Update to clang-tidy 17, codespell and CI (#29)

.clang-tidy

@@ -9,6 +9,8 @@ Checks: 'bugprone-*,
          modernize-*,
          -modernize-use-nodiscard,
          performance-*,
+         -performance-avoid-endl,
+         -performance-inefficient-string-concatenation,
          portability-*,
          readability-*,
          -readability-magic-numbers,
@@ -19,6 +21,7 @@ Checks: 'bugprone-*,
          -readability-function-cognitive-complexity'
 WarningsAsErrors: ''
 HeaderFilterRegex: '.*'
+HeaderFileExtensions: ['', "H", 'h', 'hh', 'hpp', 'hxx']
 AnalyzeTemporaryDtors: false
 FormatStyle:     none
 User:            user

.codespell-ignore-words

@@ -1,2 +1,3 @@
 inout
-nd
+nd
+alph

.codespellrc

@@ -1,3 +1,3 @@
 [codespell]
-skip = .git,*.ipynb,*.bib,*.ps,*.patch,spack-build-*,*/build,,__pycache__,.ccls,.ccls-cache,*.pdf,*.f90,*.f,*.bak
+skip = .git,*.ipynb,*.bib,*.ps,*.patch,spack-build-*,*/build,,__pycache__,.ccls,.ccls-cache,*.pdf,*.f90,*.f,*.bak,driver
 ignore-words = .codespell-ignore-words

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: TIOGA CI
+name: TIOGA-CI
 
 on:
   push:
@@ -118,6 +118,18 @@ jobs:
           echo "CCACHE_EXTRAFILES=${{github.workspace}}/.clang-tidy" >> $GITHUB_ENV
           echo "CCACHE_MAXSIZE=50M" >> $GITHUB_ENV
           echo "CTCACHE_DIR=~/.cache/ctcache" >> $GITHUB_ENV
+          echo "CLANG_TIDY_VERSION=17" >> $GITHUB_ENV
+      - name: Install clang-tidy
+        run: |
+          echo 'Acquire::Retries "3";' | sudo tee /etc/apt/apt.conf.d/80-retries
+          if [[ ! -f /etc/apt/trusted.gpg.d/apt.llvm.org.asc ]]; then
+              wget -qO- https://apt.llvm.org/llvm-snapshot.gpg.key | sudo tee /etc/apt/trusted.gpg.d/apt.llvm.org.asc
+          fi
+          source /etc/os-release # set UBUNTU_CODENAME
+          sudo add-apt-repository "deb http://apt.llvm.org/${UBUNTU_CODENAME}/ llvm-toolchain-${UBUNTU_CODENAME} main"
+          sudo add-apt-repository "deb http://apt.llvm.org/${UBUNTU_CODENAME}/ llvm-toolchain-${UBUNTU_CODENAME}-${CLANG_TIDY_VERSION} main"
+          sudo apt-get update
+          sudo apt-get install -y --no-install-recommends clang-tidy-${CLANG_TIDY_VERSION} libomp-${CLANG_TIDY_VERSION}-dev
       - name: Install Ccache
         run: |
           wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
@@ -146,6 +158,7 @@ jobs:
           -DCMAKE_C_COMPILER:STRING=mpicc \
           -DTIOGA_ENABLE_CLANG_TIDY:BOOL=ON \
           -DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
+          -DCLANG_TIDY_EXEC_NAME:STRING=clang-tidy-${CLANG_TIDY_VERSION} \
           ${{github.workspace}}
       - name: Check
         working-directory: ${{runner.workspace}}/build-clang-tidy
@@ -237,3 +250,17 @@ jobs:
           pip install codespell
       - name: Run codespell
         run: codespell
+  Save-PR-Number:
+    if: github.event_name == 'pull_request'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Save PR number
+        env:
+          PR_NUMBER: ${{ github.event.number }}
+        run: |
+          echo $PR_NUMBER > pr_number.txt
+      - uses: actions/upload-artifact@v4
+        with:
+          name: pr_number
+          path: pr_number.txt
+          retention-days: 1

.github/workflows/cleanup-cache-postpr.yml

@@ -0,0 +1,37 @@
+name: CleanUpCachePostPR
+
+on:
+  workflow_run:
+    workflows: [PostPR]
+    types:
+      - completed
+
+jobs:
+  CleanUpCcacheCachePostPR:
+    name: Clean Up Ccahe Cache Post PR
+    runs-on: ubuntu-latest
+    permissions:
+      actions: write
+      contents: read
+    env:
+      GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Clean up ccahe
+        run: |
+          gh extension install actions/gh-actions-cache
+
+          REPO=${{ github.repository }}
+
+          gh run download ${{ github.event.workflow_run.id }} -n pr_number
+          pr_number=`cat pr_number.txt`
+          BRANCH=refs/pull/${pr_number}/merge
+
+          # Setting this to not fail the workflow while deleting cache keys.
+          set +e
+
+          keys=$(gh actions-cache list -L 100 -R $REPO -B $BRANCH | cut -f 1)
+          for k in $keys
+          do
+            gh actions-cache delete $k -R $REPO -B $BRANCH --confirm
+          done

.github/workflows/cleanup-cache.yml

@@ -0,0 +1,60 @@
+name: CleanUpCache
+
+on:
+  workflow_run:
+    workflows: [TIOGA-CI]
+    types:
+      - completed
+
+jobs:
+  CleanUpCcacheCache:
+    name: Clean Up Ccache Cache for ${{ github.event.workflow_run.name }}
+    runs-on: ubuntu-latest
+    permissions:
+      actions: write
+      contents: read
+    env:
+      GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Clean up ccahe
+        run: |
+          gh extension install actions/gh-actions-cache
+
+          REPO=${{ github.repository }}
+
+          # push or pull_request or schedule or ...
+          EVENT=${{ github.event.workflow_run.event }}
+
+          # Triggering workflow run name (e.g., LinuxClang)
+          WORKFLOW_NAME=${{ github.event.workflow_run.name }}
+
+          if [[ $EVENT == "pull_request" ]]; then
+            gh run download ${{ github.event.workflow_run.id }} -n pr_number
+            pr_number=`cat pr_number.txt`
+            BRANCH=refs/pull/${pr_number}/merge
+          else
+            BRANCH=refs/heads/${{ github.event.workflow_run.head_branch }}
+          fi
+
+          # Setting this to not fail the workflow while deleting cache keys.
+          set +e
+
+          # In our cache keys, substring after `-git-` is git hash, substring
+          # before that is a unique id for jobs (e.g., `ccache-LinuxClang-configure-2d`).
+          # The goal is to keep the last used key of each job and delete all others.
+
+          # something like ccache-LinuxClang-
+          keyprefix=ccache-${WORKFLOW_NAME}-
+
+          cached_jobs=$(gh actions-cache list -L 100 -R $REPO -B $BRANCH --key $keyprefix | awk -F '-git-' '{print $1}' | sort | uniq)
+
+          # cached_jobs is something like "ccache-LinuxClang-configure-1d ccache-LinuxClang-configure-2d".
+          for j in $cached_jobs
+          do
+            old_keys=$(gh actions-cache list -L 100 -R $REPO -B $BRANCH --key ${j}-git- --sort last-used | cut -f 1 | tail -n +2)
+            for k in $old_keys
+            do
+              gh actions-cache delete $k -R $REPO -B $BRANCH --confirm
+            done
+          done

.github/workflows/post-pr.yml

@@ -0,0 +1,20 @@
+name: PostPR
+on:
+  pull_request:
+    types:
+      - closed
+
+jobs:
+  cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Save PR number
+        env:
+          PR_NUMBER: ${{ github.event.number }}
+        run: |
+          echo $PR_NUMBER > pr_number.txt
+      - uses: actions/upload-artifact@v4
+        with:
+          name: pr_number
+          path: pr_number.txt
+          retention-days: 1

CMakeLists.txt

@@ -66,17 +66,18 @@ if (BUILD_GRIDGEN_EXE)
 endif()
 
 if(TIOGA_ENABLE_CLANG_TIDY)
-  find_program(CLANG_TIDY_EXE NAMES "clang-tidy")
+  set(CLANG_TIDY_EXEC_NAME "clang-tidy" CACHE STRING "Name of the clang-tidy executable")
+  find_program(CLANG_TIDY_EXE NAMES "${CLANG_TIDY_EXEC_NAME}")
   if(CLANG_TIDY_EXE)
-    message(STATUS "clang-tidy found: ${CLANG_TIDY_EXE}")
+    message(STATUS "${CLANG_TIDY_EXEC_NAME} found: ${CLANG_TIDY_EXE}")
     #find_program (CLANG_TIDY_CACHE_EXE NAMES "clang-tidy-cache")
     #if(CLANG_TIDY_CACHE_EXE)
     #  message(STATUS "clang-tidy-cache found: ${CLANG_TIDY_CACHE_EXE}")
     #  set(CLANG_TIDY_EXE "${CLANG_TIDY_CACHE_PATH};${CLANG_TIDY_EXE}"
     #      CACHE STRING "A combined command to run clang-tidy with caching wrapper")
     #endif()
   else()
-    message(WARNING "clang-tidy not found.")
+    message(WARNING "${CLANG_TIDY_EXEC_NAME} not found.")
   endif()
 endif()
 if(CLANG_TIDY_EXE)

README.md

@@ -1,6 +1,6 @@
 # TIOGA - Topology Independent Overset Grid Assembler
 
-[![TIOGA CI](https://github.com/Exawind/tioga/actions/workflows/ci.yml/badge.svg)](https://github.com/Exawind/tioga/actions/workflows/ci.yml)
+[![TIOGA-CI](https://github.com/Exawind/tioga/actions/workflows/ci.yml/badge.svg)](https://github.com/Exawind/tioga/actions/workflows/ci.yml)
 
 TIOGA is a library for overset grid assembly on parallel distributed systems
 Copyright (C) 2015 Jay Sitaraman

src/CartBlock.C

@@ -73,7 +73,7 @@ void CartBlock::getInterpolatedData(int *nints,int *nreals,int **intData,
        for(i=0;i<(*nreals);i++) tmpreal[i]=(*realData)[i];
        //
        TIOGA_FREE((*intData));
-       TIOGA_FREE((*realData)); // didnt free this before ??
+       TIOGA_FREE((*realData)); // didn't free this before ??
        //  
       }
       (*nints)+=interpCount;

src/CartGrid.C

@@ -132,7 +132,7 @@ void CartGrid::registerData(int nfin,int *idata,double *rdata,int ngridsin)
 
 //
 // Bare bone preprocessor now
-// willl add more support data structures
+// will add more support data structures
 // to promote efficient search once the concept
 // works
 //

src/cartOps.C

@@ -317,7 +317,7 @@ void MeshBlock::getInterpolatedSolutionAMR(int *nints,int *nreals,int **intData,
      for(i=0;i<(*nreals);i++) tmpreal[i]=(*realData)[i];
      //
      TIOGA_FREE((*intData));
-     TIOGA_FREE((*realData)); // didnt free this before ??
+     TIOGA_FREE((*realData)); // didn't free this before ??
      //
    }
    (*nints)+=interpCount;

src/holeMap.C

@@ -34,7 +34,7 @@ using namespace TIOGA;
 /**
  * Create hole maps for all grids
  * this routine is not efficient
- * since it does mutiple global reduce ops
+ * since it does multiple global reduce ops
  * have to change it at a later date when
  * there is more time to develop code
  */

src/tioga.h

@@ -42,7 +42,7 @@
 #define TIOGA_HAS_NGP_IFACE 1
 
 /**
- * Topology Indpendent Overset Grid Assembler (TIOGA)
+ * Topology Independent Overset Grid Assembler (TIOGA)
  * Base class and dependencies
  * The methods of this class are invoked from tiogaInterface.C
  *
@@ -100,7 +100,7 @@ class tioga {
   //! Intersect block unique ID to index lookup mapping
   std::map<int, int> intBoxMap;
 
-  //! Parallel comms to obblist indicies
+  //! Parallel comms to obblist indices
   std::vector<int> ibsPerProc;
   std::vector<std::vector<int>> ibProcMap;
   //! q-variables registered
@@ -111,7 +111,7 @@ class tioga {
   int ihighGlobal;
   int iamrGlobal;
   int mexclude, nfringe;
-  /** basic constuctor */
+  /** basic constructor */
   tioga()
   /*
   : mblocks(0),

src/tiogaInterface.C

@@ -227,7 +227,7 @@ extern "C" {
        }
       else
       {
-        printf("Data udpate between high-order near-body and AMR cartesian Not implemented yet\n");
+        printf("Data update between high-order near-body and AMR cartesian Not implemented yet\n");
       }
     }
   }