feature/SOF 7894 tests

[VsevolodX]

• chore: old deps
• update: fix condition
• chore: possible fixes

Summary by CodeRabbit

Bug Fixes

• Fixed invalid JSON formatting in experiment data file by removing trailing comma.

Updates

• Updated SCF job monitoring example to use default timeout behavior.
• Improved output file detection in workflow example using substring matching.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 98889d6e-a973-4a63-87e0-75ca66ef55aa

📥 Commits

Reviewing files that changed from the base of the PR and between 1b19d02 and b7342a9.

📒 Files selected for processing (1)

• utils/jupyterlite.py

📝 Walkthrough

Walkthrough

This PR contains two independent, minimal changes: the SCF calculation notebook is updated to use default timeout behavior and substring matching for output files, while a JSON data file is corrected by removing an invalid trailing comma.

Changes

Example Updates and Data Fixes

Layer / File(s)	Summary
SCF job monitoring adjustments examples/workflow/qe_scf_calculation.ipynb	The wait_for_jobs_to_finish_async call removes its explicit timeout parameter to rely on the helper's default, and output file detection switches from exact filename equality ("pw.out") to substring matching ("pw.out" in file["name"]).
JSON syntax cleanup other/experiments/jupyterlite/uploads/C(001)-Ni(111)-Interface.json	Trailing comma after the unitCellFormula property is removed, fixing JSON syntax before the closing brace.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~3 minutes

Possibly related PRs

• Exabyte-io/api-examples#301: Both PRs modify the same notebook's SCF job-wait logic—switching to or updating usage of wait_for_jobs_to_finish_async—so they are related.
• Exabyte-io/api-examples#298: Both PRs modify the job-wait call in examples/workflow/qe_scf_calculation.ipynb—switching to wait_for_jobs_to_finish_async (and here removing the explicit timeout)—so they are related.
• Exabyte-io/api-examples#285: Main PR's notebook change (removing the explicit timeout and relying on the helper's default) directly relates to the retrieved PR's modification of wait_for_jobs_to_finish_async behavior, so they are related.

Suggested reviewers

• timurbazhirov

Poem

A timeout removed, now default takes the lead,
Substring matching grants the files their need,
A trailing comma fixed, JSON breathes deep,
Small tweaks that keep the workflows neat! 🐰✨

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 inconclusive)

Check name	Status	Explanation	Resolution
Title check	❓ Inconclusive	The title 'feature/SOF 7894 tests' is vague and non-descriptive. It references a ticket number and generic term 'tests' without conveying what was actually changed or fixed in the changeset.	Replace with a more descriptive title that clarifies the actual changes, such as 'Fix SCF job monitoring and JSON serialization in examples' or 'Update notebook timeout handling and fix JSON formatting'.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch feature/SOF-7894-tests

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Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@examples/workflow/qe_scf_calculation.ipynb`:
- Around line 359-363: The current loop that finds the pw.out uses substring
matching on file["name"] and can pick the wrong file; replace that with a
deterministic check (e.g. match the basename or use
file["name"].endswith("pw.out")) when iterating the list returned by
job_endpoints.list_files(JOB_RESP["_id"]) to assign output_file_metadata, and
after the loop fail fast (raise/return an error) if no exact pw.out was found so
downstream parsing doesn't run on the wrong file.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: da36e9d1-b11e-4b2e-9586-6afeaa377729

📥 Commits

Reviewing files that changed from the base of the PR and between cc16a58 and 1b19d02.

📒 Files selected for processing (2)

• examples/workflow/qe_scf_calculation.ipynb
• other/experiments/jupyterlite/uploads/C(001)-Ni(111)-Interface.json

[coderabbitai]

⚠️ Potential issue | 🟠 Major | ⚡ Quick win

Use deterministic pw.out matching to avoid parsing the wrong file.

On Line 361, substring matching can pick unintended files and silently parse incorrect data. Select by basename/ending and fail fast if not found.

Proposed fix

 files = job_endpoints.list_files(JOB_RESP["_id"])
-for file in files:
-    if "pw.out" in file["name"]:
-        output_file_metadata = file
+output_file_metadata = next(
+    (file for file in files if file["name"] == "pw.out" or file["name"].endswith("/pw.out")),
+    None,
+)
+if output_file_metadata is None:
+    raise FileNotFoundError("Could not find 'pw.out' in job output files")

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@examples/workflow/qe_scf_calculation.ipynb` around lines 359 - 363, The
current loop that finds the pw.out uses substring matching on file["name"] and
can pick the wrong file; replace that with a deterministic check (e.g. match the
basename or use file["name"].endswith("pw.out")) when iterating the list
returned by job_endpoints.list_files(JOB_RESP["_id"]) to assign
output_file_metadata, and after the loop fail fast (raise/return an error) if no
exact pw.out was found so downstream parsing doesn't run on the wrong file.