v0.3.0 release

gao-lab · Dec 20, 2024 · dfb2b01 · dfb2b01
1 parent b189393
commit dfb2b01
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Showing 4 changed files with 7 additions and 9 deletions.
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -67,4 +67,4 @@ jobs:
           context: .
           dockerfile: ./Dockerfile
           push: true
-          tags: huhansan666666/decipher:latest
+          tags: huhansan666666/slat:latest
diff --git a/Dockerfile b/Dockerfile
@@ -3,7 +3,7 @@ FROM nvcr.io/nvidia/rapidsai/base:24.04-cuda11.8-py3.11
 # Update and install dependencies
 USER root
 RUN apt-get update \
-    && DEBIAN_FRONTEND=noninteractive apt-get install gcc g++ git -y \
+    && DEBIAN_FRONTEND=noninteractive apt-get install gcc g++ git libgl1 -y \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 

diff --git a/README.md b/README.md
@@ -7,8 +7,11 @@
 
 
 # scSLAT: single cell spatial alignment tools
+
 **scSLAT** package implements the **SLAT** (**S**patial **L**inked **A**lignment **T**ool) model to align single cell spatial omics data.
 
+Please check our paper ***Spatial-linked alignment tool (SLAT) for aligning heterogenous slices*** on [*Nature Communications*](https://www.nature.com/articles/s41467-023-43105-5).
+
 ![Model architecture](docs/_static/Model.png)
 
 ## Directory structure
@@ -27,7 +30,7 @@
 └── README.md
 ```
 
-## Tutorial
+## [Tutorial](https://slat.readthedocs.io/en/latest/tutorials.html)
 Tutorial of `scSLAT` is [here](https://slat.readthedocs.io/en/latest/tutorials.html), if you have any question please open an issue on github
 
 <img src='docs/_static/imgalignment.gif' width='400'>
@@ -66,9 +69,6 @@ pip install -e ".[dev,docs]"
 install_pyg_dependencies
 ```
 
-### Conda (Ongoing)
-We plan to provide a conda package of `scSLAT` in the near future.
-
 
 ## Reproduce manuscript results
 1. Please follow the [`env/README.md`](env/README.md) to install all dependencies. Please checkout the repository to v0.2.1 before install `scSLAT`.

diff --git a/scSLAT/viz/multi_dataset.py b/scSLAT/viz/multi_dataset.py
@@ -14,7 +14,7 @@
 from .color import godsnot_102, vega_10_scanpy, vega_20_scanpy, zeileis_28
 
 
-def get_color(n=1, cmap: str = "scanpy", seed: int = 0):
+def get_color(n:int = 1, cmap: str = "scanpy", seed: int = 0):
     r"""
     Get color
 
@@ -644,8 +644,6 @@ def draw_lines(
         self,
         ax,
         show_error,
-        show_celltype,
-        default_color,
         line_width: float = 0.3,
         line_alpha: float = 0.7,
     ) -> None: