quarto-julia — Создание воспроизводимых документов с Julia

--- name: quarto-julia description: 'Quarto + Julia Skill' version: 1.0.0 --- # Quarto + Julia Skill **Status**: Production Ready **Trit**: 0 (ERGODIC - coordinator/synthesizer) **Purpose**: Reproducible documents with Julia code blocks and GF(3) skill tracking --- ## Overview Quarto is a scientific publishing system that renders `.qmd` files to HTML, PDF, and more. Combined with Julia, it enables: 1. **Executable documents** - Julia code blocks run during render 2. **Skill activation logs** - Track GF(3) triads in rendered output 3. **Reproducible research** - Same seed = same colors = same results ## Two Julia Engines | Feature | `julia` Engine (NEW) | `jupyter` Engine | |---------|---------------------|------------------| | Execute Julia code | ✅ | ✅ | | Keep sessions alive | ✅ | ✅ | | No Python required | ✅ | ❌ | | No global pkg install | ✅ | ❌ | | juliaup integration | ✅ | ❌ | | Python/R via PythonCall/RCall | ✅ | ❌ | | QuartoTools.jl expandable cells | ✅ | ❌ | **Recommendation**: Use `engine: julia` for new projects. ## Installation (No Homebrew) ```bash # Download and extract cd /tmp curl -sL https://github.com/quarto-dev/quarto-cli/releases/download/v1.6.42/quarto-1.6.42-macos.tar.gz -o quarto.tar.gz tar -xzf quarto.tar.gz # Install to ~/bin with proper structure mkdir -p ~/bin/quarto-1.6.42 cp -r bin share ~/bin/quarto-1.6.42/ # Create wrapper script (critical for path resolution) cat > ~/bin/quarto << 'EOF' #!/bin/bash export QUARTO_SHARE_PATH="$HOME/bin/quarto-1.6.42/share" exec "$HOME/bin/quarto-1.6.42/bin/quarto" "$@" EOF chmod +x ~/bin/quarto # Add to PATH echo 'export PATH="$HOME/bin:$PATH"' >> ~/.zshrc export PATH="$HOME/bin:$PATH" # Verify quarto --version # Should show 1.6.42 ``` ## Basic .qmd Document (Modern julia Engine) ```markdown --- title: "GF(3) Skill Activation Log" author: "Plurigrid ASI" date: today format: html: code-fold: true toc: true theme: cosmo engine: julia execute: echo: true cache: true --- ## Skill Triad ```{julia} #| label: gf3-triad #| code-summary: "Define GF(3) skill triad" struct SkillActivation name::String trit::Int # -1, 0, or +1 hue::Float64 end triad = [ SkillActivation("acsets", -1, 220.0), SkillActivation("bisimulation", 0, 120.0), SkillActivation("artifacts-builder", 1, 30.0) ] # Verify conservation trit_sum = sum(s.trit for s in triad) println("GF(3) sum: $trit_sum ≡ $(mod(trit_sum, 3)) (mod 3)") ``` ``` ## juliaup Version Selection ```yaml --- title: "Julia 1.11 Notebook" engine: julia julia: exeflags: ["+1.11"] # Use juliaup channel specifier --- ``` ## Commands ```bash # Render single file quarto render document.qmd # Render to specific format quarto render document.qmd --to pdf quarto render document.qmd --to docx # Live preview (watches for changes) quarto preview document.qmd # Render entire project quarto render # Check installation quarto check # Install TinyTeX for PDF output quarto install tinytex ``` ## Project Structure ``` project/ ├── _quarto.yml # Project configuration ├── index.qmd # Main document ├── skills/ │ ├── triad-1.qmd # Skill triad documentation │ └── triad-2.qmd └── _output/ # Rendered files ``` ## _quarto.yml Configuration ```yaml project: type: website output-dir: _output website: title: "Skill Activation Log" navbar: left: - href: index.qmd text: Home - href: skills/triad-1.qmd text: Triad 1 format: html: theme: cosmo css: styles.css toc: true execute: freeze: auto # Cache computations ``` ## Julia Integration Patterns ### Gay.jl Color Generation ```{julia} using Gay seed = 0x42D palette = Gay.palette(seed, 9) # 9 colors for 3 triads for (i, color) in enumerate(palette) trit = mod(i - 1, 3) - 1 # Cycle: -1, 0, +1 println("Skill $i: $(color.hex) trit=$trit") end ``` ### ACSets Schema Visualization ```{julia} using Catlab.CategoricalAlgebra using Catlab.Graphics @present SchSkillGraph(FreeSchema) begin Skill::Ob Triad::Ob belongs_to::Hom(Skill, Triad) Name::AttrType Trit::AttrType name::Attr(Skill, Name) trit::Attr(Skill, Trit) end # Render as GraphViz to_graphviz(SchSkillGraph) ``` ### Spectral Gap Computation ```{julia} using LinearAlgebra function spectral_gap(n::Int) # Cycle graph adjacency (normalized) A = zeros(n, n) for i in 1:n A[i, mod1(i+1, n)] = 0.5 A[i, mod1(i-1, n)] = 0.5 end eigs = eigvals(A) sorted = sort(real.(eigs), rev=true) return 1.0 - sorted[2] end # Find n where gap ≈ 1/4 for n in [4, 8, 9, 10, 16] gap = spectral_gap(n) marker = abs(gap - 0.25) < 0.02 ? " ← TARGET" : "" println("n=$n: gap=$(round(gap, digits=4))$marker") end ``` ## Rendering from Julia ```julia using Quarto # Single file Quarto.render("index.qmd") # With options Quarto.render("index.qmd", output_format="pdf") # Entire project Quarto.render(".") # Current directory # Preview with live reload Quarto.preview("index.qmd") ``` ## Troubleshooting ### "Cannot determine Quarto source path" This error means `QUARTO_SHARE_PATH` is not set. Use the wrapper script: ```bash # Check current setup cat ~/bin/quarto # Should contain: # export QUARTO_SHARE_PATH="$HOME/bin/quarto-1.6.42/share" # exec "$HOME/bin/quarto-1.6.42/bin/quarto" "$@" ``` ### Julia kernel not found ```bash # Install IJulia julia -e 'using Pkg; Pkg.add("IJulia")' # Register kernel julia -e 'using IJulia; IJulia.installkernel("Julia")' # List kernels jupyter kernelspec list ``` ### PDF rendering fails ```bash # Install TinyTeX quarto install tinytex # Or use system LaTeX # macOS: install MacTeX # Linux: apt install texlive-full ``` ## GF(3) Skill Tracking Template ```markdown --- title: "Skill Activation: {{< meta triad_name >}}" params: triad_name: "Database & Verification" skills: - {name: "acsets", trit: -1, hue: 220} - {name: "bisimulation", trit: 0, hue: 120} - {name: "artifacts-builder", trit: 1, hue: 30} --- ```{julia} #| label: verify-conservation skills = params.skills trit_sum = sum(s["trit"] for s in skills) @assert mod(trit_sum, 3) == 0 "GF(3) violation!" println("✓ Conservation verified: Σ = $trit_sum ≡ 0 (mod 3)") ``` ``` ## Integration with ~/worlds/ ```julia # List available worlds readdir(expanduser("~/worlds")) # Load world-specific Julia project using Pkg Pkg.activate(expanduser("~/worlds/a")) # AlgebraicJulia world ``` ## Related Skills | Skill | Trit | Integration | |-------|------|-------------| | `gay-mcp` | 0 | Deterministic colors in plots | | `acsets` | -1 | Schema visualization | | `triad-interleave` | +1 | Schedule documentation | | `algorithmic-art` | 0 | p5.js visualizations | ## References - [Quarto Documentation](https://quarto.org/docs/) - [Quarto.jl](https://github.com/quarto-dev/quarto-julia) - [Julia for Quarto](https://quarto.org/docs/computations/julia.html) --- **Skill Name**: quarto-julia **Type**: Documentation / Publishing **Trit**: 0 (ERGODIC) **Dependencies**: Julia 1.10+, IJulia, Quarto CLI 1.6+