test: reapply upstream architecture changes on synced base

[ivanmilevtues]

Test PR for CodeBoarding review behavior on top of the latest synced master baseline.\n\nThis reapplies the same substantive architecture changes from the previous test PR without the retry commits.

[github-actions]

Architecture review · 45 components changed

graph LR
    n_Experiment_Orchestration_Data_Access["Experiment Orchestration #amp; Data Access"]
    n_Core_Image_Processing_Engine["Core Image Processing Engine"]
    n_Feature_Detection_Decoding["Feature Detection #amp; Decoding"]
    n_Spatial_Quantitation_Expression["Spatial Quantitation #amp; Expression"]
    n_System_Framework_Validation["System Framework #amp; Validation"]
    n_Experiment_Orchestration_Data_Access -- "provides raw tile data for stack construction" --> n_Core_Image_Processing_Engine
    n_Experiment_Orchestration_Data_Access -- "orchestrates FOV processing into decoded datafr…" --> n_Spatial_Quantitation_Expression
    n_Experiment_Orchestration_Data_Access -- "triggers validated pipeline transformations" --> n_System_Framework_Validation
    n_Core_Image_Processing_Engine -- "requests specific tiles via lazy-loading" --> n_Experiment_Orchestration_Data_Access
    n_Feature_Detection_Decoding -- "queries image metadata and axis grouping" --> n_Core_Image_Processing_Engine
    n_Feature_Detection_Decoding -- "populates intensity tables with detected featur…" --> n_Spatial_Quantitation_Expression
    n_Feature_Detection_Decoding -- "retrieves global configuration and logging sett…" --> n_System_Framework_Validation
    n_Spatial_Quantitation_Expression -- "transforms spot intensities into expression mat…" --> n_Feature_Detection_Decoding
    n_Spatial_Quantitation_Expression -- "utilizes image levels for segmentation masks" --> n_Core_Image_Processing_Engine
    n_System_Framework_Validation -- "defines coordinate axes and transformation types" --> n_Spatial_Quantitation_Expression
    n_Spatial_Quantitation_Expression -- "calls" --> n_Experiment_Orchestration_Data_Access
    n_Core_Image_Processing_Engine -- "provides filtered images for" --> n_Feature_Detection_Decoding
    n_Core_Image_Processing_Engine -- "supplies images for" --> n_Spatial_Quantitation_Expression
    n_System_Framework_Validation -- "validates manifests for" --> n_Experiment_Orchestration_Data_Access
    n_System_Framework_Validation -- "provides base classes for" --> n_Feature_Detection_Decoding
    n_Experiment_Orchestration_Data_Access -- "calls" --> n_Feature_Detection_Decoding
    n_Core_Image_Processing_Engine -- "calls" --> n_System_Framework_Validation
    n_Spatial_Quantitation_Expression -- "calls" --> n_System_Framework_Validation
    n_System_Framework_Validation -- "calls" --> n_Core_Image_Processing_Engine
    classDef added fill:#1f883d,stroke:#0b5d23,color:#ffffff;
    classDef modified fill:#bf8700,stroke:#7d4e00,color:#ffffff;
    classDef deleted fill:#cf222e,stroke:#82071e,color:#ffffff,stroke-dasharray:5 3;
    class n_Experiment_Orchestration_Data_Access,n_Core_Image_Processing_Engine,n_Feature_Detection_Decoding,n_Spatial_Quantitation_Expression,n_System_Framework_Validation modified;
    linkStyle 10 stroke:#0b5d23,stroke-width:2px;
    linkStyle 0,1,2,3,4,5,6,7,8,9 stroke:#7d4e00,stroke-width:2px;
    linkStyle 11,12,13,14,15,16,17,18 stroke:#82071e,stroke-width:2px,stroke-dasharray:5 3;

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Colors indicate component changes compared to master: 🟩 Added · 🟨 Modified · 🟥 Removed

Download the PR analysis artifacts from this workflow artifact.

Experiment Orchestration & Data Access : 8 files changed

• notebooks/py/smFISH.py
• starfish/core/codebook/codebook.py
• starfish/core/experiment/experiment.py
• starfish/core/image/Filter/richardson_lucy_deconvolution.py
• starfish/core/imagestack/imagestack.py
• starfish/core/imagestack/parser/xarray/init.py
• starfish/core/spacetx_format/util.py
• starfish/core/spots/FindSpots/blob.py

Core Image Processing Engine : 8 files changed

• starfish/core/experiment/experiment.py
• starfish/core/image/Filter/richardson_lucy_deconvolution.py
• starfish/core/image/Filter/zero_by_channel_magnitude.py
• starfish/core/image/Segment/watershed.py
• starfish/core/imagestack/imagestack.py
• starfish/core/spots/FindSpots/blob.py
• starfish/core/util/logging.py
• starfish/util/plot.py

Feature Detection & Decoding : 7 files changed

• starfish/core/image/Filter/richardson_lucy_deconvolution.py
• starfish/core/image/Filter/zero_by_channel_magnitude.py
• starfish/core/image/Segment/watershed.py
• starfish/core/imagestack/imagestack.py
• starfish/core/spots/FindSpots/blob.py
• starfish/core/util/logging.py
• starfish/util/plot.py

Spatial Quantitation & Expression : 8 files changed

• starfish/core/codebook/codebook.py
• starfish/core/image/Filter/richardson_lucy_deconvolution.py
• starfish/core/image/Filter/zero_by_channel_magnitude.py
• starfish/core/image/Segment/watershed.py
• starfish/core/imagestack/imagestack.py
• starfish/core/spots/FindSpots/blob.py
• starfish/core/util/logging.py
• starfish/util/plot.py

System Framework & Validation : 9 files changed

• conftest.py
• starfish/core/codebook/codebook.py
• starfish/core/experiment/experiment.py
• starfish/core/image/Filter/zero_by_channel_magnitude.py
• starfish/core/quality/assessment.py
• starfish/core/spacetx_format/util.py
• starfish/core/starfish.py
• starfish/core/util/logging.py
• starfish/util/plot.py

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_{codeboarding-action · run 27571094368}