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Update for Makie 0.24#53

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mkitti wants to merge 26 commits intomainfrom
web_makie_0_24
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Update for Makie 0.24#53
mkitti wants to merge 26 commits intomainfrom
web_makie_0_24

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@mkitti mkitti commented Sep 30, 2025 •
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Additionally:

  • Have scripts access ShroffCelegansModels.jl dependencies through ShroffCelegansModels.
  • :dash linestyle does not seem to work in WGLMakie at the moment
┌ Warning: Error in Javascript: THREE.WebGLProgram: Shader Error No error - VALIDATE_STATUS false                                                                                       
│                                                                                                                                                                                       
│ Program Info Log:                                                                                                                                                                     
│ error: declarations for uniform `_uuniform_pattern` have mismatching precision qualifiers                                                                                             
│                                                                                                                                                                                       
│                                                                                                                                                                                       
│                                                                                                                                                                                       
│                                                                                                                                                                                       
│ Fragment log:                                                                                                                                                                         
│ Vertex log:                                                                                                                                                                           
│                                                                                                                                                                                       
│ )                                                                                                                                                                                     
└ @ Bonito ~/.julia/packages/Bonito/j7uJq/src/serialization/protocol.jl:41                                                                                                              
An exception was thrown in JS: Error: WebGL error: Invalid operation                                                                                                                    
Additional message: error initializing scene                                                                                                                                            
Stack trace:
    Error: WebGL error: Invalid operation
        at eval (eval at <anonymous> (https://shroff-data.int.janelia.org/fix_annotation_ap_axis/assets/035c131b8eccc08f3cda4053e1ad7d59ad39836d-Bonito.bundled.js?48ef2248e493856810fbfc4159c00cceacdb52aa:3494:27), <anonymous>:19:23)
        at Object.flush (https://shroff-data.int.janelia.org/fix_annotation_ap_axis/assets/cfaeeb082a89e41751d0699070f4b0f5074da5f6-WGLMakie.bundled.js?9b1c640ca86b589a1f70ae8d8ad00f697957fb96:24584:13)
        at Object.insert (https://shroff-data.int.janelia.org/fix_annotation_ap_axis/assets/cfaeeb082a89e41751d0699070f4b0f5074da5f6-WGLMakie.bundled.js?9b1c640ca86b589a1f70ae8d8ad00f697957fb96:24579:14)
        at Module.execute_in_order (https://shroff-data.int.janelia.org/fix_annotation_ap_axis/assets/cfaeeb082a89e41751d0699070f4b0f5074da5f6-WGLMakie.bundled.js?9b1c640ca86b589a1f70ae8d8ad00f697957fb96:24594:21)
        at eval (eval at <anonymous> (https://shroff-data.int.janelia.org/fix_annotation_ap_axis/assets/035c131b8eccc08f3cda4053e1ad7d59ad39836d-Bonito.bundled.js?48ef2248e493856810fbfc4159c00cceacdb52aa:3494:27), <anonymous>:4:9)

@mkitti mkitti requested a review from bjarthur October 9, 2025 14:29
bjarthur
bjarthur reviewed Oct 9, 2025
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Comment thread .github/workflows/CI.yml
- '1'
- '1.10'
- '1.11'
- '1.12'
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i usually just test on 1 and 1.10

bjarthur
bjarthur reviewed Oct 9, 2025
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Comment thread src/ShroffCelegansModels.jl
using Statistics: Statistics
using StatsBase: StatsBase
using ThinPlateSplines: ThinPlateSplines
using TiffImages: TiffImages
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namespace decluttering like the above can be automated with https://github.com/JuliaTesting/ExplicitImports.jl

bjarthur
bjarthur reviewed Oct 9, 2025
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Comment thread src/demo_averaging/fix_annotation_ap_axis.jl
twisted_mesh_plot.visible = false
on(contour_mesh_toggle.active) do v
twisted_mesh_plot.visible = v
end
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@bjarthur bjarthur Oct 9, 2025 •
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consider setting twisted_mesh_plot.visible to contour_mesh_toggle.active when the former is created. like this: https://github.com/JaneliaSciComp/Transcriptome4D/blob/main/src/view-viewer.jl#L111-L112

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mkitti commented Nov 13, 2025

@dchen116 I just updated the web_makie_0_24 branch with all of the https://shroff-data.int.janelia.org/ apps working.

mkitti and others added 19 commits November 13, 2025 17:56
@mkitti
Set compat with Dates to 1
a97973b
@mkitti
Update web Manifest.toml
da10d3c
@mkitti @claude
Use 0.0.0.0 and SHROFF_HOST env var for portability
9ceb850 
Replace hardcoded shroff-data.int.janelia.org IPs and vm7249 hostname
checks with "0.0.0.0" bind addresses and SHROFF_HOST environment
variable for proxy URLs, and use relative config_path fallback.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@mkitti
Add resave_for_ben.jl
28e4625
@mkitti
Update loading.jl with config_2026_03_19_v2.json
a81429b
@mkitti
Merge branch 'web_makie_0_24' of github.com:JaneliaSciComp/ShroffCele…
0e6733b 
…gansModels.jl into Windows local
@mkitti
Updates from Windows local dev
ecee33d
@mkitti
Update Project.toml and Manifest.toml files
ffe8641
@mkitti
Update scripts
bc7b228
@mkitti
Add configuration
f9b999d
@mkitti
Enable query params in fix_annotation_ap_axis
cc8e14b 
Also use workspace for glmakie and web projects
@mkitti @claude
Add linux config v2, conversion script, and update config path
e5f8fff 
- Add config/linux/config_2026_03_19_v2.json (converted from Windows paths)
- Add config/convert_windows_paths.jl to translate Windows configs to Linux
- Add config/CHANGES.md summarizing differences from 2024-09-05 v1
- Update loading.jl to use the new linux config on non-Windows hosts

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@mkitti @claude
Add deployment directory copied from shroff-data-for-mark
b623a1a 
Dockerfile, OpenShift/K8s manifests, and README copied as-is from the
separate shroff-data-for-mark build package.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@mkitti @claude
Adapt deployment for repo-based build context
d606228 
- Dockerfile: COPY . instead of COPY ShroffCelegansModels.jl (repo root is now the build context)
- BuildConfigs: dockerfilePath updated to deployment/Dockerfile
- README: updated directory structure, oc commands, and noted merged patches

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@mkitti
Add multithreading to Julia
2358c8a
@mkitti
Use annotation and timepoint query strings
227ec07
@mkitti
Identify outlier timepoints via URL
0ddadf9
@mkitti
Create a base Docker image with just dependencies
cddd7a4
@mkitti
Add initial raw_zscore_analysis function
0a3a6ee
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