Refresh README, docs landing page, and scaling plots

[sbryngelson]

User description

Summary

• README overhaul: lead with Gordon Bell headline, hero simulation video, "Why MFC" and "Try MFC" sections, badge alt text, fix init→new, remove dead Discussions badge, remove duplicate instructions
• Scaling plots: replace Frontier-only plot with combined El Capitan/Frontier/Alps plot (with dark-mode variant via <picture> element) in both README and docs performance page
• Docs landing page: add SEO meta tags (OG/Twitter cards), Gordon Bell tagline, updated scaling plot
• YouTube integration: add YouTube badge to README, replace Vimeo links with YouTube links in docs simulation gallery

Test plan

• ./mfc.sh precheck passes (all 5 checks)
• Verify README renders correctly on GitHub (light and dark mode)
• Verify docs site builds and simulation gallery links work
• Confirm YouTube badge links to correct channel

🤖 Generated with Claude Code

---

CodeAnt-AI Description

Refresh README and docs landing to highlight exascale results, add hero video, unify scaling plots, and simplify quickstart

What Changed

• README now leads with a 2025 Gordon Bell Prize Finalist headline, an embedded hero video, a focused "Why MFC?" summary, and a compact "Try MFC" quickstart with a one-click Codespaces link and a simple first-simulation command
• Badges and images gained alt text and a YouTube badge; many example/demo links were switched from Vimeo to YouTube; DOI/Zenodo/GitHub-star badges added to promote citations and social previews
• Documentation and homepage metadata updated with OpenGraph/Twitter tags and a clearer title/description; weak-scaling figures were replaced by a single combined El Capitan/Frontier/Alps plot with a dark-mode variant
• User-facing command help text and docs reflect ./mfc.sh new (replaces init) and point to the consolidated examples and getting-started page

Impact

✅ Clearer project intro for new visitors
✅ Shorter quickstart to run first simulation (one-click Codespace + single command)
✅ Better social previews and shareable links (OG/Twitter, YouTube, DOI badges)

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Summary by CodeRabbit

• Bug Fixes

  • Fixed malformed badge URLs in documentation
  • Corrected sponsor attribution text

• New Features

  • Added YouTube badge to README header

• Documentation

  • Updated project description in documentation configuration
  • Replaced video sources with YouTube links in featured simulations
  • Updated documentation reference titles

• Style

  • Refined navigation panel layout and styling

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Caution

Review failed

The pull request is closed.

📝 Walkthrough

Walkthrough

This PR updates documentation styling, configuration, and content across multiple files. Changes include fixing image badge URLs in README, updating Doxygen configuration text, modifying documentation CSS and templates, replacing Vimeo video links with YouTube sources, and standardizing documentation reference titles.

Changes

Cohort / File(s)	Summary
README and Featured Content README.md, docs/index.html	Fixed image badge URLs (removed tab-encoded sequences), added YouTube badge block, replaced Vimeo video sources with YouTube sources for three simulations, and corrected sponsor text reference.
Doxygen Configuration and Styling docs/Doxyfile.in, docs/custom.css, docs/footer.html	Updated Doxygen project description, added CSS for narrower left navigation panel and hidden tree sync button, removed GENERATE_TREEVIEW blocks and footer attribution markup.
Documentation Generation Scripts toolchain/mfc/cli/docs_gen.py, toolchain/mfc/params/generators/docs_gen.py	Renamed documentation reference titles from "Command Line Reference" to "CLI Reference" and "Case Parameters Reference" to "Case Parameters" in generated documentation output.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

Suggested labels

size:M

Poem

🐰 With whiskers twitching, URLs I mend,
From Vimeo hops to YouTube trends,
Badges fixed with careful paw,
Doxygen styled without a flaw,
Documentation shines, as nature's law! 🎬

✨ Finishing touches

• 📝 Generate docstrings

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment

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[cubic-dev-ai]

No issues found across 5 files

Confidence score: 5/5

• Automated review surfaced no issues in the provided summaries.
• No files require special attention.

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PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 2 🔵🔵⚪⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Link Breakage The Doxygen @page title and the top-level heading were renamed for the CLI reference. Please verify that any existing internal docs links, cross-references, or sidebar entries that previously pointed to the old page title/heading still resolve correctly after regeneration. def generate_cli_reference(schema: CLISchema) -> str: """Generate complete CLI reference documentation in markdown.""" lines = [ "@page cli-reference CLI Reference", "", "# CLI Reference", "", "> **Auto-generated** from `toolchain/mfc/cli/commands.py`", "> ", "> Regenerate with: `./mfc.sh generate`", Doc Consistency The parameters page title/heading and the footer section header were renamed from “Command Line Reference” to “CLI Reference”. Ensure the generated docs do not contain stale references to the previous naming (including any links or anchors), and that the CLI search snippet still matches the actual CLI command names/options. def generate_parameter_docs() -> str: # pylint: disable=too-many-locals,too-many-statements """Generate markdown documentation for all parameters.""" # AST-extract rules from case_validator.py analysis = analyze_case_validator() by_trigger = analysis["by_trigger"] by_param = analysis["by_param"] lines = [ "@page parameters Case Parameters", "", "# Case Parameters", "", "> **Auto-generated** from parameter registry", "> ", "> Regenerate with: `./mfc.sh generate --json-schema`", "", "## Overview", "", f"MFC supports **{len(REGISTRY.all_params):,}** case parameters organized into families.", "", "**Quick search:** Use `./mfc.sh params <query>` to search parameters from the command line.", "", "## Parameter Families", "", ] # Group parameters by family families: Dict[str, List[Tuple[str, Any]]] = defaultdict(list) for name, param in sorted(REGISTRY.all_params.items()): family = _get_family(name) families[family].append((name, param)) # Sort families by size (largest first), but put "general" last sorted_families = sorted( families.items(), key=lambda x: (x[0] == "general", -len(x[1]), x[0]) ) # Table of contents lines.append("| Family | Count | Description |") lines.append("|--------|-------|-------------|") family_descriptions = { "general": "Core simulation parameters (grid, time, model, etc.)", "patch_icpp": "Initial condition patch parameters", "patch_ib": "Immersed boundary patch parameters", "patch_bc": "Boundary condition patch parameters", "fluid_pp": "Fluid material properties", "acoustic": "Acoustic source parameters", "bc_x": "X-direction boundary conditions", "bc_y": "Y-direction boundary conditions", "bc_z": "Z-direction boundary conditions", "probe": "Probe/monitoring point parameters", "integral": "Integral region parameters", "simplex_params": "Simplex noise perturbation parameters", "chem_wrt_Y": "Chemistry species output parameters", "bub_pp": "Bubble property parameters", "lag_params": "Lagrangian particle parameters", # Post-processing output flags "alpha_rho_wrt": "Partial density output flags", "alpha_rho_e_wrt": "Partial density-energy output flags", "alpha_wrt": "Volume fraction output flags", "kappa_wrt": "Curvature output flags", "schlieren_alpha": "Numerical schlieren coefficients", "mom_wrt": "Momentum output flags", "vel_wrt": "Velocity output flags", "flux_wrt": "Flux output flags", "omega_wrt": "Vorticity output flags", # Domain and output regions "x_domain": "X-direction domain parameters", "y_domain": "Y-direction domain parameters", "z_domain": "Z-direction domain parameters", "x_output": "X-direction output region", "y_output": "Y-direction output region", "z_output": "Z-direction output region", # Other "fluid_rho": "Fluid reference densities", "chem_params": "Chemistry model parameters", } for family, params in sorted_families: desc = family_descriptions.get(family, "") # Use family name directly as anchor (GitHub keeps underscores in heading anchors) lines.append(f"| [{family}](#{family}) | {len(params)} | {desc} |") lines.append("") lines.append("---") lines.append("") # Document each family for family, params in sorted_families: lines.append(f"## {family} {{#{family}}}") lines.append("") desc = family_descriptions.get(family, "") if desc: lines.append(f"*{desc}*") lines.append("") lines.append(f"**{len(params)} parameters**") lines.append("") # Group by pattern (collapse indices to N, M, etc.) patterns: Dict[str, List[str]] = defaultdict(list) for name, _ in params: pattern = _collapse_indices(name) patterns[pattern].append(name) # Use pattern view if it reduces rows, otherwise show full table if len(patterns) < len(params): # Pattern view - shows collapsed patterns # Check if any member of a pattern has constraints or math symbols pattern_has_constraints = False pattern_has_symbols = False for _pattern, examples in patterns.items(): for ex in examples: p = REGISTRY.all_params[ex] if p.constraints or ex in by_trigger or ex in by_param: pattern_has_constraints = True if get_math_symbol(ex): pattern_has_symbols = True if pattern_has_constraints and pattern_has_symbols: break lines.append("### Patterns") lines.append("") # Build header dynamically based on which optional columns are needed cols = ["Pattern", "Example", "Description"] if pattern_has_symbols: cols.append("Symbol") if pattern_has_constraints: cols.append("Constraints") lines.append("| " + " | ".join(cols) + " |") lines.append("| " + " | ".join("-" * max(3, len(c)) for c in cols) + " |") for pattern, examples in sorted(patterns.items()): example = examples[0] desc = get_description(example) or "" # Truncate long descriptions if len(desc) > 60: desc = desc[:57] + "..." # Escape % for Doxygen (even inside backtick code spans) pattern_escaped = _escape_percent(pattern) example_escaped = _escape_percent(example) desc = _escape_percent(desc) row = f"| `{pattern_escaped}` | `{example_escaped}` | {desc}" if pattern_has_symbols: sym = get_math_symbol(example) row += f" | {sym}" if pattern_has_constraints: p = REGISTRY.all_params[example] constraints = _format_constraints(p) deps = _format_validator_rules(example, by_trigger, by_param) extra = "; ".join(filter(None, [constraints, deps])) if not extra: extra = _format_tag_annotation(example, p) extra = _escape_pct_outside_backticks(extra) row += f" | {extra}" lines.append(row + " |") lines.append("") else: # Full table - no patterns to collapse # Check if any param in this family has a math symbol full_has_symbols = any(get_math_symbol(n) for n, _ in params) cols = ["Parameter", "Type", "Description"] if full_has_symbols: cols.append("Symbol") cols.append("Constraints") lines.append("| " + " | ".join(cols) + " |") lines.append("| " + " | ".join("-" * max(3, len(c)) for c in cols) + " |") for name, param in params: type_str = _type_to_str(param.param_type) desc = get_description(name) or "" # Truncate long descriptions if len(desc) > 80: desc = desc[:77] + "..." constraints = _format_constraints(param) deps = _format_validator_rules(name, by_trigger, by_param) extra = "; ".join(filter(None, [constraints, deps])) if not extra: extra = _format_tag_annotation(name, param) extra = _escape_pct_outside_backticks(extra) # Escape % for Doxygen (even inside backtick code spans) name_escaped = _escape_percent(name) desc = _escape_percent(desc) row = f"| `{name_escaped}` | {type_str} | {desc}" if full_has_symbols: sym = get_math_symbol(name) row += f" | {sym}" row += f" | {extra}" lines.append(row + " |") lines.append("") lines.append("---") lines.append("") # Add footer lines.extend([ "## CLI Reference", "", "Search parameters using the CLI:", "", "```bash", UI Regression The footer removed the nav-path and generated-by blocks that Doxygen commonly uses for breadcrumbs and attribution. Confirm this doesn’t break the doxygen-awesome theme layout, treeview navigation behavior, or any tooling that expects $navpath/$generatedby to be present. <!-- HTML footer for doxygen 1.9.1--> <!-- start footer part --> <!--BEGIN GENERATE_TREEVIEW--> <!--END GENERATE_TREEVIEW--> <!--BEGIN !GENERATE_TREEVIEW--> <!--END !GENERATE_TREEVIEW--> </body> </html>

[cubic-dev-ai]

No issues found across 7 files

Confidence score: 5/5

• Automated review surfaced no issues in the provided summaries.
• No files require special attention.

[qodo-code-review]

High-level Suggestion

The PR removes the footer from auto-generated documentation pages by emptying docs/footer.html. This change eliminates crucial breadcrumb navigation, harming site usability. [High-level, importance: 9]

Solution Walkthrough:

Before:

<!-- docs/footer.html -->
<!-- ... -->
<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
  <ul>
    $navpath
    <li class="footer">$generatedby <a href="..."><img ... alt="doxygen"/></a> $doxygenversion </li>
  </ul>
</div>
<!-- ... -->
</body>
</html>

After:

<!-- docs/footer.html -->
<!-- HTML footer for doxygen 1.9.1-->
<!-- start footer part -->
<!--BEGIN GENERATE_TREEVIEW-->
<!--END GENERATE_TREEVIEW-->
<!--BEGIN !GENERATE_TREEVIEW-->
<!--END !GENERATE_TREEVIEW-->
</body>
</html>

[qodo-code-review]

Suggestion: Restore the closing </body> and </html> tags in docs/footer.html. Removing them will produce invalid HTML for the generated documentation, which can cause browser rendering issues. [possible issue, importance: 8]

Suggested change

	<!-- HTML footer for doxygen 1.9.1-->
	<!-- start footer part -->
	<!--BEGIN GENERATE_TREEVIEW-->
	<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
	<ul>
	$navpath
	<li class="footer">$generatedby <a href="https://www.doxygen.org/index.html"><img class="footer" src="$relpath^doxygen.svg" width="104" height="31" alt="doxygen"/></a> $doxygenversion </li>
	</ul>
	</div>
	<!--END GENERATE_TREEVIEW-->
	<!--BEGIN !GENERATE_TREEVIEW-->
	<hr class="footer"/><address class="footer"><small>
	$generatedby&#160;<a href="https://www.doxygen.org/index.html"><img class="footer" src="$relpath^doxygen.svg" width="104" height="31" alt="doxygen"/></a> $doxygenversion
	</small></address>
	<!--END !GENERATE_TREEVIEW-->
	</body>
	</html>
	<!-- This file is intentionally left almost empty to remove the default Doxygen footer. -->
	<!-- It must contain the closing body and html tags for valid HTML output. -->
	</body>
	</html>

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 44.07%. Comparing base (4c52155) to head (1010b59).
⚠️ Report is 2 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1152   +/-   ##
=======================================
  Coverage   44.07%   44.07%           
=======================================
  Files          70       70           
  Lines       20431    20431           
  Branches     1974     1974           
=======================================
  Hits         9004     9004           
  Misses      10291    10291           
  Partials     1136     1136           

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