📌 v0.2.1 release

Author: xiachenrui

.gitattributes

@@ -1,2 +1,4 @@
 # ignore the special file 
-**.ipynb linguist-vendored
+**.ipynb linguist-vendored
+**.R linguist-vendored
+** .Rprofile linguist-vendored

.github/workflows/build.yml

@@ -30,8 +30,8 @@ jobs:
           sudo apt install -y libxml2-utils pandoc
           curl -sSL https://install.python-poetry.org | python3 -
           pip install --upgrade pip
-          pip install -e ".[torch]"
-          pip install -e ".[pyg,docs,dev]"
+          pip install -e ".[docs, dev]"
+          pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.0.0+cpu.html
       
       - name: Build documentation
         run: |

.github/workflows/release.yml

@@ -21,8 +21,9 @@ jobs:
       run: |
         curl -sSL https://install.python-poetry.org | python3 -
         pip install --upgrade pip
-        pip install -e ".[torch]"
-        pip install -e ".[pyg,docs,dev]"
+        pip install -e ".[docs, dev]"
+        pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.0.0+cpu.html
+
     
     - name: Build package
       run: |

.gitignore

@@ -18,6 +18,9 @@
 *.arrow
 *Weights
 *.sqlite
+*.svg
+*.gz
+*.whl
 
 # folder
 **/conda/

README.md

@@ -46,36 +46,33 @@ docker pull huhansan666666/slat:latest
 > **Note**
 > Installing `scSLAT` within a new [conda environment](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) is recommended.
 
-First, we create a clean environment and install `scSLAT` from PyPI. We need install dependency `torch` before install `pyg`.
+First, we create a clean environment and install `scSLAT` from PyPI. Then we also need install dependencies for `pyg` manually. We default install with CUDA 11.7. Please refer [here](https://pytorch-geometric.readthedocs.io/en/latest/install/installation.html#quick-start) for CPU version or different CUDA versions.
 
 > **Warning**
 > old NVIDIA driver may raise error, please update NVIDIA driver to the latest version.
 
 ```bash
 conda create -n scSLAT python=3.8 -y && conda activate scSLAT
-pip install "scSLAT[torch]"
-pip install "scSLAT[pyg]"
+pip install scSLAT
+pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.0.0+cu117.html
 ```
 
-> **Note**
-> Some dependencies such as `torch-scatter` need to compile from source, which may take a long time. Please refer our solution to accelerate the install [here](https://slat.readthedocs.io/en/latest/install.html)
-
 ### Development version
 For development purpose, clone this repo and install:
 
 ```bash
 git clone [email protected]:gao-lab/SLAT.git
 cd SLAT
-pip install -e ".[torch]"
-pip install -e ".[pyg,dev,doc]"
+pip install -e ".[dev,docs]"
+pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.0.0+cu117.html
 ```
 
 ### 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 v0.2.0 before install `scSLAT`:
-2. Download and pre-process data follow the [`data/README.md`](data/README.md)
+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`.
+2. Download and pre-process data follow the [`data/README.md`](data/README.md).
 3. Whole benchmark and evaluation procedure can be found in [`/benchmark`](benchmark/README.md) and [`/evaluation`](evaluation/README.md), respectively.
 4. Every case study is recorded in the [`/case`](case/README.md) directory in the form of jupyter notebook.

benchmark/.gitignore

@@ -4,4 +4,5 @@ results*/
 split/
 multi/
 results_bak/
-figures/
+figures/
+hetero/