GWAS tutorial

.github/workflows/build.yml

@@ -34,6 +34,11 @@ jobs:
       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/gwas_tutorial.log
     - name: Test with pytest and coverage
       run: |
         pytest -v --cov=sgkit --cov-report=term-missing

docs/Makefile

@@ -1,6 +1,8 @@
 # Minimal makefile for Sphinx documentation
 #
 
+PYPATH=${PWD}/..
+
 # You can set these variables from the command line, and also
 # from the environment for the first two.
 SPHINXOPTS    ?=
@@ -22,4 +24,4 @@ clean:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@PYTHONPATH=${PYPATH} $(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -53,6 +53,7 @@
     "scanpydoc",
     "IPython.sphinxext.ipython_console_highlighting",
     "IPython.sphinxext.ipython_directive",
+    "myst_nb",
     *[p.stem for p in (HERE / "extensions").glob("*.py")],
 ]