add some github actions

.clang-tidy

@@ -0,0 +1,43 @@
+Checks: >
+     -*,
+     bugprone-*,
+       -bugprone-easily-swappable-parameters,
+     clang-analyzer-*,
+     clang-diagnostic-*,
+     cppcoreguidelines-*,
+       -cppcoreguidelines-avoid-c-arrays,
+       -cppcoreguidelines-avoid-magic-numbers,
+       -cppcoreguidelines-avoid-non-const-global-variables,
+       -cppcoreguidelines-init-variables,
+       -cppcoreguidelines-interfaces-global-init,
+       -cppcoreguidelines-macro-usage,
+       -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-use-anonymous-namespace,
+     modernize-*,
+       -modernize-avoid-c-arrays,
+       -modernize-use-trailing-return-type,
+     performance-*,
+       -performance-avoid-endl,
+     portability-*,
+     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/check_powi.py

@@ -0,0 +1,78 @@
+import subprocess
+import sys
+import os
+import re
+
+
+def pow_to_powi(text):
+    # Finds all possible std::pow(x, n) or gcem::pow(x, n)
+    # where n is a potential integer to amrex::Math::powi<n>(x)
+
+    # Check for all positive and negative integer, whole float numbers
+    # with and without _rt
+    match_pattern = r"([^,]+),\s*(-?(?:\d+\.0*_rt?|\d))"
+
+    # Match fails when there is a nested pow, so only inner most pow is matched
+    negate_pattern = r"(?![\s\S]*(?:std|gcem)::pow\((?:[^,]+),\s*(?:-?(?:\d+\.0*_rt?|\d))\))"
+
+    # Final pattern
+    pattern = rf"(?:std|gcem)::pow\({negate_pattern}{match_pattern}\)"
+    # pattern = rf"(?:std|gcem)::pow\((?![\s\S]*(?:std|gcem)::pow\((?:[^,]+),\s*(?:-?(?:\d+\.0*_rt?|\d))\))([^,]+),\s*(-?(?:\d+\.0*_rt?|\d))\)"
+
+    def replacement(match):
+        x = match.group(1)
+        n = match.group(2)
+
+        # Only extracts out the integer part before decimal point
+        n = n.split('.')[0] if '.' in n else n
+        return f"amrex::Math::powi<{n}>({x})"
+
+    text = re.sub(pattern, replacement, text)
+    return text
+
+def process_content(dir_path):
+    # This function processes all text in the given directory
+    for root, dirs, filenames in os.walk(dir_path):
+        for filename in filenames:
+            if filename.endswith(".H") or filename.endswith(".cpp"):
+                filepath = os.path.join(root, filename)
+
+                with open(filepath, 'r') as file:
+                    old_content = file.read()
+
+                # Iterate over content until content is the same
+                # This is used to get rid of potential nested pow
+                new_content = pow_to_powi(old_content)
+                while new_content != old_content:
+                    old_content = new_content
+                    new_content = pow_to_powi(old_content)
+
+                with open(filepath, 'w') as file:
+                    file.write(new_content)
+
+def git_diff():
+    # Run git diff to see if there are any changes made
+
+    git_diff_output = subprocess.run(['git', 'diff', '--color=always'],
+                                     capture_output=True, text=True)
+
+    # Print out suggested change and raise error after detecting modification
+    if git_diff_output.stdout:
+        print("Detected potential usage to replace std::pow" +
+              "with integer powers via amrex::Math::powi\n")
+        print("Below are the suggested change:\n")
+        print(git_diff_output.stdout)
+
+        raise RuntimeError("Changes detected after modification")
+
+if __name__ == '__main__':
+
+    # Get directory paths
+    directory_paths = sys.argv[1:]
+
+    # Modify the std::pow -> amrex::Math::powi if needed
+    for dir_path in directory_paths:
+        process_content(dir_path)
+
+    # Give suggested change if there are any modifications made
+    git_diff()

.github/workflows/check_powi.yml

@@ -0,0 +1,26 @@
+name: check powi
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  check-ifdefs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+          cache: "pip"
+
+      - name: Run check_powi
+        run: |
+          python .github/workflows/check_powi.py .

.github/workflows/clang-tidy.yml

@@ -0,0 +1,50 @@
+name: "clang-tidy"
+
+on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
+jobs:
+  clang_tidy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Get AMReX
+        run: |
+          mkdir external
+          cd external
+          git clone https://github.com/AMReX-Codes/amrex.git
+          cd amrex
+          git checkout development
+          echo 'AMREX_HOME=$(GITHUB_WORKSPACE)/external/amrex' >> $GITHUB_ENV
+          echo $AMREX_HOME
+          if [[ -n "${AMREX_HOME}" ]]; then exit 1; fi
+          cd ../..
+
+      - name: Install dependencies
+        run: |
+          .github/workflows/dependencies_clang-tidy-apt-llvm.sh 17
+
+      - name: Compile convective_grad
+        run: |
+          cd source/convective_grad
+          make USE_MPI=FALSE USE_CLANG_TIDY=TRUE CLANG_TIDY=clang-tidy-17 CLANG_TIDY_WARN_ERROR=TRUE -j 4
+
+      - name: Compile eos_demo
+        run: |
+          cd source/eos_demo
+          make USE_MPI=FALSE USE_CLANG_TIDY=TRUE CLANG_TIDY=clang-tidy-17 CLANG_TIDY_WARN_ERROR=TRUE -j 4
+
+      - name: Compile fluxes
+        run: |
+          cd source/fluxes
+          make USE_MPI=FALSE USE_CLANG_TIDY=TRUE CLANG_TIDY=clang-tidy-17 CLANG_TIDY_WARN_ERROR=TRUE -j 4
+
+      - name: Compile max_enuc
+        run: |
+          cd source/max_enuc
+          make USE_MPI=FALSE USE_CLANG_TIDY=TRUE CLANG_TIDY=clang-tidy-17 CLANG_TIDY_WARN_ERROR=TRUE -j 4
+

.github/workflows/codespell.yml

@@ -0,0 +1,30 @@
+name: codespell
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  codespell:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+          cache: "pip"
+
+      - name: Install dependencies
+        run: pip install codespell
+
+      - name: Run codespell
+        run: |
+          codespell
+

.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