feature/SOF 7894 tests

[VsevolodX]

• update: add interface + use correct import
• update: load from emfs
• update: only api client
• update: fix symlink
• chore: versions
• update: revert

Summary by CodeRabbit

Release Notes

• Chores
  • Updated example notebooks including material creation and quantum espresso calculations to use improved asynchronous job-waiting operations for enhanced reliability
  • Configured new API client notebook environment with required package dependencies
  • Added new example material structure data file (C(001)-Ni(111) interface) for materials designer workflow reference

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ℹ️ Review info

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Configuration used: defaults

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Run ID: 3020da0f-1fdf-4894-9313-1a4d03350fe2

📥 Commits

Reviewing files that changed from the base of the PR and between 2a771f1 and 7f256b3.

📒 Files selected for processing (1)

• examples/material/create_material.ipynb

📝 Walkthrough

Walkthrough

This PR updates example notebooks and configuration to integrate a new API client package and adopts asynchronous job-waiting patterns. A new api_client notebook entry is configured, the material creation example switches to use it, and the workflow example moves to async job handling.

Changes

Example Notebooks and Configuration Updates

Layer / File(s)	Summary
API Client Configuration and Integration config.yml, examples/material/create_material.ipynb	A new notebook entry named api_client is added to config.yml with mat3ra-api-client package dependencies. The create_material.ipynb example is updated to install api_client instead of api_examples via the setup micropip call.
Asynchronous Job Waiting Pattern examples/workflow/qe_scf_calculation.ipynb	The qe_scf_calculation.ipynb notebook replaces the synchronous wait_for_jobs_to_finish import with the asynchronous wait_for_jobs_to_finish_async variant from utils.api, aligning with the later await usage in the notebook.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• Exabyte-io/api-examples#298: Modifies the same qe_scf_calculation.ipynb notebook to replace the synchronous wait_for_jobs_to_finish helper with the async variant.
• Exabyte-io/api-examples#285: Updates notebooks to use wait_for_jobs_to_finish_async, the async job-wait helper that is being adopted here.

Suggested reviewers

• timurbazhirov

Poem

🐇 A client awakens in config's embrace,
Examples now run at an async pace,
Jobs finish fast when we await,
With api_client, we create!

🚥 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 generic, using branch naming convention rather than describing actual changeset content; it doesn't convey what the PR meaningfully accomplishes.	Use a descriptive title that summarizes the main change, such as 'Update notebooks to use api_client and async job helpers' or similar wording that reflects the actual modifications made.

✅ 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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[coderabbitai]

Actionable comments posted: 2

🤖 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 `@config.yml`:
- Around line 75-76: The notebook mapping contains a malformed YAML entry: an
unkeyed list item "mat3ra-api-client" appears under the notebook section instead
of being the value of the api_client key; fix by making "api_client" a proper
key with "mat3ra-api-client" as its value (correct indentation and colon),
ensuring the notebook mapping contains a valid api_client: mat3ra-api-client
entry so the config loader can parse it.

In `@other/materials_designer/uploads/C`(001)-Ni(111)-Interface.json:
- Line 1: The file C(001)-Ni(111)-Interface.json currently contains a raw path
string ("../../experiments/jupyterlite/uploads/C(001)-Ni(111)-Interface.json")
instead of JSON, which will break JSON loaders; fix it by either replacing the
file contents with valid JSON data matching the expected schema for
material/interface metadata (e.g., an object with the required fields) or remove
this file and create an actual filesystem symlink pointing to the target path so
consumers read real JSON from the referenced file; ensure the final committed
file is valid JSON (or a real symlink) so JSON parsers can load it without
error.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

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

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 146c2548-5b33-4ffc-b7d8-fe9e96aac042

📥 Commits

Reviewing files that changed from the base of the PR and between 87b7706 and 2a771f1.

📒 Files selected for processing (5)

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

[coderabbitai]

⚠️ Potential issue | 🔴 Critical | ⚡ Quick win

Fix malformed YAML for api_client notebook entry.

Line 76 is an unkeyed list item under the notebook mapping, which makes this section invalid for the expected schema and can break config loading.

Suggested fix

   - name: api_client
-      - mat3ra-api-client
+    packages_common:
+      - mat3ra-api-client

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change

	- name: api_client
	- mat3ra-api-client
	- name: api_client
	packages_common:
	- mat3ra-api-client

🤖 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 `@config.yml` around lines 75 - 76, The notebook mapping contains a malformed
YAML entry: an unkeyed list item "mat3ra-api-client" appears under the notebook
section instead of being the value of the api_client key; fix by making
"api_client" a proper key with "mat3ra-api-client" as its value (correct
indentation and colon), ensuring the notebook mapping contains a valid
api_client: mat3ra-api-client entry so the config loader can parse it.

[coderabbitai]

⚠️ Potential issue | 🔴 Critical | ⚡ Quick win

*.json file is not valid JSON and will break JSON loaders.

At Line 1, the file contains a raw path string, not JSON content. If the intent is to alias another file, commit this as an actual symlink; otherwise replace it with valid JSON data.

🤖 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 `@other/materials_designer/uploads/C`(001)-Ni(111)-Interface.json at line 1,
The file C(001)-Ni(111)-Interface.json currently contains a raw path string
("../../experiments/jupyterlite/uploads/C(001)-Ni(111)-Interface.json") instead
of JSON, which will break JSON loaders; fix it by either replacing the file
contents with valid JSON data matching the expected schema for
material/interface metadata (e.g., an object with the required fields) or remove
this file and create an actual filesystem symlink pointing to the target path so
consumers read real JSON from the referenced file; ensure the final committed
file is valid JSON (or a real symlink) so JSON parsers can load it without
error.