v2.1.1 with docs

docs/source/conf.py

@@ -79,16 +79,17 @@
 
 
 theme_options = ThemeOptions(
-    logo_light= "_static/no_image.png",
-    logo_dark= "_static/no_image.png",
+    logo_light="_static/no_image.png",
+    logo_dark="_static/no_image.png",
     show_scrolltop=True,
     show_breadcrumbs=True,
     awesome_external_links=True,
     main_nav_links={
         "Installation": "installation",
         "Tutorials": "tutorials",
-        "How it Works": "howitworks",
         "API": "api",
+        "How it Works": "howitworks",
+        "Contributors": "contributors",
     },
     extra_header_link_icons={
         "GitHub": LinkIcon(
@@ -100,9 +101,7 @@
 
 html_theme_options = asdict(theme_options)
 
-html_sidebars = {
-    "**": ["sidebar_main_nav_links.html", "sidebar_toc.html"]
-}
+html_sidebars = {"**": ["sidebar_main_nav_links.html", "sidebar_toc.html"]}
 
 html_context = {"default_mode": "auto"}
 

docs/source/contributors.md

@@ -0,0 +1,10 @@
+```{toctree}
+:hidden: true
+```
+
+# {octicon}`heart` Contributors
+
+## Team
+- [Clarence Mah](https://clarencemah.me)
+- [Noorsher Ahmed](https://github.com/noor01)
+- [Dylan Lam](https://github.com/dylanclam12)

docs/source/howitworks.md

@@ -47,6 +47,8 @@ The `SpatialData` object is a container for the following elements:
 - `Shapes`: boundaries, circles, polygons
 - `Tables`: annotations, count matrices
 
+See the [Data Prep Guide](tutorial_gallery/Data_Prep_Guide.html) for more information on how to prepare `SpatialData` objects for Bento and official [SpatialData documentation](https://spatialdata.scverse.org) for more info.
+
 
 ## RNAflux
 

docs/source/index.md

@@ -3,8 +3,9 @@
 
 installation
 tutorials
-howitworks
 api
+howitworks
+contributors
 ```
 
 ```{image} https://badge.fury.io/py/bento-tools.svg
@@ -49,9 +50,7 @@ Bento is a Python toolkit for performing subcellular analysis of spatial transcr
 :::{grid-item-card} {octicon}`workflow` Tutorials
 :link: tutorials.html
 :::
-::::
 
-::::{grid} 2
 :::{grid-item-card} {octicon}`gear` How It Works
 :link: howitworks.html
 :::

docs/source/tutorials.md

@@ -7,11 +7,12 @@
 :hidden: true
 
 tutorial_gallery/Main_Guide
+tutorial_gallery/Data_Prep_Guide
 tutorial_gallery/Spatial_Plotting
 tutorial_gallery/Spatial_Features
 :::
 
-::::{grid} 3
+::::{grid} 2
 :::{grid-item-card}  Main Guide
 :link: tutorial_gallery/Main_Guide.html
 
@@ -22,6 +23,7 @@ This tutorial will walk you through how to load, visualize data, and perform sub
 :link: tutorial_gallery/Data_Prep_Guide.html
 
 This guide will explain and demonstrate how to prepare SpatialData objects for Bento.
+:::
 
 :::{grid-item-card}  Spatial Plotting
 :link: tutorial_gallery/Spatial_Plotting.html

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "bento-tools"
-version = "2.1"
+version = "2.1.1"
 description = "A toolkit for subcellular analysis of spatial transcriptomics data"
 authors = [
     { name = "ckmah", email = "[email protected]" }

tests/test_flux.py

@@ -1,4 +1,3 @@
-import os
 import pytest
 
 
@@ -32,7 +31,9 @@
     assert "flux_variance_ratio" in flux_data.table.uns
 
     # Check columns are added in cell_boundaries_raster
-    assert all(gene in flux_data.points["cell_boundaries_raster"].columns for gene in genes)
+    assert all(
+        gene in flux_data.points["cell_boundaries_raster"].columns for gene in genes
+    )
 
     for i in range(len(genes)):
         assert f"flux_embed_{i}" in flux_data.points["cell_boundaries_raster"].columns
@@ -45,7 +46,7 @@
         points_key="transcripts",
         instance_key="cell_boundaries",
         res=conftest.FLUX_RES,
-        min_count = conftest.FLUXMAP_MIN_COUNT,
+        min_count=conftest.FLUXMAP_MIN_COUNT,
         train_size=conftest.FLUXMAP_TRAIN_SIZE,
         n_clusters=conftest.FLUXMAP_N_CLUSTERS,
         plot_error=False,