Pull 26.0.1 and 26.0.2 bug fixes into main

[laemtl]

Replace #1225

[maximemulder]

Regarding the CI failures:

• The "XXX is deprecated" type checks are not blocking, you can ignore them if you want to.
• The blocking type check is Error: Import "delete_physiological_file" could not be resolved. You can either use from scripts.delete_physiological_file import xxx or (preferably) put the function you need somewhere in the lib modules.
• You can use ruff check --fix to sort imports and fix trivial formatting issues.

[maximemulder]

Thanks for updating the PR ! Small things I found while reading the code.

Halp I got it wrong.

[maximemulder]

Review take two.

[laemtl]

Will test and fix the static errors soon! Blocked.

[laemtl]

• The blocking type check is Error: Import "delete_physiological_file" could not be resolved. You can either use from scripts.delete_physiological_file import xxx or (preferably) put the function you need somewhere in the lib modules.

I left it in script because delete_physiological_file is a script, not a lib.

[maximemulder]

Thanks for the PR, I added a commit to set the new script as executable:

git update-index --chmod=+x python/scripts/delete_physiological_file.py

The new script works on my machine (although not sure if we really want to print the paths as {FilePath: '...'}) !

(loris-mri-python) lorisadmin@loris:/opt/loris/bin/mri$ delete_physiological_file.py --fileid 1 --profile database_config.py --confirm --deleteondisk

Archives
----------------------------
({'FilePath': 'bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT167/ses-V1/eeg/sub-OTT167_ses-V1_task-faceO_eeg.tgz'},)

Physiological File
----------------------------
({'FilePath': 'bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT167/ses-V1/eeg/sub-OTT167_ses-V1_task-faceO_eeg.edf'},)

Physiological Metadata File
----------------------------
()

Channels
----------------------------
({'FilePath': 'bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT167/ses-V1/eeg/sub-OTT167_ses-V1_task-faceO_channels.tsv'},)

Electrodes
----------------------------
({'FilePath': 'bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT167/ses-V1/eeg/sub-OTT167_ses-V1_task-faceO_electrodes.tsv'},)

Coordinate Systems
----------------------------
()

Event Files
----------------------------
({'FilePath': 'bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT167/ses-V1/eeg/sub-OTT167_ses-V1_task-faceO_events.tsv'},)

Event Archives
----------------------------
()

Chunks
----------------------------
({'FilePath': 'bids_imports/Face13_BIDSVersion_1.1.0_chunks/sub-OTT167_ses-V1_task-faceO_eeg.chunks'},)

Dropping all DB entries for physiological file: 1

----------------------------

Delete physiological_event_parameter_category_level

Delete physiological_event_parameter

Delete physiological_channel

Delete physiological_electrode

Delete physiological_coord_system_point_3d_rel

Delete point_3d

Delete physiological_coord_system

Delete physiological_coord_system_electrode_rel

Delete physiological_electrode

Delete physiological_parameter_file

Delete physiological_archive

Delete physiological_event_archive

Delete physiological_task_event_opt

Delete physiological_task_event_hed_rel

Delete physiological_task_event

Delete physiological_event_file

Delete physiological_file


Deleting files on disk for physiological file: 1

----------------------------

Deleting file bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT167/ses-V1/eeg/sub-OTT167_ses-V1_task-faceO_eeg.tgz

Deleting file bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT167/ses-V1/eeg/sub-OTT167_ses-V1_task-faceO_eeg.edf

Deleting file bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT167/ses-V1/eeg/sub-OTT167_ses-V1_task-faceO_channels.tsv

Deleting file bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT167/ses-V1/eeg/sub-OTT167_ses-V1_task-faceO_electrodes.tsv

Deleting file bids_imports/Face13_BIDSVersion_1.1.0/sub-OTT167/ses-V1/eeg/sub-OTT167_ses-V1_task-faceO_events.tsv