Merge branch 'development' into new_shock_flag_call

Author: zingale

.clang-tidy

@@ -13,7 +13,6 @@ Checks: >
        -cppcoreguidelines-init-variables,
        -cppcoreguidelines-interfaces-global-init,
        -cppcoreguidelines-macro-usage,
-       -cppcoreguidelines-no-malloc,
        -cppcoreguidelines-non-private-member-variables-in-classes,
        -cppcoreguidelines-owning-memory,
        -cppcoreguidelines-pro-*,
@@ -25,7 +24,6 @@ Checks: >
      modernize-*,
        -modernize-avoid-c-arrays,
        -modernize-use-trailing-return-type,
-       -modernize-use-using,
      performance-*,
        -performance-avoid-endl,
      portability-*,

.github/workflows/c-linter.yml

@@ -2,6 +2,10 @@ name: cpp-linter
 
 on: [pull_request]
 
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   cpp-linter:
     runs-on: ubuntu-latest

.github/workflows/check_pr_branch.yml

@@ -0,0 +1,20 @@
+name: check PR branch
+
+on:
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - edited
+
+jobs:
+  check-PR-branch:
+    runs-on: ubuntu-latest
+    steps:
+      - name: PRs should not target main
+        run: |
+          if [[ "${{ github.base_ref }}" == "main" ]]; then
+            echo 'Pull requests must not be made against main. Please target development instead.'
+            exit 1
+          fi

.github/workflows/clang-tidy.yml

@@ -0,0 +1,36 @@
+name: "clang-tidy"
+
+on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
+jobs:
+  clang_tidy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Get submodules
+        run: |
+          git submodule update --init
+          cd external/Microphysics
+          git fetch; git checkout development
+          echo "MICROPHYSICS_HOME=$(pwd)" >> $GITHUB_ENV
+          cd ../amrex
+          git fetch; git checkout development
+          echo "AMREX_HOME=$(pwd)" >> $GITHUB_ENV
+          cd ../..
+
+      - name: Install dependencies
+        run: |
+          .github/workflows/dependencies_clang-tidy-apt-llvm.sh 17
+
+      - name: Compile flame_wave
+        run: |
+          echo $AMREX_HOME
+          echo $MICROPHYSICS_HOME
+          cd Exec/science/subchandra
+          make USE_MPI=FALSE USE_CLANG_TIDY=TRUE CLANG_TIDY=clang-tidy-17 CLANG_TIDY_WARN_ERROR=TRUE -j 4
+

.github/workflows/compiler-warnings.yml

@@ -1,6 +1,11 @@
 name: "compiler warnings"
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   compiler_warnings:
     runs-on: ubuntu-latest

.github/workflows/dependencies_clang-tidy-apt-llvm.sh

@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+
+set -eu -o pipefail
+
+# `man apt.conf`:
+#   Number of retries to perform. If this is non-zero APT will retry
+#   failed files the given number of times.
+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}-$1 main"
+
+sudo apt-get update
+
+sudo apt-get install -y --no-install-recommends \
+    clang-tidy-$1 libomp-$1-dev

.github/workflows/detonation-sdc-compare.yml

@@ -1,6 +1,11 @@
 name: detonation-sdc
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   detonation-sdc:
     runs-on: ubuntu-latest

.github/workflows/flame_wave-compare.yml

@@ -1,6 +1,11 @@
 name: flame_wave
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   flame_wave-2d:
     runs-on: ubuntu-latest

.github/workflows/gpu_action.yml

@@ -1,6 +1,11 @@
 name: GPU compilation
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   gpu-compilation:
     runs-on: ubuntu-latest

.github/workflows/wdmerger_collision-compare.yml

@@ -1,6 +1,11 @@
 name: wdmerger_collision
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   wdmerger_collision-2d:
     runs-on: ubuntu-latest