documentation:

Extended multiple-demand network should be eMDN
extDMN is the Extended Default Mode Network.

Bug in the documentation: - Extended multiple-demand network should be `eMDN` - `extDMN` is the Extended Default Mode Network.

codecov[bot] commented

2023-10-05 08:52:03 +00:00

(Migrated from github.com)

Codecov Report

Merging #251 (47d9e52) into main (22ca06f) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             main     #251   +/-   ##
=======================================
  Coverage   93.03%   93.03%           
=======================================
  Files          84       84           
  Lines        3718     3718           
  Branches      724      724           
=======================================
  Hits         3459     3459           
  Misses        161      161           
  Partials       98       98

Flag	Coverage Δ
docs	`100.00% <ø> (ø)`

Flags with carried forward coverage won't be shown. Click here to find out more.

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fraimondo (Migrated from github.com) approved these changes

2023-10-05 08:57:03 +00:00