Merge pull request #18 from Intron7/v0.6.0

v0.6.0
scverse · Apr 18, 2023 · e2bdfff · e2bdfff
2 parents 0084310 + 1aa5eb6
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diff --git a/README.md b/README.md
@@ -1,3 +1,8 @@
+[![Stars](https://img.shields.io/github/stars/Intron7/rapids_singlecell?logo=GitHub&color=blue)](https://github.com/Intron7/rapids_singlecell/stargazers)
+[![PyPI](https://img.shields.io/pypi/v/rapids-singlecell?logo=PyPI)](https://pypi.org/project/rapids-singlecell)
+[![PyPIDownloads](https://pepy.tech/badge/rapids-singlecell)](https://pepy.tech/project/rapids-singlecell)
+[![Documentation Status](https://readthedocs.org/projects/rapids-singlecell/badge/?version=latest)](https://rapids-singlecell.readthedocs.io/en/latest/?badge=latest)
+
 # rapids-singlecell
 
 ## Background
@@ -21,7 +26,7 @@ The default installer doesn't cover RAPIDS nor cupy. Information on how to insta
 
 If you want to use RAPIDS new PyPI packages, the whole library with all dependencies can be install with:
 ````
-pip install 'rapids-singlecell[rapids]' --extra-index-url=https://pypi.ngc.nvidia.com
+pip install 'rapids-singlecell[rapids]' --extra-index-url=https://pypi.nvidia.com
 ````
 Please note that the RAPIDS PyPI packages are still considered experimental. It is important to ensure that the CUDA environment is set up correctly so that RAPIDS and Cupy can locate the necessary libraries.
 

diff --git a/docs/Installation.md b/docs/Installation.md
@@ -15,7 +15,7 @@ The default installer doesn't cover RAPIDS nor cupy. Information on how to insta
 
 If you want to use RAPIDS new PyPI packages, the whole library with all dependencies can be install with:
 ```
-pip install 'rapids-singlecell[rapids]' --extra-index-url=https://pypi.ngc.nvidia.com
+pip install 'rapids-singlecell[rapids]' --extra-index-url=https://pypi.nvidia.com
 ```
 Please note that the RAPIDS PyPI packages are still considered experimental. It is important to ensure that the CUDA environment is set up correctly so that RAPIDS and Cupy can locate the necessary libraries.
 

diff --git a/docs/_static/cunndata.svg b/docs/_static/cunndata.svg
diff --git a/docs/api.md b/docs/api.md
@@ -120,10 +120,23 @@ Basic plotting function for {class}`~rapids_singlecell.cunnData.cunnData` to ass
     tl.harmony_integrate
 ```
 
+## squidpy-GPU: `gr`
 
-## Decoupler-GPU: `dcg`
+{mod}`squidpy.gr` is a tool for the analysis of spatial molecular data. {mod}`rapids_singlecell.gr` acclerates some of these anlysis.
 
-{mod}`decoupler` is a package, that contains different statistical methods to extract biological activities. {mod}`rapids_singlecell.dcg` acclerates some of these methods.
+```{eval-rst}
+.. module:: rapids_singlecell.gr
+.. currentmodule:: rapids_singlecell
+
+.. autosummary::
+    :toctree: generated
+
+    gr.spatial_autocorr
+```
+
+## decoupler-GPU: `dcg`
+
+{mod}`decoupler` contains different statistical methods to extract biological activities. {mod}`rapids_singlecell.dcg` acclerates some of these methods.
 
 ```{eval-rst}
 .. module:: rapids_singlecell.dcg

diff --git a/docs/conf.py b/docs/conf.py
@@ -100,6 +100,7 @@
     "cugraph":('https://docs.rapids.ai/api/cugraph/stable/', None),
     "pymde":('https://pymde.org',None),
     "scanpy":("https://scanpy.readthedocs.io/en/stable/",None),
+    "squidpy":("https://squidpy.readthedocs.io/en/stable/",None),
     "seaborn":("https://seaborn.pydata.org/",None),
     "decoupler":("https://decoupler-py.readthedocs.io/en/latest/",None),
     "rmm":("https://docs.rapids.ai/api/rmm/stable/",None)

diff --git a/docs/index.md b/docs/index.md
@@ -1,3 +1,7 @@
+[![Stars](https://img.shields.io/github/stars/Intron7/rapids_singlecell?logo=GitHub&color=blue)](https://github.com/Intron7/rapids_singlecell/stargazers)
+[![PyPI](https://img.shields.io/pypi/v/rapids-singlecell?logo=PyPI)](https://pypi.org/project/rapids-singlecell)
+[![PyPIDownloads](https://pepy.tech/badge/rapids-singlecell)](https://pepy.tech/project/rapids-singlecell)
+[![Documentation Status](https://readthedocs.org/projects/rapids-singlecell/badge/?version=latest)](https://rapids-singlecell.readthedocs.io/en/latest/?badge=latest)
 ```{include} basic.md
 ```
 

diff --git a/docs/notebooks.rst b/docs/notebooks.rst
@@ -10,4 +10,5 @@ Sample notebooks
    notebooks/demo_gpu-seuratv3
    notebooks/demo_gpu-PR
    notebooks/demo_gpu-seuratv3-brain
+   notebooks/autocorr_benchmark