Copy BEM surfaces by default (don't symlink) #10531
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Several (all?) Windows users attenting a workshop we hosted yesterday were running into issues when working with BEM surfaces we had shared with them as part of a FreeSurfer subjects directory. The reason was that transferring the symlinks turned out to be problematic, and this users ended up with invalid files. They had to manually copy over the BEM surfaces from the `bem/flash` or `bem/watershed` (?) directories to `bem/` and rename them. Since our collaborators are working in highly heterogenous settings (macOS, Linux, Windows), this is indeed a huge problem for data sharing, and it's not obvious at all to a common user WHY things are not working as expected. I therefore here propose an API change without deprecation cycle, changing the default value of the `make_*_bem()` functions' `copy` parameter from `False` to `True`, to always create a copy by default (and not a symlink). I'd further like to propose we change our sample data accordingly, getting rid of the symbolic links for the BEM surfaces there as well. I'm happy to discuss this at today's office hour. cc @agramfort
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This is ready for review. I would even opt for backporting this to the 1.0 branch. |
agramfort
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Apr 15, 2022
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I tested this locally and it seems to be doing the Right Thing. |
larsoner
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Apr 15, 2022
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* upstream/main: (40 commits) FIX: Flake (mne-tools#10540) FIX: Correct link (mne-tools#10536) DOC: Update installers (mne-tools#10535) ENH: Add dark mode to website (mne-tools#10523) WIP: Copy BEM surfaces by default (don't symlink) (mne-tools#10531) Avoid lowpass=0 in brainvision data (mne-tools#10517) DOC: Update installers [skip azp] [skip actions] (mne-tools#10528) FIX: Fix for old build (mne-tools#10527) Fix line noise at wrong frequencies (mne-tools#10525) FIX : read fids in eeglab (mne-tools#10521) MAINT: Prefer PySide6 in testing (mne-tools#10513) ENH: Add overview_mode support (mne-tools#10501) MRG: Updates for qtpy in mne-qt-browser (mne-tools#10509) BUG: Fix bug with themes on macOS (mne-tools#10500) MAINT: Bump installer links (mne-tools#10511) Add metadata to combine_channels (mne-tools#10504) MAINT: Standardize tests (mne-tools#10502) CI: Test circle (mne-tools#10506) ENH: Use HiDPI splash screen on HiDPI screens (mne-tools#10503) WIP,MNT: Add support for QtPy (mne-tools#10430) ...
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* upstream/main: (52 commits) MAINT: Extra test for coreg (mne-tools#10549) BUG: Fix annot meas_date / crop (mne-tools#10491) Update latest.inc Use liblinear solver instead of lbgfs in all decodung examples [skip azp][skip actions] (mne-tools#10552) STY: Hotfix for HTML [ci skip] Allow making inverse solutions from fixed-orientation discrete forward models, enabling multi-dipole modeling (mne-tools#10464) Correct documented default number of CV splits [skip azp][skip actions] (mne-tools#10548) MRG: Add error checking to prevent the creation of montage with invalid [x, y, z] (mne-tools#10547) MRG: Add "verbose" parameter to pick_channels() method (mne-tools#10544) CI: Avoid bad PySide6 (mne-tools#10545) FIX: Flake (mne-tools#10540) FIX: Correct link (mne-tools#10536) DOC: Update installers (mne-tools#10535) ENH: Add dark mode to website (mne-tools#10523) WIP: Copy BEM surfaces by default (don't symlink) (mne-tools#10531) Avoid lowpass=0 in brainvision data (mne-tools#10517) DOC: Update installers [skip azp] [skip actions] (mne-tools#10528) FIX: Fix for old build (mne-tools#10527) Fix line noise at wrong frequencies (mne-tools#10525) FIX : read fids in eeglab (mne-tools#10521) ...
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Several (all?) Windows users attending a workshop @agramfort and I hosted yesterday were running into issues when working with BEM surfaces we had shared with them as part of a FreeSurfer subjects directory.
The reason was that transferring the symlinks turned out to be problematic, and thus, users ended up with invalid files. They had to manually copy over the BEM surfaces from the
bem/flashorbem/watershed(?) directories tobem/and rename them.Since our collaborators are working in highly heterogenous settings (macOS, Linux, Windows), this is indeed a huge problem for data sharing, and it's not obvious at all to a common user WHY things are not working as expected.
I therefore here propose an API change without deprecation cycle, changing the default value of the
make_*_bem()functions'copyparameter fromFalsetoTrue, to always create a copy by default (and not a symlink).I'd further like to propose we change our sample data accordingly, getting rid of the symbolic links for the BEM surfaces there as well.
I'm happy to discuss this at today's office hour.
cc @agramfort