Merge branch 'development' into retry_retry

.clang-tidy

@@ -0,0 +1,39 @@
+Checks: >
+     -*,
+     bugprone-*,
+       -bugprone-easily-swappable-parameters,
+     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,
+     mpi-*,
+     openmp-*
+
+HeaderFilterRegex: '(/conductivity/|/constants/|/EOS/|/integration/|/interfaces/|/networks/|/neutrinos/|/nse_solver/|/opacity/|/rates/|/screening/|/util/|^\./|^./tmp_build_dir/microphysics_sources/*/).*\.H$'

.codespell-ignore-words

@@ -0,0 +1,15 @@
+blocs
+bloc
+inout
+pres
+bion
+tye
+delt
+thi
+daa
+numer
+clen
+coul
+dum
+crate
+vie

.codespellrc

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

.github/workflows/burn_cell.yml

@@ -90,4 +90,20 @@ jobs:
           cd unit_test/burn_cell
           diff -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/aprox13_QSS_unit_test.out
 
+      - name: Compile, burn_cell (RKC, aprox13)
+        run: |
+          cd unit_test/burn_cell
+          make realclean
+          make NETWORK_DIR=aprox13 INTEGRATOR_DIR=RKC -j 4
+
+      - name: Run burn_cell (RKC, aprox13)
+        run: |
+          cd unit_test/burn_cell
+          ./main3d.gnu.ex inputs_aprox13 unit_test.temperature=2.e9 > test.out
+
+      - name: Compare to stored output (RKC, aprox13)
+        run: |
+          cd unit_test/burn_cell
+          diff -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/aprox13_RKC_unit_test.out
+
 

.github/workflows/burn_cell_primordial_chem.yml

@@ -0,0 +1,63 @@
+name: burn_cell_primordial_chem
+
+on: [pull_request]
+
+jobs:
+  burn_cell_primordial_chem:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Get AMReX
+        run: |
+          mkdir external
+          cd external
+          git clone https://github.com/AMReX-Codes/amrex.git
+          cd amrex
+          git checkout development
+          echo 'AMREX_HOME=$(GITHUB_WORKSPACE)/external/amrex' >> $GITHUB_ENV
+          echo $AMREX_HOME
+          if [[ -n "${AMREX_HOME}" ]]; then exit 1; fi
+          cd ../..
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update -y -qq
+          sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0
+
+      - name: Compile and run
+        run: |
+          cd unit_test/burn_cell_primordial_chem
+          make -j 2
+          ./main1d.gnu.DEBUG.ex inputs_primordial_chem > test.out
+
+      - name: Compare to stored output
+        run: |
+          set -e
+          cd unit_test/burn_cell_primordial_chem
+          line_numbers=(456 458 460 463 465 471 476)
+          threshold=0.01
+          error_found=false
+          for line_number in "${line_numbers[@]}"; do
+
+            value1=$(awk 'NR=='"$line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH); else print 0}' test.out)
+            value2=$(awk 'NR=='"$line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH)}' reference_solution.out)
+
+            difference=$(awk -v val1="$value1" -v val2="$value2" 'BEGIN { printf "%.2f", (val1 - val2) / val2 }')
+            
+            if (( $(echo "$difference > $threshold" | bc -l) )); then
+              echo "Line number: $line_number"
+              echo "Value in test.out: $value1"
+              echo "Value in reference_solution.out: $value2"
+              echo "Difference between test and reference value is more than allowed threshold of $threshold"
+              echo
+              error_found=true
+            fi
+          done
+          if [[ $error_found == true ]]; then
+            exit 1
+          fi
+

.github/workflows/c-linter.yml

@@ -0,0 +1,49 @@
+name: cpp-linter
+
+on: [pull_request]
+
+jobs:
+  cpp-linter:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Get AMReX
+        run: |
+          mkdir external
+          cd external
+          git clone https://github.com/AMReX-Codes/amrex.git
+          cd amrex
+          git checkout development
+          echo 'AMREX_HOME=$(GITHUB_WORKSPACE)/external/amrex' >> $GITHUB_ENV
+          echo $AMREX_HOME
+          if [[ -n "${AMREX_HOME}" ]]; then exit 1; fi
+          cd ../..
+
+      - name: Install dependencies
+        run: |
+          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
+
+      - name: Run cpp linter
+        uses: AMReX-Astro/cpp-linter-action@main
+        with:
+          build_path: 'unit_test/test_react'
+          make_options: '-j 2 USE_OMP=FALSE USE_MPI=FALSE USE_CUDA=FALSE DEBUG=TRUE'
+          ignore_files: 'amrex'
+          header_filter: '(/conductivity/|/constants/|/EOS/|/integration/|/interfaces/|/networks/|/neutrinos/|/nse_solver/|/opacity/|/rates/|/screening/|/util/|^\./).*\.H$'
+          config_file: ${GITHUB_WORKSPACE}/.clang-tidy
+
+      - name: Archive clang tidy report
+        uses: actions/upload-artifact@v1
+        with:
+          name: clang-tidy-report
+          path: clang-tidy-report.txt
+
+      - name: Archive cppcheck report
+        uses: actions/upload-artifact@v1
+        with:
+          name: cppcheck-report
+          path: cppcheck-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 +1,113 @@
+#!/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__":
+
+    try:
+        good_defines_file = sys.argv[1]
+    except IndexError:
+        good_defines_file = None
+
+    # read in the list of good defines
+
+    good_defines = []
+    if good_defines_file:
+        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/cmake_build_cell_primordial_chem.yml

@@ -0,0 +1,22 @@
+name: cmake_burn_cell_primordial_chem
+
+on: [pull_request]
+jobs:
+  burn_cell:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update -y -qq
+          sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0 libopenmpi-dev
+
+      - name: Compile and run
+        run: |
+          mkdir build && cd build
+          cmake .. -DBUILD_UNIT_TEST=true -DBUILD_AMREX=true
+          make -j2
+          ctest --output-on-failure