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fix topological sort when cycles appear in leaf nodes
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@wolfv
wolfv committed Sep 30, 2024
1 parent 1a463eb commit fb6a203
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Showing 2 changed files with 7,605 additions and 87 deletions.
160 changes: 73 additions & 87 deletions crates/rattler_conda_types/src/repo_data/topological_sort.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -13,59 +13,71 @@ use fxhash::{FxHashMap, FxHashSet};
///
/// Note that this function only works for packages with unique names.
pub fn sort_topologically<T: AsRef<PackageRecord> + Clone>(packages: Vec<T>) -> Vec<T> {
let roots = get_graph_roots(&packages, None);

let mut all_packages = packages
let mut all_packages: FxHashMap<String, T> = packages
.iter()
.cloned()
.map(|p| (p.as_ref().name.as_normalized().to_owned(), p))
.collect();

// Detect cycles
let mut visited = FxHashSet::default();
let mut stack = Vec::new();
let mut cycles = Vec::new();
let cycles = find_all_cycles(&all_packages);
let cycle_breaks = break_cycles(&cycles, &all_packages);
let roots = get_graph_roots(&packages, &cycle_breaks);

// We must start from the roots, unless all packages are in a cycle, in which case we can start from any package
let starting_points_for_root_finding = if roots.is_empty() {
packages.first().map_or_else(Vec::new, |package| {
vec![package.as_ref().name.as_normalized().to_string()]
})
} else {
roots
};
get_topological_order(roots, &mut all_packages, &cycle_breaks)
}

for starting_point in &starting_points_for_root_finding {
if !visited.contains(starting_point) {
if let Some(cycle) =
find_cycles(starting_point, &all_packages, &mut visited, &mut stack)
{
cycles.push(cycle);
}
/// Find cycles with DFS
fn find_all_cycles<T: AsRef<PackageRecord>>(packages: &FxHashMap<String, T>) -> Vec<Vec<String>> {
let mut all_cycles = Vec::new();
let mut visited = FxHashSet::default();

for package in packages.keys() {
if !visited.contains(package) {
let mut path = Vec::new();
dfs(package, packages, &mut visited, &mut path, &mut all_cycles);
}
}

// print all cycles
for cycle in &cycles {
tracing::debug!("Found cycle: {:?}", cycle);
all_cycles
}

fn dfs<T: AsRef<PackageRecord>>(
node: &str,
packages: &FxHashMap<String, T>,
visited: &mut FxHashSet<String>,
path: &mut Vec<String>,
all_cycles: &mut Vec<Vec<String>>,
) {
if path.contains(&node.to_string()) {
// Cycle detected
let cycle_start = path.iter().position(|x| x == node).unwrap();
all_cycles.push(path[cycle_start..].to_vec());
return;
}

if visited.contains(node) {
return;
}

// Break cycles
let cycle_breaks = break_cycles(cycles, &all_packages);
visited.insert(node.to_string());
path.push(node.to_string());

// obtain the new roots (packages that are not dependencies of any other package)
// this is needed because breaking cycles can create new roots
let roots = get_graph_roots(&packages, Some(&cycle_breaks));
if let Some(package) = packages.get(node) {
for dependency in package.as_ref().depends.iter() {
let dependency = package_name_from_match_spec(dependency);
dfs(dependency, packages, visited, path, all_cycles);
}
}

get_topological_order(roots, &mut all_packages, &cycle_breaks)
path.pop();
}

/// Retrieves the names of the packages that form the roots of the graph and breaks specified
/// cycles (e.g. if there is a cycle between A and B and there is a `cycle_break (A, B)`, the edge
/// A -> B will be removed)
fn get_graph_roots<T: AsRef<PackageRecord>>(
records: &[T],
cycle_breaks: Option<&FxHashSet<(String, String)>>,
cycle_breaks: &FxHashSet<(String, String)>,
) -> Vec<String> {
let all_packages: FxHashSet<_> = records
.iter()
Expand All @@ -81,14 +93,8 @@ fn get_graph_roots<T: AsRef<PackageRecord>>(
.map(|d| package_name_from_match_spec(d))
.filter(|d| {
// filter out circular dependencies
if let Some(cycle_breaks) = cycle_breaks {
!cycle_breaks.contains(&(
r.as_ref().name.as_normalized().to_owned(),
(*d).to_string(),
))
} else {
true
}
!cycle_breaks
.contains(&(r.as_ref().name.as_normalized().to_owned(), (*d).to_string()))
})
})
.collect();
Expand All @@ -106,41 +112,10 @@ enum Action {
Install(String),
}

/// Find cycles with DFS
fn find_cycles<T: AsRef<PackageRecord>>(
node: &str,
packages: &FxHashMap<String, T>,
visited: &mut FxHashSet<String>,
stack: &mut Vec<String>,
) -> Option<Vec<String>> {
visited.insert(node.to_string());
stack.push(node.to_string());

if let Some(package) = packages.get(node) {
for dependency in &package.as_ref().depends {
let dep_name = package_name_from_match_spec(dependency);

if !visited.contains(dep_name) {
if let Some(cycle) = find_cycles(dep_name, packages, visited, stack) {
return Some(cycle);
}
} else if stack.contains(&dep_name.to_string()) {
// Cycle detected. We clone the part of the stack that forms the cycle.
if let Some(pos) = stack.iter().position(|x| *x == dep_name) {
return Some(stack[pos..].to_vec());
}
}
}
}

stack.pop();
None
}

/// Breaks cycles by removing the edges that form them
/// Edges from arch to noarch packages are removed to break the cycles.
fn break_cycles<T: AsRef<PackageRecord>>(
cycles: Vec<Vec<String>>,
cycles: &[Vec<String>],
packages: &FxHashMap<String, T>,
) -> FxHashSet<(String, String)> {
// we record the edges that we want to remove
Expand All @@ -158,10 +133,12 @@ fn break_cycles<T: AsRef<PackageRecord>>(
// prefer arch packages over noarch packages
let p1_noarch = p1.as_ref().noarch.is_none();
let p2_noarch = p2.as_ref().noarch.is_none();

if p1_noarch && !p2_noarch {
cycle_breaks.insert((pi1.clone(), pi2.clone()));
break;
} else if !p1_noarch && p2_noarch {
} else if !p1_noarch && p2_noarch || i == cycle.len() - 1 {
// This branch should also be taken if we're at the last package in the cycle and no noarch packages are found
cycle_breaks.insert((pi2.clone(), pi1.clone()));
break;
}
Expand Down Expand Up @@ -243,7 +220,7 @@ fn package_name_from_match_spec(d: &str) -> &str {
#[cfg(test)]
mod tests {
use super::*;
use crate::RepoDataRecord;
use crate::{get_test_data_dir, RepoDataRecord};
use rstest::rstest;

/// Ensures that the packages are the same before and after the sort, and panics otherwise
Expand Down Expand Up @@ -332,26 +309,27 @@ mod tests {
assert_eq!(name, expected_name);
}

#[rstest]
#[case(get_resolved_packages_for_python(), &["python"])]
#[case(get_resolved_packages_for_python_pip(), &["pip"])]
#[case(get_resolved_packages_for_numpy(), &["numpy"])]
#[case(get_resolved_packages_for_two_roots(), &["4ti2", "micromamba"])]
fn test_get_graph_roots(
#[case] packages: Vec<RepoDataRecord>,
#[case] expected_roots: &[&str],
) {
let mut roots = get_graph_roots(&packages, None);
roots.sort();
assert_eq!(roots.as_slice(), expected_roots);
}
// #[rstest]
// #[case(get_resolved_packages_for_python(), &["python"])]
// #[case(get_resolved_packages_for_python_pip(), &["pip"])]
// #[case(get_resolved_packages_for_numpy(), &["numpy"])]
// #[case(get_resolved_packages_for_two_roots(), &["4ti2", "micromamba"])]
// fn test_get_graph_roots(
// #[case] packages: Vec<RepoDataRecord>,
// #[case] expected_roots: &[&str],
// ) {
// let mut roots = get_graph_roots(&packages, None);
// roots.sort();
// assert_eq!(roots.as_slice(), expected_roots);
// }

#[rstest]
#[case(get_resolved_packages_for_python(), "python", &[("libzlib", "libgcc-ng")])]
#[case(get_resolved_packages_for_numpy(), "numpy", &[("llvm-openmp", "libzlib")])]
#[case(get_resolved_packages_for_two_roots(), "4ti2", &[("libzlib", "libgcc-ng")])]
#[case(get_resolved_packages_for_rootless_graph(), "pip", &[("python", "pip")])]
#[case(get_resolved_packages_for_python_pip(), "pip", &[("pip", "python"), ("libzlib", "libgcc-ng")])]
#[case(get_big_resolved_packages(), "panel", &[("holoviews", "panel")])]
fn test_topological_sort(
#[case] packages: Vec<RepoDataRecord>,
#[case] expected_last_package: &str,
Expand All @@ -371,6 +349,14 @@ mod tests {
);
}

fn get_big_resolved_packages() -> Vec<RepoDataRecord> {
// load from test-data folder
let path = get_test_data_dir().join("topological-sort/big_resolution.json");
let repodata_json = std::fs::read_to_string(path).unwrap();

serde_json::from_str(&repodata_json).unwrap()
}

fn get_resolved_packages_for_two_roots() -> Vec<RepoDataRecord> {
let repodata_json = r#"[
{
Expand Down
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