merged development

.github/workflows/burn_cell.yml

@@ -5,7 +5,7 @@ jobs:
   burn_cell:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/burn_cell_primordial_chem.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/burn_cell_sdc.yml

@@ -5,7 +5,7 @@ jobs:
   burn_cell_sdc:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/c-linter.yml

@@ -6,7 +6,7 @@ jobs:
   cpp-linter:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -34,13 +34,13 @@ jobs:
           cppcheck_options: '-U_OPENMP -UAMREX_USE_GPU -UAMREX_USE_CUDA -UAMREX_USE_HIP -U_MSC_VER'
 
       - name: Archive clang tidy report
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v4
         with:
           name: clang-tidy-report
           path: clang-tidy-report.txt
 
       - name: Archive cppcheck report
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v4
         with:
           name: cppcheck-report
           path: cppcheck-report.txt

.github/workflows/castro-development.yml

@@ -0,0 +1,85 @@
+name: Castro development
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-apps-dev
+  cancel-in-progress: true
+
+jobs:
+  castro-development:
+    name: Castro development
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Download Castro
+      uses: actions/checkout@v4
+      with:
+        repository: 'AMReX-Astro/Castro'
+        ref: development
+        path: 'Castro'
+    - name: Download AMReX
+      uses: actions/checkout@v4
+      with:
+        repository: 'AMReX-Codes/amrex'
+        ref: development
+        path: 'amrex'
+    - name: Dependencies
+      run: |
+        .github/workflows/dependencies/dependencies.sh
+        .github/workflows/dependencies/dependencies_ccache.sh
+    - name: Set Up Cache
+      uses: actions/cache@v3
+      with:
+        path: ~/.cache/ccache
+        key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
+        restore-keys: |
+             ccache-${{ github.workflow }}-${{ github.job }}-git-
+    - name: Build flame_wave
+      run: |
+        export CCACHE_COMPRESS=1
+        export CCACHE_COMPRESSLEVEL=10
+        export CCACHE_MAXSIZE=75M
+        export CCACHE_LOGFILE=${{ github.workspace }}/ccache.log.txt
+        ccache -z
+
+        export AMREX_HOME=${PWD}/amrex
+        export MICROPHYSICS_HOME=${PWD}
+
+        cd Castro/Exec/science/flame_wave/
+        make -j2 CCACHE=ccache USE_MPI=FALSE
+
+        ccache -s
+        du -hs ~/.cache/ccache
+
+    - name: Build subchandra
+      run: |
+        export CCACHE_COMPRESS=1
+        export CCACHE_COMPRESSLEVEL=10
+        export CCACHE_MAXSIZE=75M
+        export CCACHE_LOGFILE=${{ github.workspace }}/ccache.log.txt
+        ccache -z
+
+        export AMREX_HOME=${PWD}/amrex
+        export MICROPHYSICS_HOME=${PWD}
+
+        cd Castro/Exec/science/subchandra/
+        make -j2 CCACHE=ccache USE_MPI=FALSE
+
+        ccache -s
+        du -hs ~/.cache/ccache
+
+  save_pr_number:
+    if: github.event_name == 'pull_request'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Save PR number
+        env:
+          PR_NUMBER: ${{ github.event.number }}
+        run: |
+          echo $PR_NUMBER > pr_number.txt
+      - uses: actions/upload-artifact@v3
+        with:
+          name: pr_number
+          path: pr_number.txt
+          retention-days: 1

.github/workflows/castro.yml

@@ -11,19 +11,19 @@ jobs:
     name: Castro
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Get Latest Release Tag
       run: |
         AMREX_TAG=$(wget https://github.com/AMReX-Codes/amrex/releases/latest 2>&1 | grep Location: | awk '{print $2}' | awk -F/ '{print $NF}')
         echo "AMREX_TAG=$AMREX_TAG" >> $GITHUB_ENV
     - name: Download Castro
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: 'AMReX-Astro/Castro'
         ref: development
         path: 'Castro'
     - name: Download AMReX
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: 'AMReX-Codes/amrex'
         ref: ${{env.AMREX_TAG}}

.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_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 +1,37 @@
+name: check powi
+
+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_powi
+        run: |
+          python .github/workflows/check_powi.py .

.github/workflows/cmake_build_cell_primordial_chem.yml

@@ -5,7 +5,7 @@ jobs:
   burn_cell:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/codespell.yml

@@ -14,23 +14,15 @@ 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'
+          cache: "pip"
 
       - name: Install dependencies
         run: pip install codespell

.github/workflows/compile_action.yml

@@ -5,7 +5,7 @@ jobs:
   compilation:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -28,4 +28,4 @@ jobs:
 
       - name: Compile problems
         run: |
-          python3 .github/workflows/find_changed_files.py ${{ github.event.pull_request.base.sha }} ${{ github.event.pull_request.head.sha }}
+          python3 .github/workflows/find_changed_files.py ${{ github.event.pull_request.base.sha }} ${{ github.event.pull_request.head.sha }}

.github/workflows/compiler-warnings.yml

@@ -5,7 +5,7 @@ jobs:
   compiler_warnings:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/create_release.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Get the version
         id: get_version
@@ -33,4 +33,4 @@ jobs:
           release_name: Release ${{ github.ref }}
           body: ${{ env.RELEASE_TXT }}
           draft: false
-          prerelease: false
+          prerelease: false

.github/workflows/cuda.yml

@@ -11,7 +11,7 @@ jobs:
     name: CUDA@11.7 GCC
     runs-on: ubuntu-22.04
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Get AMReX
         run: |