legume-numeric 0.8.11

/// Default `env_logger` filter when verbose mode is on. Promotes everything to
/// info. (The k-NN backend, instant-distance, emits no `log` output, so no
/// per-crate pin is needed here.) Override via `RUST_LOG=...`.
pub const VERBOSE_LOG_FILTER: &str = "info";

/// Default `env_logger` filter when verbose mode is off.
pub const QUIET_LOG_FILTER: &str = "warn";

use flate2::read::MultiGzDecoder;
use rayon::prelude::*;
use std::ffi::OsStr;
use std::fs::File;
use std::io::{BufRead, BufReader, BufWriter, Write};
use std::path::Path;
use tempfile::tempdir;

#[cfg(test)]
mod tests;

/// Define a Delimiter enum to handle both &str and `Vec<char>`
pub enum Delimiter {
    Str(String),
    Chars(Vec<char>),
}

impl From<&str> for Delimiter {
    fn from(s: &str) -> Self {
        Delimiter::Str(s.to_string())
    }
}

impl From<Vec<char>> for Delimiter {
    fn from(chars: Vec<char>) -> Self {
        Delimiter::Chars(chars)
    }
}

impl From<&[char]> for Delimiter {
    fn from(chars: &[char]) -> Self {
        Delimiter::Chars(chars.to_vec())
    }
}

impl<const N: usize> From<&[char; N]> for Delimiter {
    fn from(chars: &[char; N]) -> Self {
        Delimiter::Chars(chars.to_vec())
    }
}

///
/// Read every line of the input_file into memory
///
/// * `input_file` - file name--either gzipped or not
///
pub fn read_lines(input_file_path: &str) -> anyhow::Result<Vec<Box<str>>> {
    let buf: Box<dyn BufRead> = open_buf_reader(input_file_path)?;
    let mut lines = vec![];
    for x in buf.lines() {
        lines.push(x?.into_boxed_str());
    }
    Ok(lines)
}

///
/// Write every line into the output_file
///
/// * `lines` - vector of lines
/// * `output_file` - file name--either gzipped or not
///
pub fn write_lines(lines: &Vec<Box<str>>, output_file_path: &str) -> anyhow::Result<()> {
    write_types(lines, output_file_path)
}

///
/// Write every line into the output_file
///
/// * `lines` - vector of lines
/// * `output_file` - file name--either gzipped or not
///
pub fn write_types<T>(lines: &Vec<T>, output_file_path: &str) -> anyhow::Result<()>
where
    T: std::fmt::Display,
{
    let mut buf = open_buf_writer(output_file_path)?;
    for line in lines {
        if let Err(e) = writeln!(buf, "{}", line) {
            if e.kind() == std::io::ErrorKind::BrokenPipe {
                return Ok(());
            } else {
                return Err(anyhow::anyhow!("unexpected error: {}", e));
            }
        }
    }
    buf.flush()?;
    Ok(())
}

pub struct ReadLinesOut<T: Send> {
    pub lines: Vec<Vec<T>>,
    pub header: Vec<Box<str>>,
}

///
/// Generic function to read lines and parse them into a vector of words or types.
///
/// * `input_file` - file name--either gzipped or not
/// * `hdr_line` - location of a header line (-1 = no header line)
/// * `parse_fn` - function to parse each line into the desired type
///
pub fn read_lines_of_words_generic<T>(
    input_file: &str,
    hdr_line: i64,
    parse_header_fn: impl Fn(&str) -> Vec<Box<str>> + Sync,
    parse_fn: impl Fn(&str) -> Vec<T> + Sync,
) -> anyhow::Result<ReadLinesOut<T>>
where
    T: Send,
{
    let buf_reader: Box<dyn BufRead> = open_buf_reader(input_file)?;

    fn is_not_comment_line(line: &str) -> bool {
        if line.starts_with('#') || line.starts_with('%') {
            return false;
        }
        true
    }

    let lines_raw: Vec<Box<str>> = buf_reader
        .lines()
        .map_while(Result::ok)
        .map(|x| x.into_boxed_str())
        .filter(|x| is_not_comment_line(x.as_ref()))
        .collect();

    let mut header = vec![];

    // Parsing takes more time, so split them into parallel jobs
    let mut lines: Vec<(usize, Vec<T>)> = if hdr_line < 0 {
        lines_raw
            .iter()
            .enumerate()
            .par_bridge()
            .map(|(i, s)| (i, parse_fn(s)))
            .collect()
    } else {
        let n_skip = hdr_line as usize;
        if lines_raw.len() < (n_skip + 1) {
            return Err(anyhow::anyhow!("not enough data"));
        }

        header.extend(parse_header_fn(&lines_raw[n_skip]));

        lines_raw[(n_skip + 1)..]
            .iter()
            .enumerate()
            .par_bridge()
            .map(|(i, s)| (i, parse_fn(s)))
            .collect()
    };

    if lines.len() > 100_000 {
        lines.par_sort_by_key(|&(i, _)| i);
    } else {
        lines.sort_by_key(|&(i, _)| i);
    }

    let lines = lines.into_iter().map(|(_, x)| x).collect();
    Ok(ReadLinesOut { lines, header })
}

///
/// Specialized function to read lines and parse them into a vector of types.
///
/// * `input_file` - file name--either gzipped or not
/// * `delim` - delimiter
/// * `hdr_line` - location of a header line (-1 = no header line)
///
pub fn read_lines_of_types<T>(
    input_file: &str,
    delim: impl Into<Delimiter>,
    hdr_line: i64,
) -> anyhow::Result<ReadLinesOut<T>>
where
    T: Send + std::str::FromStr + std::fmt::Display,
    <T as std::str::FromStr>::Err: std::fmt::Debug,
{
    let delim = delim.into(); // Convert the input delimiter into the Delimiter enum

    let parse_fn = move |line: &str| -> Vec<T> {
        match &delim {
            Delimiter::Str(s) => line
                .split(s.as_str())
                .map(|x| x.parse::<T>().expect("failed to parse"))
                .collect(),
            Delimiter::Chars(chars) => line
                .split(chars.as_slice())
                .map(|x| x.parse::<T>().expect("failed to parse"))
                .collect(),
        }
    };

    let parse_header_fn = |line: &str| -> Vec<Box<str>> {
        line.split_whitespace()
            .map(|x| x.to_owned().into_boxed_str())
            .collect()
    };

    read_lines_of_words_generic(input_file, hdr_line, parse_header_fn, parse_fn)
}

///
/// Specialized function to read lines and parse them into a vector of words.
///
/// * `input_file` - file name--either gzipped or not
/// * `hdr_line` - location of a header line (-1 = no header line)
///
pub fn read_lines_of_words(
    input_file: &str,
    hdr_line: i64,
) -> anyhow::Result<ReadLinesOut<Box<str>>> {
    let parse_fn = |line: &str| -> Vec<Box<str>> {
        line.split_whitespace()
            .map(|x| x.to_owned().into_boxed_str())
            .collect()
    };

    read_lines_of_words_generic(input_file, hdr_line, parse_fn, parse_fn)
}

///
/// Specialized function to read lines and parse them into a vector of words.
///
/// * `input_file` - file name--either gzipped or not
/// * `delim` - delimiter
/// * `hdr_line` - location of a header line (-1 = no header line)
///
/// Trim a field and strip one pair of symmetric quotes.
///
/// Only a field quoted at BOTH ends is a quoted field. Trimming either end
/// on its own corrupts content that merely happens to start or finish with a
/// quote: a GTF attribute column reads `gene_id "X"; gene_name "Y"`, which
/// ends in a quote it needs, and losing it leaves the attribute unparseable.
/// This is the same rule the delimited tokenizer applies to every field, so
/// any caller inspecting raw lines (header sniffing, previews) can match it.
pub fn unquote_field(x: &str) -> &str {
    let t = x.trim();
    for q in ['"', '\''] {
        if t.len() >= 2 && t.starts_with(q) && t.ends_with(q) {
            return &t[q.len_utf8()..t.len() - q.len_utf8()];
        }
    }
    t
}

pub fn read_lines_of_words_delim(
    input_file: &str,
    delim: impl Into<Delimiter>,
    hdr_line: i64,
) -> anyhow::Result<ReadLinesOut<Box<str>>> {
    let delim = delim.into(); // Convert the input delimiter into the Delimiter enum

    // Outer quotes come off here, once, rather than at each consumer.
    //
    // A csv writer that quotes every field yields `"x"` where the caller asked
    // for `x`, so a name match fails and a reader that falls back to reading by
    // POSITION then silently takes whichever columns happen to sit there. The
    // name-list reader in this same file already unquoted; the general reader
    // did not, which is the inconsistency this removes.
    //
    // This splitter cannot honour a quoted field containing the delimiter
    // anyway, so trimming the outer quotes loses nothing it had.
    // Every field is also trimmed. That is wider than unquoting and worth
    // stating: it is what removes the trailing \r on CRLF input, and it applies
    // to every delimited file the workspace reads through here.
    //
    // Only a field quoted at BOTH ends is a quoted field. Trimming either end
    // on its own corrupts content that merely happens to start or finish with a
    // quote: a GTF attribute column reads `gene_id "X"; gene_name "Y"`, which
    // ends in a quote it needs, and losing it leaves the attribute unparseable.
    let parse_fn = |line: &str| -> Vec<Box<str>> {
        match &delim {
            Delimiter::Str(s) => line
                .split(s.as_str())
                .map(|x| unquote_field(x).to_owned().into_boxed_str())
                .collect(),
            Delimiter::Chars(chars) => line
                .split(chars.as_slice())
                .map(|x| unquote_field(x).to_owned().into_boxed_str())
                .collect(),
        }
    };

    read_lines_of_words_generic(input_file, hdr_line, parse_fn, parse_fn)
}

////////////////////////////////////////////////////////////
// Name lists (a column of feature / gene names)           //
////////////////////////////////////////////////////////////

/// Header labels recognized as the name-bearing column of a name list, matched
/// case-insensitively.
const NAME_LIST_HEADERS: [&str; 12] = [
    "gene",
    "genes",
    "gene_name",
    "gene_names",
    "gene_id",
    "gene_symbol",
    "feature",
    "features",
    "feature_name",
    "symbol",
    "name",
    "id",
];

/// Position of the name-bearing column in `header`, if one is labelled.
fn name_list_column(header: &[Box<str>]) -> Option<usize> {
    header.iter().position(|h| {
        let h = h.trim().trim_matches('"').to_ascii_lowercase();
        NAME_LIST_HEADERS.contains(&h.as_str())
    })
}

/// Read a flat list of names (genes / features) from a file, keeping one column
/// and dropping every other.
///
/// The format is inferred from the extension: `.parquet`, else delimited text —
/// tab, comma, or whitespace, optionally gzipped (`.txt`, `.tsv`, `.csv`,
/// `.tsv.gz`, …). A header whose label is gene-like (`gene`, `feature`,
/// `symbol`, …) selects the column to read; without one the first column is
/// used. Every other column is ignored, so a two-column `gene<TAB>celltype`
/// marker table doubles as a plain gene list. Names are de-duplicated, keeping
/// first-seen order.
///
/// Names are returned verbatim — matching them against a data vocabulary
/// (symbol / Ensembl / case) is the caller's job.
pub fn read_name_list(file_path: &str) -> anyhow::Result<Vec<Box<str>>> {
    let is_parquet = Path::new(file_path)
        .extension()
        .and_then(OsStr::to_str)
        .is_some_and(|e| e.eq_ignore_ascii_case("parquet"));

    let names: Vec<Box<str>> = if is_parquet {
        let header = crate::matrix::parquet::peek_parquet_field_names(file_path)?;
        let col = name_list_column(&header).unwrap_or(0);
        crate::matrix::parquet::read_parquet_string_column(file_path, col)?
    } else {
        let raw = read_lines(file_path)?;
        let data_lines: Vec<&str> = raw
            .iter()
            .map(|line| line.trim())
            .filter(|line| !line.is_empty() && !line.starts_with('#') && !line.starts_with('%'))
            .collect();

        // Sniff ONE delimiter from the first row — tab, else comma, else whitespace.
        // Splitting on all three at once would tear a value like `T cell` into two
        // fields and shift every column after it.
        let delim: &[char] = match data_lines.first() {
            Some(first) if first.contains('\t') => &['\t'],
            Some(first) if first.contains(',') => &[','],
            _ => &[' ', '\t'],
        };

        // Blank fields (repeated or leading delimiters) are dropped before the column
        // is indexed, so ragged indentation does not shift it either.
        let rows: Vec<Vec<&str>> = data_lines
            .iter()
            .map(|line| {
                line.split(delim)
                    .map(|w| w.trim().trim_matches('"'))
                    .filter(|w| !w.is_empty())
                    .collect::<Vec<&str>>()
            })
            .filter(|row| !row.is_empty())
            .collect();

        // A gene-like label in the first row means it is a header: read the column it
        // names and skip it. Otherwise the file is headerless and data starts at row 0
        // — treating that first row as a header would silently drop a gene.
        let header: Vec<Box<str>> = rows
            .first()
            .map(|row| row.iter().map(|w| (*w).into()).collect())
            .unwrap_or_default();
        let (col, skip) = match name_list_column(&header) {
            Some(col) => (col, 1),
            None => (0, 0),
        };

        rows.iter()
            .skip(skip)
            .filter_map(|row| row.get(col).map(|w| (*w).into()))
            .collect()
    };

    let mut seen: std::collections::HashSet<Box<str>> = std::collections::HashSet::new();
    let names: Vec<Box<str>> = names
        .into_iter()
        .filter(|n| !n.is_empty())
        .filter(|n| seen.insert(n.clone()))
        .collect();

    if names.is_empty() {
        return Err(anyhow::anyhow!("no names found in {file_path}"));
    }
    Ok(names)
}

///
/// Open a file for reading, and return a buffered reader
/// * `input_file` - file name--either gzipped or not
pub fn open_buf_reader(input_file: &str) -> anyhow::Result<Box<dyn BufRead>> {
    // take a look at the extension
    // return buffered reader accordingly
    let ext = Path::new(input_file).extension().and_then(|x| x.to_str());
    match ext {
        Some("gz") | Some("bgz") | Some("bgzf") => {
            let input_file = File::open(input_file)?;
            // `MultiGzDecoder`, not `GzDecoder`: BGZF and anything else
            // written by `bgzip` is a concatenation of gzip members, and a
            // decoder that stops after the first one drops the rest of the
            // file silently, with no error and no short read.
            let decoder = MultiGzDecoder::new(input_file);
            // A wide buffer over the inflater: a body read one line at a time
            // would otherwise refill through it every few kilobytes.
            Ok(Box::new(BufReader::with_capacity(1 << 20, decoder)))
        }
        _ => {
            // dbg!(input_file);
            let input_file = File::open(input_file)?;
            Ok(Box::new(BufReader::new(input_file)))
        }
    }
}

////////////////////////////////////
// First-line inspection of a table //
////////////////////////////////////

/// The first line of a delimited file, split on `delimiters`, unquoted and
/// trimmed, empty fields dropped. Reads through gzip.
///
/// For error messages and for header detection. It makes no claim about
/// whether that line is a header; it only shows what the file actually holds.
pub fn first_line_fields(path: &str, delimiters: &[char]) -> anyhow::Result<Vec<Box<str>>> {
    let mut first = String::new();
    open_buf_reader(path)?.read_line(&mut first)?;
    Ok(first
        .trim_end_matches(['\n', '\r'])
        .split(delimiters)
        .map(|f| unquote_field(f).to_string().into_boxed_str())
        .filter(|f| !f.is_empty())
        .collect())
}

/// Is the first line a header? Decided by type, not by guessing intent: a line
/// whose fields after column 0 fail to parse as numbers cannot be a data row.
///
/// Column 0 is skipped because a row-name column is non-numeric either way.
/// Fields are unquoted with the tokenizer's own rule first, so a fully quoted
/// numeric field (`"100.5"`) reads as numeric and a quoted headerless file does
/// not lose its first data row to a phantom header. Reads through gzip.
///
/// `Some(0)` when the first line is a header; `None` when every field after
/// column 0 is numeric, or the file cannot be read.
pub fn detect_header_row_numeric(file_path: &str, delimiters: &[char]) -> Option<usize> {
    let mut first = String::new();
    open_buf_reader(file_path)
        .ok()?
        .read_line(&mut first)
        .ok()?;
    let fields: Vec<&str> = first
        .trim_end_matches(['\n', '\r'])
        .split(delimiters)
        .map(unquote_field)
        .collect();
    let any_non_numeric_after_col0 = fields
        .iter()
        .skip(1)
        .any(|t| !t.is_empty() && !is_numeric_or_missing(t));
    // Both outcomes are logged WITH the fields, so a header swallowed as data
    // (all-numeric sample IDs) or a data row taken as a header shows up in the
    // log next to the evidence, not only as a wrong row count later.
    let preview = fields
        .iter()
        .take(6)
        .copied()
        .collect::<Vec<_>>()
        .join(", ");
    if any_non_numeric_after_col0 {
        log::info!("{file_path}: first line treated as a header (non-numeric): [{preview}]");
        Some(0)
    } else {
        log::info!(
            "{file_path}: first line treated as data (all numeric after column 0): [{preview}]"
        );
        None
    }
}

/// A field a count row may legitimately hold: a number, or one of the missing
/// value spellings R and friends write (`NA`, `N/A`; `NaN` already parses).
fn is_numeric_or_missing(t: &str) -> bool {
    t.parse::<f64>().is_ok() || matches!(t, "NA" | "N/A" | "na" | "n/a")
}

///
/// Open a file for writing, and return a buffered writer
/// * `output_file` - file name--either gzipped or not
pub fn open_buf_writer(output_file: &str) -> anyhow::Result<Box<dyn std::io::Write>> {
    // we can simply override with stdout
    if output_file.eq_ignore_ascii_case("stdout") {
        return Ok(Box::new(std::io::BufWriter::new(std::io::stdout())));
    }

    if output_file.eq_ignore_ascii_case("stderr") {
        return Ok(Box::new(std::io::BufWriter::new(std::io::stderr())));
    }

    // take a look at the extension
    let output_file = Path::new(output_file);
    let ext = output_file.extension().and_then(|x| x.to_str());

    match ext {
        Some("gz") => {
            let output_file = File::create(output_file)?;
            let encoder =
                flate2::write::GzEncoder::new(output_file, flate2::Compression::default());
            Ok(Box::new(BufWriter::new(encoder)))
        }
        _ => {
            let output_file = File::create(output_file)?;
            Ok(Box::new(BufWriter::new(output_file)))
        }
    }
}

///
/// Create a directory if needed
/// * `file` - file name
///
pub fn mkdir(file: &str) -> anyhow::Result<()> {
    let path = Path::new(file);
    std::fs::create_dir_all(path)?;
    Ok(())
}

/// Ensure the parent directory of an output path/prefix exists.
///
/// CLI subcommands typically take an `--out` value used as a *file
/// prefix* (e.g. `results/run1` → writes `results/run1.foo.parquet`).
/// Creates the parent directory tree (`results/`) if missing, but
/// never creates a directory named after the prefix itself
/// (`results/run1/`).
///
/// `Path::parent()` returns `Some("")` for a bare filename like
/// `"run1"`; `create_dir_all` would error on that, so skip it.
pub fn mkdir_parent(path: &str) -> anyhow::Result<()> {
    if let Some(parent) = Path::new(path).parent() {
        if !parent.as_os_str().is_empty() {
            std::fs::create_dir_all(parent)?;
        }
    }
    Ok(())
}

pub trait PathOsToStr {
    #[allow(clippy::wrong_self_convention)]
    fn into_boxed_str(&self) -> Box<str>;
}

impl PathOsToStr for Path {
    fn into_boxed_str(&self) -> Box<str> {
        self.to_str()
            .expect("failed to convert to string")
            .to_string()
            .into_boxed_str()
    }
}

impl PathOsToStr for OsStr {
    fn into_boxed_str(&self) -> Box<str> {
        self.to_str()
            .expect("failed to convert to string")
            .to_string()
            .into_boxed_str()
    }
}

/// more general file/directory copy function
pub fn recursive_copy(src_path: &str, dst_path: &str) -> anyhow::Result<()> {
    let src = Path::new(src_path);
    let dst = Path::new(dst_path);

    if src.is_dir() {
        mkdir(dst_path)?;
        for entry in std::fs::read_dir(src)? {
            let entry = entry?;
            if let (Some(src_path), Some(dst_path)) =
                (entry.path().to_str(), dst.join(entry.file_name()).to_str())
            {
                let file_type = entry.file_type()?;
                if file_type.is_dir() {
                    recursive_copy(src_path, dst_path)?;
                } else if file_type.is_file() {
                    std::fs::copy(src_path, dst_path)?;
                }
            }
        }
    } else if src.is_file() {
        if let Some(dir) = dirname(dst_path).as_deref() {
            mkdir(dir)?;
        }
        std::fs::copy(src, dst)?;
    } else if src.is_symlink() {
        if let Ok(abs_src) = std::fs::read_link(src) {
            if let Some(abs_src_path) = abs_src.to_str() {
                recursive_copy(abs_src_path, dst_path)?;
            }
        }
    }

    Ok(())
}

/// Unzip `zip_path` into the `extract_path` If `extract_path` is
/// `None`, just use a current directory.
/// * Returns `extract_path`
pub fn unzip_dir(zip_path: &str, extract_path: Option<&str>) -> anyhow::Result<Box<str>> {
    let zip_file = std::fs::File::open(zip_path)?;
    let mut archive = zip::ZipArchive::new(zip_file)?;

    let extract_path = extract_path
        .map(std::path::PathBuf::from)
        .unwrap_or(std::env::current_dir()?);

    for i in 0..archive.len() {
        let mut file = archive.by_index(i)?;
        let out_path = extract_path.join(file.name());
        // println!("{}", out_path.to_str().unwrap());
        if file.is_dir() {
            std::fs::create_dir_all(&out_path)?;
        } else {
            if let Some(parent) = out_path.parent() {
                std::fs::create_dir_all(parent)?;
            }
            let mut outfile = std::fs::File::create(&out_path)?;
            std::io::copy(&mut file, &mut outfile)?;
        }
    }

    Ok(extract_path.into_boxed_str())
}

/// Zip a directory into a zip archive using `Stored` compression
/// (zarr chunks are already zstd-compressed internally). In-zip entries are
/// prefixed with the source directory's basename.
pub fn zip_dir(source_dir: &str, zip_path: &str) -> anyhow::Result<()> {
    zip_dir_as(source_dir, zip_path, None)
}

/// Like [`zip_dir`] but lets the caller override the in-zip root name, so the
/// archive can use a different prefix than the source directory's basename
/// without renaming or moving the source on disk.
pub fn zip_dir_as(
    source_dir: &str,
    zip_path: &str,
    entry_root: Option<&str>,
) -> anyhow::Result<()> {
    use std::io::Write;
    use zip::write::SimpleFileOptions;
    use zip::ZipWriter;

    let file = std::fs::File::create(zip_path)?;
    let mut zip = ZipWriter::new(file);
    let options = SimpleFileOptions::default().compression_method(zip::CompressionMethod::Stored);
    let source = Path::new(source_dir);

    fn collect_entries(dir: &Path, out: &mut Vec<std::path::PathBuf>) -> std::io::Result<()> {
        for entry in std::fs::read_dir(dir)? {
            let entry = entry?;
            let path = entry.path();
            out.push(path.clone());
            // Use entry.file_type() (does not follow symlinks) to avoid
            // infinite recursion on circular symlinks.
            if entry.file_type()?.is_dir() {
                collect_entries(&path, out)?;
            }
        }
        Ok(())
    }

    let mut entries = vec![];
    collect_entries(source, &mut entries)?;
    entries.sort();

    let root_name =
        entry_root.unwrap_or_else(|| source.file_name().and_then(|s| s.to_str()).unwrap_or(""));

    for path in &entries {
        let rel_under_source = path.strip_prefix(source).unwrap_or(path);
        let rel = if root_name.is_empty() {
            rel_under_source.to_path_buf()
        } else {
            Path::new(root_name).join(rel_under_source)
        };
        if path.symlink_metadata()?.is_dir() {
            zip.add_directory(format!("{}/", rel.display()), options)?;
        } else {
            zip.start_file(rel.display().to_string(), options)?;
            let data = std::fs::read(path)?;
            zip.write_all(&data)?;
        }
    }

    zip.finish()?;
    Ok(())
}

/// just get the directory (parent) name
pub fn dirname(file_path: &str) -> Option<Box<str>> {
    Path::new(file_path).parent().map(|x| x.into_boxed_str())
}

///
/// Take the parent directory, basename, and extension of a file
/// * `file` - file name
///
pub fn dir_base_ext(file_path: &str) -> anyhow::Result<(Box<str>, Box<str>, Box<str>)> {
    let path = Path::new(file_path);

    let dir = path
        .parent()
        .map_or(".".to_string().into_boxed_str(), |x| x.into_boxed_str());

    let ext = path
        .extension()
        .map_or("".to_string().into_boxed_str(), |x| x.into_boxed_str());

    let base = path
        .file_stem()
        .and_then(|x| x.to_str())
        .map(|x| strip_data_ext(x).to_string().into_boxed_str())
        .ok_or(anyhow::anyhow!("failed to find base here: {}", file_path))?;

    Ok((dir, base, ext))
}

///
/// Take the basename of a file
/// * `file` - file name
///
pub fn basename(file: &str) -> anyhow::Result<Box<str>> {
    let path = Path::new(file);
    if let Some(base) = path.file_stem().and_then(|s| s.to_str()) {
        Ok(strip_data_ext(base).to_string().into_boxed_str())
    } else {
        Err(anyhow::anyhow!("no file stem"))
    }
}

/// Strip a leftover sparse-data extension (`.zarr`, `.h5`, `.h5ad`) that
/// `Path::file_stem` leaves behind on doubly-extended paths like
/// `sample.zarr.zip` (file_stem → `sample.zarr`).
fn strip_data_ext(stem: &str) -> &str {
    for sfx in [".zarr", ".h5ad", ".h5"] {
        if let Some(s) = stem.strip_suffix(sfx) {
            return s;
        }
    }
    stem
}

///
/// Take the extension of a file
/// * `file` - file name
///
pub fn file_ext(file: &str) -> anyhow::Result<Box<str>> {
    let path = Path::new(file);
    if let Some(ext) = path.extension() {
        Ok(ext.into_boxed_str())
    } else {
        Err(anyhow::anyhow!("failed to extract extension"))
    }
}

///
/// Create a temporary directory and suggest a file name
/// * `suffix` - suffix of the file name
///
pub fn create_temp_dir_file(suffix: &str) -> anyhow::Result<std::path::PathBuf> {
    let temp_dir = tempdir()?.path().to_path_buf();
    std::fs::create_dir_all(&temp_dir)?;
    let temp_file = tempfile::Builder::new()
        .suffix(suffix)
        .tempfile_in(temp_dir)?
        .path()
        .to_owned();

    Ok(temp_file)
}

///
/// Remove a file if it exists
/// * `file` - file name
///
pub fn remove_file(file: &str) -> anyhow::Result<()> {
    let path = Path::new(file);
    if path.exists() {
        if path.is_file() {
            std::fs::remove_file(path)?;
        } else {
            std::fs::remove_dir_all(path)?;
        }
    }
    Ok(())
}

///
/// Remove a file if it exists
/// * `files` - file name
///
pub fn remove_all_files(files: &Vec<Box<str>>) -> anyhow::Result<()> {
    for file in files {
        remove_file(file)?;
    }
    Ok(())
}

/// Extensions a data file's name is read through, stripped from the end of
/// the name repeatedly by [`file_stem`]; dots inside the name stay.
pub const DATA_FILE_EXTENSIONS: &[&str] = &[
    "gz", "bgz", "bz2", "zst", "tsv", "csv", "txt", "tab", "gaf", "gmt", "obo", "bed", "vcf",
    "parquet", "pq",
];

/// The file name minus its known extensions
/// (`a/b/goa_human.gaf.gz` → `goa_human`, `c2.cp.v1.symbols.gmt` → `c2.cp.v1.symbols`):
/// the name tools derive a relation or a source label from, so they agree.
pub fn file_stem(path: &str) -> String {
    let mut stem = std::path::Path::new(path)
        .file_name()
        .map(|s| s.to_string_lossy().into_owned())
        .unwrap_or_else(|| path.to_string());
    loop {
        let Some((base, ext)) = stem.rsplit_once('.') else {
            break;
        };
        if base.is_empty() || !DATA_FILE_EXTENSIONS.contains(&ext.to_lowercase().as_str()) {
            break;
        }
        stem.truncate(base.len());
    }
    stem
}