Run All Mycelia Tutorials

This script executes all Mycelia tutorials in sequence. Use with caution - may take significant time and resources. External tool steps are gated by MYCELIA_RUN_EXTERNAL=true.

Usage

# Run all tutorials
julia --project=. tutorials/run_all_tutorials.jl

# Run specific tutorial
julia --project=. tutorials/01_data_acquisition.jl

# Convert to notebooks
julia --project=. -e 'include("tutorials/run_all_tutorials.jl"); convert_all_to_notebooks()'

import Pkg
if isinteractive()
    Pkg.activate("..")
end

import Dates
import Literate

List of all tutorials in execution order

TUTORIALS = [
    "01_data_acquisition.jl",
    "02_quality_control.jl",
    "03_kmer_analysis.jl",
    "04_genome_assembly.jl",
    "04_graph_type_tutorials.jl",
    "05_assembly_validation.jl",
    "06_gene_annotation.jl",
    "07_comparative_genomics.jl",
    "08_tool_integration.jl",
    "09_round_trip_01_string_graphs.jl",
    "09_round_trip_02_ngram_to_string.jl",
    "09_round_trip_03_fasta_sequences.jl",
    "09_round_trip_04_kmer_to_sequence.jl",
    "09_round_trip_05_fastq_graphs.jl",
    "09_round_trip_06_qualmer_graphs.jl",
    "10_viroid_assembly_workflow.jl",
    "11_reduced_amino_acid_alphabets.jl",
    "12_coverm_coverage.jl",
    "13_rhizomorph_assembly.jl",
    "14_binning_workflow.jl",
    "14_mash_classification.jl",
    "15_round_trip_benchmarking.jl",
    "16_un_corpus_ngram_vs_token_graphs.jl",
    "17_viroid_sketch_round_trip.jl",
    "18_advanced_assembly_theory_and_practice.jl",
]

"""
    run_all_tutorials()

Execute all tutorials in sequence, collecting timing and status information.
"""
function run_all_tutorials()
    println("=== Running All Mycelia Tutorials ===")
    println("Start time: $(Dates.now())")
    println()

    results = []
    total_start = time()

    for tutorial in TUTORIALS
        if isfile(tutorial)
            println("Running $tutorial...")
            start_time = time()

            try
                # Execute tutorial
                include(tutorial)

                elapsed = time() - start_time
                push!(results, (tutorial, :success, elapsed))
                println("✓ $tutorial completed in $(round(elapsed, digits=2))s")

            catch e
                elapsed = time() - start_time
                push!(results, (tutorial, :error, elapsed, e))
                println("✗ $tutorial failed after $(round(elapsed, digits=2))s")
                println("  Error: $e")
            end

            println()
        else
            println("⚠ $tutorial not found, skipping...")
            push!(results, (tutorial, :not_found, 0.0))
        end
    end

    total_elapsed = time() - total_start

    # Print summary
    println("=== Tutorial Execution Summary ===")
    println("Total time: $(round(total_elapsed, digits=2))s")
    println()

    successful = 0
    for (tutorial, status, elapsed, error...) in results
        if status == :success
            println("✓ $tutorial ($(round(elapsed, digits=2))s)")
            successful += 1
        elseif status == :error
            println("✗ $tutorial ($(round(elapsed, digits=2))s) - $(error[1])")
        else
            println("⚠ $tutorial (not found)")
        end
    end

    println()
    println("Successful: $successful/$(length(TUTORIALS))")
    println("End time: $(Dates.now())")

    return results
end

"""
    convert_all_to_notebooks()

Convert all tutorials to Jupyter notebooks using Literate.jl.
"""
function convert_all_to_notebooks()
    println("=== Converting Tutorials to Notebooks ===")

    # Create notebooks directory if it doesn't exist
    notebooks_dir = "notebooks"
    if !isdir(notebooks_dir)
        mkdir(notebooks_dir)
    end

    for tutorial in TUTORIALS
        if isfile(tutorial)
            println("Converting $tutorial to notebook...")

            try
                # Convert to notebook
                Literate.notebook(tutorial, notebooks_dir, execute=false)
                println("✓ Converted $tutorial")

            catch e
                println("✗ Failed to convert $tutorial: $e")
            end
        else
            println("⚠ $tutorial not found, skipping...")
        end
    end

    println()
    println("Notebooks saved to: $notebooks_dir")
end

"""
    run_tutorial(tutorial_name)

Run a specific tutorial by name.
"""
function run_tutorial(tutorial_name)
    if !endswith(tutorial_name, ".jl")
        tutorial_name *= ".jl"
    end

    if isfile(tutorial_name)
        println("Running $tutorial_name...")
        start_time = time()

        try
            include(tutorial_name)
            elapsed = time() - start_time
            println("✓ $tutorial_name completed in $(round(elapsed, digits=2))s")
            return true
        catch e
            elapsed = time() - start_time
            println("✗ $tutorial_name failed after $(round(elapsed, digits=2))s")
            println("  Error: $e")
            return false
        end
    else
        println("✗ $tutorial_name not found")
        return false
    end
end

Main execution

if abspath(PROGRAM_FILE) == @__FILE__
    # Only run if this script is executed directly
    if length(ARGS) == 0
        # Run all tutorials
        results = run_all_tutorials()
    elseif ARGS[1] == "convert"
        # Convert to notebooks
        convert_all_to_notebooks()
    else
        # Run specific tutorial
        tutorial_name = ARGS[1]
        run_tutorial(tutorial_name)
    end
end