Hublabel by electricEpilith · Pull Request #239 · vgteam/libbdsg

electricEpilith · 2026-04-07T21:38:16Z

libbdsg changes to go with merging the hublabel branch of vg

…it returns, and which is a different size on mac

…rs that validate it

… debugging

…ost_graph

…opefully query off the right orientations

…ng the net graph

…ses that all can run

…apes and cases

…rtices from a net graph child. Add a bunch of comments exlaining why I am confused by the distance index orientation bookkeeping.

…nd do it

…ord access attempts

…arlRecord

…t that instead of unpicking it

…ue root handle

planned by Claude Opus 4.7

fix typos Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>

Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>

planning help from Claude Opus 4.7

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

…ations' error Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

adamnovak

The changes since my last review look pretty good, but there still seem to be a bunch of unaddressed comments from my last review, like missing include guards and commented-out code.

adamnovak · 2026-05-15T19:29:34Z

These files are auto-generated, so you can run the formatter on them, but the changed will be clobbered when we next regenerate them.

It might make sense to include the formatter script in the repo somewhere at some point, so we can keep around a command line that formats the real code and ignores the synthetic code.

The formatter is clang-format, you'd have to install it on your own machine

adamnovak · 2026-05-15T19:32:29Z

 * an orientation of a node, as a source or destination.
 */
-NODE_UINT bgid(const handle_t& h, const bdsg::HashGraph& hg);
+NODE_UINT bgid(const handle_t &h, const bdsg::HashGraph &hg);


Is this a configurable switch of the formatter? We almost always use the ampersand on the type, and I don't think we want to go through and touch all the code to put it on the variable instead, so having the formatter come through and change it in some files is probably making things worse instead of better.

Will need to look at clang-format docs

Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>

electricEpilith and others added 30 commits December 9, 2025 12:54

add hublabel build and query code, get tests to build

c48617d

replace placeholder getter stuff, rewrite hhlquery to take iterator

9a5bbd3

Merge remote-tracking branch 'upstream/master' into hublabel

28add14

debugging etc.

3e009fa

Change hub_labels to a size_t vector, which the function to generate …

6755f44

…it returns, and which is a different size on mac

Merge remote-tracking branch 'upstream/hublabel' into hublabel

37492aa

Define a type for the complex temporary X index indexing, and accesso…

0065e97

…rs that validate it

Use indexing accessors in make_boost_graph()

420c9e9

Add const accessors and fix build errors

5edfaa0

Write some hub labeling interface docs as I remember it, and add some…

b9ba500

… debugging

Add synthetic debug logging and synthetic analysis results to make_bo…

23e6745

…ost_graph

Synthesize code to allocate vertices and avoid wasting them, and to h…

ad43882

…opefully query off the right orientations

Redesign to only think of indexing inward-facing handles for converti…

0e6aa47

…ng the net graph

Teach CMake about Boost dependency

3619491

Stop putting negative-unsigned entries in the hub labels

7e33257

Define what to do for asking about a node to itself, and test it

9a88f8f

Qualify std::move calls to appease compiler

ac07468

Const-ify arguments to label building

3b84fb0

De-comment the existing hub labeling test cases into distinct test ca…

227e4d1

…ses that all can run

Add some synthetic unit tests, with revisions, for some more graph sh…

9b33554

…apes and cases

Fix signature mismatch

385efa8

Fix type name

9ae76d4

Merge remote-tracking branch 'origin/master' into hublabel

1d50a68

Rework HHL vertex ID computation so we can actually find the right ve…

fb774f2

…rtices from a net graph child. Add a bunch of comments exlaining why I am confused by the distance index orientation bookkeeping.

Be clear about who is responsible for initializing NodeProp fields, a…

a5c20a8

…nd do it

Produce more descriptive errors for out of bounds temporary snarl rec…

9a7e4c3

…ord access attempts

Fix cases where simple snarls could be accesed with the non-simple Sn…

a868f92

…arlRecord

Figure out ChainRecord is used to decode snarls sometimes and documen…

f8de1dc

…t that instead of unpicking it

Stop trying to report types we aren't allowed to compute

41ccdf3

Handle ROOT record type as also needing to canonicalize to the one tr…

a3948d4

…ue root handle

adamnovak and others added 5 commits April 22, 2026 18:06

Address some of my own review comments

a7602fd

prevent sdsl conflicts

a169eca

planned by Claude Opus 4.7

prevent libhandlegraph conflicts

531e77e

planned by Claude Opus 4.7

prevent hopscotch conflicts

5aff1a5

planned by Claude Opus 4.7

prevent mio conflicts

789ad6d

planned by Claude Opus 4.7

adamnovak mentioned this pull request May 7, 2026

Hublabel vgteam/vg#4870

Open

electricEpilith and others added 12 commits May 8, 2026 15:07

Update bdsg/include/bdsg/internal/indexing_iterator.hpp

78584c4

fix typos Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>

Fix collections misspelling

d6dffdd

Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>

Fix typos

9882957

Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>

Fix collections typo

90289e8

Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>

Update bdsg/include/bdsg/internal/indexing_iterator.hpp

772d34c

Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>

CI needs to have Boost to support contraction hierarchy code

2d12064

consolidate contraction-hierarchy/hub-labeling stuff

83cea1f

planning help from Claude Opus 4.7

fix errors caused by const conflicts

8e57a39

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

fix PYBIND11_MAKE_OPAQUE 'a type specifier is required for all declar…

467ab3d

…ations' error Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

format code

b5abb87

uncomment non-hub-labeling tests

91b0e91

mention Boost dep

1c35a3b

adamnovak reviewed May 15, 2026

View reviewed changes

electricEpilith and others added 11 commits May 15, 2026 14:20

Remove unnecessary assert

78b6d68

Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>

add include guard

768a6a0

mention Boost in dep list

b06d1e1

reject v4 indexes

4fbdd5a

convert /// comments to doc comments

7a41612

convert /// comment to doc comment

421ea29

remove TODO, we're not making separate RecordWriter for oversized snarls

a9ccb25

fix commenting errors

1b72048

better file comment

376501a

not a test file

d650c3f

remove unnecessary comment

ed24eed

Provide feedback

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Hublabel#239

Hublabel#239
electricEpilith wants to merge 83 commits into
masterfrom
hublabel

electricEpilith commented Apr 7, 2026

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electricEpilith commented Apr 7, 2026

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