Merge branch 'hybrid_eta_deltaJ' into dsmc_simpler_charge_exchange

.clang-tidy

@@ -24,23 +24,10 @@ Checks: '
     misc-*,
         -misc-no-recursion,
         -misc-non-private-member-variables-in-classes,
-    modernize-avoid-bind,
-    modernize-concat-nested-namespaces,
-    modernize-deprecated-headers,
-    modernize-deprecated-ios-base-aliases,
-    modernize-loop-convert,
-    modernize-make-shared,
-    modernize-make-unique,
-    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-shrink-to-fit,
-    modernize-unary-static-assert,
-    modernize-use-nullptr,
+    modernize-*,
+        -modernize-avoid-c-arrays,
         -modernize-return-braced-init-list,
+        -modernize-use-trailing-return-type,
     mpi-*,
     performance-faster-string-find,
     performance-for-range-copy,

.github/workflows/clang_tidy.yml

@@ -16,28 +16,26 @@ jobs:
     - name: install dependencies
       run: |
         .github/workflows/dependencies/clang14.sh
-    - name: build WarpX using clang-tidy
+    - name: set up cache
+      uses: actions/cache@v3
+      with:
+        path: ~/.cache/ccache
+        key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
+        restore-keys: |
+             ccache-${{ github.workflow }}-${{ github.job }}-git-
+    - name: build WarpX & run clang-tidy
       run: |
-
+        export CCACHE_COMPRESS=1
+        export CCACHE_COMPRESSLEVEL=10
+        export CCACHE_MAXSIZE=300M
+        export CCACHE_EXTRAFILES=${{ github.workspace }}/.clang-tidy
+        export CCACHE_LOGFILE=${{ github.workspace }}/ccache.log.txt
+        ccache -z
 
         export CXX=$(which clang++)
         export CC=$(which clang)
 
-        # The following wrapper ensures that only source files
-        # in WarpX/Source/* are actually processed by clang-tidy
-        #_______________________________
-        cat > clang_tidy_wrapper << EOF
-        #!/bin/bash
-        REGEX="[a-z_A-Z0-9\/]*WarpX\/Source[a-z_A-Z0-9\/]+.cpp"
-        if [[ \$4 =~ \$REGEX ]];then
-          clang-tidy \$@
-        fi
-        EOF
-        chmod +x clang_tidy_wrapper
-        #_____________________________________
-
         cmake -S . -B build_clang_tidy \
-          -DCMAKE_CXX_CLANG_TIDY="$PWD/clang_tidy_wrapper;--system-headers=0;--config-file=$PWD/.clang-tidy" \
           -DCMAKE_VERBOSE_MAKEFILE=ON  \
           -DWarpX_DIMS="1;2;3;RZ"      \
           -DWarpX_MPI=ON               \
@@ -46,9 +44,30 @@ jobs:
           -DWarpX_QED=ON               \
           -DWarpX_QED_TABLE_GEN=ON     \
           -DWarpX_OPENPMD=ON           \
-          -DWarpX_PRECISION=SINGLE
+          -DWarpX_PRECISION=SINGLE     \
+          -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
+
+        cmake --build build_clang_tidy -j 2
 
-        cmake --build build_clang_tidy -j 2 2> build_clang_tidy/clang-tidy.log
+        ${{github.workspace}}/.github/workflows/source/makeMakefileForClangTidy.py --input ${{github.workspace}}/ccache.log.txt
+        make -j2 -f clang-tidy-ccache-misses.mak \
+            CLANG_TIDY=clang-tidy \
+            CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
 
-        cat build_clang_tidy/clang-tidy.log
-        if [[ $(wc -m <build_clang_tidy/clang-tidy.log) -gt 1 ]]; then exit 1; fi
+        ccache -s
+        du -hs ~/.cache/ccache
+
+  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@v3
+        with:
+          name: pr_number
+          path: pr_number.txt
+          retention-days: 1

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

@@ -0,0 +1,40 @@
+name: CleanUpCachePostPR
+
+on:
+  workflow_run:
+    workflows: [PostPR]
+    types:
+      - completed
+
+jobs:
+  CleanUpCcacheCachePostPR:
+    name: Clean Up Ccache Cache Post PR
+    runs-on: ubuntu-latest
+    permissions:
+      actions: write
+      contents: read
+    env:
+      GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Clean up ccache
+        run: |
+          gh extension install actions/gh-actions-cache
+
+          REPO=${{ 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)
+          # $keys might contain spaces. Thus we set IFS to \n.
+          IFS=$'\n'
+          for k in $keys
+          do
+            gh actions-cache delete "$k" -R $REPO -B $BRANCH --confirm
+          done
+          unset IFS

.github/workflows/cleanup-cache.yml

@@ -0,0 +1,63 @@
+name: CleanUpCache
+
+on:
+  workflow_run:
+    workflows: [🧹 clang-tidy, 🔍 CodeQL, 🐧 CUDA, 🐧 HIP, 🐧 Intel, 🍏 macOS, 🐧 OpenMP]
+    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: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Clean up ccache
+        run: |
+          gh extension install actions/gh-actions-cache
+
+          REPO=${{ 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 $1}' | sort | uniq)
+
+          # cached_jobs is something like "ccache-LinuxClang-configure-1d ccache-LinuxClang-configure-2d".
+          # It might also contain spaces. Thus we set IFS to \n.
+          IFS=$'\n'
+          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
+          unset IFS

.github/workflows/codeql.yml

@@ -35,13 +35,22 @@ jobs:
         if: ${{ matrix.language == 'cpp' }}
         run: |
           sudo apt-get update
-          sudo apt-get install --yes cmake openmpi-bin libopenmpi-dev libhdf5-openmpi-dev libadios-openmpi-dev
+          sudo apt-get install --yes cmake openmpi-bin libopenmpi-dev libhdf5-openmpi-dev libadios-openmpi-dev ccache
 
           python -m pip install --upgrade pip
           python -m pip install --upgrade wheel
           python -m pip install --upgrade cmake
           export CMAKE="$HOME/.local/bin/cmake" && echo "CMAKE=$CMAKE" >> $GITHUB_ENV
 
+      - name: Set Up Cache
+        if: ${{ matrix.language == 'cpp' }}
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/ccache
+          key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
+          restore-keys: |
+               ccache-${{ github.workflow }}-${{ github.job }}-git-
+
       - name: Configure (C++)
         if: ${{ matrix.language == 'cpp' }}
         run: |
@@ -61,6 +70,19 @@ jobs:
       - name: Build (C++)
         if: ${{ matrix.language == 'cpp' }}
         run: |
+          export CCACHE_COMPRESS=1
+          export CCACHE_COMPRESSLEVEL=10
+          export CCACHE_MAXSIZE=100M
+          ccache -z
+
+          $CMAKE --build build -j 2
+
+          ccache -s
+          du -hs ~/.cache/ccache
+
+          # Make sure CodeQL has something to do
+          touch Source/Utils/WarpXVersion.cpp
+          export CCACHE_DISABLE=1
           $CMAKE --build build -j 2
 
       - name: Perform CodeQL Analysis
@@ -88,3 +110,18 @@ jobs:
         uses: github/codeql-action/upload-sarif@v2
         with:
           sarif_file: sarif-results/${{ matrix.language }}.sarif
+
+  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@v3
+        with:
+          name: pr_number
+          path: pr_number.txt
+          retention-days: 1