Merge branch 'master' of https://github.com/theislab/single-cell-best…

…-practices

.github/workflows/build_book.yml

@@ -6,15 +6,17 @@ jobs:
   build-book:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v4
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Setup environment
-        run: pip install --upgrade jupyter-book jupytext beautifulsoup4
+        run: |
+          pip install uv
+          uv pip install --system jupyter-book jupytext beautifulsoup4
 
       - name: Cache jupyter-cache folder
         uses: actions/cache@v2
@@ -35,25 +37,25 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v4
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install Python dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install jupyter-book jupytext beautifulsoup4
+          python -m pip install --upgrade uv
+          uv pip install --system jupyter-book jupytext beautifulsoup4
 
       - name: Install Headless Chrome dependencies
         run: |
           sudo apt-get update
           sudo apt-get install -yq $(cat .github/workflows/pyppeteer_requirements.txt)
 
       - name: Install Chromium
-        run: pip install pyppeteer
+        run: uv pip install --system pyppeteer
 
       - name: Build PDF from HTML (Docs)
         run: make pdf

.github/workflows/build_environments.yml

@@ -27,7 +27,7 @@ jobs:
             "jupyter-book/multimodal_integration/advanced_integration.yml",
           ]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install Conda environment with Micromamba
         uses: mamba-org/setup-micromamba@v1

.github/workflows/labeler.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v2.3.3
+        uses: actions/checkout@v4
 
       - name: Run Labeler
         uses: crazy-max/[email protected]

.github/workflows/pre_commit.yml

@@ -6,6 +6,6 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v3
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
       - uses: pre-commit/[email protected]

.github/workflows/publish_book.yml

@@ -9,15 +9,15 @@ jobs:
   build-book:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v2
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.11
 
       - name: Setup environment
-        run: pip install --upgrade jupyter-book==0.13.2 jupytext beautifulsoup4
+        run: pip install --upgrade jupyter-book jupytext beautifulsoup4
 
       - name: Cache jupyter-cache folder
         uses: actions/cache@v2

.pre-commit-config.yaml

@@ -10,12 +10,6 @@ repos:
     rev: v2.5.1
     hooks:
       - id: prettier
-        # Newer versions of node don't work on systems that have an older version of GLIBC
-        # (in particular Ubuntu 18.04 and Centos 7)
-        # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
-        # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
-        # https://github.com/jupyterlab/jupyterlab/issues/12675
-        language_version: "17.9.1"
   - repo: https://github.com/psf/black
     rev: 22.3.0
     hooks:

environment.yml

@@ -3,7 +3,7 @@ channels:
   - defaults
   - conda-forge
 dependencies:
-  - conda-forge::python=3.10.6
-  - conda-forge::jupyter-book==0.13.1
-  - conda-forge::jupytext==1.14.4
-  - conda-forge::beautifulsoup4==4.11.1
+  - conda-forge::python=3.11.8
+  - conda-forge::jupyter-book==1.0.0
+  - conda-forge::jupytext==1.16.1
+  - conda-forge::beautifulsoup4==4.12.3

jupyter-book/conditions/perturbation_modeling.yml

@@ -4,10 +4,8 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::python=3.9.15
-  - conda-forge::scanpy=1.9.1
+  - conda-forge::python=3.11.8
   - conda-forge::jupyterlab=3.5.0
   - pip:
-      - scgen==2.1.0
-      - pertpy==0.2.0
+      - pertpy==0.7.0
       - session_info

jupyter-book/introduction/raw_data_processing.md

@@ -150,6 +150,8 @@ A good (left) and a bad (right) per sequence quality score plot. The plot on the
 
 ```
 
+Multiple FastQC reports can be combined into a single report using the tool [`MultiQC`](https://multiqc.info).
+
 (raw-proc:aln-map)=
 
 ## Alignment and mapping