Merge branch 'development' into new_shock_flag_call

.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/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/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

Diagnostics/DustCollapse/analytic.f90

@@ -1,6 +1,6 @@
 ! Print out the analytic solution for the homologous dust collapse problem,
 ! from Colgate and White 1966, ApJ, 143, 626.
-! 
+!
 ! This will yield r(t) as a function of t
 
 module constants_module
@@ -18,7 +18,7 @@ module constants_module
 
   ! we try to do equal timesteps, but eventually, the radius of the
   ! sphere is changing so quickly that we need to adjust the size of
-  ! the timestep.  The code will take nstep timesteps, with the 
+  ! the timestep.  The code will take nstep timesteps, with the
   ! initial timestep to be (t_f - t_i)/(nstep - 1).  Once the radius
   ! begins to change significantly, we will begin halving the timestep
   ! as needed.
@@ -111,7 +111,7 @@ function f(r,t) result (func)
   use constants_module
 
   implicit none
-  
+
   double precision, intent(in) :: r, t
   double precision :: func
 
@@ -130,7 +130,7 @@ function dfdr(r,t) result (dfuncdr)
   use constants_module
 
   implicit none
-  
+
   double precision, intent(in) :: r, t
   double precision :: dfuncdr
 
@@ -145,4 +145,4 @@ function dfdr(r,t) result (dfuncdr)
 end function dfdr
 
 
-  
+