Update scRNA tutorial

.github/workflows/execute-nbs.yaml

@@ -28,30 +28,31 @@ jobs:
           filter: blob:none
           fetch-depth: 0
       - name: Cache conda
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         env:
           # Increase this value to reset cache if env file has not changed
           CACHE_NUMBER: 0
         with:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
       - name: Cache notebooks
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         env:
           # Increase this value to reset cache if env file has not changed
           CACHE_NUMBER: 0
         with:
           path: .jupyter_cache
           key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: tutorials
-          channel-priority: strict
+          channel-priority: flexible
           environment-file: environment.yml
           miniforge-variant: Mambaforge
           miniforge-version: latest
           use-mamba: true
-          use-only-tar-bz2: true # This needs to be set for caching to work properly!
+          # some important packages are not available as .tar.bz2 anymore
+          # use-only-tar-bz2: true # This needs to be set for caching to work properly!
 
       - name: execute notebooks
         run: |

.gitignore

@@ -17,6 +17,9 @@ __pycache__/
 /docs/generated/
 /docs/_build/
 
+# User configuration
+/hatch.toml
+
 # IDEs
 /.idea/
 /.vscode/

.readthedocs.yaml

@@ -6,10 +6,10 @@ build:
     python: "3.11"
 sphinx:
   configuration: docs/conf.py
-  # disable this for more lenient docs builds
   fail_on_warning: true
 python:
   install:
+    - requirements: docs/patched-deps.txt
     - method: pip
       path: .
       extra_requirements:

docs/notebooks/scverse_data_interoperability.ipynb

@@ -121,7 +121,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.6"
+   "version": "3.12.4"
   }
  },
  "nbformat": 4,

docs/patched-deps.txt

@@ -0,0 +1,2 @@
+# fix from here: https://github.com/executablebooks/MyST-NB/pull/597
+myst-nb @ git+https://github.com/flying-sheep/MyST-NB@eval-metadata

environment.yml

@@ -3,18 +3,19 @@ name: tutorials
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
+  - python=3.12
   - jupyter-cache
   - ipykernel
   - ipython
+  - jupyterlab-myst
   - jupytext
-  - pip
+  - pip>=24.2
   - pip:
-      - "pandas<2"
-      - scanpy
+      - scanpy>=1.10
       - scrublet
       - leidenalg
-      - decoupler
+      # We need this commit: https://github.com/saezlab/decoupler-py/commit/0b3d9a975e06230ebbc32a6f97810be1730b8562
+      - decoupler @ git+https://github.com/saezlab/decoupler-py.git
       - celltypist
       - seaborn
       - mudata

pyproject.toml

@@ -43,13 +43,21 @@ docs = [
     "sphinx-copybutton",
 ]
 
+[tool.hatch.envs.default]
+installer = "uv"
+
 [tool.hatch.envs.registry]
 features = ["registry"]
 [tool.hatch.envs.registry.scripts]
 validate = "python tutorial-registry/validate.py {args}"
 
 [tool.hatch.envs.docs]
 features = ["docs"]
+extra-dependencies = [
+    "setuptools",  # undeclared dependency in pybtex
+    # fix from here: https://github.com/executablebooks/MyST-NB/pull/597
+    "myst-nb @ git+https://github.com/flying-sheep/MyST-NB.git@eval-metadata",
+]
 [tool.hatch.envs.docs.scripts]
 build = "sphinx-build -M html docs docs/_build {args}"