Merge branch 'development' into true_sdc_normalization

.clang-tidy

@@ -0,0 +1,41 @@
+Checks: >
+     -*,
+     bugprone-*,
+       -bugprone-easily-swappable-parameters,
+       -bugprone-implicit-widening-of-multiplication-result,
+     clang-analyzer-*,
+     clang-diagnostic-*,
+     cppcoreguidelines-*,
+       -cppcoreguidelines-avoid-c-arrays,
+       -cppcoreguidelines-avoid-goto,
+       -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-*,
+     modernize-*,
+       -modernize-avoid-c-arrays,
+       -modernize-use-trailing-return-type,
+       -modernize-use-using,
+     performance-*,
+     readability-*,
+       -readability-avoid-const-params-in-decls,
+       -readability-braces-around-statements,
+       -readability-else-after-return,
+       -readability-function-cognitive-complexity,
+       -readability-function-size,
+       -readability-identifier-length,
+       -readability-implicit-bool-conversion,
+       -readability-isolate-declaration,
+       -readability-magic-numbers,
+       -readability-named-parameter,
+       -readability-simplify-boolean-expr,
+       -readability-static-accessed-through-instance,
+     mpi-*,
+     openmp-*
+
+HeaderFilterRegex: '(/Source/*/|/Util/model_parser|^\./|^tmp_build_dir/castro_sources/*/).*\.H$'

.codespell-ignore-words

@@ -0,0 +1,14 @@
+blocs
+bloc
+inout
+als
+truns
+pres
+dum
+fom
+fromm
+thi
+nd
+ue
+bion
+aas

.codespellrc

@@ -0,0 +1,5 @@
+[codespell]
+skip = .git,*.ipynb,*.bib,*.ps
+ignore-words = .codespell-ignore-words
+
+

.github/workflows/c-linter.yml

@@ -1,20 +1,21 @@
 name: cpp-linter
 
 on: [pull_request]
+
 jobs:
   cpp-linter:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
-      - name: Get submodules 
+      - name: Get submodules
         run: |
           git submodule update --init
           cd external/Microphysics
           git fetch; git checkout development
-          cd ../amrex 
+          cd ../amrex
           git fetch; git checkout development
           cd ../..
 
@@ -23,11 +24,21 @@ 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: Get cpp linter repo 
+      - 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 2
+          make install
+          cd ../../
+
+      - name: Get cpp linter repo
         run: |
-          cd external 
+          cd external
           git clone https://github.com/AMReX-Astro/cpp-linter-action.git
-          cd .. 
+          cd ..
 
       - name: Check header includes
         run: |
@@ -36,10 +47,16 @@ jobs:
           if [[ -n "${HEADER_INCLUDES}" ]]; then exit 1; fi
 
       - name: Run cpp linter
-        run: python3 external/cpp-linter-action/run_on_changed_files.py ${{ github.event.pull_request.base.sha }} ${{ github.event.pull_request.head.sha }} -header-filter=Castro -ignore-files="amrex|Microphysics" -run-linter
-
+        run: |
+          export AMREX_HYPRE_HOME=${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|^\./' \
+          -run-linter
+
       - name: Archive clang tidy report
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v3
         with:
           name: clang-tidy-report
-          path: clang-tidy-report.txt
+          path: clang-tidy-report.txt

.github/workflows/check-ifdefs.yml

@@ -0,0 +1,37 @@
+name: check ifdefs
+
+on:
+  push:
+    branches:
+      - development
+      - main
+  pull_request:
+    branches:
+      - development
+
+jobs:
+  check-ifdefs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        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-
+
+      - name: Run check-ifdefs
+        run: |
+          python .github/workflows/check_ifdefs.py .github/workflows/good_defines.txt

.github/workflows/check_ifdefs.py

@@ -0,0 +1,109 @@
+#!/bin/env python
+
+import re
+import sys
+
+from pathlib import Path
+
+
+def find_source_files():
+    p = Path("./")
+    files = list(p.glob(r"**/*.cpp"))
+    files += list(p.glob(r"**/*.H"))
+    return files
+
+def check_file(filename):
+
+    # this is a general check to see if we should further examine a line
+    if_general_re = re.compile(r"^(?:#if|#elif)", re.IGNORECASE|re.DOTALL)
+
+    # this checks something of the form "#ifdef NAME"
+    ifdef_re = re.compile(r"^#if[n]*def\s+([a-z_0-9]+)", re.IGNORECASE|re.DOTALL)
+
+    # this checks something of the form
+    # #if (NAME == X)
+    if_re = re.compile(r"^(?:#if|#elif)\s+[\(]?([a-z_0-9]+)", re.IGNORECASE|re.DOTALL)
+
+    # together these check something of the form
+    # #if defined(NAME1) || !defined(NAME2)
+    if_defined_re1 = re.compile(r"^(?:#if|#elif)\s+[!]?(?:defined)", re.IGNORECASE|re.DOTALL)
+    if_defined_re2 = re.compile(r"[!]?(?:defined)\s*[\(]?([a-z_0-9]+)[\)]?", re.IGNORECASE|re.DOTALL)
+
+    ierr = 0
+    defines = []
+
+    with open(filename) as cf:
+        for line in cf:
+            if if_general_re.search(line):
+
+                # check each of the patterns
+                if if_defined_re1.search(line):
+                    g = if_defined_re2.findall(line)
+                    defines += g
+                    continue
+
+                if g := ifdef_re.search(line):
+                    defines.append(g.group(1))
+                    continue
+
+                if g := if_re.search(line):
+                    defines.append(g.group(1))
+                    continue
+
+
+                # if we made it here, then we didn't handle things
+                ierr = 1
+                print(f"unhandled, file: {filename} | {line}")
+
+    return ierr, set(defines)
+
+if __name__ == "__main__":
+
+    good_defines_file = sys.argv[1]
+
+    # read in the list of good defines
+
+    good_defines = []
+    with open(good_defines_file) as gd:
+        for line in gd:
+            good_defines.append(line.strip())
+
+    all_defines = []
+    total_errors = 0
+    for f in find_source_files():
+        if "tmp_build_dir" in f.parts:
+            # skip generated files
+            continue
+        ierr, defines = check_file(f)
+        all_defines += defines
+        total_errors += ierr
+
+    # remove any header guards
+
+    defines = []
+    for d in all_defines:
+        if d.endswith("_H") or d.endswith("_H_"):
+            continue
+        if len(d) == 1 and d.isdigit():
+            continue
+        defines.append(d)
+
+    defines = sorted(set(defines))
+
+    print("found defines:")
+    for d in defines:
+        print(d)
+
+    # now check to make sure that all the defines we found are okay
+
+    invalid = []
+    for d in defines:
+        if d not in good_defines:
+            invalid.append(d)
+
+    if invalid or total_errors > 0:
+        if invalid:
+            print("\ninvalid defines:")
+        for bad in invalid:
+            print(bad)
+        sys.exit(1)

.github/workflows/codespell.yml

@@ -0,0 +1,41 @@
+name: codespell
+
+on:
+  push:
+    branches:
+      - development
+      - main
+  pull_request:
+    branches:
+      - development
+
+jobs:
+  codespell:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        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-
+
+      - name: Install dependencies
+        run: pip install -r ./requirements.txt
+
+      - name: Run codespell
+        run: |
+          codespell
+

.github/workflows/compiler-warnings.yml

@@ -0,0 +1,39 @@
+name: "compiler warnings"
+
+on: [pull_request]
+jobs:
+  compiler_warnings:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        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 Detonation
+        run: |
+          cd Exec/science/Detonation
+          make USE_MPI=FALSE USE_OMP=FALSE DEBUG=TRUE WARN_ALL=TRUE WARN_ERROR=TRUE -j 2
+
+      - 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
+
+      - 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

.github/workflows/create_release.yml

@@ -2,8 +2,8 @@ on:
   push:
     # Sequence of patterns matched against refs/tags
     tags:
-      - '[0-9][0-9].[0-9][0-9]' 
-  
+      - '[0-9][0-9].[0-9][0-9]'
+
 name: Create Release
 
 jobs:
@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Get the version
         id: get_version