test: reapply upstream architecture changes

[ivanmilevtues]

Test PR for the CodeBoarding review workflow. Base is the older synced master baseline; this PR reapplies the larger upstream merge plus a small new quality assessment module so the review action has a meaningful architectural diff to analyze.

[github-actions]

Architecture review · 42 components changed

graph LR
    n_Experiment_Orchestration_Data_Access["Experiment Orchestration #amp; Data Access"]
    n_Image_Processing_Engine["Image Processing Engine"]
    n_Feature_Detection_Extraction["Feature Detection #amp; Extraction"]
    n_Decoding_Quantitation["Decoding #amp; Quantitation"]
    n_Spatial_Morphology_Segmentation["Spatial Morphology #amp; Segmentation"]
    n_Pipeline_Infrastructure_Validation["Pipeline Infrastructure #amp; Validation"]
    n_Experiment_Orchestration_Data_Access -- "orchestrates image transformations on FOVs" --> n_Image_Processing_Engine
    n_Experiment_Orchestration_Data_Access -- "triggers conversion of spatial data to decoded…" --> n_Decoding_Quantitation
    n_Experiment_Orchestration_Data_Access -- "provides coordinate selectors for biological bo…" --> n_Spatial_Morphology_Segmentation
    n_Image_Processing_Engine -- "requests raw image tiles via lazy-loading" --> n_Experiment_Orchestration_Data_Access
    n_Image_Processing_Engine -- "provides image data for mask generation" --> n_Spatial_Morphology_Segmentation
    n_Feature_Detection_Extraction -- "iterates over image axes to identify spot inten…" --> n_Image_Processing_Engine
    n_Feature_Detection_Extraction -- "populates IntensityTables with extracted spot d…" --> n_Decoding_Quantitation
    n_Decoding_Quantitation -- "maps feature dataframes to genetic targets" --> n_Feature_Detection_Extraction
    n_Spatial_Morphology_Segmentation -- "utilizes image intensity levels for watershed s…" --> n_Image_Processing_Engine
    n_Pipeline_Infrastructure_Validation -- "validates image stack configurations and schemas" --> n_Image_Processing_Engine
    n_Image_Processing_Engine -- "provides filtered and registered 5D tensors for" --> n_Feature_Detection_Extraction
    n_Spatial_Morphology_Segmentation -- "provides cell masks to aggregate spots into" --> n_Decoding_Quantitation
    n_Pipeline_Infrastructure_Validation -- "validates input manifests for" --> n_Experiment_Orchestration_Data_Access
    n_Experiment_Orchestration_Data_Access -- "calls" --> n_Feature_Detection_Extraction
    n_Experiment_Orchestration_Data_Access -- "calls" --> n_Pipeline_Infrastructure_Validation
    n_Image_Processing_Engine -- "calls" --> n_Decoding_Quantitation
    n_Feature_Detection_Extraction -- "calls" --> n_Spatial_Morphology_Segmentation
    n_Decoding_Quantitation -- "calls" --> n_Image_Processing_Engine
    n_Decoding_Quantitation -- "calls" --> n_Pipeline_Infrastructure_Validation
    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_Image_Processing_Engine,n_Decoding_Quantitation,n_Spatial_Morphology_Segmentation,n_Pipeline_Infrastructure_Validation modified;
    linkStyle 0,1,2,3,4,5,6,7,8,9 stroke:#7d4e00,stroke-width:2px;
    linkStyle 10,11,12,13,14,15,16,17,18 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 : 5 files changed

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

Image Processing Engine : 9 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/imagestack/parser/xarray/init.py
• starfish/core/spots/FindSpots/blob.py
• starfish/core/util/logging.py
• starfish/util/plot.py

Decoding & Quantitation : 3 files changed

• starfish/core/codebook/codebook.py
• starfish/core/experiment/experiment.py
• starfish/core/spacetx_format/util.py

Spatial Morphology & Segmentation : 2 files changed

• starfish/core/image/Segment/watershed.py
• starfish/core/util/logging.py

Pipeline Infrastructure & Validation : 6 files changed

• conftest.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 27568064495}