kuva 0.2.0

/// Integration tests for the `kuva` CLI binary.
///
/// Each test spawns the binary as a child process and checks stdout/stderr/exit code.
use std::fs;
use std::io::Write;
use std::process::{Command, Stdio};

fn kuva_bin() -> Command {
    // Use the debug build produced by `cargo build --bin kuva`.
    let bin = env!("CARGO_BIN_EXE_kuva");
    Command::new(bin)
}

/// Feed `input` to the binary's stdin and return (stdout, stderr, exit_code).
fn run_with_stdin(args: &[&str], input: &str) -> (String, String, i32) {
    let mut cmd = kuva_bin();
    cmd.args(args)
        .stdin(Stdio::piped())
        .stdout(Stdio::piped())
        .stderr(Stdio::piped());

    let mut child = cmd.spawn().expect("failed to spawn kuva");
    child
        .stdin
        .take()
        .expect("stdin")
        .write_all(input.as_bytes())
        .expect("write stdin");

    let out = child.wait_with_output().expect("wait");
    (
        String::from_utf8_lossy(&out.stdout).into_owned(),
        String::from_utf8_lossy(&out.stderr).into_owned(),
        out.status.code().unwrap_or(-1),
    )
}

/// Run the binary with a file argument.
fn run_with_file(args: &[&str]) -> (String, String, i32) {
    let out = kuva_bin().args(args).output().expect("failed to run kuva");
    (
        String::from_utf8_lossy(&out.stdout).into_owned(),
        String::from_utf8_lossy(&out.stderr).into_owned(),
        out.status.code().unwrap_or(-1),
    )
}

/// Return the absolute path to an example data file.
fn data(filename: &str) -> String {
    format!("{}/examples/data/{}", env!("CARGO_MANIFEST_DIR"), filename)
}

// ─── tests ────────────────────────────────────────────────────────────────────

/// Piping a TSV scatter through stdin should produce valid SVG on stdout.
#[test]
fn test_scatter_stdout() {
    let tsv = "x\ty\n1\t2\n3\t4\n5\t3\n";
    let (stdout, _stderr, code) = run_with_stdin(
        &[
            "scatter",
            "--title",
            "Scatter Plot",
            "--x-label",
            "X",
            "--y-label",
            "Y",
        ],
        tsv,
    );
    assert_eq!(code, 0, "exit code should be 0");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

/// Writing to a file path should produce a valid SVG file.
#[test]
fn test_bar_to_file() {
    let tsv = "label\tvalue\nApples\t3\nBananas\t5\nCherries\t2\n";
    let tmp = std::env::temp_dir().join("kuva_test_bar.svg");
    let path_str = tmp.to_str().unwrap();

    // Write input to a temp TSV so we can pass it as a positional arg.
    let input_path = std::env::temp_dir().join("kuva_test_bar_input.tsv");
    fs::write(&input_path, tsv).unwrap();

    let (_, stderr, code) = run_with_file(&[
        "bar",
        input_path.to_str().unwrap(),
        "--label-col",
        "label",
        "--value-col",
        "value",
        "--title",
        "Fruit Counts",
        "--x-label",
        "Fruit",
        "--y-label",
        "Count",
        "-o",
        path_str,
    ]);

    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(tmp.exists(), "output file should have been created");
    let content = fs::read_to_string(&tmp).unwrap();
    assert!(content.starts_with("<svg"), "file should contain valid SVG");

    let _ = fs::remove_file(&tmp);
    let _ = fs::remove_file(&input_path);
}

/// Histogram with explicit bin count should produce SVG with rect elements (bars).
#[test]
fn test_histogram_bins() {
    let tsv = "1.5\n2.3\n2.7\n3.2\n3.8\n3.9\n4.0\n1.5\n2.1\n3.5\n";
    let (stdout, stderr, code) = run_with_stdin(
        &[
            "histogram",
            "--bins",
            "5",
            "--title",
            "Value Distribution",
            "--x-label",
            "Value",
            "--y-label",
            "Count",
        ],
        tsv,
    );
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(
        stdout.contains("<rect"),
        "histogram SVG should contain <rect elements for bars"
    );
}

/// --color-by should produce SVG with two distinct fill colors.
#[test]
fn test_scatter_color_by() {
    let tsv = "x\ty\tgroup\n1\t2\tA\n2\t3\tA\n3\t1\tB\n4\t4\tB\n";
    let (stdout, stderr, code) = run_with_stdin(
        &[
            "scatter",
            "--x",
            "x",
            "--y",
            "y",
            "--color-by",
            "group",
            "--title",
            "Groups",
            "--x-label",
            "X",
            "--y-label",
            "Y",
        ],
        tsv,
    );
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");

    // Extract all fill="#..." values (circle points), filter out backgrounds.
    let fills: Vec<&str> = stdout
        .split("fill=\"")
        .skip(1)
        .map(|s| s.split('"').next().unwrap_or(""))
        .filter(|s| s.starts_with('#'))
        .collect();

    let unique: std::collections::HashSet<_> = fills.iter().collect();
    assert!(
        unique.len() >= 2,
        "expected at least 2 distinct fill colors for 2 groups; got: {unique:?}"
    );
}

/// Requesting PNG output without the 'png' feature should exit with code 1
/// and print a helpful error containing "--features png".
///
/// Ignored by default: `env!("CARGO_BIN_EXE_kuva")` may point to a stale
/// binary built with `--features png`, causing a false-positive exit 0.
/// Run explicitly after building the binary *without* the png feature:
///   cargo test --test cli_basic test_missing_feature_error -- --ignored
#[test]
#[ignore = "requires binary freshly built without --features png; stale binary causes false-positive"]
#[cfg(not(feature = "png"))]
fn test_missing_feature_error() {
    let tsv = "x\ty\n1\t2\n3\t4\n";
    let tmp_png = std::env::temp_dir().join("kuva_test_missing.png");

    let (_, stderr, code) = run_with_stdin(&["scatter", "-o", tmp_png.to_str().unwrap()], tsv);
    assert_ne!(code, 0, "should fail when png feature is missing");
    assert!(
        stderr.contains("--features png") || stderr.contains("png"),
        "error message should mention how to enable png; got: {stderr}"
    );

    let _ = fs::remove_file(&tmp_png);
}

// ─── Tier 1: SVG output tests ─────────────────────────────────────────────────

#[test]
fn test_line_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "line",
        &data("measurements.tsv"),
        "--x",
        "time",
        "--y",
        "value",
        "--color-by",
        "group",
        "--title",
        "Growth Curves",
        "--x-label",
        "Time",
        "--y-label",
        "Value",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_box_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "box",
        &data("samples.tsv"),
        "--group-col",
        "group",
        "--value-col",
        "expression",
        "--title",
        "Expression by Group",
        "--x-label",
        "Group",
        "--y-label",
        "Expression",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_violin_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "violin",
        &data("samples.tsv"),
        "--group-col",
        "group",
        "--value-col",
        "expression",
        "--title",
        "Expression Distribution",
        "--x-label",
        "Group",
        "--y-label",
        "Expression",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_pie_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "pie",
        &data("pie.tsv"),
        "--label-col",
        "feature",
        "--value-col",
        "percentage",
        "--title",
        "Genome Composition",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_strip_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "strip",
        &data("samples.tsv"),
        "--group-col",
        "group",
        "--value-col",
        "expression",
        "--title",
        "Expression Spread",
        "--x-label",
        "Group",
        "--y-label",
        "Expression",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_waterfall_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "waterfall",
        &data("waterfall.tsv"),
        "--label-col",
        "process",
        "--value-col",
        "log2fc",
        "--title",
        "Log2 Fold Change",
        "--x-label",
        "Process",
        "--y-label",
        "log2FC",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_stacked_area_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "stacked-area",
        &data("stacked_area.tsv"),
        "--x-col",
        "week",
        "--group-col",
        "species",
        "--y-col",
        "abundance",
        "--title",
        "Species Abundance",
        "--x-label",
        "Week",
        "--y-label",
        "Abundance",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_volcano_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "volcano",
        &data("volcano.tsv"),
        "--name-col",
        "gene",
        "--x-col",
        "log2fc",
        "--y-col",
        "pvalue",
        "--title",
        "Differential Expression",
        "--x-label",
        "log2 Fold Change",
        "--y-label=-log10(p-value)",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_manhattan_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "manhattan",
        &data("gene_stats.tsv"),
        "--chr-col",
        "chr",
        "--pvalue-col",
        "pvalue",
        "--title",
        "GWAS Results",
        "--x-label",
        "Chromosome",
        "--y-label=-log10(p-value)",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_candlestick_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "candlestick",
        &data("candlestick.tsv"),
        "--label-col",
        "date",
        "--open-col",
        "open",
        "--high-col",
        "high",
        "--low-col",
        "low",
        "--close-col",
        "close",
        "--title",
        "Stock Price",
        "--x-label",
        "Date",
        "--y-label",
        "Price (USD)",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_heatmap_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "heatmap",
        &data("heatmap.tsv"),
        "--title",
        "Gene Expression Heatmap",
        "--x-label",
        "Sample",
        "--y-label",
        "Gene",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_hist2d_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "hist2d",
        &data("hist2d.tsv"),
        "--x",
        "x",
        "--y",
        "y",
        "--title",
        "2D Density",
        "--x-label",
        "X",
        "--y-label",
        "Y",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_contour_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "contour",
        &data("contour.tsv"),
        "--x",
        "x",
        "--y",
        "y",
        "--z",
        "density",
        "--title",
        "Density Contour",
        "--x-label",
        "X",
        "--y-label",
        "Y",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_dot_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "dot",
        &data("dot.tsv"),
        "--x-col",
        "pathway",
        "--y-col",
        "cell_type",
        "--size-col",
        "pct_expressed",
        "--color-col",
        "mean_expr",
        "--title",
        "Gene Expression by Cell Type",
        "--x-label",
        "Pathway",
        "--y-label",
        "Cell Type",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_upset_svg() {
    let (stdout, stderr, code) =
        run_with_file(&["upset", &data("upset.tsv"), "--title", "Set Intersections"]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_chord_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "chord",
        &data("chord.tsv"),
        "--title",
        "Cell Type Co-occurrence",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_sankey_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "sankey",
        &data("sankey.tsv"),
        "--source-col",
        "source",
        "--target-col",
        "target",
        "--value-col",
        "value",
        "--title",
        "Flow Diagram",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_sankey_alluvium_svg() {
    let tsv = "\
tissue\tcluster\tsex\tcount
B CELL\t4\tmale\t9
BRAIN\t1\tfemale\t1
BRAIN\t1\tmale\t1
HEART\t3\tmale\t3
STOMACH\t2\tfemale\t3
";
    let (stdout, stderr, code) = run_with_stdin(
        &[
            "sankey",
            "--axis-col",
            "tissue",
            "--axis-col",
            "cluster",
            "--axis-col",
            "sex",
            "--value-col",
            "count",
            "--node-order",
            "crossings",
            "--node-order-seed",
            "42",
            "--coloring",
            "left",
            "--title",
            "Alluvium",
        ],
        tsv,
    );
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_phylo_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "phylo",
        &data("phylo.tsv"),
        "--parent-col",
        "parent",
        "--child-col",
        "child",
        "--length-col",
        "length",
        "--title",
        "Phylogenetic Tree",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_synteny_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "synteny",
        &data("synteny_seqs.tsv"),
        "--blocks-file",
        &data("synteny_blocks.tsv"),
        "--title",
        "Synteny Map",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_network_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "network",
        &data("network.tsv"),
        "--source-col",
        "source",
        "--target-col",
        "target",
        "--title",
        "Gene Regulatory Network",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_network_has_circles() {
    let (stdout, _stderr, code) = run_with_file(&[
        "network",
        &data("network.tsv"),
        "--source-col",
        "source",
        "--target-col",
        "target",
        "--labels",
    ]);
    assert_eq!(code, 0);
    assert!(
        stdout.contains("<circle"),
        "network SVG should contain <circle elements for nodes"
    );
    assert!(
        stdout.contains("<text"),
        "network SVG with --labels should contain <text elements"
    );
}

#[test]
fn test_network_matrix_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "network",
        &data("network_matrix.tsv"),
        "--matrix",
        "--directed",
        "--labels",
        "--title",
        "Matrix Network",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
    assert!(
        stdout.contains("<circle"),
        "matrix network should have nodes"
    );
}

#[test]
fn test_network_kk_layout() {
    let (stdout, stderr, code) = run_with_file(&[
        "network",
        &data("network.tsv"),
        "--source-col",
        "source",
        "--target-col",
        "target",
        "--layout",
        "kk",
        "--labels",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_network_directed_weighted() {
    let (stdout, stderr, code) = run_with_file(&[
        "network",
        &data("network.tsv"),
        "--source-col",
        "source",
        "--target-col",
        "target",
        "--weight-col",
        "weight",
        "--directed",
        "--labels",
        "--group-col",
        "group",
        "--legend",
        "pathway",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(
        stdout.contains("<path"),
        "directed network should have arrowhead paths"
    );
}

#[test]
fn test_network_bad_layout_errors() {
    let (_stdout, stderr, code) = run_with_file(&[
        "network",
        &data("network.tsv"),
        "--source-col",
        "source",
        "--target-col",
        "target",
        "--layout",
        "bogus",
    ]);
    assert_ne!(code, 0, "bad layout should fail");
    assert!(
        stderr.contains("unknown layout"),
        "error should mention unknown layout"
    );
}

// ─── Tier 2: Content verification tests ──────────────────────────────────────

#[test]
fn test_scatter_has_circles() {
    let tsv = "x\ty\n1\t2\n3\t4\n5\t3\n";
    let (stdout, _stderr, code) = run_with_stdin(
        &[
            "scatter",
            "--title",
            "Scatter",
            "--x-label",
            "X",
            "--y-label",
            "Y",
        ],
        tsv,
    );
    assert_eq!(code, 0);
    assert!(
        stdout.contains("<circle"),
        "scatter SVG should contain <circle elements"
    );
}

#[test]
fn test_line_has_path() {
    let (stdout, stderr, code) = run_with_file(&[
        "line",
        &data("measurements.tsv"),
        "--x",
        "time",
        "--y",
        "value",
        "--color-by",
        "group",
        "--title",
        "Growth Curves",
        "--x-label",
        "Time",
        "--y-label",
        "Value",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(
        stdout.contains("<path"),
        "line SVG should contain <path elements"
    );
}

#[test]
fn test_bar_has_rects_and_labels() {
    let (stdout, stderr, code) = run_with_file(&[
        "bar",
        &data("bar.tsv"),
        "--label-col",
        "category",
        "--value-col",
        "count",
        "--title",
        "Category Counts",
        "--x-label",
        "Category",
        "--y-label",
        "Count",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(
        stdout.contains("<rect"),
        "bar SVG should contain <rect elements"
    );
    assert!(
        stdout.contains("DNA repair"),
        "bar SVG should contain category label 'DNA repair'"
    );
}

#[test]
fn test_sankey_alluvium_cli_content() {
    let tsv = "\
tissue\tcluster\tsex\tcount
Wildlings\tCamp\tWildlings\t10
North\tCastle\tNorth\t8
Wildlings\tCastle\tNorth\t3
North\tCamp\tWildlings\t2
";
    let (stdout, stderr, code) = run_with_stdin(
        &[
            "sankey",
            "--axis-col",
            "tissue",
            "--axis-col",
            "cluster",
            "--axis-col",
            "sex",
            "--value-col",
            "count",
            "--node-order",
            "crossings",
            "--coloring",
            "left",
            "--title",
            "Alluvium",
        ],
        tsv,
    );
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(
        stdout.contains("<path"),
        "alluvium SVG should contain ribbon paths"
    );
    assert!(
        stdout.contains("Wildlings") && stdout.contains("Castle"),
        "alluvium SVG should contain axis labels and node labels"
    );
}

#[test]
fn test_heatmap_has_grid_cells() {
    let (stdout, stderr, code) = run_with_file(&[
        "heatmap",
        &data("heatmap.tsv"),
        "--title",
        "Expression Heatmap",
        "--x-label",
        "Sample",
        "--y-label",
        "Gene",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    let rect_count = stdout.matches("<rect").count();
    assert!(
        rect_count >= 30,
        "heatmap SVG should have at least 30 <rect elements; got {rect_count}"
    );
}

#[test]
fn test_volcano_threshold_line() {
    let (stdout, stderr, code) = run_with_file(&[
        "volcano",
        &data("volcano.tsv"),
        "--name-col",
        "gene",
        "--x-col",
        "log2fc",
        "--y-col",
        "pvalue",
        "--title",
        "Differential Expression",
        "--x-label",
        "log2 Fold Change",
        "--y-label=-log10(p-value)",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(
        stdout.contains("stroke-dasharray"),
        "volcano SVG should contain dashed threshold lines"
    );
}

#[test]
fn test_manhattan_chromosome_labels() {
    let (stdout, stderr, code) = run_with_file(&[
        "manhattan",
        &data("gene_stats.tsv"),
        "--chr-col",
        "chr",
        "--pvalue-col",
        "pvalue",
        "--title",
        "GWAS Results",
        "--x-label",
        "Chromosome",
        "--y-label=-log10(p-value)",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(
        stdout.contains("chr1"),
        "manhattan SVG should contain chromosome label text 'chr1'"
    );
}

#[test]
fn test_pie_has_paths_and_legend() {
    let (stdout, stderr, code) = run_with_file(&[
        "pie",
        &data("pie.tsv"),
        "--label-col",
        "feature",
        "--value-col",
        "percentage",
        "--legend",
        "--title",
        "Genome Composition",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(
        stdout.contains("<path"),
        "pie SVG should contain <path elements"
    );
    assert!(
        stdout.contains("Intron"),
        "pie SVG should contain legend entry 'Intron'"
    );
}

// ─── Tier 3: Terminal output tests ───────────────────────────────────────────
//
// All tests pass --term-width and --term-height explicitly so the running
// terminal's dimensions never influence the output.

fn is_terminal_output(s: &str) -> bool {
    // Terminal output contains ANSI escape sequences; it must NOT look like SVG.
    !s.trim_start().starts_with("<svg") && !s.is_empty()
}

#[test]
fn test_scatter_terminal() {
    let tsv = "x\ty\n1\t2\n3\t4\n5\t3\n2\t5\n4\t1\n";
    let (stdout, stderr, code) = run_with_stdin(
        &[
            "scatter",
            "--terminal",
            "--term-width",
            "80",
            "--term-height",
            "24",
            "--x-label",
            "X",
            "--y-label",
            "Y",
        ],
        tsv,
    );
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(
        is_terminal_output(&stdout),
        "expected terminal output, not SVG"
    );
    assert!(
        stdout
            .chars()
            .any(|c| ('\u{2800}'..='\u{28FF}').contains(&c)),
        "scatter terminal output should contain braille dots"
    );
}

#[test]
fn test_bar_terminal() {
    let tsv = "label\tvalue\nA\t10\nB\t20\nC\t15\n";
    let (stdout, stderr, code) = run_with_stdin(
        &[
            "bar",
            "--label-col",
            "label",
            "--value-col",
            "value",
            "--terminal",
            "--term-width",
            "80",
            "--term-height",
            "24",
        ],
        tsv,
    );
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(
        is_terminal_output(&stdout),
        "expected terminal output, not SVG"
    );
    assert!(
        stdout.contains('█'),
        "bar terminal output should contain block characters"
    );
}

#[test]
fn test_histogram_terminal() {
    let tsv = "1.5\n2.3\n2.7\n3.2\n3.8\n3.9\n4.0\n1.5\n2.1\n3.5\n";
    let (stdout, stderr, code) = run_with_stdin(
        &[
            "histogram",
            "--bins",
            "5",
            "--terminal",
            "--term-width",
            "80",
            "--term-height",
            "24",
        ],
        tsv,
    );
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(
        is_terminal_output(&stdout),
        "expected terminal output, not SVG"
    );
    assert!(
        stdout.contains('█'),
        "histogram terminal output should contain block characters"
    );
}

#[test]
fn test_line_terminal() {
    let (stdout, stderr, code) = run_with_file(&[
        "line",
        &data("measurements.tsv"),
        "--x",
        "time",
        "--y",
        "value",
        "--color-by",
        "group",
        "--terminal",
        "--term-width",
        "80",
        "--term-height",
        "24",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(
        is_terminal_output(&stdout),
        "expected terminal output, not SVG"
    );
}

#[test]
fn test_pie_terminal() {
    let (stdout, stderr, code) = run_with_file(&[
        "pie",
        &data("pie.tsv"),
        "--label-col",
        "feature",
        "--value-col",
        "percentage",
        "--terminal",
        "--term-width",
        "80",
        "--term-height",
        "24",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(
        is_terminal_output(&stdout),
        "expected terminal output, not SVG"
    );
    assert!(
        stdout
            .chars()
            .any(|c| ('\u{2800}'..='\u{28FF}').contains(&c)),
        "pie terminal output should contain braille arcs"
    );
}

#[test]
fn test_box_terminal() {
    let (stdout, stderr, code) = run_with_file(&[
        "box",
        &data("samples.tsv"),
        "--group-col",
        "group",
        "--value-col",
        "expression",
        "--terminal",
        "--term-width",
        "80",
        "--term-height",
        "24",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(
        is_terminal_output(&stdout),
        "expected terminal output, not SVG"
    );
}

#[test]
fn test_violin_terminal() {
    let (stdout, stderr, code) = run_with_file(&[
        "violin",
        &data("samples.tsv"),
        "--group-col",
        "group",
        "--value-col",
        "expression",
        "--terminal",
        "--term-width",
        "80",
        "--term-height",
        "24",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(
        is_terminal_output(&stdout),
        "expected terminal output, not SVG"
    );
}

#[test]
fn test_volcano_terminal() {
    let (stdout, stderr, code) = run_with_file(&[
        "volcano",
        &data("volcano.tsv"),
        "--name-col",
        "gene",
        "--x-col",
        "log2fc",
        "--y-col",
        "pvalue",
        "--terminal",
        "--term-width",
        "80",
        "--term-height",
        "24",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(
        is_terminal_output(&stdout),
        "expected terminal output, not SVG"
    );
}

#[test]
fn test_heatmap_terminal() {
    let (stdout, stderr, code) = run_with_file(&[
        "heatmap",
        &data("heatmap.tsv"),
        "--terminal",
        "--term-width",
        "80",
        "--term-height",
        "24",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(
        is_terminal_output(&stdout),
        "expected terminal output, not SVG"
    );
    assert!(
        stdout.contains('█'),
        "heatmap terminal output should contain block characters"
    );
}

#[test]
fn test_strip_terminal() {
    let (stdout, stderr, code) = run_with_file(&[
        "strip",
        &data("samples.tsv"),
        "--group-col",
        "group",
        "--value-col",
        "expression",
        "--terminal",
        "--term-width",
        "80",
        "--term-height",
        "24",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(
        is_terminal_output(&stdout),
        "expected terminal output, not SVG"
    );
}

// ─── Tier 4: Error-path tests ─────────────────────────────────────────────────

#[test]
fn test_bad_column_name() {
    let tsv = "x\ty\n1\t2\n3\t4\n";
    let (_, stderr, code) = run_with_stdin(&["scatter", "--x", "nonexistent_col"], tsv);
    assert_ne!(code, 0, "should fail when column name does not exist");
    assert!(
        stderr.contains("nonexistent_col"),
        "error message should mention the bad column name; got: {stderr}"
    );
}

#[test]
fn test_empty_stdin() {
    let (_, stderr, code) = run_with_stdin(&["scatter"], "");
    assert_ne!(code, 0, "should fail on empty input");
    assert!(
        !stderr.is_empty(),
        "stderr should be non-empty on empty input"
    );
}

/// Ignored by default: same stale-binary caveat as `test_missing_feature_error`.
/// Run explicitly after building without --features pdf:
///   cargo test --test cli_basic test_missing_feature_pdf -- --ignored
#[test]
#[ignore = "requires binary freshly built without --features pdf; stale binary causes false-positive"]
#[cfg(not(feature = "pdf"))]
fn test_missing_feature_pdf() {
    let tsv = "x\ty\n1\t2\n3\t4\n";
    let tmp_pdf = std::env::temp_dir().join("kuva_test_missing.pdf");

    let (_, stderr, code) = run_with_stdin(&["scatter", "-o", tmp_pdf.to_str().unwrap()], tsv);
    assert_ne!(code, 0, "should fail when pdf feature is missing");
    assert!(
        stderr.contains("pdf"),
        "error message should mention pdf; got: {stderr}"
    );

    let _ = fs::remove_file(&tmp_pdf);
}

// ── forest ───────────────────────────────────────────────────────────────────

#[test]
fn test_forest_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "forest",
        &data("forest.tsv"),
        "--label-col",
        "study",
        "--estimate-col",
        "estimate",
        "--ci-lower-col",
        "ci_lower",
        "--ci-upper-col",
        "ci_upper",
        "--title",
        "Meta-Analysis",
        "--x-label",
        "Effect Size",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_forest_has_lines_and_circles() {
    let (stdout, stderr, code) = run_with_file(&[
        "forest",
        &data("forest.tsv"),
        "--label-col",
        "study",
        "--estimate-col",
        "estimate",
        "--ci-lower-col",
        "ci_lower",
        "--ci-upper-col",
        "ci_upper",
        "--weight-col",
        "weight",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(
        stdout.contains("<line"),
        "SVG should contain line elements (CI whiskers)"
    );
    assert!(
        stdout.contains("<rect"),
        "SVG should contain rect elements (point estimates)"
    );
    assert!(
        stdout.contains("stroke-dasharray"),
        "SVG should contain dashed null line"
    );
}

// ── scatter3d ────────────────────────────────────────────────────────────────

#[test]
fn test_scatter3d_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "scatter3d",
        &data("scatter3d.tsv"),
        "--x",
        "x",
        "--y",
        "y",
        "--z",
        "z",
        "--title",
        "3D Scatter",
        "--x-label",
        "X",
        "--y-label",
        "Y",
        "--z-label",
        "Z",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_scatter3d_has_circles_and_lines() {
    let (stdout, stderr, code) = run_with_file(&[
        "scatter3d",
        &data("scatter3d.tsv"),
        "--x",
        "x",
        "--y",
        "y",
        "--z",
        "z",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(
        stdout.contains("<circle"),
        "SVG should contain circle markers"
    );
    assert!(
        stdout.contains("<line"),
        "SVG should contain line elements (box edges)"
    );
}

#[test]
fn test_scatter3d_color_by() {
    let (stdout, stderr, code) = run_with_file(&[
        "scatter3d",
        &data("scatter3d.tsv"),
        "--x",
        "x",
        "--y",
        "y",
        "--z",
        "z",
        "--color-by",
        "group",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
    assert!(
        stdout.contains("<circle"),
        "SVG should contain circle markers"
    );
}

// ── surface3d ────────────────────────────────────────────────────────────────

#[test]
fn test_surface3d_svg() {
    let (stdout, stderr, code) = run_with_file(&[
        "surface3d",
        &data("surface3d.tsv"),
        "--x",
        "x",
        "--y",
        "y",
        "--z",
        "z",
        "--z-color",
        "viridis",
        "--title",
        "3D Surface",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(stdout.starts_with("<svg"), "output should start with <svg");
}

#[test]
fn test_surface3d_has_paths() {
    let (stdout, stderr, code) = run_with_file(&[
        "surface3d",
        &data("surface3d.tsv"),
        "--x",
        "x",
        "--y",
        "y",
        "--z",
        "z",
    ]);
    assert_eq!(code, 0, "exit code should be 0; stderr: {stderr}");
    assert!(
        stdout.contains("<path"),
        "SVG should contain path elements (surface faces)"
    );
}

// ── colormap string parsing via CLI ──────────────────────────────────────────

/// Diverging colormap names should be accepted by `kuva heatmap --colormap` and
/// produce valid SVG.  Tests each diverging name plus representative aliases.
#[test]
fn test_heatmap_colormap_diverging_names() {
    // Each entry: (--colormap value, description)
    let cases: &[&str] = &[
        "brown-green",
        "browngreen",
        "brbg",
        "pink-green",
        "pinkgreen",
        "piyg",
        "purple-green",
        "purplegreen",
        "prgn",
        "purple-orange",
        "purpleorange",
        "puor",
        "red-blue",
        "redblue",
        "rdbu",
        "red-grey",
        "redgrey",
        "rdgy",
        "red-yellow-blue",
        "rdylbu",
        "red-yellow-green",
        "rdylgn",
        "spectral",
    ];

    // Long-format TSV: (row, col, value) triples; use --long-format
    let tsv =
        "row\tcol\tvalue\nA\tX\t-3.0\nA\tY\t0.0\nA\tZ\t3.0\nB\tX\t-1.0\nB\tY\t0.0\nB\tZ\t1.0\n";

    for name in cases {
        let (stdout, stderr, code) =
            run_with_stdin(&["heatmap", "--long-format", "--colormap", name], tsv);
        assert_eq!(code, 0, "--colormap {name} should exit 0; stderr: {stderr}");
        assert!(
            stdout.starts_with("<svg"),
            "--colormap {name} output should start with <svg"
        );
        // No unknown-colormap warning should appear for recognized names
        assert!(
            !stderr.contains("unknown colormap"),
            "--colormap {name} emitted unknown colormap warning: {stderr}"
        );
    }
}

/// `parse_colormap` aliases: hyphens, no-separator, and d3 abbreviations
/// should all resolve without an "unknown colormap" warning on stderr.
#[test]
fn test_heatmap_colormap_sequential_aliases() {
    let tsv = "row\tcol\tval\nA\tX\t5\nA\tY\t10\nB\tX\t15\nB\tY\t20\n";
    let aliases: &[&str] = &[
        "viridis",
        "inferno",
        "magma",
        "plasma",
        "cividis",
        "turbo",
        "warm",
        "cool",
        "cubehelix",
        "blues",
        "greens",
        "grayscale",
        "grey",
        "gray",
        "oranges",
        "purples",
        "reds",
        "blue-green",
        "bugn",
        "orange-red",
        "orrd",
        "yellow-green",
        "ylgn",
        "yellow-orange-red",
        "ylorrd",
        "rainbow",
        "sinebow",
    ];

    for name in aliases {
        let (_, stderr, code) =
            run_with_stdin(&["heatmap", "--long-format", "--colormap", name], tsv);
        assert_eq!(code, 0, "--colormap {name} exit code; stderr: {stderr}");
        assert!(
            !stderr.contains("unknown colormap"),
            "--colormap {name} should not warn 'unknown colormap'; stderr: {stderr}"
        );
    }
}

/// An unrecognized colormap name should warn on stderr but still exit 0 and
/// produce SVG (falls back to Viridis).
#[test]
fn test_heatmap_colormap_unknown_warns_but_succeeds() {
    let tsv = "x\ty\tv\n1\t1\t5\n1\t2\t10\n";
    let (stdout, stderr, code) = run_with_stdin(
        &["heatmap", "--long-format", "--colormap", "notacolormap"],
        tsv,
    );
    assert_eq!(code, 0, "unknown colormap should still exit 0");
    assert!(stdout.starts_with("<svg"), "should still produce SVG");
    assert!(
        stderr.contains("unknown colormap"),
        "should warn about unknown colormap; stderr: {stderr}"
    );
}

// ── misc ─────────────────────────────────────────────────────────────────────

#[test]
fn test_unknown_subcommand() {
    let (_, _, code) = run_with_file(&["notaplot"]);
    assert_ne!(code, 0, "unknown subcommand should exit with non-zero code");
}