Jupyter notebooks

.github/workflows/build.yml

@@ -39,7 +39,7 @@ jobs:
           python -m pip install -r requirements.txt
           python -m pip install -e .
           python -m pip install  \
-            pytest-timeout pytest-xdist
+            pytest-timeout pytest-xdist nbval ipympl
       - name: Gusto tests
         run: |
           . /home/firedrake/firedrake/bin/activate
@@ -58,8 +58,20 @@ jobs:
         if: always()
         run: |
           mkdir logs
-          cd /tmp/pytest-of-firedrake/pytest-0/
+          cd /tmp/pytest-of-firedrake/pytest-*/
           find . -name "*.log" -exec cp --parents {} /__w/gusto/gusto/logs/ \;
+      - name: Gusto jupyter_notebooks
+        run: |
+          . /home/firedrake/firedrake/bin/activate
+          export GUSTO_PARALLEL_LOG=FILE
+          python -m pytest \
+            -n 4 --dist loadscope \
+            --timeout=1200 \
+            --timeout-method=thread \
+            -o faulthandler_timeout=1260 \
+            --nbval-lax \
+            --nbval-cell-timeout=3000 \
+            -v jupyter_notebooks
       - name: Upload artifact
         if: always()
         uses: actions/upload-pages-artifact@v3

.github/workflows/lint.yml

@@ -21,7 +21,7 @@ jobs:
         uses: rbialon/flake8-annotations@v1
       - name: Install linter
         run: |
-          pip install flake8 pylint
+          pip install flake8 pylint nbqa
       - name: Lint codebase
         run: |
           make lint GITHUB_ACTIONS_FORMATTING=1

.gitignore

@@ -57,3 +57,7 @@ docs/_build/
 target/
 /docs/source/teamgrid.rst
 /docs/source/gusto.rst
+
+# Gusto specific
+jupyter_notebooks/results
+jupyter_notebooks/.ipynb_checkpoints

Makefile

@@ -1,7 +1,7 @@
 # Adds file annotations to Github Actions (only useful on CI)
 GITHUB_ACTIONS_FORMATTING=0
 ifeq ($(GITHUB_ACTIONS_FORMATTING), 1)
-	FLAKE8_FORMAT=--format='::error file=%(path)s,line=%(row)d,col=%(col)d,title=%(code)s::%(path)s:%(row)d:%(col)d: %(code)s %(text)s'
+	FLAKE8_FORMAT=--format '::error file=%(path)s,line=%(row)d,col=%(col)d,title=%(code)s::%(path)s:%(row)d:%(col)d: %(code)s %(text)s'
 else
 	FLAKE8_FORMAT=
 endif
@@ -17,23 +17,42 @@ lint:
 	@python3 -m flake8 $(FLAKE8_FORMAT) integration-tests
 	@echo "    Linting gusto plotting scripts"
 	@python3 -m flake8 $(FLAKE8_FORMAT) plotting
+	@echo "    Linting gusto notebooks"
+	@python3 -m nbqa flake8 jupyter_notebooks/*.ipynb $(FLAKE8_FORMAT)
 
-test:
-	@echo "    Running all tests"
-	@python3 -m pytest unit-tests integration-tests examples $(PYTEST_ARGS)
+test: unit_test integration_test example notebook_test
 
-unit_test:
+clean_cache:
+	@echo "    Cleaning caches"
+	@firedrake-clean
+
+unit_test: clean_cache
 	@echo "    Running all unit-tests"
 	@python3 -m pytest unit-tests $(PYTEST_ARGS)
 
-integration_test:
+integration_test: clean_cache
 	@echo "    Running all integration-tests"
 	@python3 -m pytest integration-tests $(PYTEST_ARGS)
 
-example:
+example: clean_cache
 	@echo "    Running all examples"
 	@python3 -m pytest examples -v -m "not parallel" $(PYTEST_ARGS)
 
 parallel_example:
 	@echo "    Running all parallel examples"
 	@python3 -m pytest examples -v -m "parallel" $(PYTEST_ARGS)
+
+notebook_test: clean_cache
+	@echo "    Running all Jupyter notebooks"
+	@python3 -m pytest --nbval-lax -v jupyter_notebooks $(PYTEST_ARGS)
+
+reset_notebooks:
+	@jupyter-nbconvert --clear-output ./jupyter_notebooks/*.ipynb
+	@rm -rf ./jupyter_notebooks/results
+	@env OMP_NUM_THREADS=1 jupyter-nbconvert \
+		--execute \
+		--ClearMetadataPreprocessor.enabled=True \
+		--allow-errors \
+		--to notebook \
+		--inplace \
+		./jupyter_notebooks/*.ipynb