diff --git a/.DS_Store b/.DS_Store
index ca989f4..ceda1da 100644
Binary files a/.DS_Store and b/.DS_Store differ
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 1e5d3b3..2017561 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -16,7 +16,7 @@ jobs:
strategy:
fail-fast: false
matrix:
- python-version: ["3.10", "3.11"]
+ python-version: ["3.11", "3.12"]
steps:
- uses: actions/checkout@v4
diff --git a/.gitignore b/.gitignore
index 6d317bd..0137429 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,5 @@
test/test_check_with_R_data.py
rawdata/snRNAseq_cellsWithSubtype.h5ad
docs/source/notebooks/rawdata/snRNAseq_cellsWithSubtype.h5ad
+docs/source/notebooks/output/HMI_example/Human_Myocardial_Infarction_analysed.h5ad
+tutorials/output/HMI_example/Human_Myocardial_Infarction_analysed.h5ad
diff --git a/.readthedocs.yml b/.readthedocs.yml
index 8b28a1f..5739965 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -4,7 +4,7 @@ version: 2
build:
os: ubuntu-22.04
tools:
- python: "3.10"
+ python: "3.11"
# You can also specify other tool versions:
# nodejs: "19"
# rust: "1.64"
diff --git a/dist/.DS_Store b/dist/.DS_Store
new file mode 100644
index 0000000..5008ddf
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diff --git a/dist/pycrosstalker-0.2.0-py3-none-any.whl b/dist/pycrosstalker-0.2.0-py3-none-any.whl
deleted file mode 100644
index b9fe95c..0000000
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diff --git a/dist/pycrosstalker-0.2.0.tar.gz b/dist/pycrosstalker-0.2.0.tar.gz
deleted file mode 100644
index ba9cb37..0000000
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diff --git a/dist/pycrosstalker-1.0.1-py3-none-any.whl b/dist/pycrosstalker-1.0.1-py3-none-any.whl
deleted file mode 100644
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diff --git a/dist/pycrosstalker-2.0.0-py3-none-any.whl b/dist/pycrosstalker-2.0.0-py3-none-any.whl
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index 1d19ccc..0000000
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diff --git a/dist/pycrosstalker-2.0.0.tar.gz b/dist/pycrosstalker-2.0.0.tar.gz
deleted file mode 100644
index 19c5205..0000000
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diff --git a/dist/pycrosstalker-2.1.0-py3-none-any.whl b/dist/pycrosstalker-2.1.0-py3-none-any.whl
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index 0000000..115a171
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diff --git a/dist/pycrosstalker-2.1.0.tar.gz b/dist/pycrosstalker-2.1.0.tar.gz
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diff --git a/docs/requirements.txt b/docs/requirements.txt
index 5073517..cc1ee93 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -7,3 +7,4 @@ sphinx-rtd-size
gprofiler-official
sankeyflow
nbformat
+anndata
diff --git a/docs/source/index.md b/docs/source/index.md
index 4e2b1b6..995992a 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -54,7 +54,7 @@ libgeos-dev
```
-## Features v2.0.0
+## Features v2.1.0
- Single and Comparative Reports
@@ -64,6 +64,7 @@ libgeos-dev
- All measures and PC table
- PC1 and PC2 based barplot
- LR pair visualization plot can be done
+ - Store analysis results directly in AnnData and export to `.h5ad`
# References
diff --git a/docs/source/notebooks/Human_Myelofibrosis.ipynb b/docs/source/notebooks/Human_Myelofibrosis.ipynb
index f58cc2a..185a1c4 100644
--- a/docs/source/notebooks/Human_Myelofibrosis.ipynb
+++ b/docs/source/notebooks/Human_Myelofibrosis.ipynb
@@ -26,13 +26,6 @@
"scrolled": true
},
"outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "/opt/miniconda3/envs/pyCrossTalkeR2/lib/python3.12/site-packages/requests/__init__.py:86: RequestsDependencyWarning: Unable to find acceptable character detection dependency (chardet or charset_normalizer).\n"
- ]
- },
{
"data": {
"text/html": [
@@ -40,7 +33,7 @@
" window.PlotlyConfig = {MathJaxConfig: 'local'};\n",
" if (window.MathJax && window.MathJax.Hub && window.MathJax.Hub.Config) {window.MathJax.Hub.Config({SVG: {font: \"STIX-Web\"}});}\n",
" \n",
- " \n",
- "