Override notebooks within Jenkinsfile

[Zeitsperre]

Overview

This PR adds a new filtering mechanism to make it easier to quickly run tests against individual notebooks.

Changes

• Modifies the Jenkinsfile to accept a new ALLOWLIST_NOTEBOOKS field for providing a filter for notebooks to be run

Testing Checklist

• Manually tested and verified working on Jenkins

Related Issue / Discussion

The functionality was already possible by setting a gist with a filtering function and setting CONFIG_PARAMETERS_SCRIPT_URL to pick up the script, overriding existing settings.

The changes here make it so that this can simply be performed directly on Jenkins.

[Zeitsperre]

@tlvu

I get the feeling you know where I'm going with this PR. Can you explain to me how I can pass environment variables from the Jenkins UI so that they're only expanded in the testall shell script?

[tlvu]

Minor suggestions. I'll need to test this myself once you are done. But this looks good to me. Let me know what's not working?

[tlvu]

Can you explain to me how I can pass environment variables from the Jenkins UI so that they're only expanded in the testall shell script?

I think in the current state things should work. What's not working?

[tlvu]

Please remove the boilerplate in the PR description. That boilerplate was for a new Jupyter env docker image release. It's not for this case. Please summarize your change short and sweet in the PR description. No need for that boilerplate.

[Zeitsperre]

I think in the current state things should work. What's not working?

Specifically, the environment variables from the Jenkins UI are not being expanded in the testall shell script:

http://jenkins.ouranos.ca/job/PAVICS-e2e-workflow-tests/job/config-override-notebooks/9/console

For pytest:

10:56:26  + py.test --rootdir=. --nbval $PAVICS_SDI_DIR/docs/source/notebooks/subset-user-input.ipynb $PAVICS_SDI_DIR/docs/source/notebooks/subsetting.ipynb --nbval-sanitize-with notebooks/output-sanitize.cfg --dist=loadscope --numprocesses=0
10:56:29  ERROR: file or directory not found: $PAVICS_SDI_DIR/docs/source/notebooks/subset-user-input.ipynb
10:56:29  
10:56:29  ============================= test session starts ==============================
10:56:29  platform linux -- Python 3.11.12, pytest-8.3.5, pluggy-1.5.0
10:56:29  rootdir: /home/jenkins/agent/workspace/_tests_config-override-notebooks@2
10:56:29  plugins: anyio-4.9.0, dash-3.0.3, nbval-0.11.0, tornasync-0.6.0.post2, xdist-3.6.1
10:56:29  collected 0 items
10:56:29  
10:56:29  ============================ no tests ran in 0.01s =============================
10:56:29  + EXIT_CODE=4

for nbconvert:

10:56:31  + enable_resulting_nb $PAVICS_SDI_DIR/docs/source/notebooks/subsetting.ipynb
10:56:31  + [ x$PAVICS_SDI_DIR/docs/source/notebooks/subsetting.ipynb = xpavics-sdi-master/docs/source/notebooks/FAQ_dask_parallel.ipynb ]
10:56:31  + [ x$PAVICS_SDI_DIR/docs/source/notebooks/subsetting.ipynb = xPAVICS-landing-master/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-3Climate-Indicators.ipynb ]
10:56:31  + return 0
10:56:31  + jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=240 --allow-errors --output-dir buildout --output $PAVICS_SDI_DIR/docs/source/notebooks/subsetting.output.ipynb $PAVICS_SDI_DIR/docs/source/notebooks/subsetting.ipynb
10:56:32  [NbConvertApp] WARNING | pattern '$PAVICS_SDI_DIR/docs/source/notebooks/subsetting.ipynb' matched no files
10:56:32  This application is used to convert notebook files (*.ipynb)
10:56:32          to various other formats.
...

[Zeitsperre]

Please remove the boilerplate in the PR description. That boilerplate was for a new Jupyter env docker image release. It's not for this case. Please summarize your change short and sweet in the PR description. No need for that boilerplate.

I'm going to propose some new templates for Pull Requests.

[tlvu]

Specifically, the environment variables from the Jenkins UI are not being expanded in the testall shell script

Ah ! True, you'll need to eval that new CUSTOM_NOTEBOOKS var before you can use it.

[tlvu]

@Zeitsperre Going through my old PRs to review, I've replied to you for this one. Have you tried it? Why is this PR in Draft mode by the way? Not sure you want to productize it?

[tlvu]

Please just fix the PR description before merge.