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Add a start-here guide, troubleshooting page, and references with bibtex support. Wire the new pages into the Sphinx index and requirements.
Reviewer's GuideExpands LEED-IV onboarding documentation and introduces centralized bibliography support via sphinxcontrib-bibtex, wiring new pages into the Sphinx docs and adding scientific references. File-Level Changes
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WalkthroughAdds bibliography support to Sphinx documentation and introduces three new documentation pages: a "start here" guide for LEED-IV users, a troubleshooting section for common issues, and a references page. Includes new BibTeX entries and updates navigation to link new pages. Changes
Estimated code review effort🎯 2 (Simple) | ⏱️ ~12 minutes Possibly related issues
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Clarifications for #34:
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Actionable comments posted: 3
🤖 Fix all issues with AI agents
In @doc/conf.py:
- Line 37: The requirements entry for the bibtex extension is too low for Sphinx
>=7.2; update the dependency string 'sphinxcontrib-bibtex>=2.5,<3' to
'sphinxcontrib-bibtex>=2.6,<3' so the added extension 'sphinxcontrib.bibtex' is
supported by the required Sphinx versions.
In @doc/references.bib:
- Around line 1-18: Update the bibliographic metadata for the two BibTeX
entries: for entry key pendry1980 replace the incorrect doi value with
10.1088/0022-3719/13/5/024; for entry key vanhove1984 change year to 1979,
replace isbn with 978-3-642-67197-5, and add series = {Springer Series in
Chemical Physics} and volume = {2} (keep author, title, and publisher as-is);
ensure fields are valid BibTeX keys and values for keys pendry1980 and
vanhove1984.
In @doc/start_here.rst:
- Around line 3-5: The title decorators are too short for the title text "Start
here: LEED-IV in CLEED"; update the overline and underline to be at least as
long as the title (e.g., change the 27 asterisks to 29 asterisks) or shorten the
title so the decorator length matches, ensuring the reStructuredText title
markup uses matching-length decoration.
📜 Review details
Configuration used: Organization UI
Review profile: ASSERTIVE
Plan: Pro
📒 Files selected for processing (7)
doc/conf.pydoc/index.rstdoc/references.bibdoc/references.rstdoc/requirements.txtdoc/start_here.rstdoc/troubleshooting.rst
🧰 Additional context used
📓 Path-based instructions (1)
doc/**/*.rst
📄 CodeRabbit inference engine (AGENTS.md)
doc/**/*.rst: Documentation sources underdoc/must use reStructuredText (*.rst), not Markdown; whitespace/indentation and blank lines are part of the syntax
Prefer.. toctree::navigation over.. include::in reStructuredText so pages are addressable and cross-references behave predictably
In reStructuredText documentation, avoid tabs; use spaces (tabs can create accidental block quotes / unexpected indentation)
Refer to repo-specific reStructuredText conventions and common pitfalls inskills/restructured-text/SKILL.md
Files:
doc/start_here.rstdoc/references.rstdoc/index.rstdoc/troubleshooting.rst
🧠 Learnings (3)
📓 Common learnings
Learnt from: CR
Repo: Liam-Deacon/CLEED PR: 0
File: doc/AGENTS.md:0-0
Timestamp: 2025-12-20T09:06:56.386Z
Learning: Applies to doc/CLEED_Manual.pdf : Keep `doc/CLEED_Manual.pdf` tracked in git as the canonical reference manual for the original CLEED program suite
📚 Learning: 2025-12-20T09:06:56.386Z
Learnt from: CR
Repo: Liam-Deacon/CLEED PR: 0
File: doc/AGENTS.md:0-0
Timestamp: 2025-12-20T09:06:56.386Z
Learning: Applies to doc/CLEED_Manual.pdf : Keep `doc/CLEED_Manual.pdf` tracked in git as the canonical reference manual for the original CLEED program suite
Applied to files:
doc/start_here.rstdoc/references.rstdoc/references.bibdoc/troubleshooting.rst
📚 Learning: 2026-01-07T13:38:38.082Z
Learnt from: CR
Repo: Liam-Deacon/CLEED PR: 0
File: AGENTS.md:0-0
Timestamp: 2026-01-07T13:38:38.082Z
Learning: Applies to doc/**/*.rst : Prefer `.. toctree::` navigation over `.. include::` in reStructuredText so pages are addressable and cross-references behave predictably
Applied to files:
doc/index.rst
🪛 GitHub Actions: Docs (Sphinx)
doc/start_here.rst
[error] 3-3: Sphinx warning treated as error: Title overline too short.
⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (1)
- GitHub Check: Codacy Static Code Analysis
🔇 Additional comments (7)
doc/requirements.txt (1)
3-3: LGTM!The sphinxcontrib-bibtex dependency is correctly versioned and necessary for bibliography support introduced in the new documentation files.
doc/troubleshooting.rst (1)
1-41: LGTM!The troubleshooting guide follows proper reStructuredText conventions with correct header underline alignment, clear section labels, and actionable guidance. The practical problem-solution format is well-suited for first-time users.
doc/start_here.rst (1)
17-18: No issues found. The citation syntax:cite:p:vanhove1984and `:cite:p:`pendry1980is correct for sphinxcontrib-bibtex >=2.5 and follows the documented parenthetical citation role format.doc/references.rst (1)
1-12: Bibliography structure is correct; consider expanding the collection.The reStructuredText syntax is correct, and the bibliography directive properly references
references.bibwith the:all:option. However, the description states it "collects primary sources referenced throughout the CLEED manual and tutorials," yet only two entries are currently included. This aligns with the follow-up items mentioned in the PR objectives about expanding the bibliography with additional algorithm-specific references.Verify that the two included citations are sufficient for the current documentation scope, or consider adding placeholder entries for commonly referenced works in LEED-IV analysis.
doc/index.rst (2)
19-19: LGTM! Logical placement of start_here guide.The
start_hereentry is well-positioned after the introduction, providing a natural onboarding flow for new LEED-IV users.
26-27: LGTM! Troubleshooting and references sections complete the documentation structure.The placement of
troubleshootingandreferencesafter the main content sections (downloads) follows a logical documentation structure, making these resources easily accessible.doc/conf.py (1)
99-100: LGTM! Bibliography configuration is correct.The
bibtex_bibfilesconfiguration correctly points toreferences.bibwith a clear comment explaining the purpose. The relative path is appropriate since both files reside in thedoc/directory.
| 'sphinx.ext.intersphinx', | ||
| 'sphinx.ext.mathjax', | ||
| 'sphinx.ext.viewcode', | ||
| 'sphinxcontrib.bibtex', |
There was a problem hiding this comment.
🧩 Analysis chain
🏁 Script executed:
#!/bin/bash
# Check sphinxcontrib-bibtex and Sphinx version requirements
echo "=== Content of doc/requirements.txt ==="
cat doc/requirements.txt
echo -e "\n=== Checking for version specifications ==="
grep -i "sphinx" doc/requirements.txt | head -20Repository: Liam-Deacon/CLEED
Length of output: 283
🌐 Web query:
sphinxcontrib-bibtex 2.5 compatibility Sphinx 7.2
💡 Result:
Short answer: No — sphinxcontrib-bibtex 2.5 is not guaranteed compatible with Sphinx 7.2. Upgrade to a maintained release (2.6.x or later) that documents support for newer Sphinx versions.
Evidence:
- Sphinx 7.2 release notes (Sphinx 7.x series) — release date and changes. [1]
- sphinxcontrib-bibtex project documentation shows more recent 2.6.x releases (active maintenance) and changelog entries after 2.5; use a current release for compatibility with recent Sphinx. [2]
If you want, I can check the exact minimum/maximum Sphinx requirement declared in the sphinxcontrib-bibtex 2.5 package metadata (setup.cfg/pyproject) and list any breaking changes between 2.5 and the current sphinxcontrib-bibtex.
Update sphinxcontrib-bibtex minimum version requirement to 2.6+
The extension addition is correct, but doc/requirements.txt specifies sphinxcontrib-bibtex>=2.5,<3, which is incompatible with the required Sphinx version (>=7.2,<9). Version 2.5 does not provide documented support for Sphinx 7.2+. Update the requirement to sphinxcontrib-bibtex>=2.6,<3 to ensure compatibility.
🤖 Prompt for AI Agents
In @doc/conf.py at line 37, The requirements entry for the bibtex extension is
too low for Sphinx >=7.2; update the dependency string
'sphinxcontrib-bibtex>=2.5,<3' to 'sphinxcontrib-bibtex>=2.6,<3' so the added
extension 'sphinxcontrib.bibtex' is supported by the required Sphinx versions.
| @article{pendry1980, | ||
| author = {Pendry, J. B.}, | ||
| title = {Reliability factors for LEED calculations}, | ||
| journal = {Journal of Physics C: Solid State Physics}, | ||
| volume = {13}, | ||
| number = {5}, | ||
| pages = {937-944}, | ||
| year = {1980}, | ||
| doi = {10.1088/0022-3719/13/5/012} | ||
| } | ||
|
|
||
| @book{vanhove1984, | ||
| author = {Van Hove, M. A. and Tong, S. Y.}, | ||
| title = {Surface Crystallography by LEED}, | ||
| publisher = {Springer}, | ||
| year = {1984}, | ||
| isbn = {978-3-540-13380-0} | ||
| } |
There was a problem hiding this comment.
🧩 Analysis chain
🏁 Script executed:
#!/bin/bash
# Description: Verify the DOI and ISBN for the bibliography entries
echo "=== Verifying Pendry 1980 DOI ==="
curl -s -L "https://doi.org/10.1088/0022-3719/13/5/012" -I 2>&1 | head -n 5
echo -e "\n=== Checking ISBN format for Van Hove 1984 ==="
# ISBN-13 format check: 978-3-540-13380-0
isbn="978-3-540-13380-0"
echo "ISBN: $isbn"
# Remove hyphens and verify it's 13 digits
digits=$(echo "$isbn" | tr -d '-')
echo "Digits: $digits (length: ${#digits})"
if [ ${#digits} -eq 13 ]; then
echo "✓ ISBN-13 format is valid"
else
echo "✗ ISBN format is invalid"
fiRepository: Liam-Deacon/CLEED
Length of output: 178
🌐 Web query:
Pendry 1980 "Reliability factors for LEED calculations" Journal of Physics C
💡 Result:
Here’s the reference and where to find it:
- J. B. Pendry, "Reliability factors for LEED calculations," Journal of Physics C: Solid State Physics, vol. 13, no. 5, pp. 937–944, Feb. 1980. DOI: 10.1088/0022-3719/13/5/024. [1]
Online records / access:
- IOP Stacks entry / PDF (journal page). [1]
- bibliographic listing (summary entry). [2]
Sources:
[1] CiNii / IOP Stacks bibliographic record (DOI 10.1088/0022-3719/13/5/024).
[2] Low-energy electron diffraction — reference list (Pendry 1980).
🌐 Web query:
Van Hove Tong 1984 "Surface Crystallography by LEED" Springer
💡 Result:
Bibliographic details:
Van Hove, M. A.; Tong, S. Y. Surface Crystallography by LEED: Theory, Computation and Structural Results. Springer‑Verlag, Springer Series in Chemical Physics, Vol. 2. DOI: 10.1007/978-3-642-67195-1. (Original Springer publication: 1979; paperback reprint/ISBN 978-3-642-67197-5). [1][2]
Sources: Springer book page and product listings. [1] [2]
BibTeX structure is correct, but bibliographic metadata contains errors that must be fixed.
The entries follow proper BibTeX syntax, but verification revealed significant inaccuracies in the citation data:
- Pendry 1980: DOI is incorrect. The entry lists
10.1088/0022-3719/13/5/012, but the correct DOI is10.1088/0022-3719/13/5/024. - Van Hove & Tong: The year is wrong (listed as 1984, but the original publication was 1979). The ISBN
978-3-540-13380-0does not match published editions. The correct ISBN for the paperback reprint is978-3-642-67197-5, and the work is published as part of Springer Series in Chemical Physics, Vol. 2.
Both entries need correction before merging.
🤖 Prompt for AI Agents
In @doc/references.bib around lines 1 - 18, Update the bibliographic metadata
for the two BibTeX entries: for entry key pendry1980 replace the incorrect doi
value with 10.1088/0022-3719/13/5/024; for entry key vanhove1984 change year to
1979, replace isbn with 978-3-642-67197-5, and add series = {Springer Series in
Chemical Physics} and volume = {2} (keep author, title, and publisher as-is);
ensure fields are valid BibTeX keys and values for keys pendry1980 and
vanhove1984.
| ************************** | ||
| Start here: LEED-IV in CLEED | ||
| ************************** |
There was a problem hiding this comment.
Fix title overline/underline length.
The Sphinx build is failing because the title decorators (27 asterisks) are shorter than the title text (29 characters). reStructuredText requires decorators to be at least as long as the title.
🐛 Proposed fix
-**************************
+*****************************
Start here: LEED-IV in CLEED
-**************************
+*****************************📝 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.
| ************************** | |
| Start here: LEED-IV in CLEED | |
| ************************** | |
| ***************************** | |
| Start here: LEED-IV in CLEED | |
| ***************************** |
🧰 Tools
🪛 GitHub Actions: Docs (Sphinx)
[error] 3-3: Sphinx warning treated as error: Title overline too short.
🤖 Prompt for AI Agents
In @doc/start_here.rst around lines 3 - 5, The title decorators are too short
for the title text "Start here: LEED-IV in CLEED"; update the overline and
underline to be at least as long as the title (e.g., change the 27 asterisks to
29 asterisks) or shorten the title so the decorator length matches, ensuring the
reStructuredText title markup uses matching-length decoration.
1 participant
Problem
Issue #34 calls for improved onboarding docs, troubleshooting, and inline scientific references for LEED-IV users, plus a bibliography system in Sphinx.
Solution
Testing
Follow-ups
Summary by Sourcery
Expand and restructure the Sphinx documentation to improve onboarding for LEED-IV users and introduce a citation-backed references system.
New Features:
Enhancements:
Build:
Summary by CodeRabbit
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