Merge branch 'development' into change_ionization_balance

Author: RemiLehe

.azure-pipelines.yml

@@ -7,13 +7,21 @@ trigger:
   branches:
     include:
     - development
+  paths:
+    exclude:
+    - 'Docs/**'
+    - 'Tools/machines/**'
+    - '**/*.rst'
+    - '**/*.md'
 pr:
   autoCancel: true
   drafts: false
   paths:
     exclude:
-    - Docs
+    - 'Docs/**'
+    - 'Tools/machines/**'
     - '**/*.rst'
+    - '**/*.md'
 
 jobs:
 - job:

.github/ISSUE_TEMPLATE/blank_issue.md

@@ -1,5 +1,5 @@
 ---
-name: Blank issue
+name: 🗒️ Blank issue
 about: Ask us a question
 labels: [question]
 ---

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,5 +1,5 @@
 ---
-name: Bug report
+name: 🐛 Bug report
 about: Report a bug or unexpected behavior.
 labels: [bug]
 ---

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,5 +1,5 @@
 ---
-name: Feature request
+name: 💡 Feature request
 about: Suggest a new feature or enhancement.
 labels: [enhancement]
 ---

.github/ISSUE_TEMPLATE/installation-issue.md

@@ -1,5 +1,5 @@
 ---
-name: Installation issue
+name: 🔧 Installation issue
 about: Report an issue with installing or setting up WarpX.
 labels: [install]
 ---

.github/workflows/check_changes.yml

@@ -20,8 +20,9 @@ jobs:
           filters: |
             non_docs:
               - '!Docs/**'
-              - '!**.md'
+              - '!Tools/machines/**'
               - '!**.rst'
+              - '!**.md'
           predicate-quantifier: 'every'
       - id: set-output
         run: |

.github/workflows/clang_sanitizers.yml

@@ -5,6 +5,7 @@ on:
     branches:
       - "development"
   pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
 
 concurrency:
   group: ${{ github.ref }}-${{ github.head_ref }}-clangsanitizers
@@ -71,11 +72,12 @@ jobs:
         #MPI implementations often leak memory
         export "ASAN_OPTIONS=detect_leaks=0"
 
-        mpirun -n 2 ./build/bin/warpx.rz Examples/Physics_applications/laser_acceleration/inputs_base_rz
-        mpirun -n 2 ./build/bin/warpx.1d Examples/Physics_applications/laser_acceleration/inputs_base_1d
-        mpirun -n 2 ./build/bin/warpx.2d Examples/Physics_applications/laser_acceleration/inputs_base_2d
-        mpirun -n 2 ./build/bin/warpx.3d Examples/Physics_applications/laser_acceleration/inputs_base_3d
-        mpirun -n 2 ./build/bin/warpx.2d Examples/Tests/implicit/inputs_test_2d_theta_implicit_jfnk_vandb
+        # Print stacktrace for easier debugging
+        export UBSAN_OPTIONS=print_stacktrace=1
+
+        git clone https://github.com/ECP-WarpX/warpx-data ../warpx-data
+
+        ctest --test-dir build/Examples/Physics_applications/ -R ".*\.run" --output-on-failure
 
   build_thread_sanitizer:
     name: Clang thread sanitizer

.github/workflows/clang_tidy.yml

@@ -5,6 +5,7 @@ on:
     branches:
       - "development"
   pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
 
 concurrency:
   group: ${{ github.ref }}-${{ github.head_ref }}-clangtidy
@@ -24,31 +25,33 @@ jobs:
     runs-on: ubuntu-24.04
     timeout-minutes: 250
     needs: check_changes
-    if: ${{ github.event.pull_request.draft == false && needs.check_changes.outputs.has_non_docs_changes == 'true' }}
+    if: ${{ github.event.pull_request.draft == false }}
     steps:
     - uses: actions/checkout@v4
+      if: ${{ needs.check_changes.outputs.has_non_docs_changes == 'true' }}
     - name: install dependencies
+      if: ${{ needs.check_changes.outputs.has_non_docs_changes == 'true' }}
       run: |
         .github/workflows/dependencies/clang.sh 17
     - name: set up cache
+      if: ${{ needs.check_changes.outputs.has_non_docs_changes == 'true' }}
       uses: actions/cache@v4
       with:
         path: ~/.cache/ccache
         key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
         restore-keys: |
              ccache-${{ github.workflow }}-${{ github.job }}-git-
     - name: build WarpX & run clang-tidy
+      if: ${{ needs.check_changes.outputs.has_non_docs_changes == 'true' }}
       run: |
         export CCACHE_COMPRESS=1
         export CCACHE_COMPRESSLEVEL=10
         export CCACHE_MAXSIZE=300M
         export CCACHE_EXTRAFILES=${{ github.workspace }}/.clang-tidy
         export CCACHE_LOGFILE=${{ github.workspace }}/ccache.log.txt
         ccache -z
-
         export CXX=$(which clang++-17)
         export CC=$(which clang-17)
-
         cmake -S . -B build_clang_tidy      \
           -DCMAKE_VERBOSE_MAKEFILE=ON       \
           -DWarpX_DIMS="${{ matrix.dim }}"  \
@@ -60,13 +63,10 @@ jobs:
           -DWarpX_OPENPMD=ON                \
           -DWarpX_PRECISION=SINGLE          \
           -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
-
         cmake --build build_clang_tidy -j 4
-
         ${{github.workspace}}/.github/workflows/source/makeMakefileForClangTidy.py --input ${{github.workspace}}/ccache.log.txt
         make -j4 --keep-going -f clang-tidy-ccache-misses.mak \
             CLANG_TIDY=clang-tidy-17 \
             CLANG_TIDY_ARGS="--config-file=${{github.workspace}}/.clang-tidy --warnings-as-errors=*"
-
         ccache -s
         du -hs ~/.cache/ccache

.github/workflows/codeql.yml

@@ -5,8 +5,7 @@ on:
     branches: [ "development" ]
   pull_request:
     branches: [ "development" ]
-  schedule:
-    - cron: "27 3 * * 0"
+    types: [opened, synchronize, reopened, ready_for_review]
 
 concurrency:
   group: ${{ github.ref }}-${{ github.head_ref }}-codeql

.github/workflows/cuda.yml

@@ -5,6 +5,7 @@ on:
     branches:
       - "development"
   pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
 
 concurrency:
   group: ${{ github.ref }}-${{ github.head_ref }}-cuda
@@ -127,7 +128,9 @@ jobs:
         which nvcc || echo "nvcc not in PATH!"
 
         git clone https://github.com/AMReX-Codes/amrex.git ../amrex
-        cd ../amrex && git checkout --detach e59329031fdad45285ebe04fb7101e62f77a49d9 && cd -
+        dependencies_file="./dependencies.json"
+        amrex_commit=$(jq -r '.commit_amrex' "${dependencies_file}")
+        cd ../amrex && git checkout --detach ${amrex_commit} && cd -
         make COMP=gcc QED=FALSE USE_MPI=TRUE USE_GPU=TRUE USE_OMP=FALSE USE_FFT=TRUE USE_CCACHE=TRUE -j 4
 
         ccache -s