git pull && git annex get . at forked source

I fetched upstream spine-generic:data-multi-subject into https://github.com/renelabounek/data-multi-subject. Then I called
git pull && git annex get .

and have got following errors saying me that re-defaced T1w images were not downloaded throught the git annex:
get sub-amu01/anat/sub-amu01_T1w.nii.gz (not available)
  No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-amu02/anat/sub-amu02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-amu03/anat/sub-amu03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-amu04/anat/sub-amu04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-amu05/anat/sub-amu05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-balgrist01/anat/sub-balgrist01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-balgrist02/anat/sub-balgrist02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-balgrist03/anat/sub-balgrist03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-balgrist04/anat/sub-balgrist04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-balgrist05/anat/sub-balgrist05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-balgrist06/anat/sub-balgrist06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-brnoCeitec01/anat/sub-brnoCeitec01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-brnoCeitec02/anat/sub-brnoCeitec02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-brnoCeitec03/anat/sub-brnoCeitec03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-brnoCeitec04/anat/sub-brnoCeitec04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-brnoCeitec05/anat/sub-brnoCeitec05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-brnoCeitec06/anat/sub-brnoCeitec06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-brnoUhb01/anat/sub-brnoUhb01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-brnoUhb02/anat/sub-brnoUhb02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-brnoUhb03/anat/sub-brnoUhb03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-brnoUhb04/anat/sub-brnoUhb04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-brnoUhb05/anat/sub-brnoUhb05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-brnoUhb06/anat/sub-brnoUhb06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-brnoUhb07/anat/sub-brnoUhb07_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-brnoUhb08/anat/sub-brnoUhb08_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-cmrra01/anat/sub-cmrra01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-cmrra02/anat/sub-cmrra02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-cmrra03/anat/sub-cmrra03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-cmrra04/anat/sub-cmrra04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-cmrra05/anat/sub-cmrra05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-cmrra06/anat/sub-cmrra06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-cmrrb01/anat/sub-cmrrb01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-cmrrb02/anat/sub-cmrrb02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-cmrrb03/anat/sub-cmrrb03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-cmrrb04/anat/sub-cmrrb04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-cmrrb05/anat/sub-cmrrb05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-cmrrb06/anat/sub-cmrrb06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-cmrrb07/anat/sub-cmrrb07_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-dresden01/anat/sub-dresden01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-dresden02/anat/sub-dresden02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-geneva01/anat/sub-geneva01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-geneva02/anat/sub-geneva02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-geneva03/anat/sub-geneva03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-geneva04/anat/sub-geneva04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-geneva05/anat/sub-geneva05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-geneva06/anat/sub-geneva06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-juntendo750w01/anat/sub-juntendo750w01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-juntendo750w02/anat/sub-juntendo750w02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-juntendo750w03/anat/sub-juntendo750w03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-juntendo750w04/anat/sub-juntendo750w04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-juntendo750w05/anat/sub-juntendo750w05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-juntendo750w06/anat/sub-juntendo750w06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-nottwil01/anat/sub-nottwil01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-nottwil02/anat/sub-nottwil02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-nottwil03/anat/sub-nottwil03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-nottwil04/anat/sub-nottwil04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-nottwil05/anat/sub-nottwil05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-nottwil06/anat/sub-nottwil06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-nwu01/anat/sub-nwu01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-nwu02/anat/sub-nwu02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-nwu03/anat/sub-nwu03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-nwu04/anat/sub-nwu04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-nwu05/anat/sub-nwu05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-nwu06/anat/sub-nwu06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-oxfordFmrib01/anat/sub-oxfordFmrib01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-oxfordFmrib02/anat/sub-oxfordFmrib02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-oxfordFmrib03/anat/sub-oxfordFmrib03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-oxfordFmrib04/anat/sub-oxfordFmrib04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-oxfordFmrib05/anat/sub-oxfordFmrib05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-oxfordFmrib06/anat/sub-oxfordFmrib06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-oxfordFmrib07/anat/sub-oxfordFmrib07_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-oxfordFmrib08/anat/sub-oxfordFmrib08_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-oxfordFmrib09/anat/sub-oxfordFmrib09_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-oxfordFmrib10/anat/sub-oxfordFmrib10_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-oxfordFmrib11/anat/sub-oxfordFmrib11_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-oxfordOhba01/anat/sub-oxfordOhba01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-oxfordOhba02/anat/sub-oxfordOhba02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-oxfordOhba03/anat/sub-oxfordOhba03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-oxfordOhba04/anat/sub-oxfordOhba04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-oxfordOhba05/anat/sub-oxfordOhba05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-pavia01/anat/sub-pavia01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-perform01/anat/sub-perform01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-perform02/anat/sub-perform02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-perform03/anat/sub-perform03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-perform04/anat/sub-perform04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-perform05/anat/sub-perform05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-perform06/anat/sub-perform06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-queensland01/anat/sub-queensland01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-queensland02/anat/sub-queensland02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-queensland03/anat/sub-queensland03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-queensland04/anat/sub-queensland04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-queensland05/anat/sub-queensland05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-queensland06/anat/sub-queensland06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-sherbrooke01/anat/sub-sherbrooke01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-sherbrooke02/anat/sub-sherbrooke02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-sherbrooke03/anat/sub-sherbrooke03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-sherbrooke04/anat/sub-sherbrooke04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-sherbrooke05/anat/sub-sherbrooke05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-sherbrooke06/anat/sub-sherbrooke06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-sherbrooke07/anat/sub-sherbrooke07_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-stanford01/anat/sub-stanford01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-stanford02/anat/sub-stanford02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-stanford03/anat/sub-stanford03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-stanford04/anat/sub-stanford04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-stanford05/anat/sub-stanford05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-stanford06/anat/sub-stanford06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-strasbourg01/anat/sub-strasbourg01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-strasbourg02/anat/sub-strasbourg02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-strasbourg03/anat/sub-strasbourg03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-strasbourg04/anat/sub-strasbourg04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-strasbourg05/anat/sub-strasbourg05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-strasbourg06/anat/sub-strasbourg06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-tokyo750w01/anat/sub-tokyo750w01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-tokyo750w02/anat/sub-tokyo750w02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-tokyo750w03/anat/sub-tokyo750w03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-tokyo750w04/anat/sub-tokyo750w04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-tokyo750w05/anat/sub-tokyo750w05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-tokyo750w06/anat/sub-tokyo750w06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-tokyo750w07/anat/sub-tokyo750w07_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-tokyoIngenia01/anat/sub-tokyoIngenia01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-tokyoIngenia02/anat/sub-tokyoIngenia02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-tokyoIngenia03/anat/sub-tokyoIngenia03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-tokyoIngenia04/anat/sub-tokyoIngenia04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-tokyoIngenia06/anat/sub-tokyoIngenia06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-tokyoIngenia07/anat/sub-tokyoIngenia07_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-tokyoSkyra01/anat/sub-tokyoSkyra01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-tokyoSkyra02/anat/sub-tokyoSkyra02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-tokyoSkyra03/anat/sub-tokyoSkyra03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-tokyoSkyra04/anat/sub-tokyoSkyra04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-tokyoSkyra05/anat/sub-tokyoSkyra05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-tokyoSkyra06/anat/sub-tokyoSkyra06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-tokyoSkyra07/anat/sub-tokyoSkyra07_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-ubc01/anat/sub-ubc01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-ubc02/anat/sub-ubc02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-ubc03/anat/sub-ubc03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-ubc04/anat/sub-ubc04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-ubc05/anat/sub-ubc05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-ubc06/anat/sub-ubc06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-unf01/anat/sub-unf01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-unf02/anat/sub-unf02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-unf03/anat/sub-unf03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-unf04/anat/sub-unf04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-unf05/anat/sub-unf05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-unf06/anat/sub-unf06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-unf07/anat/sub-unf07_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-vallHebron01/anat/sub-vallHebron01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-vallHebron02/anat/sub-vallHebron02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-vallHebron03/anat/sub-vallHebron03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-vallHebron04/anat/sub-vallHebron04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-vallHebron05/anat/sub-vallHebron05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-vallHebron06/anat/sub-vallHebron06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-vallHebron07/anat/sub-vallHebron07_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-vuiisAchieva01/anat/sub-vuiisAchieva01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-vuiisAchieva02/anat/sub-vuiisAchieva02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-vuiisAchieva03/anat/sub-vuiisAchieva03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-vuiisAchieva04/anat/sub-vuiisAchieva04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-vuiisAchieva05/anat/sub-vuiisAchieva05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-vuiisAchieva06/anat/sub-vuiisAchieva06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-vuiisIngenia01/anat/sub-vuiisIngenia01_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-vuiisIngenia02/anat/sub-vuiisIngenia02_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-vuiisIngenia03/anat/sub-vuiisIngenia03_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-vuiisIngenia04/anat/sub-vuiisIngenia04_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-vuiisIngenia05/anat/sub-vuiisIngenia05_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed
get sub-vuiisIngenia06/anat/sub-vuiisIngenia06_T1w.nii.gz (not available)
No other repository is known to contain the file.
(Note that these git remotes have annex-ignore set: origin upstream)
failed

Hi @renelabounek, thanks for reporting this issue. There are (at least) two things happening here:

We recently changed how the access permissions work on Amazon S3, where these files are stored, so currently they're not able to be downloaded. We'll get this fixed quickly, and we'll let you know as soon as things are back to normal.
But that's not the error message you're getting. Instead, it seems that git-annex has decided to ignore the origin and upstream repositories, so it's not even trying to download the files from Amazon S3. (git-annex tends to start ignoring a remote whenever it encounters problems with it.) You can confirm this by looking at the output of the following command (run inside the repository):git config --list | grep '^remote'

If it contains lines with annex-ignore, those remotes are currently ignored by git-annex. You can undo this with commands like:git config --unset remote.origin.annex-ignore
git config --unset remote.upstream.annex-ignore

You don't need to try this right now though; we'll let you know once the Amazon S3 permissions issue is fixed.

Hi @renelabounek, thanks for reporting this issue. There are (at least) two things happening here:

We recently changed how the access permissions work on Amazon S3, where these files are stored, so currently they're not able to be downloaded. We'll get this fixed quickly, and we'll let you know as soon as things are back to normal.

But that's not the error message you're getting. Instead, it seems that git-annex has decided to ignore the origin and upstream repositories, so it's not even trying to download the files from Amazon S3. (git-annex tends to start ignoring a remote whenever it encounters problems with it.) You can confirm this by looking at the output of the following command (run inside the repository):
git config --list | grep '^remote'

If it contains lines with annex-ignore, those remotes are currently ignored by git-annex. You can undo this with commands like:
git config --unset remote.origin.annex-ignore
git config --unset remote.upstream.annex-ignore

You don't need to try this right now though; we'll let you know once the Amazon S3 permissions issue is fixed.

Ok I will do step 2, when you let me know that the issue 1 is fixed. Thanks, Rene

Ok, I think we don't need the origin and upstream remotes, at least for now, so please ignore step 2 from my previous comment. Can you try these commands:
git annex enableremote amazon public=yes
git annex get sub-amu01/anat/sub-amu01_T1w.nii.gz

If that works, then you should be able to retry downloading everything:
git annex get .

Otherwise, could you post the results of these commands please?
git config --list | grep '^remote'
git annex whereis sub-amu01/anat/sub-amu01_T1w.nii.gz

It di not pass. STDOUTs are below. I have not done the step 2 (i.e. the git config --unset commands), as you said not to do.
(base) [labounek@porto data-multi-subject]$ git annex enableremote amazon public=yes
enableremote amazon ok
(recording state in git...)
(base) [labounek@porto data-multi-subject]$ git annex get sub-amu01/anat/sub-amu01_T1w.nii.gz
get sub-amu01/anat/sub-amu01_T1w.nii.gz (not available)
  No other repository is known to contain the file.

  (Note that these git remotes have annex-ignore set: origin upstream)
failed
get: 1 failed
(base) [labounek@porto data-multi-subject]$

(base) [labounek@porto data-multi-subject]$ git config --list | grep '^remote'
remote.origin.url=https://github.com/renelabounek/data-multi-subject.git
remote.origin.fetch=+refs/heads/*:refs/remotes/origin/*
remote.origin.annex-ignore=true
remote.amazon.annex-s3=true
remote.amazon.annex-uuid=5a5447a8-a9b8-49bc-8276-01a62632b502
remote.amazon.annex-ignore=false
remote.amazon.skipfetchall=true
remote.upstream.url=https://github.com/spine-generic/data-multi-subject
remote.upstream.fetch=+refs/heads/*:refs/remotes/upstream/*
remote.upstream.annex-ignore=true
remote.upstream.annex-readonly=true
(base) [labounek@porto data-multi-subject]$

(base) [labounek@porto data-multi-subject]$ git annex whereis sub-amu01/anat/sub-amu01_T1w.nii.gz
whereis sub-amu01/anat/sub-amu01_T1w.nii.gz (0 copies) failed
whereis: 1 failed
(base) [labounek@porto data-multi-subject]$

Ok, I can reproduce this problem, and I have some idea why it's happening, and a potential way to fix it (though not 100%).
The problem:

git-annex stores a lot of metadata in a git branch called git-annex (including, where to find contents of files).
By default, I think git pull only gets data from remotes for the master branch, not for the git-annex branch.
Your fork, which is under github.com/renelabounek, and which is called origin on your computer, only contains metadata updates until November 2021, in its git-annex branch.
The original, which is under github.com/spine-generic, and which is called upstream on your computer, contains a lot more metadata updates, in its git-annex branch. This includes information about where to find the file sub-amu01/anat/sub-amu01_T1w.nii.gz, for example.
Unfortunately, I'm not sure (yet) how to bring the origin/git-annex branch up to date with the upstream/git-annex branch. Normally I would use this link to do a Github pull request from our repository to your fork, but there's a "Can’t automatically merge." error message. I'll have to look into this more later.
Thankfully, it looks like maybe you can still get the files without fixing this. The following command should tell your computer to get the current metadata from upstream/git-annex:git fetch upstream git-annex

After running that, do the following commands work?git annex whereis sub-amu01/anat/sub-amu01_T1w.nii.gz
git annex get sub-amu01/anat/sub-amu01_T1w.nii.gz

Nope, I am still not able to get the files.
(base) [labounek@porto data-multi-subject]$ git fetch upstream git-annex
remote: Enumerating objects: 57723, done.
remote: Counting objects: 100% (7627/7627), done.
remote: Compressing objects: 100% (6890/6890), done.
remote: Total 57723 (delta 41), reused 7624 (delta 39), pack-reused 50096
Receiving objects: 100% (57723/57723), 8.92 MiB | 1.80 MiB/s, done.
Resolving deltas: 100% (19046/19046), completed with 4 local objects.
From https://github.com/spine-generic/data-multi-subject
 * branch            git-annex  -> FETCH_HEAD
(base) [labounek@porto data-multi-subject]$

(base) [labounek@porto data-multi-subject]$ git annex whereis sub-amu01/anat/sub-amu01_T1w.nii.gz
whereis sub-amu01/anat/sub-amu01_T1w.nii.gz (0 copies) failed
whereis: 1 failed
(base) [labounek@porto data-multi-subject]$

(base) [labounek@porto data-multi-subject]$ git annex get sub-amu01/anat/sub-amu01_T1w.nii.gz
get sub-amu01/anat/sub-amu01_T1w.nii.gz (not available)
  No other repository is known to contain the file.

  (Note that these git remotes have annex-ignore set: origin upstream)
failed
get: 1 failed
(base) [labounek@porto data-multi-subject]$

I'm having trouble reproducing this problem on my computer. Could you tell me the output of the following commands, so that I have a better idea what's happening?
git log -n 5 git-annex
git log -n 5 origin/git-annex
git log -n 5 upstream/git-annex

Thanks.

Thanks for your help.  After trying to reproduce the problem on my computer, I think we can try to merge the information from the upstream/git-annex branch into the local git-annex branch with the following commands:

Start the automatic merging process, which we expect to fail (we'll fix this with the following commands).git checkout git-annex
git merge --no-edit --allow-unrelated-histories upstream/git-annex

We expect this to produce lots of output, ending with:...
Automatic merge failed; fix conflicts and then commit the result.

Fix the conflicts like this:git -c 'mergetool.custom.cmd=(echo "$MERGED" | grep -Eq [.]log$) && cat "$LOCAL" "$REMOTE" | sort -nu > "$MERGED"' \
    -c mergetool.custom.trustExitCode \
    -c mergetool.keepBackup=false \
    mergetool --tool=custom

This will probably take several minutes, and produce lots of output like this:Normal merge conflict for 'ffd/627/SHA256E-s2732168--10acedb4cccb4804dd8b34d4a3ca6fb846528e291a045cb4140eccb2d4e305eb.nii.gz.log':
  {local}: modified file
  {remote}: modified file

Normal merge conflict for 'ffd/736/SHA256E-s1897274--090e2c5f0d417e6e858297cbf92ba6e2ecd8c2b80e86a21d88f9f06bb053e332.nii.gz.log':
  {local}: modified file
  {remote}: modified file

Normal merge conflict for 'ffd/c3d/SHA256E-s1592114--0202f1d6b6a8e937730f21641398ee338fe071f3d1866837f189fd7beb9f31f3.nii.gz.log':
  {local}: modified file
  {remote}: modified file

Save the results:git -c core.editor=/bin/true merge --continue

This should produce a single line of output, like:[git-annex 693c29b0e] Merge remote-tracking branch 'upstream/git-annex' into git-annex

Get back to the master branch, and check if git-annex now knows that files exist on amazon:git checkout master
git annex whereis sub-amu01/anat/sub-amu01_T1w.nii.gz

If this succeeds, you may want to save the results to your fork on github, with the following command:git push origin git-annex:git-annex

If it still doesn't work I would need to know exactly which version of git-annex you have, which is in the output of the following command:
git annex version

Start the automatic merging process, which we expect to fail (we'll fix this with the following commands).
git checkout git-annex
git merge --no-edit --allow-unrelated-histories upstream/git-annex

We expect this to produce lots of output, ending with:
...
Automatic merge failed; fix conflicts and then commit the result.

My expected outputs started to appear different within the first set of commands. My git does not know allow-unrelated-histories. Should I continue? Or do we need to fix this first?
(base) [labounek@porto data-multi-subject]$ git checkout git-annex
Switched to branch 'git-annex'
Your branch is ahead of 'upstream/git-annex' by 5 commits.
  (use "git push" to publish your local commits)
(base) [labounek@porto data-multi-subject]$

(base) [labounek@porto data-multi-subject]$ git merge --no-edit --allow-unrelated-histories upstream/git-annex
error: unknown option `allow-unrelated-histories'
usage: git merge [options] [<commit>...]
   or: git merge [options] <msg> HEAD <commit>
   or: git merge --abort

    -n                    do not show a diffstat at the end of the merge
    --stat                show a diffstat at the end of the merge
    --summary             (synonym to --stat)
    --log[=<n>]           add (at most <n>) entries from shortlog to merge commit message
    --squash              create a single commit instead of doing a merge
    --commit              perform a commit if the merge succeeds (default)
    -e, --edit            edit message before committing
    --ff                  allow fast-forward (default)
    --ff-only             abort if fast-forward is not possible
    --rerere-autoupdate   update the index with reused conflict resolution if possible
    --verify-signatures   Verify that the named commit has a valid GPG signature
    -s, --strategy <strategy>
                          merge strategy to use
    -X, --strategy-option <option=value>
                          option for selected merge strategy
    -m, --message <message>
                          merge commit message (for a non-fast-forward merge)
    -v, --verbose         be more verbose
    -q, --quiet           be more quiet
    --abort               abort the current in-progress merge
    --progress            force progress reporting
    -S, --gpg-sign[=<key id>]
                          GPG sign commit
    --overwrite-ignore    update ignored files (default)

(base) [labounek@porto data-multi-subject]$

I assume it is a git version issue. Unfortunatelly, I am not admin at the server where the database is stored. So update git can be tricky or even impossible for me. Any other possibility before I will write to server admins the update request?
(base) [labounek@porto data-multi-subject]$ git --version
git version <IP_ADDRESS>
(base) [labounek@porto data-multi-subject]$

Yes, it looks like a git version issue. Thankfully, that option is only
needed for recent versions of git to make them act like older versions of
git, so you can safely remove just that option and try again.
(Thanks for including your exact git version, that will help with fixing
things.)
On Thu., Jul. 21, 2022, 11:19 a.m. Rene Labounek, @.***>
wrote:

Start the automatic merging process, which we expect to fail (we'll
fix this with the following commands).
git checkout git-annex
git merge --no-edit --allow-unrelated-histories upstream/git-annex
We expect this to produce lots of output, ending with:
...
Automatic merge failed; fix conflicts and then commit the result.
My expected outputs started to appear different within the first set of
commands. My git does not know allow-unrelated-histories. Should I
continue? Or do we need to fix this first?
(base) @.*** data-multi-subject]$ git checkout git-annex
Switched to branch 'git-annex'
Your branch is ahead of 'upstream/git-annex' by 5 commits.
(use "git push" to publish your local commits)
(base) @.*** data-multi-subject]$
(base) @.*** data-multi-subject]$ git merge --no-edit --allow-unrelated-histories upstream/git-annex
error: unknown option `allow-unrelated-histories'
usage: git merge [options] [...]
or: git merge [options]  HEAD
or: git merge --abort
-n                    do not show a diffstat at the end of the merge
--stat                show a diffstat at the end of the merge
--summary             (synonym to --stat)
--log[=<n>]           add (at most <n>) entries from shortlog to merge commit message
--squash              create a single commit instead of doing a merge
--commit              perform a commit if the merge succeeds (default)
-e, --edit            edit message before committing
--ff                  allow fast-forward (default)
--ff-only             abort if fast-forward is not possible
--rerere-autoupdate   update the index with reused conflict resolution if possible
--verify-signatures   Verify that the named commit has a valid GPG signature
-s, --strategy <strategy>
                      merge strategy to use
-X, --strategy-option <option=value>
                      option for selected merge strategy
-m, --message <message>
                      merge commit message (for a non-fast-forward merge)
-v, --verbose         be more verbose
-q, --quiet           be more quiet
--abort               abort the current in-progress merge
--progress            force progress reporting
-S, --gpg-sign[=<key id>]
                      GPG sign commit
--overwrite-ignore    update ignored files (default)

(base) @.*** data-multi-subject]$
I assume it is a git version issue
https://stackoverflow.com/questions/41356766/unknown-option-allow-unrelated-histories.
Unfortunatelly, I am not admin at the server where the database is stored.
So update git can be tricky or even impossible for me. Any other
possibility before I will write to server admins the update request?
(base) @.*** data-multi-subject]$ git --version
git version <IP_ADDRESS>
(base) @.*** data-multi-subject]$
—
Reply to this email directly, view it on GitHub
https://github.com/spine-generic/data-multi-subject/issues/125#issuecomment-1191619144,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AAHCXZWTZRZMNTAWV6XNNTLVVFS7XANCNFSM53TMY4DA
.
You are receiving this because you were assigned.Message ID:
@.***>

First two commands appears that everythin is up to date. The third command does not know flag --continue. Possibly, again, version issue.
(base) [labounek@porto data-multi-subject]$ git merge --no-edit upstream/git-annex
Already up-to-date.
(base) [labounek@porto data-multi-subject]$

(base) [labounek@porto data-multi-subject]$ git -c 'mergetool.custom.cmd=(echo "$MERGED" | grep -Eq [.]log$) && cat "$LOCAL" "$REMOTE" | sort -nu > "$MERGED"' \
>     -c mergetool.custom.trustExitCode \
>     -c mergetool.keepBackup=false \
>     mergetool --tool=custom
No files need merging
(base) [labounek@porto data-multi-subject]$

(base) [labounek@porto data-multi-subject]$ git -c core.editor=/bin/true merge --continue
error: unknown option `continue'
usage: git merge [options] [<commit>...]
   or: git merge [options] <msg> HEAD <commit>
   or: git merge --abort

    -n                    do not show a diffstat at the end of the merge
    --stat                show a diffstat at the end of the merge
    --summary             (synonym to --stat)
    --log[=<n>]           add (at most <n>) entries from shortlog to merge commit message
    --squash              create a single commit instead of doing a merge
    --commit              perform a commit if the merge succeeds (default)
    -e, --edit            edit message before committing
    --ff                  allow fast-forward (default)
    --ff-only             abort if fast-forward is not possible
    --rerere-autoupdate   update the index with reused conflict resolution if possible
    --verify-signatures   Verify that the named commit has a valid GPG signature
    -s, --strategy <strategy>
                          merge strategy to use
    -X, --strategy-option <option=value>
                          option for selected merge strategy
    -m, --message <message>
                          merge commit message (for a non-fast-forward merge)
    -v, --verbose         be more verbose
    -q, --quiet           be more quiet
    --abort               abort the current in-progress merge
    --progress            force progress reporting
    -S, --gpg-sign[=<key id>]
                          GPG sign commit
    --overwrite-ignore    update ignored files (default)

(base) [labounek@porto data-multi-subject]$

From the output of your commands, it looks like the git-annex branch on
your computer already contains all the information from both
origin/git-annex and upstream/git-annex, with no conflicts. So, the
first command git merge correctly and successfully did nothing (but I was
expecting a merge conflict); the second command also saw no conflicts and
did nothing; and the third command git merge --continue didn't recognize
the --continue flag (probably a git version issue, yes), but in this
situation that command didn't need to do anything so that's ok.
Can you try the next commands? And whether or not it succeeds, if you can
do the last command (for saving the git-annex state to your fork on
github), at least I should be able to examine the state myself to figure
out what's going on.
On Thu., Jul. 21, 2022, 11:49 a.m. Rene Labounek, @.***>
wrote:

First two commands appears that everythin is up to date. The third command
does not know flag --continue. Possibly, again, version issue.
(base) @.*** data-multi-subject]$ git merge --no-edit upstream/git-annex
Already up-to-date.
(base) @.*** data-multi-subject]$
(base) @.*** data-multi-subject]$ git -c 'mergetool.custom.cmd=(echo "$MERGED" | grep -Eq [.]log$) && cat "$LOCAL" "$REMOTE" | sort -nu > "$MERGED"' \

-c mergetool.custom.trustExitCode \
-c mergetool.keepBackup=false \
mergetool --tool=custom

No files need merging
(base) @.*** data-multi-subject]$
(base) @.*** data-multi-subject]$ git -c core.editor=/bin/true merge --continue
error: unknown option `continue'
usage: git merge [options] [...]
or: git merge [options]  HEAD
or: git merge --abort
-n                    do not show a diffstat at the end of the merge
--stat                show a diffstat at the end of the merge
--summary             (synonym to --stat)
--log[=<n>]           add (at most <n>) entries from shortlog to merge commit message
--squash              create a single commit instead of doing a merge
--commit              perform a commit if the merge succeeds (default)
-e, --edit            edit message before committing
--ff                  allow fast-forward (default)
--ff-only             abort if fast-forward is not possible
--rerere-autoupdate   update the index with reused conflict resolution if possible
--verify-signatures   Verify that the named commit has a valid GPG signature
-s, --strategy <strategy>
                      merge strategy to use
-X, --strategy-option <option=value>
                      option for selected merge strategy
-m, --message <message>
                      merge commit message (for a non-fast-forward merge)
-v, --verbose         be more verbose
-q, --quiet           be more quiet
--abort               abort the current in-progress merge
--progress            force progress reporting
-S, --gpg-sign[=<key id>]
                      GPG sign commit
--overwrite-ignore    update ignored files (default)

(base) @.*** data-multi-subject]$
—
Reply to this email directly, view it on GitHub
https://github.com/spine-generic/data-multi-subject/issues/125#issuecomment-1191654317,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AAHCXZWY7ZNXPSPFNARWOTDVVFWQFANCNFSM53TMY4DA
.
You are receiving this because you were assigned.Message ID:
@.***>

@mguaypaq, sorry for ym delay. I was not around computer much through the weekend. File download failed again. Bellow are the outputs.
Thanks, Rene
(base) [labounek@porto data-multi-subject]$ git checkout master
Checking out files: 100% (7613/7613), done.
Switched to branch 'master'
(base) [labounek@porto data-multi-subject]$

(base) [labounek@porto data-multi-subject]$ git annex whereis sub-amu01/anat/sub-amu01_T1w.nii.gz
whereis sub-amu01/anat/sub-amu01_T1w.nii.gz (0 copies) failed
whereis: 1 failed
(base) [labounek@porto data-multi-subject]$

(base) [labounek@porto data-multi-subject]$ git annex version
git-annex version: 8.20211012-geb95ed486
build flags: Assistant Webapp Pairing Inotify DBus DesktopNotify TorrentParser MagicMime Feeds Testsuite S3 WebDAV
dependency versions: aws-0.22 bloomfilter-<IP_ADDRESS> cryptonite-0.26 DAV-1.3.4 feed-<IP_ADDRESS> ghc-8.8.4 http-client-<IP_ADDRESS> persistent-sqlite-<IP_ADDRESS> torrent-10000.1.1 uuid-1.3.13 yesod-<IP_ADDRESS>
key/value backends: SHA256E SHA256 SHA512E SHA512 SHA224E SHA224 SHA384E SHA384 SHA3_256E SHA3_256 SHA3_512E SHA3_512 SHA3_224E SHA3_224 SHA3_384E SHA3_384 SKEIN256E SKEIN256 SKEIN512E SKEIN512 BLAKE2B256E BLAKE2B256 BLAKE2B512E BLAKE2B512 BLAKE2B160E BLAKE2B160 BLAKE2B224E BLAKE2B224 BLAKE2B384E BLAKE2B384 BLAKE2BP512E BLAKE2BP512 BLAKE2S256E BLAKE2S256 BLAKE2S160E BLAKE2S160 BLAKE2S224E BLAKE2S224 BLAKE2SP256E BLAKE2SP256 BLAKE2SP224E BLAKE2SP224 SHA1E SHA1 MD5E MD5 WORM URL X*
remote types: git gcrypt p2p S3 bup directory rsync web bittorrent webdav adb tahoe glacier ddar git-lfs httpalso borg hook external
operating system: linux x86_64
supported repository versions: 8
upgrade supported from repository versions: 0 1 2 3 4 5 6 7
local repository version: 8
(base) [labounek@porto data-multi-subject]$

Ah, examining the previous output you gave me more carefully, I see that git fetch upstream git-annex did not do exactly what I expected, probably because of the older git version. I'm sorry. Can you try the following command:
git fetch upstream

After that, I would be curious if the following command now works (and the output):
git annex whereis sub-amu01/anat/sub-amu01_T1w.nii.gz

If it fails, the output of the following commands could help me figure out what's going on:
git status
git show master:sub-amu01/anat/sub-amu01_T1w.nii.gz
git show git-annex:8db/012/SHA256E-s15565632--20fa8ec26515317c0871c129300c3ca6a44a20b8c48275e07ba46a0b9d22210a.nii.gz.log
git show origin/git-annex:8db/012/SHA256E-s15565632--20fa8ec26515317c0871c129300c3ca6a44a20b8c48275e07ba46a0b9d22210a.nii.gz.log
git show upstream/git-annex:8db/012/SHA256E-s15565632--20fa8ec26515317c0871c129300c3ca6a44a20b8c48275e07ba46a0b9d22210a.nii.gz.log

This really helped. See outputs bellow. Sorry for the hessle. But in summary, what was generally different for the forked database when compared to the README.md method? Just to start with the git fetch upstream before git pull && git annex get .. Or was there something else needed to be done?
@mguaypaq, thank you very much for your time and help.
Rene
(base) [labounek@porto data-multi-subject]$ git fetch upstream
remote: Enumerating objects: 63657, done.
remote: Counting objects: 100% (13269/13269), done.
remote: Compressing objects: 100% (11272/11272), done.
remote: Total 63657 (delta 1165), reused 13254 (delta 1159), pack-reused 50388
Receiving objects: 100% (63657/63657), 9.57 MiB | 2.91 MiB/s, done.
Resolving deltas: 100% (20171/20171), completed with 271 local objects.
From https://github.com/spine-generic/data-multi-subject
 * [new branch]      af/fix_images -> upstream/af/fix_images
 * [new branch]      af/update_participants_tsv -> upstream/af/update_participants_tsv
 * [new branch]      af/update_sub-ucl06_GH_direct -> upstream/af/update_sub-ucl06_GH_direct
 + e40f90c...15efe2d git-annex  -> upstream/git-annex  (forced update)
 * [new branch]      master     -> upstream/master
 * [new branch]      mt-entity  -> upstream/mt-entity
 * [new branch]      ng/ci-cache -> upstream/ng/ci-cache
 * [new branch]      renelabounek-master -> upstream/renelabounek-master
 * [new branch]      rl/height-weight -> upstream/rl/height-weight
 * [new branch]      sb/121-move-derivatives -> upstream/sb/121-move-derivatives
 * [new branch]      synced/af/csfseg_json -> upstream/synced/af/csfseg_json
 * [new branch]      synced/jca/17-defacing -> upstream/synced/jca/17-defacing
 * [new branch]      synced/jca/21-travis -> upstream/synced/jca/21-travis
 * [new branch]      synced/jca/7-check-data-consistency -> upstream/synced/jca/7-check-data-consistency
 * [new branch]      synced/jca/derivatives-r20200830-mts -> upstream/synced/jca/derivatives-r20200830-mts
 * [new branch]      synced/jca/participants -> upstream/synced/jca/participants
 * [new branch]      synced/jca/readme -> upstream/synced/jca/readme
 * [new branch]      synced/jca/reupload-disc-labels -> upstream/synced/jca/reupload-disc-labels
 * [new branch]      synced/jca/update-derivatives -> upstream/synced/jca/update-derivatives
 * [new tag]         r20201001  -> r20201001
 * [new tag]         r20201130  -> r20201130
 * [new tag]         r20211125  -> r20211125
 * [new tag]         r20220125  -> r20220125
(base) [labounek@porto data-multi-subject]$

(base) [labounek@porto data-multi-subject]$ git annex whereis sub-amu01/anat/sub-amu01_T1w.nii.gz
(merging upstream/git-annex into git-annex...)
(recording state in git...)
whereis sub-amu01/anat/sub-amu01_T1w.nii.gz (3 copies)
  	5a5447a8-a9b8-49bc-8276-01a62632b502 -- [amazon]
   	e405e14e-33b2-4a35-b7a7-3eeec054f0d4 -- sebeda@joplin.neuro.polymtl.ca:/mnt/nvme/sebeda/data-multi-subject
   	fc75435d-eb11-4c5a-9b68-debf6e68df2a -- alex@MacBook.local:~/data/data-multi-subject

  amazon: https://data-multi-subject---spine-generic---neuropoly.s3.ca-central-1.amazonaws.com/SHA256E-s15565632--20fa8ec26515317c0871c129300c3ca6a44a20b8c48275e07ba46a0b9d22210a.nii.gz
ok
(base) [labounek@porto data-multi-subject]$

(base) [labounek@porto data-multi-subject]$ git annex get sub-amu01/anat/sub-amu01_T1w.nii.gz
get sub-amu01/anat/sub-amu01_T1w.nii.gz (from amazon...)

ok
(recording state in git...)
(base) [labounek@porto data-multi-subject]$

Great! I'm so glad it works now :tada:

But in summary, what was generally different for the forked database when compared to the README.md method? Just to start with the git fetch upstream before git pull && git annex get .. Or was there something else needed to be done?

I think that's the main thing, yes, just doing git fetch upstream along with git pull before doing git annex get. The reason is:

git pull gets the contents of small files and hashes of the contents of big files into your local master branch (on your computer) from the origin/master branch (on your github fork). Possibly, depending on your settings, it also gets this from the upstream/master branch (on the original github repo), but typically your fork's origin/master is kept up to date with upstream/master so it doesn't matter.
git fetch upstream gets the locations of the contents of big files (for example, "the file contents that hashes to 12FA32 is available on amazon") into your local git-annex branch, from the upstream/git-annex branch. This was the missing part in your case. Github makes it easy to synchronize your fork's origin/master branch with upstream/master, but it doesn't do this by default for other branches, like origin/git-annex and upstream/git-annex. In fact, your fork's origin/git-annex branch is very much older than upstream/git-annex, so it doesn't have information about the location of newer file contents.
Once you have all this, git annex get looks at the hash of a file contents in master, uses this to look up a location in git-annex, and contacts this location (amazon, in this case) to get the actual contents.

Hopefully that explains this a bit!

A bit, yes... :-D I have the data updated, so we can close this issue. Only question remain, if my case was just too specific or if it would be worth to add the potential neccesity of the git fetch upstream command into README.md

Indeed! I'll open a separate issue for that. Thanks again for your patience!


Operator does not check if nodeAgent(s) are removed when reconciling a CR of the same name

Describe the bug:
When upgrading a 3.9.4 chart with Windows nodeAgent(s) installed, if the nodeAgent has been removed from the Logging CR in-use, the operator will not clean up the existing nodeAgent(s). This behavior is most likely the same for Linux nodeAgents as well.
Expected behaviour:
Similar to removing a fluentbit field from a Logging CR and running helm upgrade, running helm upgrade after removing a nodeAgent should result in the deletion of that nodeAgent.
Steps to reproduce the bug:

Install the Logging Operator 3.9.4 chart with a Logging CR bundled (this needs at least one nodeAgent (this was only tested with Windows)
Delete nodeAgent from the Logging CR
Run helm upgrade
nodeAgent will not be deleted

Additional context:
The Logging CR was bundled with the chart when this issue was first encountered.
Environment details:

Kubernetes version (e.g. v1.15.2): v.1.20.5
Cloud-provider/provisioner (e.g. AKS, GKE, EKS, PKE etc): n/a
logging-operator version (e.g. 2.1.1): 3.9.4
Install method (e.g. helm or static manifests): helm
Logs from the misbehaving component (and any other relevant logs): logs show no errors
Resource definition (possibly in YAML format) that caused the issue, without sensitive data: Logging CRD v1beta1

/kind bug

We had some discussions internally, but not yet finalized on what should we do about this.

We have an option to rewrite the reconciler core, which is a slightly bigger/riskier change and not yet put it on the roadmap.
The other option is to implement a more specific check into the reconcile loop, that would notice the difference between the desired state and the actual nodeagent resources and removes them. The problem is, that since we don't remove an actual resource, but only an item in the list, the Kubernetes GC won't notice.

Thank you for looking into this @pepov! Either option would be suitable for us; we have a workaround at the moment as well via our documentation.

The problem is, that since we don't remove an actual resource, but only an item in the list, the Kubernetes GC won't notice.
Is it an anti-pattern for the reconcile loop to have a "Delete If Exists" style of function? This function could be called when the difference between the desired state and the actual state check is trigged, and the nodeAgents being removed from the list are explicitly deleted.

Is it an anti-pattern for the reconcile loop to have a "Delete If Exists" style of function? This function could be called when the difference between the desired state and the actual state check is trigged, and the nodeAgents being removed from the list are explicitly deleted.

Not an anti-pattern just not natively embedded into the controller-runtime tooling as far as we know. Client tools all do this slighlty differently. We have an approach for this, it just evolved after the logging operator core had been established so now we have to refactor a bit to have it.
By the way it works by grouping resources into components and adding a specific annotation to each resource on create/update. After reconciling a component we remove all the resources with matching annotations that are not included in the actual list of desired resources.

Thank you for the clarification on the deletion pattern for the operator. That makes sense to me!

By the way it works by grouping resources into components and adding a specific annotation to each resource on create/update. After reconciling a component we remove all the resources with matching annotations that are not included in the actual list of desired resources.

Ah, this should work for us as another workaround. I'll try it, and see if we run into the same thing again (we shouldn't, from what I can see in the code). Thank you.

Seeing this issue as well. Not sure how to resolve this? or will there be a chart update that addresses this?

This is going to be officially supported in 4.3

NodeAgents are not going to be supported in the future and will be marked for deletion from the API in the next major release.


border image

look at this
how didnt i know this beforeeeeee
this means two changes

buttons
inputs

guess who gets to remake this~ me..
im crying but hey
no pain no gain
border image might just been the thing thats missing, you see, on linux and on phone they look really scuffed, so this might actually be the missing piece in the Puzzle
sorry for my bad grammar, just woke up from a nap

oh yeah since i am taking a break from dc, leave your freedback as a comment, team

:3

done :3


pydantic.error_wrappers.ValidationError: cannot parse boolean value in WSL

Checks

[x] I added a descriptive title to this issue
[x] I have searched (google, github) for similar issues and couldn't find anything
[x] I have read and followed the docs and still think this is a bug

Bug
Output of python -c "import pydantic.utils; print(pydantic.utils.version_info())":
Loading .env environment variables…
             pydantic version: 1.8.2
            pydantic compiled: True
                 install path: /mnt/i/Leadbook/scoring_model/env/lib/python3.9/site-packages/pydantic
               python version: 3.9.9 (main, Nov 16 2021, 03:05:18)  [GCC 7.5.0]
                     platform: Linux-4.4.0-19041-Microsoft-x86_64-with-glibc2.27
     optional deps. installed: ['dotenv', 'typing-extensions']

We are deploying a uvicorn app from WSL. But when we do that, we get pydantic.error_wrappers.ValidationError which further says value could not be parsed to a boolean (type=type_error.bool). However, this problem does not occur in Linux or macOS.
from pydantic import BaseSettings
class Settings(BaseSettings):
    debug: bool = False
...

I encountered this bug as well. I deleted my project, cloned it again from github, made a new virtual environment and installed the requirements.txt and this fixed my issue.

Based on @kenzo47's comment I'm going to assume this was an issue with the environment and close this issue.
If you (or others) are still having this problem, I think we would need a more detailed description of how to reproduce the issue in order to attempt to resolve it.

I see the validation error consistently (even in fresh env creation etc.) where pydantic is installed via langroid on macOS.
ref: https://github.com/langroid/langroid/issues/594


Crashes related to speech prefs

Even a freshly built Pester crashed for me because of an uncaught exception on launch.
I deleted a 2-year old Pester plist and lockfile in ~/Library/Preferences, but that didn't stop the crashes.
Seeing the mentions of voice-related difficulties in the webpage and in the stack trace, I tried going into the speech preferences and fumbled a bit. And then Pester managed to launch.
I am not sure what I changed to fix things. The only maybe-interesting thing I saw is that VoiceOver Utility showed as default in the Speech section a voice which didn't seem to be really installed (Fiona compact; I did have Fiona installed, but not the compact version). Once I went into the Dictation & Speech prefs and selected another voice, VoiceOver Utility shows that voice.
XCode 7.1beta on Mac OS X 10.10.5

Ouch. I really thought I had fixed all of these problems. Could you attach a copy of a crash report? Thanks.

GitHub is not allowing me to attach the crash report even once renamed to .txt. So I created a gist.
https://gist.github.com/hmijail/6664a9ee91fcbfcab88a

I had no idea that VoiceOver Utility had its own speech popup menu.  It does seem to be different from the one in System Preferences in that it lists the compact voices separately, rather than as an unchecked "Upgrade to enhanced quality" checkbox.  SpeechObjects.framework in /System/Library/PrivateFrameworks exposes all this stuff, which means it's unfortunately not available for use by third-party apps.  As is, I'm reverse-engineering the speech file format to make the voice popup menu in Pester look even reasonably decent.  It's infuriating and gets worse every OS X version with the addition of more and more voices.
Your mention of Fiona was quite helpful.  It turns out Scottish is not a country but a variant (en-scotland), which shows up as "Scottish Standard English" in the popup menu, and I hadn't tested with any of those voices.
I may have to release yet another build of 1.1b19 with this change, but I need to get b20 out in the next couple days before El Capitan ships, so it should be in a release soon.  I'd ordinarily build you a copy but I think you can probably do that yourself :-)
Thanks again!

So I guess we were lucky that I typed "voice" instead of "speech" in Spotlight - that's how I learnt about VoiceOver Utility and found about the voice mismatch :).
No build needed, thanks. Good luck with the rest, it really sounds hairy.


net: sockets: Add dummy shutdown() implementation.

shutdown() itself is described as just marking RX or TX path of a
socket as not available. For the first approximation, we implement
it just as a dummy function, to allow build existing POSIX
applications which use it.
Signed-off-by: Paul Sokolovsky<EMAIL_ADDRESS>

Codecov Report

:exclamation: No coverage uploaded for pull request base (master@d5b71ca). Click here to learn what that means.
The diff coverage is 0%.

@@            Coverage Diff            @@
##             master   #13184   +/-   ##
=========================================
  Coverage          ?   48.87%
=========================================
  Files             ?      317
  Lines             ?    46748
  Branches          ?    10798
=========================================
  Hits              ?    22848
  Misses            ?    19337
  Partials          ?     4563

Impacted Files
Coverage Δ

include/net/socket.h
100% <ø> (ø)

subsys/net/lib/sockets/sockets.c
51.16% <0%> (ø)

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update d5b71ca...0fc4074. Read the comment docs.


2024-winter

Create pull request from edited branch of to main branch of your fork
By the way, see example in repo readme, format is wrong


Adding Maintainer notes

modify CONTRIBUTING to include how to structure commits
modify package.json Versions to include majors, where it should be included
modify README to include how this package is Versioned
adding "Notes to Maintainers" to know how the processes work

@Ben305 i would need to know which version of the merge method is / should / will be used and to confirm that the versioning is correct

Coverage decreased (-0.8%) to 85.176% when pulling 2b55c9d24753a4f278944366648823673856064a on hasezoey:feature/maintain into a3c7ceedc1e4818fe6282fef9218b23a00e73e74 on szokodiakos:master.

Note: i dont know why coveralls reports that there is a -0.8%, when not even modifying the code

@hasezoey I prefer squash and merge to keep the history clean.

@Ben305, i would prefer if it would be "ff", but only if the commits are correctly structured :)
and #359, i "couldnt" use ff or squash, because i wanted that all the issues & prs are "preserved" and closed (and showed as merged and not closed)

@Ben305 is that acceptable now? (if you dont know what "ff" does compared to "no-ff": "no-ff" adds always an merge commit, and "ff" does never add a merge commit and tries to just put the commits into the timeline without modifying them, so i added an case for that) :)

@Ben305 2 questions for you:

i noticed you still have the branch release-5.7.2 in this repo, is this still needed?
and i noticed that you make a new branch (example "v5.9.0", or is this a tag?), because the travis deploy is never run because of that ...

@Ben305 would this be right if i let it so as the final version? (use Fast-Forward, when possible and fits the style?)


How to add accounts

How do i implement or add accounts to the bot to lvl it up ?

Take a look at issue #20, I am planning on adding a file to resources that can be used as an easy example/drop in replacement for the accounts.py file. in the mean time it just requires a little coding to do.


Stop tracking openstack-utils for Queens and Rocky

openstack-utils is a RedHat utility that hasn't been updated in two
years. We don't use it directly nor do we reference it in our
documentation. Let's stop being concerned about it.

wow, we still have that??! we only used it for crudini, which we however now have as a separate package. we should remove it alltogether.


Improvement for node close to metric

The latest indicator added, which shows a point one unit close to a metric, is currently working for all metrics.
Perhaps it could be useful to skip some metrics based on the case of the layer?
If case == 1 : #Uppercase
    ignore xHeight

if case == 2 : #Lowercase
    ignore CapHeight

Good idea. There are some tricky edge cases, though. I’ll see what I can do.


Support the API of CopyPart

Is this a BUG REPORT or FEATURE REQUEST?:

/kind feature

Anything else we need to know?:
CopyPart API: Uploads a part by copying data from an existing object as data source. the requirement is from https://docs.aws.amazon.com/AmazonS3/latest/API/API_UploadPartCopy.html. Precondition feature for CopyPart is supported in the PR
Environment:

Gelato(release/branch) version:
OS (e.g. from /etc/os-release):
Kernel (e.g. uname -a):
Install tools:
Others:

It's fixed by PR#818


Disconnecting App stops running print.

Rebooting your iPad shouldn’t stop a print that was never started via the app.
Poor design flaw.
I’m uninstalling till that issue is fixed.

Hi @stitzebr,
OctoPod or any other client cannot stop a print by closing the app or rebooting your iPhone or iPad. I do not know what happened in your case so cannot provide much help. :( The only way to cancel a print from OctoPod or any client is to 1) press Cancel button (and you should see a warning dialog) or 2) by clicking Disconnect which will disconnect OctoPrint from the printer.
Maybe you did #2 thinking that you were disconnecting OctoPod?
Regards,
Gaston

I ran into this problem as well today, @gdombiak . Clicking "Disconnect" doesn't do what a newbie expects it to.
After googling, I've found numerous issues that have been opened for this problem. It seems everyone mistakes what the "Disconnect" button does. Everyone expects it to disconnect OctoPod from OctoPrint, nobody expects it to disconnect OctoPrint from the Printer. Even the confirmation dialog text doesn't trigger alarm bells in my head that this will disconnect OctoPrint from the printer.
The reason why people are having this issue, is that nobody ever clicks the "Disconnect" button in the "Connection" section of the OctoPrint Web UI, but they click "Disconnect" in apps talking to web-servers all the time. The default idea in everyone's head is that disconnecting is harmless.
It's great that this function exists, but it needs to be buried in a sub-menu, in the Advanced settings, or something! It should definitely not be front and centre on main screen of the app, when pressing it can explode a nuclear bomb in the middle of your print.
Outside of this, great app! Many thanks for your hard work!!


[HOW-TO] Cleanly Close and Configure Cameras with Arducam Multicam v2.2

Describe what it is that you want to accomplish
I have (2) OV5647 cameras that are attached to an Arducam Multi Camera Adapter Module V2.2. I wish to preview from Camera 0 and capture an image and then switch to showing a preview and capture an image from Camera 1.
However, whenever I try to start Camera 1 after stopping Camera 0, I get a V4L2 device or resource is busy error.
ERROR V4L2 v4l2_videodevice.cpp:1047 /dev/video0[26:cap]: Unable to set format: Device or resource busy
Describe alternatives you've considered
If I close() camera 0 instead of stopping, I am able to switch to camera 1 without issue. But that requires me to reinitialize/reallocate the Picamera2(0) the next time I want to switch back which is slow.
Additional context
I am using a Raspi 4b running 64-bit Bullseye and a Waveshare 2.8 HDMI display.
In my config.txt I am using dtoverlay=camera-mux-4port,cam0-ov5647,cam1-ov5647 and camera_auto_detect=0 to enable the multi camera adapter.
libcamera-hello -t 0 --camera 0 and  libcamera-hello -t 0 --camera 1 both work successfully from the terminal.
print(Picamera2.global_camera_info()) produces
[{'Model': 'ov5647', 'Location': 2, 'Rotation': 0, 'Id': '/base/soc/i2c0mux/i2c@1/pca@70/i2c@0/ov5647@36'}, {'Model': 'ov5647', 'Location': 2, 'Rotation': 0, 'Id': '/base/soc/i2c0mux/i2c@1/pca@70/i2c@1/ov5647@36'}]
This is a minimal code example that reproduces the error. It occurs even with just trying to capture images without displaying the preview.
from picamera2 import Picamera2
import time

cam0 = Picamera2(0)
cam1 = Picamera2(1)

cam0.start()
cam0.capture_file("cam0.jpg")
cam0.stop()
#code succeeds if this is cam0.close()

time.sleep(5)

cam1.start()
cam1.capture_file("cam1.jpg")
cam1.stop()

Traceback (most recent call last):
  File "/home/me/tests/test.py", line 15, in <module>
    cam1.start()
  File "/usr/lib/python3/dist-packages/picamera2/picamera2.py", line 1049, in start
    self.configure(config)
  File "/usr/lib/python3/dist-packages/picamera2/picamera2.py", line 1004, in configure
    self.configure_(camera_config)
  File "/usr/lib/python3/dist-packages/picamera2/picamera2.py", line 943, in configure_
    if self.camera.configure(libcamera_config):
RuntimeError: Failed to configure camera: Device or resource busy

How do I cleanly stop() camera 0 or force a reconfigure so that I can use camera 1 without deallocating camera 0 entirely?

Hi, and thanks for the question.
I think basically I have only bad news for you here. Two cameras show up because you've put them in your device tree, but unfortunately, to the Linux kernel these are the same device - that fact that there's some "magic" on the adpater board is completely unknown to it. There's no way you can have one device "left open" but use what you think is a second device but which to the kernel, is the same device - all those /dev/video<N> nodes are the same in both cases, so they all have to be closed and re-opened.
libcamera-hello works as you describe because it does a complete shutdown when the process quits, just like quitting your Python process and starting over. So far as I know, there is no difference in this respect between using libcamera directly or Picamera2.
I think these are just the limits of adapter boards like this. You could get round this using a Pi with two physically distinct camera connectors, such as a Compute Module (or Pi 5). Beyond that, I guess if there's something particularly slow about closing one camera and opening another, then maybe there's something there that can be investigated. Do you have any further data on this?


TODO List #8

Provides a button to clear custom sets once not needed anymore.

Rad, screenshot of this?

Regardless of how likely will you face that kind of Zekrom, all what we care about here is the "Clear Custom Sets" button that shows up instantly as the custom set is added.
Now after clicking the button, POOF all the sets disappeared, the magic button did its job so it quietly hides back (hence the display set to none when done, we don't want from it to bloat the HTML). When looking up the custom set of Zekrom we had crafted :

It isn't there anymore.
And by the way, thank you very much for the support, I just try my hardest to be what I'm here for : helping :D.

Regardless of how legitimate this set is, this is how the page should look like once a custom set has been imported. Notice the "Clear Sets" button that is the pivotal thing in the whole story.
Once clicked, I try again to look for the custom set I've crafted for Zekrom (second image below), aaaand nope, no "Custom Set" appears, it has been deleted successfully, as the alert mentioned when the button was clicked.
Oh, and thanks for the nice word, glad I could help :D.

This only clears the sets after a refresh. It would be optimal for a refresh to be unneeded but for now this is good

@Ntonio36 Hmm in the request for this, they wanted specific sets, is that something you could work on as well?

I successfully found a way to separately store custom sets all alone, but I couldn't figure out at all how to make them get loaded into the Pokémon name area... That's a TODO I should set for myself, for the least that I can say. But don't expect anything from it, though.

@Ntonio36 try looking at how customsets is currently done there


header: Fix dark mode header box-shadow.

Followup to 239b6737c0a58e3d86d2c0d1c9e684fe994ad72b
I forgot to add darkmode support to my previous followup, sorry about that.
Current state of main:

with this PR:

@timabbott would be good to get this merged soon, since the issue is currently on main but not deployed on CZO yet.

@shameondev I'm pretty confident it's just this rule -- I updated it for light mode in https://github.com/zulip/zulip/commit/239b6737c0a58e3d86d2c0d1c9e684fe994ad72b and forgot to make the dark mode change for the same thing.


Equals without childrens content?

With the React test utils (with chai-jsx to do the assertion) I could do:
const renderer = TestUtils.createRenderer()
renderer.render(<Foo/>)
expect(renderer.getRenderOutput()).to.deep.equal(

    <Bar/>

) // succeeds

However with enzyme shallow equals:
expect(shallow(<Foo/>).equals(

    <Bar/>

)) // fails

This fails because you need to specify also the contents of Bar. I don't think this should be the behaviour for shallow rendering? You should not care about the contents of Bar.
Is there a way to get the same behaviour in enzyme? Because I like all the other features that enzyme has that the test utils from React do not provide (at least not when shallow rendering).,

Is there a reason why you want to check the whole structure at once and can't just check if a <Bar /> component was rendered as a part of <Foo />?
expect(shallow(<Foo />).find(Bar)).to.have.length(1);

or to be more specific
expect(shallow(<Foo />).find('div').find(Bar)).to.have.length(1);

This fails because you need to specify also the contents of Bar.
@ngerritsen I can't be sure from the example, but this should not be the case...

This would fail if you don't specify the children of <Bar>. ie, you would essentially need to replicate the render method of Foo (not that I recommend that).
Can you provide working code for your example? Either there is a legitimate bug going on here, or one of us is misunderstanding.
Thanks  for taking the time to file an issue.

It is not a bug, it's a different way of doing the equal.
@Markionium sometimes with small components it's just convenient do do an equal with the whole component sometimes, but just querying the component for specific elements is also fine.
Let's close this for now.


Set bwa-mem2 batch size for reproducibility

improve reproducibility for bwa-mem2 alignments by setting -K
this ensures that the number of input bases in each batch is consistent
the parameter value was selected to match configuration used in Sarek

I've undertaken a brief investigation of the impact that batch size has on output BAMs to better understand the need to set a consistent batch size (i.e. applying the -K option).
For further background, by default bwa-mem2 loads some number of reads into memory (known as a batch) so that the input data can be processed in manageable chunks. The number of reads loaded into memory is determined by a batch size parameter, which by default scales with the number of threads used. It has been reported that running bwa-mem2 on the same input data with different thread counts (and hence batch size) can introduce discrepancies in the output BAMs. However, using the -K option to set a constant batch size is said to ameliorate these discrepancies when re-running bwa-mem2 on the same data even when setting different thread counts.
To investigate and explore this at a high-level I have done the following:

simulated 500,000 reads from the GRCh38_hmf genome
aligned with bwa-mem2 as we do in oncoanalyser but varying thread count and running with or without -K
compared at a high-level with checksums of resulting BAMs

I found BAMs with different checksums were generated when varying thread count without setting a constant batch size (Table 1). When applying a constant batch size, checksums of all BAMs were identical regardless of thread count. The BAMs did not differ within replicates, ruling out any other confounding effect.
Table 1. MD5 checksums of BAMs generated from the same input data with varying thread counts and -K

batch_size
threads
iteration
md5_chksm

default
4
1
b93eaa49ade96ef6f04daace9d383f96

default
4
2
b93eaa49ade96ef6f04daace9d383f96

default
8
1
e103d1007a18af7deebf7d50effacafe

default
8
2
e103d1007a18af7deebf7d50effacafe

100000000
4
1
29f237e841d4adb51d42bce163941acf

100000000
4
2
29f237e841d4adb51d42bce163941acf

100000000
8
1
29f237e841d4adb51d42bce163941acf

100000000
8
2
29f237e841d4adb51d42bce163941acf

Given that -K reduces variability in output BAMs and improves reproducibility, it is clear that this option is beneficial in that regard.
One important consideration is that if a batch size is set, it must be reasonably done as not to be so small that inefficiencies are introduced nor too great that relatively large amounts of memory are used for low thread counts. From observations made during the above investigation, a batch size of 100,000,000 appears to fit well for our use case.

Commands used to generate data (click to expand)
Download required data
mkdir -p reference_data/

curl https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.1/bwa_index/2.2.1.tar.gz | tar --strip-components 1 -xzvf - -C reference_data/
wget -P reference_data/ https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/24.0/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna

Init work directory
mkdir -p 1_reads/ 2_alignments/

Simulate reads
wgsim -S 0 -1 151 -2 151 -N 500000 reference_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna 1_reads/sim.500_000.R1.fastq 1_reads/sim.500_000.R2.fastq 1>/dev/null

Generate read alignments
align_reads() {
  reads_fwd=${1};
  reads_rev=${2};
  threads=${3};
  batch_size=${4};
  replicate=${5};

  reads_fwd_fn=${reads_fwd##*/};
  name=${reads_fwd_fn/.R1.fastq/};

  k_arg='';
  if [[ ${batch_size} != none ]]; then k_arg="-K ${batch_size}"; fi;

  output_fn=${name}.${threads}.${batch_size}.${replicate}.bam

  bwa-mem2 mem 2>2_alignments/${output_fn}.log \
    -Y \
    -t ${threads} \
    ${k_arg} \
    reference_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
    ${reads_fwd} \
    ${reads_rev} | \
    \
    sambamba view \
      --sam-input \
      --format bam \
      --compression-level 0 \
      --nthreads 1 \
      /dev/stdin | \
    \
    sambamba sort \
      --nthreads 1 \
      --out 2_alignments/${output_fn} \
      /dev/stdin
}

align_reads 1_reads/sim.500_000.R{1,2}.fastq 4 none 1
align_reads 1_reads/sim.500_000.R{1,2}.fastq 4 none 2
align_reads 1_reads/sim.500_000.R{1,2}.fastq 8 none 1
align_reads 1_reads/sim.500_000.R{1,2}.fastq 8 none 2
align_reads 1_reads/sim.500_000.R{1,2}.fastq 4 100000000 1
align_reads 1_reads/sim.500_000.R{1,2}.fastq 4 100000000 2
align_reads 1_reads/sim.500_000.R{1,2}.fastq 8 100000000 1
align_reads 1_reads/sim.500_000.R{1,2}.fastq 8 100000000 2

Compare output BAMs
parallel 'echo {} $(samtools view {} | md5sum)' ::: *500_000*bam | sort -nk2,2 | column -t

# sim.500_000.4.none.1.bam       b93eaa49ade96ef6f04daace9d383f96  -
# sim.500_000.4.none.2.bam       b93eaa49ade96ef6f04daace9d383f96  -
# sim.500_000.8.none.1.bam       e103d1007a18af7deebf7d50effacafe  -
# sim.500_000.8.none.2.bam       e103d1007a18af7deebf7d50effacafe  -
# sim.500_000.4.100000000.1.bam  29f237e841d4adb51d42bce163941acf  -
# sim.500_000.4.100000000.2.bam  29f237e841d4adb51d42bce163941acf  -
# sim.500_000.8.100000000.1.bam  29f237e841d4adb51d42bce163941acf  -
# sim.500_000.8.100000000.2.bam  29f237e841d4adb51d42bce163941acf  -

/cc @charlesshale

@scwatts I would recommend using the nf-core modules for it and setting up the -k with args

Thanks @maxulysse, I'll take a look at doing this next week.
We're using a fairly different approach to sorting/compressing and read group assignment, and the nf-core bwa-mem2/mem module would need to be heavily patched to maintain that functionality - I'd been a bit hesitant to apply that much patching to any nf-core module since I felt that it defeated their purpose, opting instead to use local modules in those cases instead. Did you have any thoughts around that?
I totally agree with implementing this via ext.args

oh, I see you have added sambamba within the same process, haven't looked at the full module.


login Screen wont show up

Register works well in the database is my account but after logout or reconnect the login screen wont show up!

It is problem of GT-MP.
Just wait...or reconect. It's normaly.


Deal With NA When Write Into HBaseTable

Hi Man,
When I try to save a rdd into hbase , how could I get rid of the NA (like "", "null", "NA" or else) value?
    trdd.toHBaseTable("mbk_user_label")
      .toColumns("mobikeno", "registertime", "ts", "progress", "nation", "status", "citycode")
      .inColumnFamily("attrs")
      .save()

trdd: org.apache.spark.rdd.RDD[(String, String, String, String, String, String, String, String)]
Should I  change my trdd into Option[String]?
Thx.

I change to use option to fix the NA like problem with a func.
However when all the data are None, it will raise a Error.
Does it possible to cover this situation in your proj?

Technically, you cannot have a empty row id, so you should not put Optional values on them. If you need to use Optionals also on row id, you can just filter them out (rdd.filter(_._1.nonEmpty).toColumns... before writing them to the store.
I'd not like to suppress the error as it may indicate a problem with your code.

Thx.
Sorry for not explain the problem clear. I give a real row id but all the field value is None. Now I add filter func before load data into HBase.
Make it right as your suggest.


Non recoverable error

Problem Description

Reproduction
No response

Hello, thanks for the report. This is a dupe of #219, which I'll fix soon.


Incorrect handling of accented letters with mtg.wtf syntax

Running json-to-mse '=b:isd,soi' fails with card not found: Seance. This is because magic-search-engine's find_cards outputs the card as Seance, but it's listed as Séance in MTG JSON.

This is fixed in https://github.com/taw/magic-search-engine/commit/8ea785d96ec8629e988d1859af8c2ee42c47f96e. Now the reason this invocation fails is #7.


install-chef-suse: Remove creation of symlinks to SMT mirror

This is moved to crowbar itself now.
Depends on https://github.com/crowbar/crowbar-core/pull/133

:+1:

:+1:

+1

Needs rebase

rebased

@mjura @rsalevsky @tboerger just checking: are your +1 from before the rebase still valid?

Yes, I'm happy +1


Panels on indexes not working on master

In commit 7cd7f440ab043a19cd485ad3be1f8365fdd2f641 (December 26th), I forked the project to do some research and mokeying around, when I updated back to master over here, the panel I configured on my index is no longer rendering the text from the partial.  I created a new project to validate that this is the case as well on the current master.

actionmailer (3.1.3)
actionpack (3.1.3)
activeadmin (0.3.4 8b69d68)
activemodel (3.1.3)
activerecord (3.1.3)
activeresource (3.1.3)
activesupport (3.1.3)
ansi (1.4.1)
archive-tar-minitar (0.5.2)
arel (2.2.1)
bcrypt-ruby (3.0.1)
bourbon (1.3.6)
builder (3.0.0)
bundler (1.0.21)
coffee-rails (3.1.1)
coffee-script (2.2.0)
coffee-script-source (1.2.0)
columnize (0.3.6)
devise (2.0.0)
erubis (2.7.0)
execjs (1.3.0)
fastercsv (1.5.4)
formtastic (2.0.2)
has_scope (0.5.1)
hike (1.2.1)
i18n (0.6.0)
inherited_resources (1.2.2)
jquery-rails (1.0.19)
json (1.6.5)
kaminari (0.13.0)
linecache19 (0.5.12)
mail (2.3.0)
meta_search (1.1.2)
mime-types (1.17.2)
multi_json (1.0.4)
orm_adapter (0.0.6)
polyamorous (0.5.0)
polyglot (0.3.3)
rack (1.3.6)
rack-cache (1.1)
rack-mount (0.8.3)
rack-ssl (1.3.2)
rack-test (0.6.1)
rails (3.1.3)
railties (3.1.3)
rake (<IP_ADDRESS>)
rdoc (3.12)
responders (0.6.5)
ruby-debug-base19 (0.11.25)
ruby-debug19 (0.11.6)
ruby_core_source (0.1.5)
sass (3.1.12)
sass-rails (3.1.5)
sprockets (2.0.3)
sqlite3 (1.3.5)
thor (0.14.6)
tilt (1.3.3)
treetop (1.4.10)
turn (0.8.2)
tzinfo (0.3.31)
uglifier (1.2.2)
warden (1.1.0)

Sorry, here's the related code that's chopped down to just the panel here (it's in a blank project, so I didn't do the columns as it displays the behavior even without).
index :as => :table, :download_links => false do |oath|
panel "Test" do
render :partial => "shared/test_partial"
end
end

That did it.  Thanks!


Deep get/filter to mask Map using a nested object.

I was wondering if it is possible to do something like the following:
let data = {
  "posts": [
    {
      "id": 1,
      "title": "Cool post",
      "content": "This post content!"
    },
    {
      "id": 2,
      "title": "Cool post 2",
      "content": "This is post 2 content!"
    }
  ],
  "someOtherData": [...]
};
let imData = Immutable.fromJS(data);

// Create mask
let mask = Immutable.fromJS({
  "posts": ["id", "title"]
}

// Filter / deep get ?
let result = imData.get(mask).toJS();

// Result now being:
{
  "posts":
    [
      {"id": 1, "title": "Cool post"},
      {"id": 2, "title": "Cool post 2"}
    ]
}

For arbitrarily deep masks btw.

Closing this aging issue - sorry for not getting to your question

Is that a resounding no? or a "yeah, that is obvious" affirmation?


Ember CP validation does not support ember octane with glimmer component

Issue :-
Ember cp validation does not supporting ember octane with glimmer component.. How to applied cp validation on glimmer component and controller,  Please suggest
Environment

Ember Version:  3.20
Ember CLI Version: 3.20
Ember CP Validations Version: 4.0.0-beta.10

Steps to Reproduce

It appears cp-validations is deprecated.

It appears cp-validations is deprecated.

Is there a replacement package for Octane edition?

there is a few workarounds:
https://gist.github.com/lifeart/941c3988e152624b0f2eff385d2553d0
https://gist.github.com/lifeart/bb254ce172d0913b1b275e24861bb20e

@fsmanuel can this issue be closed now?


feature request: Add revert reason to FailedRelayedMessage event

Is your feature request related to a problem? Please describe.
It's a real pain to debug L1->L2 messages that revert when they're relayed. This is because they just show a generic "evm execution reverted" error.
Example: https://kovan-optimistic.etherscan.io/tx/0x647991fe8282b4ddd1fdb8dd201c412adc6cbb92eba021f47be182a8a0dfe00e/advanced
Describe the solution you'd like
Adding the error message into FailedRelayedMessage would allow block explorers or the watcher to alert users and devs of why the relay failed, making it easier to debug.
Describe alternatives you've considered
Doing a trace and looking directly for the revert in l2geth and exposing this to etherscan?

In bedrock the L1 to L2 messages have their own deposit txs, and the relay / entry-point on L2 is customizable. (there will likely be an encouraged default though that can replay failed deposit execution, and there this feedback is still useful). cc @maurelian


MSI Installer Doesn't Remove Previous Builds of OpenJDK / JRE Runtime

When installing the latest build, the previous versions aren't removed for the JRE.
For example, if JRE 8 Update 202 was installed and you upgrade to 212 it leaves the previous version installed as well.
Is there a command line in the MSI you can enable to auto remove previous builds during an upgrade?

see https://github.com/AdoptOpenJDK/openjdk-installer/issues/88


Make different payment options available

Describe the solution you'd like
As Azure subscriptions is ONLY available on 88 countries, this deprives many users from the ability to leverage VS App Center. We would like to be able to create an account from regular credit cards like many other Microsoft platforms do (Office365, Skype) OR have the link to Microsoft Store
Describe alternatives you've considered
We have no alternative solution as the link to Azure is the unique way by which you can subscribe to build/test plans .
Additional context
N/A

Hi @malouly, thanks for reaching out, and I see your point. Azure billing is currently commercially available in 140 countries and regions , and most of what App Center offers is backed by Azure. May I ask what region you are currently in?
In the meantime, I'll let @ricduong and @Zakeelm add more details about billing.

Thank you very much,
I’m from Mauritania (west Africa :  https://en.wikipedia.org/wiki/Mauritania https://en.wikipedia.org/wiki/Mauritania ) and we don’t see our country name in the supported countries list. We appreciate very much your help to include it to the list.
Cordialement / Best regards
LOULY  Mohamed-Abdallahi
Directeur Général / CEO
GTI international (GTI)
Tel : (+222)  26 300 300
<EMAIL_ADDRESS><EMAIL_ADDRESS>  |   http://www.gti-intl.com http://www.gti-intl.com/
De : Amanda Chew<EMAIL_ADDRESS>Envoyé : jeudi 29 août 2019 22:52
À : microsoft/appcenter<EMAIL_ADDRESS>Cc : malouly<EMAIL_ADDRESS>Mention<EMAIL_ADDRESS>Objet : Re: [microsoft/appcenter] Make different payment options available (#949)
Hi @malouly https://github.com/malouly , thanks for reaching out, and I see your point. Azure billing is currently commercially available in 140 countries and regions  https://azure.microsoft.com/en-us/free/free-account-faq/ , and most of what App Center offers is backed by Azure. May I ask what region you are currently in?
In the meantime, I'll let @ricduong https://github.com/ricduong  and @Zakeelm https://github.com/Zakeelm  add more details about billing.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub https://github.com/microsoft/appcenter/issues/949?email_source=notifications&email_token=ANASKTI72UHNQCJQLDOBV3DQHBHJPA5CNFSM4IQLYI5KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5QBGOQ#issuecomment-526390074 , or mute the thread https://github.com/notifications/unsubscribe-auth/ANASKTIKV5RNNDBPOQDINQLQHBHJPANCNFSM4IQLYI5A .  https://github.com/notifications/beacon/ANASKTPKJVCEH6EYDEXFW5DQHBHJPA5CNFSM4IQLYI5KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5QBGOQ.gif