Merge branch 'develop' into bugfix/su2py-correctness-tools

Author: shbhmexe

.github/workflows/code-style.yml

@@ -14,7 +14,7 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v5
       - name: Setup python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
          python-version: '3.10'
          check-latest: true

.github/workflows/codeql.yml

@@ -37,20 +37,20 @@ jobs:
         run: ./meson.py setup build --optimization=1
 
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v3
+        uses: github/codeql-action/init@v4
         with:
           languages: ${{ matrix.language }}
           queries: +security-and-quality
 
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v3
+        uses: github/codeql-action/autobuild@v4
         if: ${{ matrix.language == 'python' }}
 
       - name: Build cpp
         if: ${{ matrix.language == 'cpp' }}
         run: ./ninja -C build
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v3
+        uses: github/codeql-action/analyze@v4
         with:
           category: "/language:${{ matrix.language }}"

.github/workflows/regression-arm64.yml

@@ -10,4 +10,4 @@ jobs:
     name: Run the jobs on Linux ARM64
     uses: './.github/workflows/regression.yml'
     with:
-      runner: 'ARM64'
+      runner: 'ubuntu-24.04-arm'

.github/workflows/regression.yml

@@ -65,7 +65,7 @@ jobs:
       - name: Compress binaries
         run: tar -zcvf install_bin.tgz install/*
       - name: Upload Binaries
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: ${{ matrix.config_set }}
           path: install_bin.tgz
@@ -76,7 +76,7 @@ jobs:
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
   build_tsan:
     name: Build SU2 (tsan)
-    if: inputs.runner != 'ARM64'
+    if: ${{ !contains(inputs.runner, 'arm') }}
     strategy:
       fail-fast: false
       matrix:
@@ -108,7 +108,7 @@ jobs:
       - name: Compress binaries
         run: tar -zcvf install_bin.tgz install/*
       - name: Upload Binaries
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: ${{ matrix.config_set }}
           path: install_bin.tgz
@@ -146,7 +146,7 @@ jobs:
       - name: Compress binaries
         run: tar -zcvf install_bin.tgz install/*
       - name: Upload Binaries
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: ${{ matrix.config_set }}
           path: install_bin.tgz
@@ -218,7 +218,7 @@ jobs:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
   discadj_tape_tests:
-    if: inputs.runner != 'ARM64'
+    if: ${{ !contains(inputs.runner, 'arm') }}
     runs-on: ${{ inputs.runner || 'ubuntu-latest' }}
     name: Tape Tests
     needs: build
@@ -236,7 +236,7 @@ jobs:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
       - name: Download All artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v5
       - name: Uncompress and Move Binaries
         run: |
           BIN_FOLDER="$PWD/install/bin"
@@ -267,7 +267,7 @@ jobs:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
   thread_sanitizer_tests:
-    if: inputs.runner != 'ARM64'
+    if: ${{ !contains(inputs.runner, 'arm') }}
     runs-on: ${{ inputs.runner || 'ubuntu-latest' }}
     name: Thread Sanitizer Tests
     needs: build_tsan

.github/workflows/release-management.yml

@@ -44,7 +44,7 @@ jobs:
           zip -r ../${{matrix.os_bin}}.zip bin/*
         # Uploads binaries as artifacts (just as a backup)
       - name: Upload Binaries
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: ${{matrix.os_bin}}
           path: ${{matrix.os_bin}}.zip

Common/include/CConfig.hpp

@@ -1,4 +1,4 @@
-/*!
+/*!
  * \file CGeometry.hpp
  * \brief Headers of the main subroutines for creating the geometrical structure.
  *        The subroutines and functions are in the <i>CGeometry.cpp</i> file.
@@ -51,6 +51,7 @@ extern "C" {
 #include <climits>
 #include <memory>
 #include <unordered_map>
+#include <cstdint>
 
 #include "primal_grid/CPrimalGrid.hpp"
 #include "dual_grid/CDualGrid.hpp"

Common/include/geometry/CGeometry.hpp

@@ -28,11 +28,11 @@
 
 #pragma once
 
+#include <cstdint>
 #include <iostream>
 #include <vector>
 #include <limits>
 #include <cstdlib>
-#include <limits>
 #include <memory>
 
 #include "../../option_structure.hpp"

Common/include/geometry/primal_grid/CPrimalGrid.hpp

@@ -233,18 +233,19 @@ class COptionEnumList final : public COptionBase {
 
 template <class Type>
 class COptionArray final : public COptionBase {
-  string name;     // Identifier for the option
-  const int size;  // Number of elements
-  Type* field;     // Reference to the field
+  string name;             // Identifier for the option
+  const int size;          // Number of elements
+  const bool allow_fewer;  // Allow smaller size
+  Type* field;             // Reference to the field
 
  public:
-  COptionArray(string option_field_name, const int list_size, Type* option_field)
-      : name(option_field_name), size(list_size), field(option_field) {}
+  COptionArray(string option_field_name, const int list_size, const bool allow_fewer, Type* option_field)
+      : name(std::move(option_field_name)), size(list_size), allow_fewer(allow_fewer), field(option_field) {}
 
   string SetValue(const vector<string>& option_value) override {
     COptionBase::SetValue(option_value);
     // Check that the size is correct
-    if (option_value.size() != (unsigned long)this->size) {
+    if ((option_value.size() < size_t(size) && !allow_fewer) || option_value.size() > size_t(size)) {
       string newstring;
       newstring.append(this->name);
       newstring.append(": wrong number of arguments: ");
@@ -258,7 +259,7 @@ class COptionArray final : public COptionBase {
       newstring.append(" found");
       return newstring;
     }
-    for (int i = 0; i < this->size; i++) {
+    for (size_t i = 0; i < option_value.size(); i++) {
       istringstream is(option_value[i]);
       if (!(is >> field[i])) {
         return badValue(" array", this->name);

Common/include/option_structure.inl

@@ -479,13 +479,16 @@ T createNaturalColoring(Index_t numInnerIndexes) {
  *        pattern is returned.
  * \param[in] pattern - Sparse pattern to be colored.
  * \param[in] groupSize - Size of the outer index groups, default 1.
+ * \param[in] includeOuterIdx - If the outer indices are the same type of entity as
+ *            the inner indices this must be true. For example, when both are point
+ *            indices, i.e. the pattern is the adjacency matrix.
  * \param[in] balanceColors - Try to balance number of indexes per color,
  *            tends to result in worse locality (thus false by default).
  * \param[out] indexColor - Optional, vector with colors given to the outer indices.
  * \return Coloring in the same type of the input pattern.
  */
 template <typename Color_t = unsigned char, size_t MaxColors = 255, size_t MaxMB = 128, class T>
-T colorSparsePattern(const T& pattern, size_t groupSize = 1, bool balanceColors = false,
+T colorSparsePattern(const T& pattern, size_t groupSize = 1, bool includeOuterIdx = false, bool balanceColors = false,
                      std::vector<Color_t>* indexColor = nullptr) {
   static_assert(std::is_integral<Color_t>::value, "");
   static_assert(std::numeric_limits<Color_t>::max() >= MaxColors, "");
@@ -538,6 +541,11 @@ T colorSparsePattern(const T& pattern, size_t groupSize = 1, bool balanceColors
 
       for (; it != searchOrder.end(); ++it) {
         bool free = true;
+        if (includeOuterIdx) {
+          for (Index_t k = iOuter; k < grpEnd && free; ++k) {
+            free = !innerInColor[*it][k];
+          }
+        }
         /*--- Traverse entire group as a large outer index. ---*/
         for (Index_t k = outerPtr[iOuter]; k < outerPtr[grpEnd] && free; ++k) {
           free = !innerInColor[*it][innerIdx[k] - minIdx];