Merge pull request #379 from seoklab/clang-tools-19

chore(dev): bump clang-tools version to v19

.clang-tidy

@@ -5,7 +5,7 @@
 
 # Require clang-tidy v15
 ---
-Checks: "-*,abseil-*,boost-*,bugprone-*,clang-*,concurrency-*,cppcoreguidelines-*,google-*,misc-*,modernize-*,openmp-*,performance-*,portability-*,readability-*,-bugprone-assignment-in-if-condition,-bugprone-easily-swappable-parameters,-cppcoreguidelines-avoid-do-while,-cppcoreguidelines-avoid-c-arrays,-cppcoreguidelines-init-variables,-cppcoreguidelines-narrowing-conversions,-cppcoreguidelines-pro-*,-cppcoreguidelines-rvalue-reference-param-not-moved,-cppcoreguidelines-use-default-member-init,-google-explicit-constructor,-misc-no-recursion,-modernize-avoid-c-arrays,-modernize-return-braced-init-list,-modernize-loop-convert,-modernize-concat-nested-namespaces,-modernize-pass-by-value,-modernize-raw-string-literal,-modernize-use-trailing-return-type,-modernize-use-auto,-modernize-use-default-member-init,-modernize-use-emplace,-modernize-use-equals-delete,-modernize-use-nodiscard,-readability-isolate-declaration,-readability-identifier-length,-readability-qualified-auto,-*-magic-numbers"
+Checks: "-*,abseil-*,boost-*,bugprone-*,clang-*,concurrency-*,cppcoreguidelines-*,google-*,misc-*,modernize-*,openmp-*,performance-*,portability-*,readability-*,-boost-use-ranges,-bugprone-assignment-in-if-condition,-bugprone-crtp-constructor-accessibility,-bugprone-easily-swappable-parameters,-clang-analyzer-optin.core.EnumCastOutOfRange,-cppcoreguidelines-avoid-do-while,-cppcoreguidelines-avoid-c-arrays,-cppcoreguidelines-init-variables,-cppcoreguidelines-narrowing-conversions,-cppcoreguidelines-pro-*,-cppcoreguidelines-rvalue-reference-param-not-moved,-cppcoreguidelines-use-default-member-init,-google-explicit-constructor,-misc-no-recursion,-modernize-avoid-c-arrays,-modernize-return-braced-init-list,-modernize-loop-convert,-modernize-concat-nested-namespaces,-modernize-pass-by-value,-modernize-raw-string-literal,-modernize-use-trailing-return-type,-modernize-use-auto,-modernize-use-default-member-init,-modernize-use-emplace,-modernize-use-equals-delete,-modernize-use-nodiscard,-performance-enum-size,-readability-isolate-declaration,-readability-identifier-length,-readability-qualified-auto,-readability-math-missing-parentheses,-readability-avoid-nested-conditional-operator,-*-magic-numbers"
 FormatStyle: "file"
 # If these flags are updated, .clangd should be updated as well
 ExtraArgsBefore:
@@ -24,6 +24,7 @@ ExtraArgsBefore:
   - -Wno-unused-macros
   - -Wno-disabled-macro-expansion
   - -Wno-unsafe-buffer-usage
+  - -Wno-switch-default
   - -fno-sanitize=all
 CheckOptions:
   - key: bugprone-stringview-nullptr.IncludeStyle

.clangd

@@ -24,6 +24,7 @@ CompileFlags:
     - -Wno-unused-macros
     - -Wno-disabled-macro-expansion
     - -Wno-unsafe-buffer-usage
+    - -Wno-switch-default
   Remove:
     - "-fsanitize=*"
     - "-flto*"
@@ -43,3 +44,9 @@ InlayHints:
   Enabled: Yes
   ParameterNames: Yes
   DeducedTypes: Yes
+---
+If:
+  PathMatch: "third_party/.*"
+Diagnostics:
+  Suppress: "*"
+  UnusedIncludes: None

.github/workflows/_run-clang-tools.yaml

@@ -16,7 +16,7 @@ on:
         default: false
       version:
         type: string
-        default: "17"
+        default: "19"
 
 defaults:
   run:

include/nuri/core/geometry.h

@@ -206,7 +206,7 @@ auto cdist(const ML1 &a, const ML2 &b) {
 }
 
 namespace internal {
-  constexpr inline double safe_normalizer(double sqn, double eps = 1e-12) {
+  constexpr double safe_normalizer(double sqn, double eps = 1e-12) {
     return sqn > eps ? 1 / std::sqrt(sqn) : 0;
   }
 

include/nuri/core/graph.h

@@ -1003,8 +1003,8 @@ NodesErased Graph<NT, ET>::erase_nodes(Iterator begin, Iterator end) {
   // E = O(V).
   if (begin == end) {
     return {
-      {num_nodes(), {}},
-      {num_edges(), {}},
+      { num_nodes(), {} },
+      { num_edges(), {} },
     };
   }
 
@@ -1028,7 +1028,7 @@ NodesErased Graph<NT, ET>::erase_nodes(Iterator begin, Iterator end) {
   auto edge_info =
       erase_nodes_common(node_keep, first_erased_id, erase_trailing);
   return {
-    {erase_trailing ? first_erased_id : -1, std::move(node_keep)},
+    { erase_trailing ? first_erased_id : -1, std::move(node_keep) },
     std::move(edge_info),
   };
 }
@@ -1044,8 +1044,8 @@ NodesErased Graph<NT, ET>::erase_nodes(const const_iterator begin,
   // This will also handle size() == 0 case correctly.
   if (begin >= end) {
     return {
-      {num_nodes(), {}},
-      {num_edges(), {}},
+      { num_nodes(), {} },
+      { num_edges(), {} },
     };
   }
 
@@ -1073,7 +1073,7 @@ NodesErased Graph<NT, ET>::erase_nodes(const const_iterator begin,
   auto edge_info =
       erase_nodes_common(node_keep, first_erased_id, erase_trailing);
   return {
-    {erase_trailing ? first_erased_id : -1, std::move(node_keep)},
+    { erase_trailing ? first_erased_id : -1, std::move(node_keep) },
     std::move(edge_info),
   };
 }
@@ -2170,7 +2170,7 @@ class Subgraph {
    * @note If the node is already in the subgraph, this is a no-op. If the
    * node id is out of range, the behavior is undefined.
    */
-  void add_node(int id) { return nodes_.insert(id); }
+  void add_node(int id) { nodes_.insert(id); }
 
   /**
    * @brief Add nodes to the subgraph

src/algo/rings.cpp

@@ -289,9 +289,9 @@ namespace {
   }
 
   template <class MoleculeLike, class Iter>
-  auto make_dst_iterator(Iter it) {
+  auto make_dst_iterator(Iter &&it) {
     return internal::make_transform_iterator<
-        extract_did<typename MoleculeLike::Neighbor>>(it);
+        extract_did<typename MoleculeLike::Neighbor>>(std::forward<Iter>(it));
   }
 
   template <class MoleculeLike, class Pred>

src/core/geometry.cpp

@@ -311,14 +311,14 @@ namespace {
       kTol = 1e-2, kEps = 1e-8, kEps2 = 1e-16;
 
   constexpr int kIp2[2][2] = {
-    {0, 1},
-    {1, 2},
+    { 0, 1 },
+    { 1, 2 },
   };
 
   constexpr int kIp3[3][3] = {
-    {0, 1, 3},
-    {1, 2, 4},
-    {3, 4, 5},
+    { 0, 1, 3 },
+    { 1, 2, 4 },
+    { 3, 4, 5 },
   };
   constexpr int kIp2312[] = { 1, 2, 0, 1 };
 

src/fmt/mol2.cpp

@@ -683,7 +683,7 @@ SubstructInfo resolve_substructs(const Molecule &mol) {
 struct NameMapEntry {
   int first_idx;
   int count = 1;
-  std::string safe_name = {};
+  std::string safe_name = {};  // NOLINT(readability-redundant-member-init)
 };
 
 template <class C, class NameFunc>

src/fmt/pdb.cpp

@@ -485,7 +485,7 @@ struct PDBAtomInfoTemplate {
   std::string_view name;
   int atomic_number;
   int implicit_hydrogens;
-  std::string_view altname {};
+  std::string_view altname {};  // NOLINT(readability-redundant-member-init)
   constants::Hybridization hyb = constants::kSP3;
   int formal_charge = 0;
   bool conjugated = false;
@@ -1597,7 +1597,7 @@ class AtomicLine {
 public:
   AtomicLine(std::string_view line, int serial)
       : serial_(serial), line_(line), id_ {
-          {safe_atoi(slice(line_, 22, 26)), line_[21], line_[26]},
+          { safe_atoi(slice(line_, 22, 26)), line_[21], line_[26] },
           slice_strip(line_, 11, 16)
   } {
     ABSL_DCHECK(line.size() >= 47) << "Invalid ATOM/HETATM record: " << line;
@@ -2042,9 +2042,10 @@ void update_substructures(Molecule &mol, std::vector<Substructure> &subs,
   for (int i = 0; i < atom_data.size(); ++i) {
     ResidueId id = atom_data[i].first().id().res;
 
-    auto [cit, _] = insert_sorted(chains, { id.chain, {} }, [](auto a, auto b) {
-      return a.first < b.first;
-    });
+    auto [cit, _] = insert_sorted(chains, { id.chain, {} },
+                                  [](const auto &a, const auto &b) {
+                                    return a.first < b.first;
+                                  });
     cit->second.push_back(i);
   }
 

src/fmt/sdf.cpp

@@ -70,8 +70,7 @@ struct HeaderReadResult {
   static HeaderReadResult failure() { return HeaderReadResult(); }
 
   static HeaderReadResult success(int version, int natoms, int nbonds) {
-    return HeaderReadResult(static_cast<int>(version), static_cast<int>(natoms),
-                            static_cast<int>(nbonds));
+    return HeaderReadResult(version, natoms, nbonds);
   }
 
   int version() const { return version_; }

src/fmt/smiles.cpp

@@ -346,7 +346,7 @@ void handle_ring(Ctx &ctx, int ring_idx) {
   const char bond_data = x3::get<last_bond_data_tag>(ctx);
   RingMap &map = x3::get<ring_map_tag>(ctx);
   auto [it, is_new] = map.insert({
-      ring_idx, {bond_data, current_idx}
+      ring_idx, { bond_data, current_idx }
   });
 
   // New ring index, nothing to do.

test/.clang-tidy

@@ -2,8 +2,8 @@
 # Project NuriKit - Copyright 2023 SNU Compbio Lab.
 # SPDX-License-Identifier: Apache-2.0
 #
-Checks: "-cppcoreguidelines-avoid-non-const-global-variables,-cppcoreguidelines-owning-memory,-cppcoreguidelines-special-member-functions,-readability-function-cognitive-complexity,-readability-identifier-naming,-*-non-private-member-variables-in-classes"
+Checks: "-cppcoreguidelines-avoid-non-const-global-variables,-cppcoreguidelines-owning-memory,-cppcoreguidelines-special-member-functions,-readability-function-cognitive-complexity,-readability-identifier-naming,-*-non-private-member-variables-in-classes,-*-macro-usage"
 InheritParentConfig: true
-ExtraArgs:
+ExtraArgsBefore:
   - -Wno-gnu-zero-variadic-macro-arguments
   - -Wno-unused-member-function

test/algo/guess_test.cpp

@@ -120,17 +120,17 @@ class ARGTestParam: public AATestParam {
 
   std::vector<std::pair<int, int>> bonds() const override {
     return {
-      {0,  1},
-      {1,  2},
-      {1,  4},
-      {2,  3},
-      {2, 11},
-      {4,  5},
-      {5,  6},
-      {6,  7},
-      {7,  8},
-      {8,  9},
-      {8, 10},
+      { 0,  1 },
+      { 1,  2 },
+      { 1,  4 },
+      { 2,  3 },
+      { 2, 11 },
+      { 4,  5 },
+      { 5,  6 },
+      { 6,  7 },
+      { 7,  8 },
+      { 8,  9 },
+      { 8, 10 },
     };
   }
 
@@ -206,17 +206,17 @@ class HISTestParam: public AATestParam {
 
   std::vector<std::pair<int, int>> bonds() const override {
     return {
-      {0,  1},
-      {1,  2},
-      {1,  4},
-      {2,  3},
-      {2, 10},
-      {4,  5},
-      {5,  6},
-      {5,  7},
-      {6,  8},
-      {7,  9},
-      {8,  9},
+      { 0,  1 },
+      { 1,  2 },
+      { 1,  4 },
+      { 2,  3 },
+      { 2, 10 },
+      { 4,  5 },
+      { 5,  6 },
+      { 5,  7 },
+      { 6,  8 },
+      { 7,  9 },
+      { 8,  9 },
     };
   }
 
@@ -274,14 +274,14 @@ class PROTestParam: public AATestParam {
 
   std::vector<std::pair<int, int>> bonds() const override {
     return {
-      {0, 1},
-      {0, 6},
-      {1, 2},
-      {1, 4},
-      {2, 3},
-      {2, 7},
-      {4, 5},
-      {5, 6},
+      { 0, 1 },
+      { 0, 6 },
+      { 1, 2 },
+      { 1, 4 },
+      { 2, 3 },
+      { 2, 7 },
+      { 4, 5 },
+      { 5, 6 },
     };
   }
 
@@ -353,19 +353,19 @@ class TYRTestParam: public AATestParam {
 
   std::vector<std::pair<int, int>> bonds() const override {
     return {
-      { 0,  1},
-      { 1,  2},
-      { 1,  4},
-      { 2,  3},
-      { 2, 12},
-      { 4,  5},
-      { 5,  6},
-      { 5,  7},
-      { 6,  8},
-      { 7,  9},
-      { 8, 10},
-      { 9, 10},
-      {10, 11},
+      {  0,  1 },
+      {  1,  2 },
+      {  1,  4 },
+      {  2,  3 },
+      {  2, 12 },
+      {  4,  5 },
+      {  5,  6 },
+      {  5,  7 },
+      {  6,  8 },
+      {  7,  9 },
+      {  8, 10 },
+      {  9, 10 },
+      { 10, 11 },
     };
   }
 
@@ -441,22 +441,22 @@ class TRPTestParam: public AATestParam {
 
   std::vector<std::pair<int, int>> bonds() const override {
     return {
-      { 0,  1},
-      { 1,  2},
-      { 1,  4},
-      { 2,  3},
-      { 2, 14},
-      { 4,  5},
-      { 5,  6},
-      { 5,  7},
-      { 6,  8},
-      { 7,  9},
-      { 7, 10},
-      { 8,  9},
-      { 9, 11},
-      {10, 12},
-      {11, 13},
-      {12, 13},
+      {  0,  1 },
+      {  1,  2 },
+      {  1,  4 },
+      {  2,  3 },
+      {  2, 14 },
+      {  4,  5 },
+      {  5,  6 },
+      {  5,  7 },
+      {  6,  8 },
+      {  7,  9 },
+      {  7, 10 },
+      {  8,  9 },
+      {  9, 11 },
+      { 10, 12 },
+      { 11, 13 },
+      { 12, 13 },
     };
   }