update: fix citations

[VsevolodX]

Summary by CodeRabbit

• Documentation
  • Updated multiple references in the Introduction notebook to current research materials.

[review-notebook-app]

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📝 Walkthrough

Walkthrough

This PR updates three bibliography entries ([5], [9], [14]) in the References section of a Jupyter notebook, replacing them with different papers and metadata while preserving the reference structure. Changes are limited to markdown text only, with no structural or functional modifications.

Changes

Cohort / File(s)	Summary
Reference Updates other/materials_designer/specific_examples/Introduction.ipynb	Replaced three reference entries: [5] and [14] with different papers (preserving reference IDs and DOI fields), and [9] with a new paper including updated year, author list, title, volume/issue, and page range.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~3 minutes

Possibly related PRs

• update: restructure according to MCODE #280: Modifies the same notebook's References section with content and formatting changes.

Suggested reviewers

• timurbazhirov
• pranabdas

Poem

🐰 References renewed, so fresh and bright,
Five, nine, and fourteen shine with light,
Old papers fade, new knowledge flows,
The notebook blooms where wisdom grows! 📚✨

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'update: fix citations' accurately describes the main change—correcting citation entries in the notebook's References section by replacing three outdated or incorrect citations with updated ones.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch feature/SOF-7869-1

Warning

There were issues while running some tools. Please review the errors and either fix the tool's configuration or disable the tool if it's a critical failure.

🔧 Ruff (0.15.6)

other/materials_designer/specific_examples/Introduction.ipynb

Unexpected end of JSON input

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🧹 Nitpick comments (3)

other/materials_designer/specific_examples/Introduction.ipynb (3)

65-65: Formatting inconsistency: Journal name missing italics.

The journal name "Physical Review B" should be wrapped in asterisks (*Physical Review B*) to match the formatting of other citations in this file (e.g., lines 57, 59, 67).

Proposed fix

-    "<a id=\"ref5\"></a>[5] Kang, Y.-J., Kang, J., & Chang, K. J. (2008). Electronic structure of graphene and doping effect on SiO₂. Physical Review B, 78(11), 115404. https://doi.org/10.1103/PhysRevB.78.115404\n",
+    "<a id=\"ref5\"></a>[5] Kang, Y.-J., Kang, J., & Chang, K. J. (2008). Electronic structure of graphene and doping effect on SiO₂. *Physical Review B*, 78(11), 115404. https://doi.org/10.1103/PhysRevB.78.115404\n",

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@other/materials_designer/specific_examples/Introduction.ipynb` at line 65,
The citation for reference [5] (anchor "ref5") is missing italic formatting for
the journal name; edit the citation string that starts with "[5] Kang, Y.-J.,
Kang, J., & Chang, K. J. (2008)..." and wrap "Physical Review B" with asterisks
(e.g., *Physical Review B*) so it matches the formatting used by other
citations.

---

73-73: Formatting inconsistency: Journal name missing italics.

The journal name "Nano Letters" should be wrapped in asterisks (*Nano Letters*) to match the formatting of other citations.

Additionally, please verify this citation is the intended reference for the "Twisted BN Nanoribbon Bilayer" entry (line 34). The cited paper discusses twisted bilayer boron nitride in general, while the table entry specifically references nanoribbons.

Proposed formatting fix

-    "<a id=\"ref9\"></a>[9] Xian, L., Kennes, D. M., Tancogne-Dejean, N., Altarelli, M., & Rubio, A. (2019). Multiflat Bands and Strong Correlations in Twisted Bilayer Boron Nitride: Doping-Induced Correlated Insulator and Superconductor. Nano Letters, 19(8), 4934-4940. https://doi.org/10.1021/acs.nanolett.9b00986\n",
+    "<a id=\"ref9\"></a>[9] Xian, L., Kennes, D. M., Tancogne-Dejean, N., Altarelli, M., & Rubio, A. (2019). Multiflat Bands and Strong Correlations in Twisted Bilayer Boron Nitride: Doping-Induced Correlated Insulator and Superconductor. *Nano Letters*, 19(8), 4934-4940. https://doi.org/10.1021/acs.nanolett.9b00986\n",

,

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@other/materials_designer/specific_examples/Introduction.ipynb` at line 73,
The citation line containing "Xian, L., Kennes, D. M., Tancogne-Dejean, N.,
Altarelli, M., & Rubio, A. (2019). Multiflat Bands and Strong Correlations in
Twisted Bilayer Boron Nitride: Doping-Induced Correlated Insulator and
Superconductor. Nano Letters, 19(8), 4934-4940.
https://doi.org/10.1021/acs.nanolett.9b00986" should be updated to format the
journal name as *Nano Letters* (wrap "Nano Letters" with asterisks) to match
other citations, and then verify that this reference is the correct source for
the "Twisted BN Nanoribbon Bilayer" entry (the table entry referenced as
"Twisted BN Nanoribbon Bilayer"); if it is not, replace it with the correct
paper specific to nanoribbons or adjust the table entry to reflect the cited
paper.

---

83-83: Formatting inconsistency: Journal name missing italics.

The journal name "Physical Review B" should be wrapped in asterisks (*Physical Review B*) to match the formatting of other citations.

Proposed fix

-    "<a id=\"ref14\"></a>[14] Sangiovanni, D. G., Mei, A. B., Edstrom, D., Hultman, L., Chirita, V., Petrov, I., & Greene, J. E. (2018). Effects of surface vibrations on interlayer mass transport: Ab initio molecular dynamics investigation of Ti adatom descent pathways and rates from TiN/TiN(001) islands. Physical Review B, 97(3), 035406. https://doi.org/10.1103/PhysRevB.97.035406\n",
+    "<a id=\"ref14\"></a>[14] Sangiovanni, D. G., Mei, A. B., Edstrom, D., Hultman, L., Chirita, V., Petrov, I., & Greene, J. E. (2018). Effects of surface vibrations on interlayer mass transport: Ab initio molecular dynamics investigation of Ti adatom descent pathways and rates from TiN/TiN(001) islands. *Physical Review B*, 97(3), 035406. https://doi.org/10.1103/PhysRevB.97.035406\n",

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@other/materials_designer/specific_examples/Introduction.ipynb` at line 83,
Update the citation string containing "<a id=\"ref14\"></a>[14] Sangiovanni, D.
G., Mei, A. B., Edstrom, D., Hultman, L., Chirita, V., Petrov, I., & Greene, J.
E. (2018). Effects of surface vibrations on interlayer mass transport: Ab initio
molecular dynamics investigation of Ti adatom descent pathways and rates from
TiN/TiN(001) islands. Physical Review B, 97(3), 035406.
https://doi.org/10.1103/PhysRevB.97.035406" by wrapping the journal name
"Physical Review B" in asterisks (i.e., *Physical Review B*) so it matches the
italic formatting used in other citations in the notebook cell with id "ref14".

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Nitpick comments:
In `@other/materials_designer/specific_examples/Introduction.ipynb`:
- Line 65: The citation for reference [5] (anchor "ref5") is missing italic
formatting for the journal name; edit the citation string that starts with "[5]
Kang, Y.-J., Kang, J., & Chang, K. J. (2008)..." and wrap "Physical Review B"
with asterisks (e.g., *Physical Review B*) so it matches the formatting used by
other citations.
- Line 73: The citation line containing "Xian, L., Kennes, D. M.,
Tancogne-Dejean, N., Altarelli, M., & Rubio, A. (2019). Multiflat Bands and
Strong Correlations in Twisted Bilayer Boron Nitride: Doping-Induced Correlated
Insulator and Superconductor. Nano Letters, 19(8), 4934-4940.
https://doi.org/10.1021/acs.nanolett.9b00986" should be updated to format the
journal name as *Nano Letters* (wrap "Nano Letters" with asterisks) to match
other citations, and then verify that this reference is the correct source for
the "Twisted BN Nanoribbon Bilayer" entry (the table entry referenced as
"Twisted BN Nanoribbon Bilayer"); if it is not, replace it with the correct
paper specific to nanoribbons or adjust the table entry to reflect the cited
paper.
- Line 83: Update the citation string containing "<a id=\"ref14\"></a>[14]
Sangiovanni, D. G., Mei, A. B., Edstrom, D., Hultman, L., Chirita, V., Petrov,
I., & Greene, J. E. (2018). Effects of surface vibrations on interlayer mass
transport: Ab initio molecular dynamics investigation of Ti adatom descent
pathways and rates from TiN/TiN(001) islands. Physical Review B, 97(3), 035406.
https://doi.org/10.1103/PhysRevB.97.035406" by wrapping the journal name
"Physical Review B" in asterisks (i.e., *Physical Review B*) so it matches the
italic formatting used in other citations in the notebook cell with id "ref14".

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 97951195-35b6-4098-a1d5-b1a503f1d8be

📥 Commits

Reviewing files that changed from the base of the PR and between 3f13a53 and 376fed1.

📒 Files selected for processing (1)

• other/materials_designer/specific_examples/Introduction.ipynb