Merge branch 'development' into codespell_update

.clang-tidy

@@ -28,6 +28,7 @@ Checks: >
        -modernize-use-using,
      performance-*,
        -performance-avoid-endl,
+       -performance-enum-size,
      portability-*,
      readability-*,
        -readability-avoid-const-params-in-decls,

.github/workflows/check-params.yml

@@ -0,0 +1,37 @@
+name: check runtime params
+
+on:
+  push:
+    branches:
+      - development
+      - main
+  pull_request:
+    branches:
+      - development
+
+jobs:
+  check-runtime-params:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Get submodules
+        run: |
+          git submodule update --init
+          cd external/Microphysics
+          git fetch; git checkout development
+          cd ../amrex
+          git fetch; git checkout development
+          cd ../..
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Run check-params
+        run: |
+          PYTHONPATH=external/Microphysics/util/build_scripts python .github/workflows/check_params.py .

.github/workflows/check_params.py

@@ -0,0 +1,74 @@
+import argparse
+import importlib
+import os
+import re
+from pathlib import Path
+import sys
+
+# some parameters that are not defined in _cpp_parameters
+
+whitelist = ["maestro.lo_bc",
+             "maestro.hi_bc"]
+
+# we don't have all of the radiation parametrs in the _cpp_parameters
+# yet, so we won't check these namespaces
+
+namespace_ignore = []
+
+def doit(maestroex_dir):
+
+    maestroex = Path(os.path.abspath(maestroex_dir))
+
+    # import the module that defines the MAESTROeX runtime params
+    sys.path.append(str(maestroex / "Source" / "param/"))
+    import parse_maestro_params
+
+    # read in the parameters defined in _cpp_parameters
+    param_file = maestroex / "Source" / "param" / "_cpp_parameters"
+    params = parse_maestro_params.read_param_file(str(param_file))
+
+    namespaces = set(p.namespace for p in params)
+    runtime_parameters = [f"{p.namespace}.{p.name}" for p in params]
+
+    pattern = re.compile(r"[A-Za-z0-9_]+\.[A-Za-z0-9_]+", re.IGNORECASE)
+
+    # loop over all the inputs files
+    exec_path = maestroex / "Exec"
+    for f in exec_path.glob("**/inputs*"):
+
+        if os.path.isdir(f):
+            continue
+
+        # find all the params in each namespace
+        with open(f) as infile:
+            print(f"working on {f}")
+            for line in infile:
+                # remove comments
+                idx = line.find("#")
+                if idx > 0:
+                    line = line[:idx]
+
+                found_param = pattern.match(line)
+                if not found_param:
+                    continue
+
+                p = found_param.group(0)
+                nm = p.split(".")[0]
+                if nm in namespaces and nm not in namespace_ignore:
+                    if not (p in runtime_parameters or p in whitelist):
+                        sys.exit(f"Error: {p} not valid")
+
+
+if __name__ == "__main__":
+
+    # we need the top-level MAESTROeX directory
+
+    p = argparse.ArgumentParser()
+    p.add_argument("maestroex_dir", type=str, nargs=1,
+                   help="top level MAESTROeX directory")
+
+    args = p.parse_args()
+
+    doit(args.maestroex_dir[0])
+
+

.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 wdconvect
+        run: |
+          echo $AMREX_HOME
+          echo $MICROPHYSICS_HOME
+          cd Exec/science/wdconvect
+          make USE_MPI=FALSE USE_OMP=FALSE USE_CLANG_TIDY=TRUE CLANG_TIDY=clang-tidy-17 CLANG_TIDY_WARN_ERROR=TRUE -j 4
+

.github/workflows/compiler-warnings.yml

@@ -0,0 +1,39 @@
+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@v4
+        with:
+          fetch-depth: 0
+
+      - name: Get submodules
+        run: |
+          git submodule update --init
+          cd external/Microphysics
+          git fetch; git checkout development
+          cd ../amrex
+          git fetch; git checkout development
+          cd ../..
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update -y -qq
+          sudo apt-get -qq -y install curl g++>=9.3.0
+
+      - name: Compile wdconvect
+        run: |
+          cd Exec/science/wdconvect
+          make USE_MPI=FALSE USE_OMP=FALSE DEBUG=TRUE WARN_ALL=TRUE WARN_ERROR=TRUE -j 4
+
+      - name: Compile reacting_bubble
+        run: |
+          cd Exec/test_problems/reacting_bubble
+          make USE_MPI=FALSE USE_OMP=FALSE DEBUG=TRUE DIM=2 WARN_ALL=TRUE WARN_ERROR=TRUE -j 4

.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/gpu_action.yml

@@ -37,4 +37,4 @@ jobs:
         run: |
           export PATH=$PATH:/usr/local/cuda/bin
           cd Exec/test_problems/reacting_bubble
-          make DIM=2 USE_MPI=FALSE USE_CUDA=TRUE -j 2
+          make DIM=2 USE_MPI=FALSE USE_CUDA=TRUE -j 4

.github/workflows/reacting_bubble-compare.yml

@@ -26,7 +26,7 @@ jobs:
       - name: Compile reacting_bubble
         run: |
           cd Exec/test_problems/reacting_bubble
-          make DIM=2 USE_MPI=FALSE -j 2
+          make DIM=2 USE_MPI=FALSE -j 4
 
       - name: Run reacting_bubble
         run: |
@@ -36,7 +36,7 @@ jobs:
       - name: Build the fextrema tool
         run: |
           cd external/amrex/Tools/Plotfile
-          make programs=fextrema -j 2
+          make programs=fextrema -j 4
 
       - name: Check the extrema
         run: |

.github/workflows/wdconvect-compare.yml

@@ -0,0 +1,46 @@
+name: wdconvect
+
+on: [pull_request]
+jobs:
+  wdconvect-3d:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Get submodules
+        run: |
+          git submodule update --init
+          cd external/Microphysics
+          git fetch; git checkout development
+          cd ../amrex
+          git fetch; git checkout development
+          cd ../..
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update -y -qq
+          sudo apt-get -qq -y install curl g++>=9.3.0
+
+      - name: Compile wdconvect
+        run: |
+          cd Exec/science/wdconvect
+          make USE_OMP=FALSE USE_MPI=FALSE -j 4
+
+      - name: Run wdconvect
+        run: |
+          cd Exec/science/wdconvect
+          cp model_files/kepler_new_6.25e8.hybrid.hse.320 .
+          cp inputs_files/inputs_3d_regression.2levels .
+          ./Maestro3d.gnu.ex inputs_3d_regression.2levels
+
+      - name: Build the fextrema tool
+        run: |
+          cd external/amrex/Tools/Plotfile
+          make programs=fextrema -j 4
+
+      - name: Check the extrema
+        run: |
+          cd Exec/science/wdconvect
+          ../../../external/amrex/Tools/Plotfile/fextrema.gnu.ex wdconvect_plt0000003 > fextrema.out
+          diff fextrema.out ci-benchmarks/wdconvect_3d_extrema.out
+

.zenodo.json

@@ -2,29 +2,31 @@
     "creators": [
         {
             "affiliation": "Center for Computational Sciences and Engineering, Lawrence Berkeley National Laboratory",
+            "name": "Almgren, Ann",
+            "orcid": "0000-0003-2103-312X"
+        },
+        {
+            "affiliation": "Department of Physics and Astronomy, Stony Brook University",
+            "name": "Boyd, Brendan",
+            "orcid": "0000-0002-5419-9751"
+        },
+        {
             "name": "Fan, Doreen",
             "orcid": "0000-0002-3246-4315"
         },
         {
-            "affiliation": "Center for Computational Sciences and Engineering, Lawrence Berkeley National Laboratory",
-            "name": "Nonaka, Andy",
-            "orcid": "0000-0003-1791-0265"
+            "name": "Harpole, Alice",
+            "orcid": "0000-0002-1530-781X"
         },
         {
             "affiliation": "Center for Computational Sciences and Engineering, Lawrence Berkeley National Laboratory",
-            "name": "Almgren, Ann",
-            "orcid": "0000-0003-2103-312X"
+            "name": "Nonaka, Andy",
+            "orcid": "0000-0003-1791-0265"
         },
         {
-            "affiliation": "Center for Computational Sciences and Engineering, Lawrence Berkeley National Laboratory",
             "name": "Willcox, Donald",
             "orcid": "0000-0003-2300-5165"
         },
-        {
-            "affiliation": "Department of Physics and Astronomy, Stony Brook University",
-            "name": "Harpole, Alice",
-            "orcid": "0000-0002-1530-781X"
-        },
         {
             "affiliation": "Department of Physics and Astronomy, Stony Brook University",
             "name": "Zingale, Michael",