Merge branch 'development' into plot_max_level

.clang-tidy

@@ -7,21 +7,26 @@ Checks: >
      clang-diagnostic-*,
      cppcoreguidelines-*,
        -cppcoreguidelines-avoid-c-arrays,
-       -cppcoreguidelines-avoid-goto,
+       -cppcoreguidelines-avoid-do-while,
        -cppcoreguidelines-avoid-magic-numbers,
        -cppcoreguidelines-avoid-non-const-global-variables,
        -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-*,
+     misc-*,
+       -misc-const-correctness,
+       -misc-include-cleaner,
+       -misc-non-private-member-variables-in-classes,
+       -misc-no-recursion,
      modernize-*,
        -modernize-avoid-c-arrays,
        -modernize-use-trailing-return-type,
-       -modernize-use-using,
      performance-*,
+       -performance-avoid-endl,
+     portability-*,
      readability-*,
        -readability-avoid-const-params-in-decls,
        -readability-braces-around-statements,

.github/dependabot.yml

@@ -0,0 +1,9 @@
+# Dependabot configuration
+# ref: https://docs.github.com/en/code-security/supply-chain-security/keeping-your-dependencies-updated-automatically/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    target-branch: "development"

.github/workflows/c-linter.yml

@@ -2,11 +2,15 @@ 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
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -30,7 +34,7 @@ jobs:
           tar xfz v2.28.0.tar.gz
           cd hypre-2.28.0/src
           ./configure --with-cxxstandard=17 --without-MPI
-          make -j 2
+          make -j 4
           make install
           cd ../../
 
@@ -56,7 +60,7 @@ jobs:
           -run-linter
 
       - name: Archive clang tidy report
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: clang-tidy-report
           path: clang-tidy-report.txt

.github/workflows/check-ifdefs.yml

@@ -14,23 +14,14 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
-
-      - name: Cache pip
-        uses: actions/cache@v3
-        with:
-          # this path is specific to Ubuntu
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
+          python-version: '3.11'
 
       - name: Run check-ifdefs
         run: |

.github/workflows/check-makefiles.yml

@@ -0,0 +1,29 @@
+name: check makefiles
+
+on:
+  push:
+    branches:
+      - development
+      - main
+  pull_request:
+    branches:
+      - development
+
+jobs:
+  check-ifdefs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Run check-ifdefs
+        run: |
+          python .github/workflows/check_makefiles.py
+

.github/workflows/check-params.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -28,19 +28,10 @@ jobs:
           cd ../..
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
-      - name: Cache pip
-        uses: actions/cache@v3
-        with:
-          # this path is specific to Ubuntu
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-
       - name: Run check-params
         run: |
           PYTHONPATH=external/Microphysics/util/build_scripts python .github/workflows/check_params.py .

.github/workflows/check_makefiles.py

@@ -0,0 +1,46 @@
+import re
+import sys
+from pathlib import Path
+
+correct_params = {
+    "DEBUG": "FALSE",
+    "USE_MPI": "TRUE",
+    "USE_OMP": "FALSE",
+    "COMP": "gnu",
+    "USE_CUDA": "FALSE",
+    "USE_HIP": "FALSE",
+    "PRECISION": "DOUBLE",
+    "PROFILE": "FALSE"}
+
+
+def find_source_files():
+    p = Path("./Exec")
+    files = list(p.glob(r"**/GNUmakefile"))
+    return files
+
+def check_makefile(makefile):
+
+    with open(makefile) as mf:
+        for _line in mf:
+            if idx := _line.find("#") >= 0:
+                line = _line[:idx]
+            else:
+                line = _line
+
+            for key in correct_params:
+                if key in line:
+                    try:
+                        k, v = re.split(":=|\?=|=", line)
+                    except ValueError:
+                        sys.exit(f"invalid line: {line}")
+
+                    if not v.strip() == correct_params[key]:
+                        sys.exit(f"invalid param {key} in {makefile}")
+
+if __name__ == "__main__":
+
+    for f in find_source_files():
+        check_makefile(f)
+
+
+

.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/codespell.yml

@@ -14,23 +14,15 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
-
-      - name: Cache pip
-        uses: actions/cache@v3
-        with:
-          # this path is specific to Ubuntu
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
+          cache: "pip"
 
       - name: Install dependencies
         run: pip install -r ./requirements.txt

.github/workflows/compiler-warnings.yml

@@ -1,11 +1,16 @@
 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
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -26,14 +31,14 @@ jobs:
       - name: Compile Detonation
         run: |
           cd Exec/science/Detonation
-          make USE_MPI=FALSE USE_OMP=FALSE DEBUG=TRUE WARN_ALL=TRUE WARN_ERROR=TRUE -j 2
+          make USE_MPI=FALSE USE_OMP=FALSE DEBUG=TRUE WARN_ALL=TRUE WARN_ERROR=TRUE -j 4
 
       - name: Compile subchandra
         run: |
           cd Exec/science/subchandra
-          make USE_MPI=FALSE USE_OMP=FALSE DEBUG=TRUE WARN_ALL=TRUE WARN_ERROR=TRUE -j 2
+          make USE_MPI=FALSE USE_OMP=FALSE DEBUG=TRUE WARN_ALL=TRUE WARN_ERROR=TRUE -j 4
 
       - name: Compile wdmerger
         run: |
           cd Exec/science/wdmerger
-          make USE_MPI=FALSE USE_OMP=FALSE DEBUG=TRUE WARN_ALL=TRUE WARN_ERROR=TRUE -j 2
+          make USE_MPI=FALSE USE_OMP=FALSE DEBUG=TRUE WARN_ALL=TRUE WARN_ERROR=TRUE -j 4

.github/workflows/create_release.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Get the version
         id: get_version
@@ -33,4 +33,4 @@ jobs:
           release_name: Release ${{ github.ref }}
           body: ${{ env.RELEASE_TXT }}
           draft: false
-          prerelease: false
+          prerelease: false

.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