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Every reference in the specific-example notebooks and the Introduction now matches its paper's DOI, authors, title, journal and year.

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Summary by CodeRabbit

• Documentation
  • Updated citations across materials design examples with corrected author details and fuller publication information, including journal volumes, issues, article or page numbers, and DOI links.
  • Added a publication citation to the custom silicon cutout example and linked the X-0D-CUT catalog entry to a reference.
  • Corrected spacing and punctuation in article titles and citations.

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Reviewing files that changed from the base of the PR and between e7771b2 and 8f6d8c6.

Files selected for processing: 3

• other/materials_designer/specific_examples/Introduction.ipynb
• other/materials_designer/specific_examples/defect_point_vacancy_boron_nitride_SIMULATION.ipynb
• other/materials_designer/specific_examples/optimization_interface_film_xy_position_graphene_nickel_SIMULATION.ipynb

Files skipped from review as they are similar to previous changes: 2

• other/materials_designer/specific_examples/defect_point_vacancy_boron_nitride_SIMULATION.ipynb
• other/materials_designer/specific_examples/Introduction.ipynb

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Walkthrough

Updated citations and bibliographic details in the Materials Designer Introduction and example notebooks. The changes include a new reference link, revised publication details, and author and title formatting updates.

Changes: Notebook citation updates

Layer / File(s)	Summary
Introduction reference updates other/materials_designer/specific_examples/Introduction.ipynb	The X-0D-CUT entry now links reference 25. Several reference entries have revised titles or citation details, and reference 25 was added.
Example notebook citation updates other/materials_designer/specific_examples/custom_cutout_etched_silicon.ipynb, other/materials_designer/specific_examples/defect_point_*.ipynb, other/materials_designer/specific_examples/defect_surface_*.ipynb, other/materials_designer/specific_examples/interface_3d_3d_copper_cristobalite.ipynb, other/materials_designer/specific_examples/optimization_interface_film_xy_position_graphene_nickel_SIMULATION.ipynb	Citations were added or updated with author names, journal details, article numbers, page numbers, title spacing, and DOI formatting.

Estimated code review effort: 1 (Trivial) | ~5 minutes

Change: Bug fix

Possibly related PRs

• mat3ra/api-examples#406: PR #406 uses Introduction reference 2 for a gold-cluster comparison; this PR updates that reference’s citation details.
• mat3ra/api-examples#391: PR #391 cites a paper whose citation is updated in the Pt-step notebook and Introduction reference 15.

Suggested reviewers: timurbazhirov

Merge Risk: Minimal · up to 8f6d8

No actionable merge-blocking risk is identified in these citation-only updates.

Pre-merge checks: 5

Check name	Status	Explanation
Description Check		Check skipped - CodeRabbit’s high-level summary is enabled.
Title check		The title clearly identifies the main change: fixing citations in the specific-example notebooks. It is concise and directly matches the pull request objectives.
Docstring Coverage		No eligible functions found in the changed files. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff with cyclomatic complexity of at least 2. Documentat…
Linked Issues check		Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check		Check skipped because no linked issues were found for this pull request.

Full details: Docstring Coverage

Explanation

No eligible functions found in the changed files. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff with cyclomatic complexity of at least 2. Documentation-only edits and deletions within surviving functions are included; unchanged diff context and fully deleted functions are excluded. Analyzed 0 functions across 0 files. (3 skipped: 3 unsupported.)

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Actionable comments posted: 1

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• 🪄 Fix comments: Fix CodeRabbit comments on this PR

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Inline comments:
Review comments at
@other/materials_designer/specific_examples/Introduction.ipynb:
- Line 85: Update reference 15 in the Introduction notebook to use the author
spelling Šljivančanin, Ž., matching the corresponding notebook; leave the rest
of the citation unchanged.

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Review info

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• Source mode: Auto
• Repository: Unavailable
• Branch: Unavailable
• File: No configuration file from this repository applied
• Commit: Unavailable
• Layers: defaults
• Review profile: CHILL
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• Run ID: 2f8da4a8-6273-4095-a7f3-2edfbf4b6483

Commits

Reviewing files that changed from the base of the PR and between 0d674c1 and e7771b2.

Files selected for processing: 11

• other/materials_designer/specific_examples/Introduction.ipynb
• other/materials_designer/specific_examples/custom_cutout_etched_silicon.ipynb
• other/materials_designer/specific_examples/defect_point_interstitial_tin_oxide.ipynb
• other/materials_designer/specific_examples/defect_point_interstitial_tin_oxide_SIMULATION.ipynb
• other/materials_designer/specific_examples/defect_point_substitution_graphene.ipynb
• other/materials_designer/specific_examples/defect_point_vacancy_boron_nitride.ipynb
• other/materials_designer/specific_examples/defect_point_vacancy_boron_nitride_SIMULATION.ipynb
• other/materials_designer/specific_examples/defect_surface_adatom_graphene.ipynb
• other/materials_designer/specific_examples/defect_surface_island_titanium_nitride.ipynb
• other/materials_designer/specific_examples/defect_surface_step_platinum.ipynb
• other/materials_designer/specific_examples/interface_3d_3d_copper_cristobalite.ipynb

Included review availability: This review used your included allowance. Your plan provides up to 1 included review per hour; 0 remain after this review.