📝 Build docs

Author: xiachenrui

.github/workflows/release.yml

@@ -18,10 +18,10 @@ jobs:
         python-version: '3.8'
 
     - name: Install dependencies
-      run:
+      run: |
         curl -sSL https://install.python-poetry.org | python3 -
         pip install --upgrade pip
-        pip install -e ".[cpu,docs]" 
+        pip install -e ".[cpu,docs]"
     
     - name: Build package
       run: |

.readthedocs.yml

@@ -0,0 +1,17 @@
+version: 2
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.8"
+  apt_packages:
+    - pandoc
+sphinx:
+  configuration: docs/conf.py
+python:
+  install:
+  - method: pip
+    path: .
+    extra_requirements:
+    - docs
+    - cpu
+    - dev

README.md

@@ -2,9 +2,9 @@
 [![dev-badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/xiachenrui/bc835db052fde5bd731a09270b42006c/raw/version.json)](https://gist.github.com/xiachenrui/bc835db052fde5bd731a09270b42006c)
 [![build-badge](https://github.com/gao-lab/SLAT/actions/workflows/build.yml/badge.svg)](https://github.com/gao-lab/SLAT/actions/workflows/build.yml)
 [![license-badge](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![docs-badge](https://readthedocs.org/projects/slat/badge/?version=latest)](https://salt.readthedocs.io/en/latest/?badge=latest)
 <!-- [![pypi-badge](https://img.shields.io/pypi/v/<name>)](https://pypi.org/project/<name>) -->
 <!-- [![conda-badge](https://anaconda.org/bioconda/<name>/badges/version.svg)](https://anaconda.org/bioconda/<name>) -->
-<!-- [![docs-badge](https://readthedocs.org/projects/<name>/badge/?version=latest)](https://<name>.readthedocs.io/en/latest/?badge=latest) -->
 
 # scSLAT: single cell spatial alignment tools
 
@@ -29,7 +29,7 @@
 ```
 
 ## Tutorial
-Tutorial of `scSLAT` is [here](TBD), if you have any question please open an issue on github
+Tutorial of `scSLAT` is [here](https://slat.readthedocs.io/en/latest/), if you have any question please open an issue on github
 
 ## Installation
 ### Install from PyPI

docs/index.md

@@ -15,7 +15,7 @@
    :caption: Contents:
 ```
 
-**scSLAT** package implements the **SLAT** (**S**patial **L**inked **A**lignment **T**ool) model, which aims to align single cell spatial data fast and accurate. scSLAT can extend to large dataset and various omics data easily.
+**scSLAT** package implements the **SLAT** (**S**patially-**L**inked **A**lignment **T**ool) model, which aims to align single cell spatial data fast and accurate. scSLAT can extend to large dataset and various omics data easily.
 
 ```{eval-rst}
 .. image:: _static/Model.png
@@ -24,12 +24,12 @@
 ```
 
 ## Key applications of scSLAT
-- Accurately align large (20,000+) single cell spatial data in few **seconds**.
+- Accurately align large (100,000+) single cell spatial data in few **seconds**.
 - Align **multi-platform**(such as Stereo-seq and MERFISH) and **multi-modalities** (such as ATAC and RNA) single cell spatial data.
 - Revealing spatial-temporal changes by time-series developmental spatial data alignment.
 
 ## Manuscript
-Please see our manuscript [Xia et al., 2022] at [*Biorxiv*](https://biorxiv.org) to learn more.
+Preparing
 
 ## Getting started with scSLAT
 To get started with ``scSLAT``, check out our {doc}`installation guide <install>` and {doc}`tutorials <tutorials>`.

docs/install.md

@@ -22,7 +22,7 @@ However, if you only want to run on CPU, you can directly install CPU version:
 pip install scSLAT[cpu]
 ```
 ## Docker container
-Dockerfile of `scSLAT` is available at [`env/Dockerfile`](env/Dockerfile)
+Dockerfile of `scSLAT` is available at [`env/Dockerfile`](https://github.com/gao-lab/SLAT/blob/main/env/Dockerfile)
 
 ## Install from Conda (Ongoing)
-We plan to provide a conda package of `scSLAT` in the near future.
+We plan to provide a conda package of `scSLAT` in the future.

env/README.md

@@ -7,7 +7,7 @@ If you want repeat our whole benchmark and evaluation workflow, please configure
 - dill
 - parse
 
-NOTE: Do **NOT** change install order !
+NOTE: Do **NOT** change install order !, you can see `env/envrionment.yml` for more details.
 ```
 mamba create -p ./conda python==3.8 -y && conda activate ./conda
 mamba install pytorch=1.11.0 torchvision torchaudio cudatoolkit=11.3 -c pytorch -y

env/environment.yml

@@ -0,0 +1,15 @@
+channels:
+  - pyg
+  - pytorch
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.8
+  - pytorch=1.11.0
+  - torchvision
+  - torchaudio
+  - cudatoolkit=11.3
+  - ca-certificates
+  - openssl
+  - pyg
+  - certifi