Upgrade sphinx to fix build

.github/workflows/build.yml

@@ -24,26 +24,10 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        sudo apt update -y
-        sudo apt install graphviz  # Needed for documentation
         python -m pip install --upgrade pip
-        pip install -r requirements.txt -r requirements-dev.txt -r requirements-doc.txt
+        pip install -r requirements.txt -r requirements-dev.txt
     - name: Run pre-commit
       uses: pre-commit/[email protected]
-    - name: Check for Sphinx doc warnings
-      run: |
-        cd docs
-        make html SPHINXOPTS="-W --keep-going -n"
-    - uses: actions/upload-artifact@v2
-      if: failure()
-      with:
-        name: gwas_tutorial
-        path: /home/runner/work/sgkit/sgkit/docs/_build/html/reports/examples/gwas_tutorial.err.log
-    - uses: actions/upload-artifact@v2
-      if: failure()
-      with:
-        name: relatedness_tutorial
-        path: /home/runner/work/sgkit/sgkit/docs/_build/html/reports/examples/relatedness_tutorial.err.log
     - name: Test with pytest
       run: |
         pytest -v

.github/workflows/check-docs.yml

@@ -0,0 +1,46 @@
+name: Check docs
+
+on:
+  push:
+  pull_request:
+  schedule:
+    # Run at the end of every day
+    - cron: "0 0 * * *"
+
+jobs:
+  build:
+    # Scheduled runs only on the origin org
+    if: (github.event_name == 'schedule' && github.repository_owner == 'pystatgen') || (github.event_name != 'schedule')
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9"]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        sudo apt update -y
+        sudo apt install graphviz  # Needed for documentation
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt -r requirements-dev.txt -r requirements-doc.txt
+    - name: Run pre-commit
+      uses: pre-commit/[email protected]
+    - name: Check for Sphinx doc warnings
+      run: |
+        cd docs
+        make html SPHINXOPTS="-W --keep-going -n"
+    - uses: actions/upload-artifact@v2
+      if: failure()
+      with:
+        name: gwas_tutorial
+        path: /home/runner/work/sgkit/sgkit/docs/_build/html/reports/examples/gwas_tutorial.err.log
+    - uses: actions/upload-artifact@v2
+      if: failure()
+      with:
+        name: relatedness_tutorial
+        path: /home/runner/work/sgkit/sgkit/docs/_build/html/reports/examples/relatedness_tutorial.err.log

requirements-doc.txt

@@ -1,6 +1,6 @@
 myst_nb
 pydata-sphinx-theme
-sphinx>4,<=4.2.0
+sphinx==6.2.1
 sphinx_autodoc_typehints>=1.14.0
 scanpydoc
 ipython

sgkit/io/bgen/bgen_reader.py

@@ -476,10 +476,12 @@ def rechunk_bgen(
 
     Warnings
     --------
+
     This functional is only applicable to diploid, bi-allelic BGEN datasets.
 
     Returns
     -------
+
     Dataset
         The rechunked dataset.
     """
@@ -589,10 +591,12 @@ def bgen_to_zarr(
 
     Warnings
     --------
+
     This functional is only applicable to diploid, bi-allelic BGEN datasets.
 
     Returns
     -------
+
     Dataset
         The rechunked dataset.
     """

sgkit/io/dataset.py

@@ -105,6 +105,7 @@ def load_dataset(
 
     Returns
     -------
+
     Dataset
         The dataset loaded from the Zarr store or file system.
     """