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Stop using raw pointers in the canonicalization interface (#8990)

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* change count-type from pointer to ints to vector

* change type from pointer to ints to vector

* change type from pointer to ints to vector

* change type from pointer to ints to vector

* change type from pointer to ints to vector

* use std::fill only when necessary

* delete unnecessary includes

* reformat

* re-enable a test that was accidentally disabled a few years ago

* finish getting rid of the raw pointers

* include chrono

* changes from review

---------

Co-authored-by: Anna Brünisholz <anna.bruenisholz@gmail.com>
This commit is contained in:
Greg Landrum
2025-12-12 14:00:23 +01:00
committed by GitHub
parent a8a00a1d99
commit e786ca231d
5 changed files with 159 additions and 185 deletions
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29
Code/RDGeneral/hanoiSort.h
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@@ -1,5 +1,5 @@
//
// Copyright (C) 2014 Greg Landrum
// Copyright (C) 2014-2025 Greg Landrum and other RDKit contributors
// Adapted from pseudo-code from Roger Sayle
//
// @@ All Rights Reserved @@
@@ -10,18 +10,21 @@
//
#include <RDGeneral/export.h>
#ifndef HANOISORT_H_
#define HANOISORT_H_
#ifndef HANOISORT_H
#define HANOISORT_H
#include <cstring>
#include <cassert>
#include <cstdlib>
#include <vector>
#include <span>
#if defined(_MSC_VER)
#pragma warning(push, 1)
#pragma warning(disable : 4800)
#endif
namespace RDKit {
namespace detail {
template <typename CompareFunc>
bool hanoi(int *base, int nel, int *temp, int *count, int *changed,
CompareFunc compar) {
@@ -145,17 +148,25 @@ bool hanoi(int *base, int nel, int *temp, int *count, int *changed,
}
}
}
} // namespace detail
template <typename CompareFunc>
[[deprecated("Use the overload that takes std::span and std::vector instead")]]
void hanoisort(int *base, int nel, int *count, int *changed,
CompareFunc compar) {
assert(base);
int *temp = (int *)malloc(nel * sizeof(int));
assert(temp);
if (hanoi(base, nel, temp, count, changed, compar)) {
memmove(base, temp, nel * sizeof(int));
std::vector<int> tempVec(nel);
if (detail::hanoi(base, nel, tempVec.data(), count, changed, compar)) {
memmove(base, tempVec.data(), nel * sizeof(int));
}
}
template <typename CompareFunc>
void hanoisort(std::span<int> &base, std::vector<int> &count,
std::vector<int> &changed, CompareFunc compar) {
std::vector<int> tempVec(base.size());
if (detail::hanoi(base.data(), base.size(), tempVec.data(), count.data(),
changed.data(), compar)) {
std::copy(tempVec.begin(), tempVec.end(), base.begin());
}
free(temp);
}
} // namespace RDKit