Remove Spatial Enrichment + Bootstrapping Cython

[srivarra]

This is for internal use only; if you'd like to open an issue or request a new feature, please open a bug or enhancement issue

Spatial enrichment has been issue prone and difficult to use. For now it would be ideal to remove it.

We can remove _bootstrapping.pyx. And the functions used by it downstream.

Here is a visual representation:

---
title: Bootstrapping
---
flowchart TB

    subgraph src/ark [src/ark]
        subgraph _bootstrapping.pyx [_bootstrapping.pyx]
        compute_close_num_rand
        end

        subgraph spatial_analysis_utils.py [spatial_analysis_utils.py]
        compute_close_cell_num_random
        end

        subgraph spatial_enrichment.py [spatial_enrichment.py]
        calculate_channel_spatial_enrichment --> generate_channel_spatial_enrichment_stats
        calculate_cluster_spatial_enrichment --> generate_cluster_spatial_enrichment_stats
        end
    end


    subgraph Tests [Tests]

        subgraph spatial_enrichment_test.py [spatial_enrichment_test.py]
        test_calculate_channel_spatial_enrichment
        test_calculate_cluster_spatial_enrichment
        test_generate_channel_spatial_enrichment_stats
        test_generate_cluster_spatial_enrichment_stats
        end

        subgraph spatial_analysis_utils_test.py [spatial_analysis_utils_test.py]
        test_compute_close_cell_num_random
        end

    end

    %% code dependency links
    _bootstrapping.pyx --> spatial_analysis_utils.py
    spatial_analysis_utils.py --> spatial_enrichment.py

    %% test dependency links
    compute_close_cell_num_random --> test_compute_close_cell_num_random
    calculate_channel_spatial_enrichment --> test_calculate_channel_spatial_enrichment
    calculate_cluster_spatial_enrichment --> test_calculate_cluster_spatial_enrichment
    generate_channel_spatial_enrichment_stats --> test_generate_channel_spatial_enrichment_stats
    generate_cluster_spatial_enrichment_stats --> test_generate_cluster_spatial_enrichment_stats


    %% hrefs
    click compute_close_num_rand href "https://github.com/angelolab/ark-analysis/blob/301e344f0ffbedafaad282c52c801e7713272f85/src/ark/utils/_bootstrapping.pyx#L248"
    click compute_close_cell_num_random href "https://github.com/angelolab/ark-analysis/blob/301e344f0ffbedafaad282c52c801e7713272f85/src/ark/analysis/spatial_analysis_utils.py#L287"
    click calculate_channel_spatial_enrichment href "https://github.com/angelolab/ark-analysis/blob/301e344f0ffbedafaad282c52c801e7713272f85/src/ark/analysis/spatial_enrichment.py#L102"
    click calculate_cluster_spatial_enrichment href "https://github.com/angelolab/ark-analysis/blob/301e344f0ffbedafaad282c52c801e7713272f85/src/ark/analysis/spatial_enrichment.py#L325"
    click generate_channel_spatial_enrichment_stats href "https://github.com/angelolab/ark-analysis/blob/301e344f0ffbedafaad282c52c801e7713272f85/src/ark/analysis/spatial_enrichment.py#L13"
    click generate_cluster_spatial_enrichment_stats href "https://github.com/angelolab/ark-analysis/blob/301e344f0ffbedafaad282c52c801e7713272f85/src/ark/analysis/spatial_enrichment.py#L243"
    
    click test_compute_close_cell_num_random href "https://github.com/angelolab/ark-analysis/blob/301e344f0ffbedafaad282c52c801e7713272f85/tests/analysis/spatial_analysis_utils_test.py#L201"
    click test_calculate_channel_spatial_enrichment href "https://github.com/angelolab/ark-analysis/blob/301e344f0ffbedafaad282c52c801e7713272f85/tests/analysis/spatial_enrichment_test.py#L111"
    click test_calculate_cluster_spatial_enrichment href "https://github.com/angelolab/ark-analysis/blob/301e344f0ffbedafaad282c52c801e7713272f85/tests/analysis/spatial_enrichment_test.py#L247"
    click test_generate_channel_spatial_enrichment_stats href "https://github.com/angelolab/ark-analysis/blob/301e344f0ffbedafaad282c52c801e7713272f85/tests/analysis/spatial_enrichment_test.py#L37"
    click test_generate_cluster_spatial_enrichment_stats href "https://github.com/angelolab/ark-analysis/blob/301e344f0ffbedafaad282c52c801e7713272f85/tests/analysis/spatial_enrichment_test.py#L76"

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In addition this will allow the following:

• Removal of the setup.py file
• Simplified build system on CI
  • only need one OS for building
  • No need for cibuildwheel
• Simplified user experience (no need for Visual Studio toolchains on Windows)