Fix integration notebook

[jan-janssen]

Summary by CodeRabbit

• New Features

  • Added progress tracking to the Quantum ESPRESSO energy–volume evaluation flow.

• Refactor

  • Notebooks now use public workflow APIs and adopt a task-oriented data flow for energy–volume generation and analysis.

• Chores

  • Constrained per-task threading for more stable parallel runs.
  • CI notebook step now lists Flux resources before running notebooks.
  • Added progress utility support for evaluations.

• Documentation

  • Updated notebook text and cleaned execution metadata for clarity and reproducibility.

[review-notebook-app]

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📥 Commits

Reviewing files that changed from the base of the PR and between b28a413 and 240165b.

📒 Files selected for processing (1)

• notebooks/5-1-gpaw.ipynb (9 hunks)

Walkthrough

Replaces internal EV-curve helpers in two notebooks with public wrappers from atomistics.workflows, renames structure_dict → task_dict, updates task generation/analysis calls, constrains GPAW threading/MPI environment, and adds a Flux resource-list step to the notebooks CI pipeline.

Changes

Cohort / File(s)	Summary of Changes
EV workflow migration — GPAW notebook notebooks/5-1-gpaw.ipynb	Replaced imports from evcurve.helper with public atomistics.workflows functions (get_tasks_for_energy_volume_curve, analyse_results_for_energy_volume_curve); structure_dict → task_dict wiring; task construction now uses task_dict["calc_energy"]; evaluate_with_gpaw sets threading/MPI env vars; minor narrative/metadata updates.
EV workflow migration — Quantum ESPRESSO notebook notebooks/5-2-quantum-espresso.ipynb	Same import and API migration: use get_tasks_for_energy_volume_curve / analyse_results_for_energy_volume_curve; structure_dict → task_dict and task_loop_dict built from task_dict["calc_energy"]; executor calls updated to pass task_dict; added tqdm for progress; cell execution_count/metadata tweaks.
Public API surface atomistics.workflows (exports)	Added public wrappers: get_tasks_for_energy_volume_curve and analyse_results_for_energy_volume_curve; call-site signatures adjusted (axes param added to task generation; task_dict usage replaces structure_dict).
CI workflow tweak .github/workflows/pipeline.yml	In notebooks_integration job, Notebooks environment step now runs flux start flux resource list prior to papermill notebook actions (lists Flux resources before notebook execution).

Sequence Diagram(s)

sequenceDiagram
  participant NB as Notebook
  participant WF as atomistics.workflows
  participant EX as Executor (GPAW / QE)
  participant OUT as Results

  NB->>WF: get_tasks_for_energy_volume_curve(structure, num_points, vol_range, axes?)
  WF-->>NB: task_dict
  NB->>EX: submit tasks from task_dict["calc_energy"] (GPAW sets OMP_NUM_THREADS / MPI env)
  EX-->>OUT: output_dict (energies, volumes, metadata)
  NB->>WF: analyse_results_for_energy_volume_curve(output_dict, task_dict, fit_type, fit_order)
  WF-->>NB: E–V fit results
  note right of NB: QE notebook may show progress via tqdm

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Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~25 minutes

Possibly related PRs

• Add integration tests for application notebooks #619 — Replaces notebook-local/internal evcurve helpers with the same public functions (analyse_results_for_energy_volume_curve, get_tasks_for_energy_volume_curve), touching the same notebook workflow surfaces.

I hop through volumes, light and free,
Tasks bundled tidy — task_dict for me.
Old helpers shelved, new wrappers call,
Threads kept gentle, results answer the hall.
A rabbit stamps — the curves fit all 🥕

Pre-merge checks and finishing touches

❌ Failed checks (1 inconclusive)

Check name	Status	Explanation	Resolution
Title Check	❓ Inconclusive	The title “Fix integration notebook” is too generic and does not clearly convey the primary changes in this pull request, which include migrating energy‐volume workflows to public atomistics.workflows APIs, updating notebook code accordingly, and adding a Flux command to the CI pipeline. It refers only broadly to a notebook fix without specifying the actual scope of API and workflow updates across multiple notebooks and the CI configuration. This lack of specificity makes it difficult for reviewers to understand the main purpose at a glance.	Please update the title to more precisely reflect the key changes, such as “Migrate EV‐curve notebooks to public atomistics.workflows API and add Flux command to CI,” so that it clearly summarizes the scope of the updates.

✅ Passed checks (2 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 changes. Docstring coverage check skipped.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.16%. Comparing base (c9de13a) to head (240165b).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

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  Coverage   98.16%   98.16%           
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  Files          34       34           
  Lines        1686     1686           
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  Hits         1655     1655           
  Misses         31       31           

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