Merge branch 'main' into fix_132

.github/workflows/pythonpackage.yml

@@ -1,37 +1,45 @@
 name: Python package
 
-on: [push]
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  schedule:
+    - cron: "0 5 1,15 * *"
 
 jobs:
   build:
 
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        python-version: [3.8, 3.9]
+        python-version: ["3.10", "3.12"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Install tools
+      run: python -m pip install --upgrade pip
     - name: Install dependencies
+      run: >
+        pip install
+        ".[test]"
+        git+https://github.com/bioFAM/mofapy2
+        git+https://github.com/scverse/mudata
+    - name: List dependencies
       run: |
-        python -m pip install --upgrade pip
-        python -m pip install umap-learn
-        python -m pip install .
-        # python -m pip install mofapy2
-        python -m pip install git+https://github.com/bioFAM/mofapy2
-        python -m pip install git+https://github.com/scverse/mudata
+        pip list
     - name: Lint with flake8
       run: |
-        pip install flake8
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        pip install pytest
         pytest

.gitignore

@@ -6,6 +6,9 @@ __pycache__/
 # C extensions
 *.so
 
+# cached data
+data/
+
 # Distribution / packaging
 .Python
 build/

.readthedocs.yaml

@@ -1,14 +1,15 @@
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
 # Build from the docs/ directory with Sphinx
 sphinx:
   configuration: docs/source/conf.py
 
 # Explicitly set the version of Python and its requirements
 python:
-  version: 3.8
   install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - docs
+    - requirements: docs/requirements.txt

docs/requirements.txt

@@ -0,0 +1,10 @@
+sphinx==7.2.6
+sphinx-rtd-theme==2.0.0
+commonmark==0.9.1
+recommonmark==0.7.1
+sphinx_automodapi==0.17.0
+nbsphinx==0.9.3
+readthedocs-sphinx-search==0.3.2
+sphinx-book-theme==1.1.2
+pydata-sphinx-theme==0.15.2
+muon

docs/source/changelog.rst

@@ -9,6 +9,12 @@ Release notes
 
    *
 
+
+v0.1.6
+------
+
+* Compatibility with scanpy 1.10
+
 v0.1.5
 ------
 

muon/__init__.py

@@ -13,4 +13,4 @@
 from . import atac
 from . import prot
 
-__version__ = "0.1.5"
+__version__ = "0.1.6"

muon/_atac/preproc.py

@@ -116,7 +116,7 @@ def tfidf(
     if log_tfidf:
         tf_idf = np.log1p(tf_idf)
 
-    res = np.nan_to_num(tf_idf, 0)
+    res = np.nan_to_num(tf_idf, nan=0.0)
     if not inplace:
         return res