Merge branch 'master' into v1.1.0dev

.github/workflows/load_test_upload.yml

@@ -14,10 +14,10 @@ jobs:
     - uses: actions/checkout@v2
       with:
         fetch-depth: 0
-    - name: Set up Python 3.8
+    - name: Set up Python 3.11
       uses: actions/setup-python@v2
       with:
-        python-version: 3.8
+        python-version: 3.11
     - name: Install package
       run: |
         pip install wheel
@@ -35,10 +35,10 @@ jobs:
     - uses: actions/checkout@v2
       with:
         fetch-depth: 0
-    - name: Set up Python 3.8
+    - name: Set up Python 3.11
       uses: actions/setup-python@v2
       with:
-        python-version: 3.8
+        python-version: 3.11
     - name: Install dependencies
       run: |
         sudo apt-get clean && sudo apt-get update

.readthedocs.yml

@@ -5,6 +5,11 @@
 # Required
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.7"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
@@ -13,7 +18,6 @@ formats:
   - pdf
 
 python:
-  version: 3.7
   install:
   - method: pip
     path: .

README.md

@@ -82,7 +82,7 @@ With all dependencies
 
 -`pp.find_overdispersed`, `tl.test_association`, `tl.fit`, `tl.test_fork`, `tl.activation`, `tl.test_association_covariate`, `tl.test_covariate`: Require R package mgcv interfaced via python package rpy2:
 
-    conda create -n scFates -c conda-forge -c r python=3.8 r-mgcv rpy2=3.4.2 -y
+    conda create -n scFates -c conda-forge -c r python=3.11 r-mgcv rpy2=3.4.2 -y
     conda activate scFates
     pip install scFates
 
@@ -118,10 +118,10 @@ If you have a nvidia GPU, scFates can leverage CUDA computations for speedups fo
 
 `pp.filter_cells`, `pp.batch_correct`, `pp.diffusion`, `tl.tree`, `tl.cluster`
 
-The latest version of rapids framework is required (at least 0.17) it is recommanded to create a new conda environment:
+The latest version of rapids framework is required. Create the following  conda environment:
 
-    conda create -n scFates-gpu -c rapidsai -c nvidia -c conda-forge -c defaults \
-        cuml=21.12 cugraph=21.12 python=3.8 cudatoolkit=11.0 -y
+    conda create --solver=libmamba -n scFates-gpu -c rapidsai -c conda-forge -c nvidia  \
+        cuml=23.12 cugraph=23.12 python=3.10 cuda-version=11.2
     conda activate scFates-gpu
     pip install git+https://github.com/j-bac/elpigraph-python.git
     pip install scFates

docs/installation.rst

@@ -1,7 +1,7 @@
 Installation
 ============
 
-scFates is continuously tested with python 3.7 and 3.8, it is recommended to use a Miniconda_ environment.
+scFates is continuously tested with python 3.11, it is recommended to use a Miniconda_ environment.
 
 PyPI
 ----
@@ -20,7 +20,7 @@ With all dependencies
 
 - :func:`scFates.pp.find_overdispersed`, :func:`scFates.tl.test_association`, :func:`scFates.tl.fit`, :func:`scFates.tl.test_fork`, :func:`scFates.tl.activation`: Require R package mgcv interfaced via python package rpy2::
 
-    conda create -n scFates -c conda-forge -c r python=3.8 r-mgcv rpy2 -y
+    conda create -n scFates -c conda-forge -c r python=3.11 r-mgcv rpy2 -y
     conda activate scFates
     pip install scFates
 

docs/release_notes.rst

@@ -4,11 +4,15 @@
 Release Notes
 =============
 
-Version 1.0.6 :small:`August 26, 2566/2033`
+Version 1.0.7 :small:`February 15, 2566/2024`
+--------------------------------------------
+Fixed adjustedText version to avoid error, changed tests to python 3.11
+
+Version 1.0.6 :small:`August 26, 2566/2023`
 -------------------------------------------
 Fixed exception in :func:`scFates.tl.slide_cells`
 
-Version 1.0.5 :small:`August 25, 2566/2033`
+Version 1.0.5 :small:`August 25, 2566/2023`
 -------------------------------------------
 Fix int and bool check when ordering segments in :func:`scFates.pl.trends`.
 

docs/requirements.txt

@@ -1,3 +1,4 @@
+mock
 typing_extensions
 importlib_metadata
 sphinx_rtd_theme==0.5.2
@@ -9,7 +10,7 @@ matplotlib==3.3.1
 sphinx==4.0.2
 docutils
 readthedocs-sphinx-ext
-Jinja2==2.11.3
+Jinja2==3.1.3
 nbsphinx<0.8.7
 ipython
 anndata

requirements.txt

@@ -11,7 +11,7 @@ pandas<2.0
 statsmodels>=0.11.1
 matplotlib>=3.2.1
 plotly>=4.8.1
-adjustText>=0.7.3
+adjustText==0.7.3
 cycler>=0.10.0
 python_igraph>=0.8.2
 typing_extensions