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gustaveroussy · Nov 9, 2023 · e24f7dc · e24f7dc
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -1,7 +1,7 @@
-name: ci 
+name: ci
 on:
   push:
-    tags:        
+    tags:
       - v*
 jobs:
   deploy:
@@ -36,7 +36,7 @@ jobs:
       #----------------------------------------------
       - name: Install dependencies
         if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-        run: poetry install
+        run: poetry install --extras "dev"
       #----------------------------------------------
       #              run test suite
       #----------------------------------------------

diff --git a/README.md b/README.md
@@ -2,7 +2,7 @@
   <img src="docs/assets/sopa.png" alt="sopa_logo" width="400"/>
 </p>
 
-**S**patial-**o**mics **p**reprocessing and **a**nalysis in Python. Built on top of [SpatialData](https://github.com/scverse/spatialdata), it enables processing and analyses of **any** imaging-based spatial-omics using a standard data structure and output. Sopa was designed for generability and low-memory consumption on large images (scales to `1TB+` images).
+**S**patial-**o**mics **p**ipeline and **a**nalysis in Python. Built on top of [SpatialData](https://github.com/scverse/spatialdata), it enables processing and analyses of **any** imaging-based spatial-omics using a standard data structure and output. Sopa was designed for generability and low-memory consumption on large images (scales to `1TB+` images).
 
 The pipeline outputs are composed of (i) Xenium Explorer files for interactive visualization, (ii) a HTML report for quick quality controls, and (iii) a SpatialData `.zarr` directory for further analyses.
 

diff --git a/docs/api/segmentation/shapes.md b/docs/api/segmentation/shapes.md
@@ -0,0 +1 @@
+::: sopa.segmentation.shapes.solve_conflicts
diff --git a/docs/cite_us.md b/docs/cite_us.md
@@ -0,0 +1,9 @@
+Our paper is available as an Arxiv preprint [here](TODO).
+```txt
+TODO
+```
+
+This library has been developed by Quentin Blampey, PhD student in Biomathematics / Deep Learning. The following institutions funded this work:
+
+- Lab of Mathematics and Computer Science (MICS), **CentraleSupélec** (Engineering School, Paris-Saclay University).
+- PRISM center, **Gustave Roussy Institute** (Cancer campus, Paris-Saclay University).
diff --git a/docs/cli.md b/docs/cli.md
@@ -3,19 +3,19 @@
 ```console
 // Run the Sopa CLI helper
 $ sopa --help
- Usage: sopa [OPTIONS] COMMAND [ARGS]...                                                               
-╭─ Commands ────────────────────────────────────────────────────────────╮
-│ aggregate     Count transcripts and/or average channels inside cells  │
-│ annotate      Perform cell-type annotation                            │
-│ check         Run some sanity checks                                  │
-│ crop          Crop an image based on a user-defined polygon           │
-│ explorer      Convertion to the Xenium Explorer's inputs              │
-│ patchify      Create patches with overlaps                            │
-│ read          Read any technology data + write an SpatialData object  │
-│ report        Create a HTML report of the pipeline run and some QCs   │
-│ resolve       Resolve the segmentation conflicts over patches         │
-│ segmentation  Perform cell segmentation on patches                    │
-╰───────────────────────────────────────────────────────────────────────╯
+ Usage: sopa [OPTIONS] COMMAND [ARGS]...    
+╭─ Commands ─────────────────────────────────────────────────────╮
+│ aggregate     Aggregate transcripts/channels inside cells      │
+│ annotate      Perform cell-type annotation                     │
+│ check         Run some sanity checks                           │
+│ crop          Crop an image based on a user-defined polygon    │
+│ explorer      Convertion to the Xenium Explorer's inputs       │
+│ patchify      Create patches with overlaps                     │
+│ read          Read any technology + write a SpatialData object │
+│ report        Create a web-report with figures/QCs             │
+│ resolve       Resolve the segmentation conflicts over patches  │
+│ segmentation  Perform cell segmentation on patches             │
+╰────────────────────────────────────────────────────────────────╯
 // Example: run cellpose segmentation
 $ sopa segmentation cellpose sdata.zarr
 ... [Logs] ...

diff --git a/docs/getting_started.md b/docs/getting_started.md
diff --git a/docs/index.md b/docs/index.md
@@ -1,4 +1,9 @@
-# Spatial-omics preprocessing and analysis
+# Spatial-omics pipeline and analysis
 
-!!! info
-    Read [Mkdocs Material documentation](https://squidfunk.github.io/mkdocs-material/creating-your-site/) to learn how to update the documentation.
+<p align="center">
+  <img src="./assets/sopa.png" alt="sopa_logo" width="400px"/>
+</p>
+
+**S**patial-**o**mics **p**ipeline and **a**nalysis in Python. Built on top of [SpatialData](https://github.com/scverse/spatialdata), it enables processing and analyses of **any** imaging-based spatial-omics using a standard data structure and output. Sopa was designed for generability and low-memory consumption on large images (scales to `1TB+` images).
+
+The pipeline outputs are composed of (i) Xenium Explorer files for interactive visualization, (ii) a HTML report for quick quality controls, and (iii) a SpatialData `.zarr` directory for further analyses.
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -7,9 +7,15 @@ theme:
   favicon: assets/sopa_favicon.png
 nav:
   - Home: index.md
+  - Getting Started: getting_started.md
   - CLI: cli.md
+  - API:
+    - sopa.segmentation:
+      - sopa.segmentation.shapes: api/segmentation/shapes.md
+  - Cite us: cite_us.md
 plugins:
   - search
+  - mkdocstrings
 markdown_extensions:
   - admonition
   - attr_list