Merge branch 'development' into ppm_one_sided_second

.clang-tidy

@@ -7,21 +7,27 @@ 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,
+       -performance-enum-size,
+     portability-*,
      readability-*,
        -readability-avoid-const-params-in-decls,
        -readability-braces-around-statements,
@@ -33,9 +39,11 @@ Checks: >
        -readability-isolate-declaration,
        -readability-magic-numbers,
        -readability-named-parameter,
+       -readability-redundant-inline-specifier,
+       -readability-redundant-member-init,
        -readability-simplify-boolean-expr,
        -readability-static-accessed-through-instance,
      mpi-*,
      openmp-*
 
-HeaderFilterRegex: '(/Source/*/|/Util/model_parser_cxx|^\./|^tmp_build_dir/castro_sources/*/).*\.H$'
+HeaderFilterRegex: '(/Source/*/|/Util/model_parser|^\./|^tmp_build_dir/castro_sources/*/).*\.H$'

.codespell-ignore-words

@@ -11,3 +11,5 @@ thi
 nd
 ue
 bion
+aas
+checkin

.editorconfig

@@ -0,0 +1,49 @@
+# http://EditorConfig.org
+#
+# precedence of rules is bottom to top
+
+# this is the top-most EditorConfig file
+root = true
+
+
+[*.{c,h,cpp,hpp,H,py}]
+# 4 space indentation
+indent_style = space
+indent_size = 4
+
+# Clean up trailing whitespace
+trim_trailing_whitespace = true
+
+# unix-style newlines
+end_of_line = lf
+
+# newline ending in files
+insert_final_newline = true
+
+
+[*.md]
+# two end of line whitespaces are newlines without a paragraph
+trim_trailing_whitespace = false
+
+
+[*.rst]
+# Enforce UTF-8 encoding
+charset = utf-8
+
+# Unix-style newlines
+end_of_line = lf
+
+# Newline ending in files
+insert_final_newline = true
+
+# 3 space indentation
+indent_style = space
+indent_size = 3
+
+# Clean up trailing whitespace
+trim_trailing_whitespace = true
+
+[{Makefile,GNUmakefile,Make.*}]
+# TABs are part of its syntax
+indent_style = tab
+indent_size = unset

.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
 
@@ -24,6 +28,16 @@ jobs:
           sudo apt-get update -y -qq
           sudo apt-get -qq -y install curl clang-tidy cmake jq clang cppcheck clang-format bear g++>=9.3.0 gfortran>=9.3.0
 
+      - name: Install hypre
+        run: |
+          wget -q https://github.com/hypre-space/hypre/archive/refs/tags/v2.28.0.tar.gz
+          tar xfz v2.28.0.tar.gz
+          cd hypre-2.28.0/src
+          ./configure --with-cxxstandard=17 --without-MPI
+          make -j 4
+          make install
+          cd ../../
+
       - name: Get cpp linter repo
         run: |
           cd external
@@ -38,14 +52,15 @@ jobs:
 
       - name: Run cpp linter
         run: |
+          export AMREX_HYPRE_HOME=${PWD}/hypre-2.28.0/src/hypre
           python3 external/cpp-linter-action/run_on_changed_files.py ${{ github.event.pull_request.base.sha }} ${{ github.event.pull_request.head.sha }} \
           -ignore-files="amrex|Microphysics" \
           -config-file="${GITHUB_WORKSPACE}/.clang-tidy" \
-          -header-filter='/Source/|/Util/model_parser_cxx|^\./' \
+          -header-filter='/Source/|/Util/model_parser|^\./' \
           -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

@@ -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_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_params.py

@@ -0,0 +1,76 @@
+import argparse
+import importlib
+import os
+import re
+from pathlib import Path
+import sys
+
+# some parameters that are not defined in _cpp_parameters
+
+whitelist = ["castro.lo_bc",
+             "castro.hi_bc",
+             "gravity.abs_tol",
+             "gravity.rel_tol"]
+
+# we don't have all of the radiation parametrs in the _cpp_parameters
+# yet, so we won't check these namespaces
+
+namespace_ignore = ["radiation", "radsolve"]
+
+def doit(castro_dir):
+
+    castro = Path(os.path.abspath(castro_dir))
+
+    # import the module that defines the Castro runtime params
+    sys.path.append(str(castro / "Source" / "driver/"))
+    import parse_castro_params
+
+    # read in the parameters defined in _cpp_parameters
+    param_file = castro / "Source" / "driver" / "_cpp_parameters"
+    params = parse_castro_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 = castro / "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 Castro directory
+
+    p = argparse.ArgumentParser()
+    p.add_argument("castro_dir", type=str, nargs=1,
+                   help="top level Castro directory")
+
+    args = p.parse_args()
+
+    doit(args.castro_dir[0])
+
+