Reorganise modules

Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi

* The heatmap generation does not fall cleanly within the computations or db
  modules. This commit moves it to the higher level gn3 module.

3 files changed, 27 insertions, 69 deletions

diff --git a/gn3/computations/heatmap.py b/gn3/heatmaps.py
index 8727c92..198fb45 100644
--- a/gn3/computations/heatmap.py
+++ b/gn3/heatmaps.py
@@ -275,3 +275,28 @@ def get_nearest_marker(traits_list, genotype):
 
     marker_finder = nearest_marker_finder(genotype)
     return [marker_finder(trait) for trait in traits_list]
+
+# # Grey + Blue + Red
+# def generate_heatmap():
+#     cols = 20
+#     y_axis = (["%s"%x for x in range(1, cols+1)][:-1] + ["X"]) #replace last item with x for now
+#     x_axis = heatmap_x_axis_names()
+#     data = generate_random_data(height=cols, width=len(x_axis))
+#     fig = px.imshow(
+#         data,
+#         x=x_axis,
+#         y=y_axis,
+#         width=500)
+#     fig.update_traces(xtype="array")
+#     fig.update_traces(ytype="array")
+#     # fig.update_traces(xgap=10)
+#     fig.update_xaxes(
+#         visible=True,
+#         title_text="Traits",
+#         title_font_size=16)
+#     fig.update_layout(
+#         coloraxis_colorscale=[
+#             [0.0, '#3B3B3B'], [0.4999999999999999, '#ABABAB'],
+#             [0.5, '#F5DE11'], [1.0, '#FF0D00']])
+#     fig.write_html("%s/%s"%(heatmap_dir, "test_image.html"))
+#     return fig
diff --git a/gn3/heatmaps/heatmaps.py b/gn3/heatmaps/heatmaps.py
deleted file mode 100644
index 88f546d..0000000
--- a/gn3/heatmaps/heatmaps.py
+++ /dev/null
@@ -1,67 +0,0 @@
-import random
-import plotly.express as px
-
-#### Remove these ####
-
-heatmap_dir = "heatmap_images"
-
-def generate_random_data(data_stop: float = 2, width: int = 10, height: int = 30):
-    """
-    This is mostly a utility function to be used to generate random data, useful
-    for development of the heatmap generation code, without access to the actual
-    database data.
-    """
-    return [[random.uniform(0,data_stop) for i in range(0, width)]
-            for j in range(0, height)]
-
-def generate_random_data2(data_stop: float = 2, width: int = 10, height: int = 30):
-    """
-    This is mostly a utility function to be used to generate random data, useful
-    for development of the heatmap generation code, without access to the actual
-    database data.
-    """
-    return [
-        [{
-            "value": item,
-            "category": random.choice(["C57BL/6J +", "DBA/2J +"])}
-         for item in axis]
-        for axis in generate_random_data(data_stop, width, height)]
-
-def heatmap_x_axis_names():
-    return [
-        "UCLA_BXDBXH_CARTILAGE_V2::ILM103710672",
-        "UCLA_BXDBXH_CARTILAGE_V2::ILM2260338",
-        "UCLA_BXDBXH_CARTILAGE_V2::ILM3140576",
-        "UCLA_BXDBXH_CARTILAGE_V2::ILM5670577",
-        "UCLA_BXDBXH_CARTILAGE_V2::ILM2070121",
-        "UCLA_BXDBXH_CARTILAGE_V2::ILM103990541",
-        "UCLA_BXDBXH_CARTILAGE_V2::ILM1190722",
-        "UCLA_BXDBXH_CARTILAGE_V2::ILM6590722",
-        "UCLA_BXDBXH_CARTILAGE_V2::ILM4200064",
-        "UCLA_BXDBXH_CARTILAGE_V2::ILM3140463"]
-#### END: Remove these ####
-
-# Grey + Blue + Red
-def generate_heatmap():
-    cols = 20
-    y_axis = (["%s"%x for x in range(1, cols+1)][:-1] + ["X"]) #replace last item with x for now
-    x_axis = heatmap_x_axis_names()
-    data = generate_random_data(height=cols, width=len(x_axis))
-    fig = px.imshow(
-        data,
-        x=x_axis,
-        y=y_axis,
-        width=500)
-    fig.update_traces(xtype="array")
-    fig.update_traces(ytype="array")
-    # fig.update_traces(xgap=10)
-    fig.update_xaxes(
-        visible=True,
-        title_text="Traits",
-        title_font_size=16)
-    fig.update_layout(
-        coloraxis_colorscale=[
-            [0.0, '#3B3B3B'], [0.4999999999999999, '#ABABAB'],
-            [0.5, '#F5DE11'], [1.0, '#FF0D00']])
-    fig.write_html("%s/%s"%(heatmap_dir, "test_image.html"))
-    return fig
diff --git a/tests/unit/computations/test_heatmap.py b/tests/unit/test_heatmaps.py
index 156af45..265d5a8 100644
--- a/tests/unit/computations/test_heatmap.py
+++ b/tests/unit/test_heatmaps.py
@@ -1,6 +1,6 @@
-"""Module contains tests for gn3.computations.heatmap"""
+"""Module contains tests for gn3.heatmaps.heatmaps"""
 from unittest import TestCase
-from gn3.computations.heatmap import (
+from gn3.heatmaps import (
     cluster_traits,
     export_trait_data,
     compute_traits_order,