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Self-contain 2023-bids-dicom figures; annex 32 pointer files - #31

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@yarikoptic yarikoptic commented Oct 9, 2026 •

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Closes #30.

  • 2023-bids-dicom.html: the BIDS-minder slide's upstream URL 404s (the file was removed from bids-starter-kit in [ENH] Move starter kit to new BIDS website with redirects bids-standard/bids-starter-kit#414); use our pics/BIDS-minder.svg. The two ReproIn figures on "DICOMs in BIDS" were also hotlinked from ReproNim/reproin@master; they are now annexed as pics/dbic-flow.png and pics/dbic-conversions.png.
  • pics/BIDS-minder.svg and 31 other files had been committed as git-annex pointer files (unlocked) instead of symlinks: 12 when this PR was opened, and 20 more that arrived on master since then (merged in here). tools/build_preview.py copies such files verbatim, so the PR preview served the /annex/objects/... text instead of the image. git annex lock turned them into symlinks. The keys are unchanged and all 32 are on datasets.datalad.org.

Before merging, make the two new keys available. The git-annex branch was deliberately not pushed from here, so until then the git-annex check fails for exactly these two files. Pushing only git-annex triggers no PR event, so re-run that check afterwards. The copy step keeps the datasets.datalad.org mirror from losing the images it hotlinks today:

git annex registerurl MD5E-s149431--29e378a46a7294f2f7b040a48136c9bf.png \
  https://raw.githubusercontent.com/ReproNim/reproin/fe5488b59c607ead1384da0e3efcbe57770c34e8/docs/source/images/dbic-flow.png
git annex registerurl MD5E-s293267--d7a4fa9b78b172ed35d73251763a045f.png \
  https://raw.githubusercontent.com/ReproNim/reproin/fe5488b59c607ead1384da0e3efcbe57770c34e8/docs/source/images/dbic-conversions.png
git annex get pics/dbic-flow.png pics/dbic-conversions.png
git annex copy --to datasets.datalad.org pics/dbic-flow.png pics/dbic-conversions.png
git push origin git-annex
Details
  • Our pics/BIDS-minder.svg (158781 B) differs from both upstream versions (171718 B and 203984 B, bids-starter-kit 38ce978 and 212a377). It shows the same mind map plus one extra "Zarr" leaf under "OME Zarr". Its aspect ratio is taller (1718×1234 vs 2023×1303), so at natural size the bottom branch was clipped, hence style="height:1000px". I checked this with headless-Chromium screenshots of slide #/6/2; it fits within the deck's 1920×1080 canvas (top 40 px, bottom 1030 px).
  • The ReproIn PNGs come from the commit that added them (fe5488b, 2018-03-01). They are byte-identical to current master. They went to pics/, next to the existing pics/dbic-conversions-p{1,2}.png crops, rather than pics/borrowed/, because ReproIn is a ReproNim/CON project.
  • The 20 later ones are listed in the message of commit 93ed4b9. Most are logos and webshots used by 2026-usrse-con-talk.html or its 2026-usrse-con-talk/ack-*.html pages, and two are the logos of 2026-usrse/duct-poster.html. Some had been symlinks before and were re-added with plain git add (e.g. pics/borrowed/2026-ai-intensifies.png in 8e37efd).
  • The first 12 locked files: 0000-zoom-background-qrcode.png, 2016-openfmri-dataset-datalad-howto.png, 2026-ca-origami-retreat-aicoding-qrcode.png, 2026-repronim-YODA-BIDS-webinar-qrcode.png, 2026-usrse-con-talk-qrcode.png, 202x-mvc-stack-qrcode.png, BIDS-minder.svg, borrowed/arjlover-webshot.png, con-tinuous-term-dandi-cli.png, con_logo_square_with_fuzzybackground.png, datalad-animated.gif, datalad-handbook-basics.svg.
  • I ran annex_check.py check (con/ci-actions@claude/bold-bohr-lvtger) the way CI does, in a clone with only GitHub's git-annex branch. Result on the current head: datasets.datalad.org has 32 of 34 keys, and the two ReproIn keys are missing. After the registerurl calls above: web: has 2 of 2, All annexed content is available. OK.
  • The proposed git-annex branch change was produced in a clone with annex.private=true, so it touches only the web remote and URL logs (4 files: *.log and *.log.web for the two keys). No repository UUID from this session is recorded.
  • Already true before this PR: the tall dbic-conversions.png (1254×1674) overflows the slide. A follow-up could use the existing -p1/-p2 crops as fragments, as 2022-nih-compcore.html does.
  • Left as is: the live-site iframes (e.g. BIDS steering group, DANDI team, the datalad-crawler docs). They are intentionally live.

🤖 Generated with Claude Code

https://claude.ai/code/session_01LioXKDkasSKTUKxXyXn5N1

claude added 2 commits October 9, 2026 09:01
They were committed through git's clean filter (plain `git add`), so the
tree had small "/annex/objects/KEY" pointer files (unlocked) instead of
the symlinks (locked) used everywhere else in this dataset.
tools/build_preview.py fetches content only for broken symlinks and
copies regular files verbatim, so the PR preview served the pointer text
instead of the image, e.g. pics/BIDS-minder.svg rendered blank.

`git annex lock` turns them into symlinks; keys are unchanged, and the
content of all 12 is on datasets.datalad.org.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01LioXKDkasSKTUKxXyXn5N1
- BIDS-minder slide loaded bids-standard.github.io/bids-starter-kit/
  _images/BIDS-minder.svg, which 404s since the starter kit moved to the
  BIDS website (bids-standard/bids-starter-kit#414).  Use our
  pics/BIDS-minder.svg instead (same mind map, plus a "Zarr" leaf), sized
  to fit the slide.
- "DICOMs in BIDS" slide loaded dbic-flow.png and dbic-conversions.png
  from ReproNim/reproin master.  Annex copies as pics/dbic-flow.png and
  pics/dbic-conversions.png, added from URLs pinned to the reproin commit
  that introduced them (unchanged since).  To make their content
  available (CI's git-annex check, and the datasets.datalad.org mirror):

    git annex registerurl MD5E-s149431--29e378a46a7294f2f7b040a48136c9bf.png \
      https://raw.githubusercontent.com/ReproNim/reproin/fe5488b59c607ead1384da0e3efcbe57770c34e8/docs/source/images/dbic-flow.png
    git annex registerurl MD5E-s293267--d7a4fa9b78b172ed35d73251763a045f.png \
      https://raw.githubusercontent.com/ReproNim/reproin/fe5488b59c607ead1384da0e3efcbe57770c34e8/docs/source/images/dbic-conversions.png
    git annex get pics/dbic-flow.png pics/dbic-conversions.png
    git annex copy --to datasets.datalad.org pics/dbic-flow.png pics/dbic-conversions.png
    git push origin git-annex

INDEX.md updated accordingly.

Closes #30

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01LioXKDkasSKTUKxXyXn5N1
…ing-i14q0i

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01LioXKDkasSKTUKxXyXn5N1
Same as the earlier lock of 12 pics/ files: these came in after that fix,
again via plain `git add` (some replaced symlinks, e.g.
pics/borrowed/2026-ai-intensifies.png in 8e37efd), so the tree had
unlocked "/annex/objects/KEY" pointer files that tools/build_preview.py
copies verbatim.  `git annex lock`; keys are unchanged, and the content
of all 20 is on datasets.datalad.org.

  2026-usrse/duct-poster-assets/logos/con_logo_blue_big_tight.svg
  2026-usrse/duct-poster-assets/logos/duct_logo.svg
  pics/20261019-con-website-people-webshot.png
  pics/20261019-devcon-website-people-webshot.png
  pics/borrowed/2026-ai-intensifies.png
  pics/borrowed/aws-mark.png
  pics/borrowed/dbic-logo.png
  pics/borrowed/incf-mark.png
  pics/borrowed/powered-by-aws.png
  pics/ccn-logo.svg
  pics/con-projects/bids_logo.png
  pics/con-projects/dandi_logo.png
  pics/con-projects/datalad_logo.png
  pics/con-projects/ember_logo.png
  pics/con-projects/hcp_logo.png
  pics/con-projects/incf_logo.png
  pics/con-projects/nwb_logo.png
  pics/con-projects/psychopy_logo.png
  pics/con-projects/scikit-learn_logo.png
  pics/dartmouth-logo.svg

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01LioXKDkasSKTUKxXyXn5N1
@yarikoptic-gitmate yarikoptic-gitmate changed the title Self-contain 2023-bids-dicom figures; annex 12 pointer files in pics/ Self-contain 2023-bids-dicom figures; annex 32 pointer files Oct 21, 2026
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🚀 Preview of 93ed4b9:

It will be live once the GitHub Pages deployment finishes.
Images whose git-annex content is not on datasets.datalad.org yet are listed in the build summary.
Re-run the Preview workflow to update it.

This branch has not been deployed

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bring BIDS minder in for self-containment

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