Merge branch 'development' into add_cubic_interp

.clang-tidy

@@ -7,6 +7,7 @@ Checks: >
      clang-diagnostic-*,
      cppcoreguidelines-*,
        -cppcoreguidelines-avoid-c-arrays,
+       -cppcoreguidelines-avoid-do-while,
        -cppcoreguidelines-avoid-magic-numbers,
        -cppcoreguidelines-avoid-non-const-global-variables,
        -cppcoreguidelines-init-variables,
@@ -20,6 +21,7 @@ Checks: >
        -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,

.github/workflows/c-linter.yml

@@ -2,6 +2,10 @@ 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

.github/workflows/clang-tidy.yml

@@ -0,0 +1,36 @@
+name: "clang-tidy"
+
+on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
+jobs:
+  clang_tidy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Get submodules
+        run: |
+          git submodule update --init
+          cd external/Microphysics
+          git fetch; git checkout development
+          echo "MICROPHYSICS_HOME=$(pwd)" >> $GITHUB_ENV
+          cd ../amrex
+          git fetch; git checkout development
+          echo "AMREX_HOME=$(pwd)" >> $GITHUB_ENV
+          cd ../..
+
+      - name: Install dependencies
+        run: |
+          .github/workflows/dependencies_clang-tidy-apt-llvm.sh 17
+
+      - name: Compile flame_wave
+        run: |
+          echo $AMREX_HOME
+          echo $MICROPHYSICS_HOME
+          cd Exec/science/subchandra
+          make USE_MPI=FALSE USE_CLANG_TIDY=TRUE CLANG_TIDY=clang-tidy-17 CLANG_TIDY_WARN_ERROR=TRUE -j 4
+

.github/workflows/compiler-warnings.yml

@@ -1,6 +1,11 @@
 name: "compiler warnings"
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   compiler_warnings:
     runs-on: ubuntu-latest

.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

.github/workflows/detonation-sdc-compare.yml

@@ -1,6 +1,11 @@
 name: detonation-sdc
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   detonation-sdc:
     runs-on: ubuntu-latest

.github/workflows/docs-test.yml

@@ -9,6 +9,10 @@ on:
     branches:
       - development
 
+env:
+  # enable color output from Sphinx
+  FORCE_COLOR: "1"
+
 jobs:
   docs:
     runs-on: ubuntu-latest
@@ -33,7 +37,10 @@ jobs:
       - name: Build docs
         run: |
           cd Docs/
-          make SPHINXOPTS=-v NO_DOXYGEN=TRUE html
+          # remove missing TOC entries that would otherwise be generated by
+          # doxygen to avoid warnings about missing references
+          sed -i -e 's/^   filelist$//; s/^   classlist$//' source/index.rst
+          make SPHINXOPTS='-v -W --keep-going' NO_DOXYGEN=TRUE html
 
       - name: Check links
         run: |

.github/workflows/flame_wave-compare.yml

@@ -1,6 +1,11 @@
 name: flame_wave
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   flame_wave-2d:
     runs-on: ubuntu-latest

.github/workflows/fsanitizer.yml

@@ -0,0 +1,37 @@
+name: fsanitizer
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-fsanitizer
+  cancel-in-progress: true
+
+jobs:
+  fsanitizer:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - 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 cmake jq clang g++>=9.3.0
+
+      - name: Compile subchandra
+        run: |
+          cd Exec/science/subchandra
+          make FSANITIZER=TRUE USE_MPI=FALSE -j 4
+
+      - name: Run subchandra
+        run: |
+          cd Exec/science/subchandra
+          ./Castro2d.gnu.SMPLSDC.ex inputs_2d.N14.coarse amr.max_level=1 max_step=1 amr.n_cell=320 640

.github/workflows/get_release_txt.py

@@ -26,9 +26,9 @@
                     txt = txt[m.end():].strip()
             else:
                 txt = ""
-                    
-            # we now need to substitute characters in the string so that 
-            # the action can deal with line breaks 
+
+            # we now need to substitute characters in the string so that
+            # the action can deal with line breaks
             txt = txt.replace('%', '%25')
             txt = txt.replace('\n', '%0A')
             txt = txt.replace('\r', '%0D')

.github/workflows/gpu_action.yml

@@ -1,6 +1,11 @@
 name: GPU compilation
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   gpu-compilation:
     runs-on: ubuntu-latest

.github/workflows/style.yml

@@ -0,0 +1,22 @@
+name: Style
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-style
+  cancel-in-progress: true
+
+jobs:
+  tabs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Tabs
+        run: .github/workflows/style/check_tabs.sh
+
+  trailing_whitespaces:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Trailing Whitespaces
+        run: .github/workflows/style/check_trailing_whitespaces.sh

.github/workflows/style/check_tabs.sh

@@ -0,0 +1,36 @@
+#!/usr/bin/env bash
+
+set -eu -o pipefail
+
+find . -type d \( -name .git \
+                  -o -path ./paper \
+                  -o -name build -o -name install \
+                  -o -name tmp_build_dir -o -name tmp_install_dir \
+               \) -prune -o \
+       -type f \( \( -name "*.H" -o -name "*.h" -o -name "*.hh" -o -name "*.hpp" \
+                  -o -name "*.c" -o -name "*.cc" -o -name "*.cpp" -o -name "*.cxx" \
+                  -o -name "*.f" -o -name "*.F" -o -name "*.f90" -o -name "*.F90" \
+                  -o -name "*.py" \
+                  -o -name "*.md" -o -name "*.rst" \
+                  -o -name "*.sh" \
+                  -o -name "*.tex" \
+                  -o -name "*.txt" \
+                  -o -name "*.yml" \) \
+                 -a \( ! -name "*.tab.h" -a ! -name "*.tab.nolint.H" \
+                    -a ! -name "*.lex.h" -a ! -name "*.lex.nolint.H" \) \
+               \) \
+    -exec grep -Iq . {} \; \
+    -exec sed -i 's/\t/\ \ \ \ /g' {} +
+
+gitdiff=`git diff`
+
+if [ -z "$gitdiff" ]
+then
+    exit 0
+else
+    echo -e "\nTabs are not allowed. Changes suggested by"
+    echo -e "  ${0}\n"
+    git --no-pager diff
+    echo ""
+    exit 1
+fi

.github/workflows/style/check_trailing_whitespaces.sh

@@ -0,0 +1,38 @@
+#!/usr/bin/env bash
+
+set -eu -o pipefail
+
+find . -type d \( -name .git \
+                  -o -path ./paper \
+                  -o -name build -o -name install \
+                  -o -name tmp_build_dir -o -name tmp_install_dir \
+                  -o -path ./util/gcem \
+               \) -prune -o \
+       -type f \( \( -name "*.H" -o -name "*.h" -o -name "*.hh" -o -name "*.hpp" \
+                  -o -name "*.c" -o -name "*.cc" -o -name "*.cpp" -o -name "*.cxx" \
+                  -o -name "*.f" -o -name "*.F" -o -name "*.f90" -o -name "*.F90" \
+                  -o -name "*.py" \
+                  -o -name "*.rst" \
+                  -o -name "*.sh" \
+                  -o -name "*.tex" \
+                  -o -name "*.txt" \
+                  -o -name "*.yml" \) \
+                 -a \( ! -name "*.tab.h" -a ! -name "*.tab.nolint.H" \
+                    -a ! -name "*.lex.h" -a ! -name "*.lex.nolint.H" \
+                    -a ! -path "./networks/*/reaclib_rates.H" \) \
+               \) \
+    -exec grep -Iq . {} \; \
+    -exec sed -i 's/[[:blank:]]\+$//g' {} +
+
+gitdiff=`git diff`
+
+if [ -z "$gitdiff" ]
+then
+    exit 0
+else
+    echo -e "\nTrailing whitespaces at the end of a line are not allowed. Changes suggested by"
+    echo -e "  ${0}\n"
+    git --no-pager diff
+    echo ""
+    exit 1
+fi

.github/workflows/wdmerger_collision-compare.yml

@@ -1,6 +1,11 @@
 name: wdmerger_collision
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   wdmerger_collision-2d:
     runs-on: ubuntu-latest

.gitignore

@@ -72,6 +72,8 @@ Docs/source/namespacelist.rst
 Docs/source/runtime_parameters.rst
 Docs/source/*_files.rst
 Docs/source/preprocessed_files
+Docs/source/yt_example.rst
+Docs/source/yt_example_files/
 
 
 amr_diag.out

CHANGES.md

@@ -1,3 +1,31 @@
+# 24.04
+
+  * Some clang-tidy fixes (#2779, #2780, #2781, #2784, #2786, #2787, #2790,
+    #2791, #2792, #2793, #2797, #2798, #2799, #2800, #2801, #2804)
+
+  * Fix species initialization in the Detonation problem (#2806)
+    and let it work with NSE (#2765)
+
+  * Sync up with AMReX changes (#2794)
+
+  * wdmerger now reports composition of initial stars (#2767)
+
+  * flame_wave now checks if the `atm_delta` is too small (#2782)
+    and stores X(ash) (#2773)
+
+  * a bounds issue in the true SDC integration was fixed (#2775)
+
+# 24.03
+
+  * Documentation updates (#2742, #2752, #2753)
+
+  * Fix some code warnings (#2737)
+
+  * Fixed the exact Riemann solver compilation (#2745)
+
+  * Fix an issue with large kernel sizes with ROCm in the reduction code
+    in the reactions (#2749)
+
 # 24.02
 
   * Lot's of code fixes from coverity and clang-tidy (#2736, #2734,