Merge branch 'develop' into feature_validation_sandia_jet

.clang-format

@@ -2,3 +2,4 @@ BasedOnStyle: Google
 PointerAlignment: Left
 DerivePointerAlignment: false
 ColumnLimit: 120
+SortIncludes: Never

.clang-tidy

@@ -0,0 +1,5 @@
+Checks: '-*,modernize-avoid-bind,modernize-deprecated-headers,modernize-deprecated-ios-base-aliases,modernize-macro-to-enum,modernize-pass-by-value,modernize-raw-string-literal,modernize-redundant-void-arg,modernize-replace-auto-ptr,modernize-replace-disallow-copy-and-assign-macro,modernize-replace-random-shuffle,modernize-return-braced-init-list,modernize-shrink-to-fit,modernize-unary-static-assert,modernize-use-auto,modernize-use-bool-literals,modernize-use-default-member-init,modernize-use-emplace,modernize-use-equals-default,modernize-use-equals-delete,modernize-use-noexcept,modernize-use-nullptr,modernize-use-override,modernize-use-transparent-functors,modernize-use-using,readability-const-return-type,readability-avoid-const-params-in-decls,readability-container-data-pointer,readability-container-size-empty,readability-delete-null-pointer,readability-duplicate-include,readability-non-const-parameter,readability-redundant-access-specifiers,readability-redundant-control-flow,readability-redundant-declaration,readability-redundant-function-ptr-dereference,readability-redundant-smartptr-get,readability-redundant-string-cstr,readability-redundant-string-init,readability-simplify-boolean-expr,readability-simplify-subscript-expr,readability-else-after-return,performance-*'
+CheckOptions:
+  - {key: modernize-use-override.AllowOverrideAndFinal, value: 'true'}
+  - {key: performance-unnecessary-copy-initialization.AllowedTypes, value: 'su2double'}
+  - {key: performance-unnecessary-value-param.AllowedTypes, value: 'su2double'}

.github/ISSUE_TEMPLATE/bug_report.md

@@ -26,4 +26,3 @@ assignees: ''
  - C++ compiler and version: [e.g., g++ (GCC) 4.8.5]
  - MPI implementation and version: [e.g., OpenMPI 3.0.0]
  - SU2 Version: [e.g., v6.2.0]
-

.github/pull_request_template.md

@@ -1,6 +1,6 @@
 ## Proposed Changes
 *Give a brief overview of your contribution here in a few sentences.*
- 
+
 
 
 ## Related Work
@@ -14,5 +14,6 @@
 - [ ] I am submitting my contribution to the develop branch.
 - [ ] My contribution generates no new compiler warnings (try with --warnlevel=3 when using meson).
 - [ ] My contribution is commented and consistent with SU2 style (https://su2code.github.io/docs_v7/Style-Guide/).
+- [ ] I used the pre-commit hook to prevent dirty commits and used `pre-commit run --all` to format old commits.
 - [ ] I have added a test case that demonstrates my contribution, if necessary.
 - [ ] I have updated appropriate documentation (Tutorials, Docs Page, config_template.cpp), if necessary.

.github/release.yml

@@ -17,4 +17,3 @@ changelog:
       - title: 'Other Changes'
         labels:
           - "*"
-

.github/workflows/code-style.yml

@@ -0,0 +1,30 @@
+name: Code Style
+on:
+  pull_request:
+    paths:
+      - "**.[ch]pp"
+      - "**.[ch]"
+      - "**.cfg"
+      - "**.py"
+
+jobs:
+  formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Setup python
+        uses: actions/setup-python@v4
+        with:
+         python-version: '3.10'
+         check-latest: true
+      - name: Install pre-commit
+        run: pip install pre-commit
+      - name: Run checks
+        run: pre-commit run -a -v
+      - name: Git status
+        if: always()
+        run: git status
+      - name: Full diff
+        if: always()
+        run: git diff

.github/workflows/regression.yml

@@ -26,23 +26,23 @@ jobs:
         config_set: [BaseMPI, ReverseMPI, ForwardMPI, BaseNoMPI, ReverseNoMPI, ForwardNoMPI, BaseOMP, ReverseOMP, ForwardOMP]
         include:
           - config_set: BaseMPI
-            flags: '-Denable-pywrapper=true -Denable-coolprop=true -Denable-tests=true --warnlevel=2 --werror'
+            flags: '-Denable-pywrapper=true -Denable-coolprop=true -Denable-mlpcpp=true -Denable-tests=true --warnlevel=2 --werror'
           - config_set: ReverseMPI
             flags: '-Denable-autodiff=true -Denable-normal=false -Denable-pywrapper=true -Denable-tests=true --warnlevel=3 --werror'
           - config_set: ForwardMPI
             flags: '-Denable-directdiff=true -Denable-normal=false -Denable-tests=true --warnlevel=3 --werror'
           - config_set: BaseNoMPI
-            flags: '-Denable-pywrapper=true -Denable-openblas=true -Dwith-mpi=disabled -Denable-tests=true --warnlevel=3 --werror'
+            flags: '-Denable-pywrapper=true -Denable-openblas=true -Dwith-mpi=disabled -Denable-mlpcpp=true -Denable-tests=true --warnlevel=3 --werror'
           - config_set: ReverseNoMPI
             flags: '-Denable-autodiff=true -Denable-normal=false -Dwith-mpi=disabled -Denable-pywrapper=true -Denable-tests=true --warnlevel=3 --werror'
           - config_set: ForwardNoMPI
             flags: '-Denable-directdiff=true -Denable-normal=false -Dwith-mpi=disabled -Denable-tests=true --warnlevel=3 --werror'
           - config_set: BaseOMP
             flags: '-Dwith-omp=true -Denable-mixedprec=true -Denable-pywrapper=true -Denable-tecio=false --warnlevel=3 --werror'
           - config_set: ReverseOMP
-            flags: '-Denable-autodiff=true -Denable-normal=false -Dwith-omp=true -Denable-mixedprec=true -Denable-tecio=false --warnlevel=3 --werror'
+            flags: '-Denable-autodiff=true -Denable-normal=false -Dwith-omp=true -Denable-mixedprec=true -Denable-pywrapper=true -Denable-tecio=false --warnlevel=3 --werror'
           - config_set: ForwardOMP
-            flags: '-Denable-directdiff=true -Denable-normal=false -Dwith-omp=true -Denable-mixedprec=true -Denable-tecio=false --warnlevel=3 --werror'
+            flags: '-Denable-directdiff=true -Denable-normal=false -Dwith-omp=true -Denable-mixedprec=true -Denable-pywrapper=true -Denable-tecio=false --warnlevel=3 --werror'
     runs-on: ${{ inputs.runner || 'ubuntu-latest' }}
     steps:
       - name: Cache Object Files
@@ -52,12 +52,12 @@ jobs:
           key: ${{ matrix.config_set }}-${{ github.sha }}
           restore-keys: ${{ matrix.config_set }}
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/build-su2:221224-1158
+        uses: docker://ghcr.io/su2code/su2/build-su2:230704-1323
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
       - name: Build
-        uses: docker://ghcr.io/su2code/su2/build-su2:221224-1158
+        uses: docker://ghcr.io/su2code/su2/build-su2:230704-1323
         with:
           args: -b ${{github.ref}} -f "${{matrix.flags}}"
       - name: Compress binaries
@@ -68,7 +68,50 @@ jobs:
           name: ${{ matrix.config_set }}
           path: install_bin.tgz
       - name: Post Cleanup
-        uses: docker://ghcr.io/su2code/su2/build-su2:221224-1158
+        uses: docker://ghcr.io/su2code/su2/build-su2:230704-1323
+        with:
+          entrypoint: /bin/rm
+          args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
+  build_tsan:
+    name: Build SU2 (tsan)
+    if: inputs.runner != 'ARM64'
+    strategy:
+      fail-fast: false
+      matrix:
+        config_set: [BaseOMP-tsan, ReverseOMP-tsan] #ForwardOMP-tsan
+        include:
+          - config_set: BaseOMP-tsan
+            flags: '--buildtype=debugoptimized -Dwith-omp=true -Denable-mixedprec=true -Denable-tecio=false --warnlevel=3'
+          - config_set: ReverseOMP-tsan
+            flags: '--buildtype=debugoptimized -Denable-autodiff=true -Denable-normal=false -Dwith-omp=true -Denable-mixedprec=true -Denable-tecio=false --warnlevel=3'
+          #- config_set: ForwardOMP-tsan
+          #  flags: '--buildtype=debug -Denable-directdiff=true -Denable-normal=false -Dwith-omp=true -Denable-mixedprec=true -Denable-pywrapper=true -Denable-tecio=false --warnlevel=3 --werror'
+    runs-on: ${{ inputs.runner || 'ubuntu-latest' }}
+    steps:
+      - name: Cache Object Files
+        uses: actions/cache@v3
+        with:
+          path: ccache
+          key: ${{ matrix.config_set }}-${{ github.sha }}
+          restore-keys: ${{ matrix.config_set }}
+      - name: Pre Cleanup
+        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:230704-1323
+        with:
+          entrypoint: /bin/rm
+          args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
+      - name: Build
+        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:230704-1323
+        with:
+          args: -b ${{github.ref}} -f "${{matrix.flags}}"
+      - name: Compress binaries
+        run: tar -zcvf install_bin.tgz install/bin
+      - name: Upload Binaries
+        uses: actions/upload-artifact@v3
+        with:
+          name: ${{ matrix.config_set }}
+          path: install_bin.tgz
+      - name: Post Cleanup
+        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:230704-1323
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -99,7 +142,7 @@ jobs:
             tag: OMP
     steps:
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:221224-1158
+        uses: docker://ghcr.io/su2code/su2/test-su2:230704-1323
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -125,12 +168,58 @@ jobs:
           chmod a+x $BIN_FOLDER/*
           ls -lahR $BIN_FOLDER
       - name: Run Tests in Container
-        uses: docker://ghcr.io/su2code/su2/test-su2:221224-1158
+        uses: docker://ghcr.io/su2code/su2/test-su2:230704-1323
         with:
           # -t <Tutorials-branch> -c <Testcases-branch>
           args: -b ${{github.ref}} -t develop -c feature_validation_sandia_jet -s ${{matrix.testscript}}
       - name: Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:221224-1158
+        uses: docker://ghcr.io/su2code/su2/test-su2:230704-1323
+        with:
+          entrypoint: /bin/rm
+          args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
+  thread_sanitizer_tests:
+    if: inputs.runner != 'ARM64'
+    runs-on: ${{ inputs.runner || 'ubuntu-latest' }}
+    name: Thread Sanitizer Tests
+    needs: build_tsan
+    strategy:
+      fail-fast: false
+      matrix:
+        testscript: ['hybrid_regression.py', 'hybrid_regression_AD.py']
+    steps:
+      - name: Pre Cleanup
+        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:230704-1323
+        with:
+          entrypoint: /bin/rm
+          args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
+      - name: Download All artifacts
+        uses: actions/download-artifact@v3
+      - name: Uncompress and Move Binaries
+        run: |
+          BIN_FOLDER="$PWD/install/bin"
+          mkdir -p $BIN_FOLDER
+          ls -lah $BIN_FOLDER
+          for type in Base Reverse Forward; do
+            TYPE_FOLDER="${type}OMP-tsan"
+            echo "Processing '$TYPE_FOLDER' ..."
+            if [ -d $TYPE_FOLDER ]; then
+              pushd $TYPE_FOLDER
+              ls -lah
+              tar -zxvf install_bin.tgz
+              ls -lah install/bin/
+              cp -r install/bin/* $BIN_FOLDER;
+              popd;
+            fi
+          done
+          chmod a+x $BIN_FOLDER/*
+          ls -lahR $BIN_FOLDER
+      - name: Run Tests in Container
+        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:230704-1323
+        with:
+          # -t <Tutorials-branch> -c <Testcases-branch>
+          args: -b ${{github.ref}} -t develop -c develop -s ${{matrix.testscript}} -a "--tsan"
+      - name: Cleanup
+        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:230704-1323
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -151,7 +240,7 @@ jobs:
             tag: MPI
     steps:
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:221224-1158
+        uses: docker://ghcr.io/su2code/su2/test-su2:230704-1323
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -212,11 +301,11 @@ jobs:
           echo $PWD
           ls -lahR
       - name: Run Unit Tests
-        uses: docker://ghcr.io/su2code/su2/test-su2:221224-1158
+        uses: docker://ghcr.io/su2code/su2/test-su2:230704-1323
         with:
           entrypoint: install/bin/${{matrix.testdriver}}
       - name: Post Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:221224-1158
+        uses: docker://ghcr.io/su2code/su2/test-su2:230704-1323
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}

.github/workflows/release-management.yml

@@ -35,7 +35,7 @@ jobs:
           key: ${{ matrix.os_bin }}-${{ github.sha }}
           restore-keys: ${{ matrix.os_bin }}
       - name: Build
-        uses: docker://ghcr.io/su2code/su2/build-su2-cross:221224-1158
+        uses: docker://ghcr.io/su2code/su2/build-su2-cross:230704-1323
         with:
           args: -b ${{ github.sha }} -f "${{matrix.flags}}"
       - name: Create Archive
@@ -65,4 +65,3 @@ jobs:
           asset_path: ${{matrix.os_bin}}.zip
           asset_name: SU2-${{ steps.update_release.outputs.tagname }}-${{matrix.os_bin}}.zip
           asset_content_type: application/zip
-

.github/workflows/require-labels.yml

@@ -0,0 +1,13 @@
+name: Pull Request Labels
+on:
+  pull_request:
+    types: [opened, labeled, unlabeled, synchronize]
+jobs:
+  label:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: mheap/github-action-required-labels@v3
+        with:
+          mode: exactly
+          count: 1
+          labels: "changelog:feature, changelog:fix, changelog:chore"

.gitignore

@@ -97,3 +97,9 @@ ninja
 
 # Ignore vscode folder
 .vscode/
+
+# Ignore SU2 pre-configuration timestamp created by preconfigure.py
+su2preconfig.timestamp
+
+# Clangd server files
+.cache

.gitmodules

@@ -24,3 +24,6 @@
 [submodule "externals/mel"]
 	path = externals/mel
 	url = https://github.com/pcarruscag/MEL.git
+[submodule "subprojects/MLPCpp"]
+	path = subprojects/MLPCpp
+	url = https://github.com/EvertBunschoten/MLPCpp.git

.pep8

@@ -0,0 +1,6 @@
+[pycodestyle]
+max_line_length = 120
+ignore = E402
+in-place = true
+aggressive = 2
+recursive = true

.pre-commit-config.yaml

@@ -0,0 +1,62 @@
+repos:
+  # Official repo for the clang-format hook
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: "v15.0.7"
+    hooks:
+      - id: clang-format
+        exclude: |
+            (?x)^(
+            ^Common/include/CConfig.hpp|
+            ^Common/include/option_structure.hpp|
+            ^Common/src/CConfig.cpp|
+            ^SU2_CFD|
+            ^externals|
+            ^subprojects|
+            ^TestCases|
+            ^legacy
+            )
+        types_or: [c++, c]
+  # black repo for python formatting
+  - repo: https://github.com/ambv/black
+    rev: 22.6.0
+    hooks:
+      - id: black
+        exclude: |
+            (?x)^(
+            ^SU2_CFD|
+            ^externals|
+            ^subprojects|
+            ^TestCases|
+            ^legacy
+            )
+  # Official repo for default hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.4.0"
+    hooks:
+      - id: mixed-line-ending
+        exclude: |
+            (?x)^(
+            ^SU2_CFD|
+            ^externals|
+            ^subprojects|
+            ^TestCases|
+            ^legacy
+            )
+      - id: trailing-whitespace
+        exclude: |
+            (?x)^(
+            ^SU2_CFD|
+            ^externals|
+            ^subprojects|
+            ^TestCases|
+            ^legacy
+            )
+      - id: end-of-file-fixer
+        exclude: |
+            (?x)^(
+            ^SU2_CFD|
+            ^externals|
+            ^subprojects|
+            ^TestCases|
+            ^legacy
+            )