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Marpaia/flow and mother machine integration - #38

Merged

Gonza10V merged 65 commits into

gvidal/biophysics_reviewfrom

marpaia/flow-and-mother-machine

Oct 3, 2026

Commits on Sep 24, 2026
- Add feedback/ to .gitignore
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- Establish explicit viewer dataset presentation lifecycle
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- Cap tutorial founder lengths at their sampled division thresholds
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- Keep reference grid geometry fixed within each dataset
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- Preserve channel labels across models checkpoints and scenes
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  014ffe3
- Share validated scalar ranges across cell and signal coloring
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  ef3ce89
- Combine viewer lifecycle and metadata prerequisites for replay
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  d65f848
- Preserve device visibility as a dataset presentation preference
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  af99548
- Add cooperative live-session shutdown and port reuse tests
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  ed5bda0
- Add persistent channel range editors and concentration legends
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  8ee43ab
- Combine channel metadata and scalar ranges for composite coloring
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  b0f98ee
- Pause disconnected sessions before admitting reconnects
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  283c0ee
- Specify conservative cell occupancy transport with executable reference cases
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- Add linear RGB composite species coloring and channel controls
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  1351bcc
- Export checkpoint recordings and replay verified frames offline
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  1b69e4a
- Test real Windows console interruption and port reuse
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  b50c72d
- Combine shutdown and founder initialization prerequisites for issue 24
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- Diagnose out-of-plane motion and document tutorial dimensionality
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  63adb45
- Match capsule surfaces and release replaced instance buffers
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- Preserve pending replay seeks and retry failed requested frames
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- Document and execute tutorial commands across backends and shells
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  27776ba
- Match Vite query strings in scalar range browser hook
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  e96672c
- Keep command checks float32-aware and bound failed process cleanup
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  215e87d
- Match Vite query strings in composite browser hook
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  9a27f87
- Match Vite query strings in reference grid browser hook
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  2a6bdc0
- Match Vite query strings in device visibility browser hook
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  c1cb4d6
- Record executed Windows PowerShell tutorial verification
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  5e1fdec
- Bound scene channel metadata allocation and preserve compact legacy labels
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  ae428e5
- Format new founder regression test blocks
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  2d30fc7
Commits on Sep 25, 2026
- Keep channel labels unique when names imitate index suffixes
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  f450e13
- Normalize displayed channel whitespace before disambiguation
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  9838289
- Bound WebSocket shutdown drains and abort stalled transports
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  a29ae2b
- Bound kernel send buffering in portable shutdown regression
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  4451295
- Pause probe reads before WebSocket upgrade to prevent prefetch
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  2b03f16
- Report server await chains when backpressure setup fails
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  c67ff0d
- Establish measured Windows backpressure with bounded real frame requests
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  e9e631f
- Use one bounded setup budget for native frame acknowledgements
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  4677491
- Merge pull request #26 from DRAGGON-Lab/marpaia/22
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  331b6e5
- Merge pull request #27 from DRAGGON-Lab/marpaia/20
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- Integrate landed founders and dataset controls into channel metadata
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  8dc0094
- Format merged viewer feature documentation
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  55e4e34
- Merge pull request #28 from DRAGGON-Lab/marpaia/18
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  e7c9537
- Merge pull request #31 from DRAGGON-Lab/marpaia/13
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  fbb2f4c
- Combine shutdown with landed metadata and initialization changes
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  5d586e8
- Integrate landed metadata and dataset controls with capsule rendering
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  e72dda1
- Include reviewed shutdown prerequisite before capsule landing
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  43819bc
- Integrate landed dataset and channel metadata changes
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  62c4d99
- Merge branch 'marpaia/21' into marpaia/23
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  df2834d
- Merge pull request #34 from DRAGGON-Lab/marpaia/17
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  c6a759e
- Merge pull request #36 from DRAGGON-Lab/marpaia/21
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  9bf95f5
- Combine scalar ranges with reviewed viewer prerequisites
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  7c215a2
- Integrate replay with reviewed range and rendering changes
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  5057e8d
- Merge branch 'marpaia/16' into marpaia/14
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  a18f60d
- Combine shell guidance with reviewed planarity and viewer changes
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  6ecd89b
- Merge pull request #29 from DRAGGON-Lab/marpaia/23
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  cbcc81e
- Merge pull request #30 from DRAGGON-Lab/marpaia/15
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  b0bf3ff
- Combine composite colors with landed features and integration regressions
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  8438d36
- Merge pull request #33 from DRAGGON-Lab/marpaia/16
  marpaia
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  149a26d
- Merge pull request #35 from DRAGGON-Lab/marpaia/14
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  361393e
- Decode linked Markdown as UTF-8 in Windows command validation
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  09663df
- Merge branch 'marpaia/24' into marpaia/19
  marpaia
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  89bb1f9
- Merge pull request #37 from DRAGGON-Lab/marpaia/24
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  2c0d901
- Merge pull request #32 from DRAGGON-Lab/marpaia/19
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Commits on Sep 28, 2026
- Implement the Metal/CUDA occupancy API, including geometry, conservative remapping, exchange weights, and transport ledgers.
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  35ab73c
Commits on Sep 30, 2026
- Initial commit of Media Flow and Mother Machine
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  bd13ca2

Commits

Commits on Sep 24, 2026

Commits on Sep 25, 2026

Commits on Sep 28, 2026

Commits on Sep 30, 2026