Execute notebooks individually

[jan-janssen]

Summary by CodeRabbit

• Chores
  • Improved the automated processing of Jupyter notebooks by removing an outdated script.
  • Updated the CI pipeline to execute each notebook sequentially with enhanced error handling for more reliable outcomes.

[coderabbitai]

Walkthrough

The changes remove a shell script that executed Jupyter notebooks and update the CI pipeline to call individual papermill commands. The revised pipeline now runs specific notebooks sequentially—starting a flux service where needed—while maintaining error checking through execution statuses. No changes were made to exported or public entities.

Changes

File(s)	Change Summary
.ci_support/build_notebooks.sh	Deleted the script that iterated through notebooks using papermill and tracked errors via a counter.
.github/workflows/pipeline.yml	Updated the CI pipeline to replace the removed script with sequential papermill commands, including flux service initiation for designated notebooks.

Sequence Diagram(s)

sequenceDiagram
    participant CI as CI Pipeline
    participant NP as Papermill
    participant FL as Flux Service

    CI->>NP: Execute Notebook 1 (1-single-node)
    CI->>FL: Start Flux for Notebook 2
    FL->>NP: Execute Notebook 2 (2-hpc-cluster)
    CI->>FL: Start Flux for Notebook 3
    FL->>NP: Execute Notebook 3 (3-hpc-job)
    CI->>NP: Execute Notebook 4 (4-developer)

Loading

Poem

I'm a rabbit in the CI field, leaping with glee,
Old scripts hopped away, now new steps set me free.
Flux and papermill lead my code-run parade,
Each notebook a hop in this delightful upgrade.
Crunching code with joyous hops—oh, what a day! 🐇✨
Celebrating change in my own whimsical way!

---

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 96.40%. Comparing base (8195183) to head (fbe4f07).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #617   +/-   ##
=======================================
  Coverage   96.40%   96.40%           
=======================================
  Files          28       28           
  Lines        1252     1252           
=======================================
  Hits         1207     1207           
  Misses         45       45           

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[coderabbitai]

Actionable comments posted: 0

🧹 Nitpick comments (1)

.github/workflows/pipeline.yml (1)

170-174: Ensure Robust Sequential Execution and Error Handling for Notebooks

The new commands successfully execute each notebook individually using papermill and the flux start prefix where needed. To further solidify this setup:

• Consider adding explicit error handling (for example, prepending the run block with set -euo pipefail or using || exit 1 after critical commands) so that a failure in one notebook execution halts subsequent commands.
• Verify that using flux start to wrap the papermill commands for the HPC-related notebooks is intentional and that the flux service is correctly initialized by the time these commands are executed.

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 8195183 and fbe4f07.

📒 Files selected for processing (2)

• .ci_support/build_notebooks.sh (0 hunks)
• .github/workflows/pipeline.yml (1 hunks)

💤 Files with no reviewable changes (1)

• .ci_support/build_notebooks.sh

⏰ Context from checks skipped due to timeout of 90000ms (3)

• GitHub Check: benchmark (ubuntu-latest, 3.13, .ci_support/environment-mpich.yml)
• GitHub Check: unittest_win
• GitHub Check: benchmark (ubuntu-latest, 3.13, .ci_support/environment-openmpi.yml)