Add notebooks to testing #24
Conversation
There was a problem hiding this comment.
docs/source/notebooks/example.ipynb::Cell 0
/tmp/sandpiper-venv/lib/python3.8/site-packages/jupyter_client/manager.py:66: DeprecationWarning: KernelManager._kernel_spec_manager_changed is deprecated in traitlets 4.1: use @observe and @unobserve instead.
def _kernel_spec_manager_changed(self):
-- Docs: https://docs.pytest.org/en/stable/warnings.html
I just got this warning but otherwise all the tests passed!
| @@ -5,3 +5,5 @@ venv/ | |||
| *.sqlite | |||
| .ipynb_checkpoints/ | |||
| .Rhistory | |||
| credentials.json | |||
There was a problem hiding this comment.
Good catch! It's nice that you thought of this.
| @@ -132,7 +138,7 @@ notebook-sanitizer: | |||
| .PHONY: test-notebooks | |||
| test-notebooks: notebook-sanitizer | |||
| @echo "Running notebook-based tests" | |||
| @bash -c "env WPS_URL=$(WPS_URL) pytest --nbval --verbose $(CURDIR)/docs/source/notebooks/ --sanitize-with $(CURDIR)/docs/source/output-sanitize.cfg --ignore $(CURDIR)/docs/source/notebooks/.ipynb_checkpoints" | |||
| @bash -c "source $(VENV)/bin/activate && env WPS_URL=$(WPS_URL) pytest --nbval --verbose $(CURDIR)/docs/source/notebooks/ --sanitize-with $(CURDIR)/docs/source/output-sanitize.cfg --ignore $(CURDIR)/docs/source/notebooks/.ipynb_checkpoints" | |||
There was a problem hiding this comment.
I don't see the commands are being executed when running make command. Also, I don't understand what the commands do. Could you elaborate?
There was a problem hiding this comment.
The command is mostly setup. Setting up the environment and sanitizing the notebook before running pytest with nbval to run the notebook.
| @@ -5,7 +5,8 @@ services: | |||
| image: pcic/sandpiper | |||
| ports: | |||
| - "8101:5003" | |||
|
|
|||
| volumes: | |||
| - /storage/data/climate/downscale/BCCAQ2/:/storage/data/climate/downscale/BCCAQ2/ | |||
There was a problem hiding this comment.
I wonder what this line is for. Would be appreciated if you could teach me.
There was a problem hiding this comment.
I discovered that our deployed instance of sandpiper was unable to correctly resolve the rules as it did not have access to the data. This just supplies the data as a volume that can be targeted using the same directory structure the database anticipates.
Changes
Makefilecommandsdocker-composefilesResolves #20.
Notes
Originally, we wanted the notebooks to be included in the
pytestsuite. However, a recent update to theMakefileintroduced some commands that would run the notebooks as a suite for you usingnbval. All we had to do was hook in our notebook and we were good to go.One slight complication was the password for the
connection_stringcould not be directly used in the notebook. To get around this, theMakefilewill create acredentials.jsonfile which will store the secret. There is a dummy value setup by this process and the user must manually add the correct value. This has to be done before the notebooks will work correctly. The file is in the.gitignoreso there should be no worry about exposing the passphrase publicly.