Code Spell (#3563)

Add a github action and fix various spellings.

---------

Co-authored-by: Jean M. Sexton <jmsexton@lbl.gov>

.codespell-ignore-words

@@ -0,0 +1,33 @@
+abot
+alo
+apoints
+asend
+ba
+bloc
+blocs
+boxs
+cant
+ccache
+clen
+compex
+couldnt
+fromm
+frop
+geometrys
+hist
+hsi
+infor
+inout
+ist
+lsit
+nd
+nineth
+parm
+parms
+pres
+ptd
+recuse
+siz
+structed
+te
+thi

.codespellrc

@@ -0,0 +1,3 @@
+[codespell]
+skip = .git,*.ipynb,*.bib,*.ps,*.patch,*~,CHANGES,*/Extern/SWFFT,*/Extern/hpgmg,./tmp_install_dir,./installdir,*/build,*/tmp_build_dir
+ignore-words = .codespell-ignore-words

.github/workflows/cleanup-cache-postpr.yml

@@ -8,7 +8,7 @@ on:
 
 jobs:
   CleanUpCcacheCachePostPR:
-    name: Clean Up Ccahe Cache Post PR
+    name: Clean Up Ccache Cache Post PR
     runs-on: ubuntu-latest
     permissions:
       actions: write
@@ -17,7 +17,7 @@ jobs:
       GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v3
-      - name: Clean up ccahe
+      - name: Clean up ccache
         run: |
           gh extension install actions/gh-actions-cache
 

.github/workflows/cleanup-cache.yml

@@ -8,7 +8,7 @@ on:
 
 jobs:
   CleanUpCcacheCache:
-    name: Clean Up Ccahe Cache for ${{ github.event.workflow_run.name }}
+    name: Clean Up Ccache Cache for ${{ github.event.workflow_run.name }}
     runs-on: ubuntu-latest
     permissions:
       actions: write
@@ -17,7 +17,7 @@ jobs:
       GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v3
-      - name: Clean up ccahe
+      - name: Clean up ccache
         run: |
           gh extension install actions/gh-actions-cache
 

.github/workflows/codespell.yml

@@ -0,0 +1,23 @@
+name: codespell
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-codespell
+  cancel-in-progress: true
+
+jobs:
+  codespell:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install codespell
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y --no-install-recommends python3-pip
+          pip3 install --user codespell
+
+      - name: Run codespell
+        run: codespell

Docs/sphinx_documentation/source/AmrCore.rst

@@ -238,7 +238,7 @@ Within AMReX_Interpolater.cpp/H are the derived classes:
 
 -  :cpp:`FaceLinear`
 
--  :cpp:`FaceDivFree`: This is more accurately a divergence-preserving interpolation on face centered data, i.e., it ensures the divergence of the fine ghost cells match the value of the divergence of the underlying coarse cell. All fine cells overlying a given coarse cell will have the same divergence, even when the coarse grid divergence is spatially varying. Note that when using this with :cpp:`FillPatch` for time sub-cycling, the coarse grid times may not match the fine grid time, in which case :cpp:`FillPatch` will create coarse values at the fine time before calling this interpolation and the result of the :cpp:`FillPatch` is *not* garanteed to preserve the original divergence.
+-  :cpp:`FaceDivFree`: This is more accurately a divergence-preserving interpolation on face centered data, i.e., it ensures the divergence of the fine ghost cells match the value of the divergence of the underlying coarse cell. All fine cells overlying a given coarse cell will have the same divergence, even when the coarse grid divergence is spatially varying. Note that when using this with :cpp:`FillPatch` for time sub-cycling, the coarse grid times may not match the fine grid time, in which case :cpp:`FillPatch` will create coarse values at the fine time before calling this interpolation and the result of the :cpp:`FillPatch` is *not* guaranteed to preserve the original divergence.
 
 These Interpolaters can be executed on CPU or GPU, with certain limitations:
 

Src/AmrCore/AMReX_FillPatcher.H

@@ -30,7 +30,7 @@ namespace amrex {
  * (1) This class is for filling data during time stepping, not during
  * regrid.  The fine level data passed as input must have the same BoxArray
  * and DistributionMapping as the destination.  It's OK they are the same
- * MultiFab.  For AmrLevel based codes, AmrLevel::FillPatcherFill wil try to
+ * MultiFab.  For AmrLevel based codes, AmrLevel::FillPatcherFill will try to
  * use FillPatcher if it can, and AmrLevel::FillPatch will use the fillpatch
  * functions.
  *
@@ -64,7 +64,7 @@ namespace amrex {
  * AMR levels.  This operation at the coarse/fine boundary is non-trivial
  * for RK orders higher than 2.  Note that it is expected that time stepping
  * on the coarse level is perform before any fine level time stepping, and
- * it's the user's reponsibility to properly create and destroy this object.
+ * it's the user's responsibility to properly create and destroy this object.
  * See AmrLevel::RK for an example of using the RungeKutta functions and
  * FillPatcher together.
  */
@@ -419,7 +419,7 @@ void FillPatcher<MF>::storeRKCoarseData (Real /*time*/, Real dt, MF const& S_old
     auto const& fpc = getFPinfo();
 
     for (auto& tmf : m_cf_crse_data) {
-        tmf.first = std::numeric_limits<Real>::lowest(); // because we dont' need it
+        tmf.first = std::numeric_limits<Real>::lowest(); // because we don't need it
         tmf.second = std::make_unique<MF>(make_mf_crse_patch<MF>(fpc, m_ncomp));
     }
     m_cf_crse_data[0].second->ParallelCopy(S_old, m_cgeom.periodicity());

Src/AmrCore/AMReX_FluxRegister.H

@@ -171,7 +171,7 @@ public:
                   const Geometry& geom);
 
     /**
-    * \brief /in this version the area is assumed to muliplied into the flux (if not, use scale to fix)
+    * \brief /in this version the area is assumed to multiplied into the flux (if not, use scale to fix)
     *
     * \param mflx
     * \param dir
@@ -192,7 +192,7 @@ public:
     /**
     * \brief Increment flux correction with fine data.
     *
-    * /in this version the area is assumed to muliplied into the flux (if not, use scale to fix)
+    * /in this version the area is assumed to multiplied into the flux (if not, use scale to fix)
     *
     * \param mflx
     * \param dir
@@ -230,7 +230,7 @@ public:
     /**
     * \brief Increment flux correction with fine data.
     *
-    * in this version the area is assumed to muliplied into the flux (if not, use scale to fix)
+    * in this version the area is assumed to multiplied into the flux (if not, use scale to fix)
     *
     * \param flux
     * \param dir

Src/Base/AMReX.cpp

@@ -408,8 +408,8 @@ amrex::Initialize (int& argc, char**& argv, bool build_parm_parse,
             else
             {
                 // This counts command line arguments before a "--"
-                // and only sends the preceeding arguments to ParmParse;
-                // the rest get ingored.
+                // and only sends the preceding arguments to ParmParse;
+                // the rest get ignored.
                 int ppargc = 1;
                 for (; ppargc < argc; ++ppargc) {
                     if (std::strcmp(argv[ppargc], "--") == 0) { break; }
@@ -514,7 +514,7 @@ amrex::Initialize (int& argc, char**& argv, bool build_parm_parse,
             pp.queryAdd("handle_sigfpe" , system::handle_sigfpe );
             pp.queryAdd("handle_sigill" , system::handle_sigill );
 
-            // We save the singal handlers and restore them in Finalize.
+            // We save the signal handlers and restore them in Finalize.
             if (system::handle_sigsegv) {
                 prev_handler_sigsegv = std::signal(SIGSEGV, BLBackTrace::handler);
             } else {

Src/Base/AMReX_ANSIEscCode.H

@@ -16,7 +16,7 @@ namespace Font {
     constexpr char RapidBlink  [] = "\033[6m";
 }
 
-namespace FGColor { // Forground colors
+namespace FGColor { // Foreground colors
     constexpr char Black         [] = "\033[30m";
     constexpr char Red           [] = "\033[31m";
     constexpr char Green         [] = "\033[32m";

Src/Base/AMReX_Arena.H

@@ -146,7 +146,7 @@ public:
     /**
      * \brief Does the device have enough free memory for allocating this
      * much memory?  For CPU builds, this always return true.  This is not a
-     * const funciton because it may attempt to release memory back to the
+     * const function because it may attempt to release memory back to the
      * system.
      */
     [[nodiscard]] virtual bool hasFreeDeviceMemory (std::size_t sz);

Src/Base/AMReX_BLProfiler.cpp

@@ -1281,7 +1281,7 @@ void BLProfiler::WriteCommStats(bool bFlushing, bool memCheck)
       nfiHeader.Stream() << "CommProfProc  " << myProc
                          << "  nCommStats  " << vCommStats.size()
                          << "  datafile  " << localDFileName
-                         << "  seekpos  " << nfiDatafile.SeekPos()    // ---- data file seek posotion
+                         << "  seekpos  " << nfiDatafile.SeekPos()    // ---- data file seek position
                          << "  " << procName << '\n';
       for(int ib(0); ib < CommStats::barrierNames.size(); ++ib) {
           int seekindex(CommStats::barrierNames[ib].second);

Src/Base/AMReX_CArena.H

@@ -70,7 +70,7 @@ public:
     /**
      * \brief Does the device have enough free memory for allocating this
      * much memory?  For CPU builds, this always return true.  This is not a
-     * const funciton because it may attempt to release memory back to the
+     * const function because it may attempt to release memory back to the
      * system.
      */
     [[nodiscard]] bool hasFreeDeviceMemory (std::size_t sz) final;

Src/Base/AMReX_CTOParallelForImpl.H

@@ -180,7 +180,7 @@ ParallelFor (TypeList<CTOs...> /*list_of_compile_time_options*/,
  *
  * \param ctos   list of all possible values of the parameters.
  * \param option the run time parameters.
- * \param N      an interger specifying the 1D for loop's range.
+ * \param N      an integer specifying the 1D for loop's range.
  * \param f      a callable object taking an integer and working on that iteration.
  */
 template <typename T, class F, typename... CTOs>

Src/Base/AMReX_DistributionMapping.H

@@ -405,7 +405,7 @@ DistributionMapping MakeSimilarDM (const BoxArray& ba, const MultiFab& mf, const
  *  of overlap with.
  *
  *  @param[in] ba The BoxArray we want to generate a DistributionMapping for.
- *  @param[in] src_ba The BoxArray associatied with the src DistributionMapping.
+ *  @param[in] src_ba The BoxArray associated with the src DistributionMapping.
  *  @param[in] src_dm The input DistributionMapping we want the output to be similar to.
  *  @param[in] ng The number of grow cells to use when computing intersection / overlap
  *  @return The computed DistributionMapping.

Src/Base/AMReX_FabArray.H

@@ -723,7 +723,7 @@ public:
     *
     * \param comp   component
     * \param nghost number of ghost cells
-    * \param local  If true, MPI communciation is skipped.
+    * \param local  If true, MPI communication is skipped.
     */
     template <typename F=FAB, std::enable_if_t<IsBaseFab<F>::value,int> = 0>
     typename F::value_type
@@ -1205,7 +1205,7 @@ public:
      * \param comp           starting component
      * \param ncomp          number of components
      * \param nghost         number of ghost cells
-     * \param local          If true, MPI communciation is skipped.
+     * \param local          If true, MPI communication is skipped.
      * \param ignore_covered ignore covered cells. Only relevant for cell-centered EB data.
      */
     template <typename F=FAB, std::enable_if_t<IsBaseFab<F>::value,int> = 0>
@@ -1220,7 +1220,7 @@ public:
      * \param comp   starting component
      * \param ncomp  number of components
      * \param nghost number of ghost cells
-     * \param local  If true, MPI communciation is skipped.
+     * \param local  If true, MPI communication is skipped.
      */
     template <typename IFAB, typename F=FAB, std::enable_if_t<IsBaseFab<F>::value,int> = 0>
     typename F::value_type

Src/Base/AMReX_FabArrayUtility.H

@@ -1547,7 +1547,7 @@ indexFromValue (FabArray<FAB> const& mf, int comp, IntVect const& nghost,
  * \param ycomp  starting component of y
  * \param ncomp  number of components
  * \param nghost number of ghost cells
- * \param local  If true, MPI communciation is skipped.
+ * \param local  If true, MPI communication is skipped.
  */
 template <typename FAB, std::enable_if_t<IsBaseFab<FAB>::value,int> FOO = 0>
 typename FAB::value_type

Src/Base/AMReX_GpuControl.H

@@ -150,7 +150,7 @@ namespace Gpu {
     }
 
     /**
-     * This struct provides a RAII-style mechansim for changing the number
+     * This struct provides a RAII-style mechanism for changing the number
      * of streams returned by Gpu::numStreams() to a single stream.
      */
     struct [[nodiscard]] SingleStreamRegion
@@ -166,7 +166,7 @@ namespace Gpu {
     };
 
     /**
-     * This struct provides a RAII-style mechansim for disabling GPU
+     * This struct provides a RAII-style mechanism for disabling GPU
      * synchronization in MFITer by default.  Note that explicit calls to
      * Gpu::steramSynchronize and Gpu::deviceSynchronize still work.
      */

Src/Base/AMReX_IntVect.H

@@ -108,7 +108,7 @@ public:
 
     /**
     * \brief Construct an IntVect from an Vector<int>.  It is an error if
-    * the Vector<int> doesn' t have the same dimension as this
+    * the Vector<int> doesn't have the same dimension as this
     * IntVect.
     */
     explicit IntVect (const Vector<int>& a) noexcept : vect{AMREX_D_DECL(a[0],a[1],a[2])} {

Src/Base/AMReX_MultiFabUtilI.H

@@ -64,7 +64,7 @@ namespace amrex::MFUtil {
 
 
         //! Regrid (by duplication) class T (which must be either of type
-        //! MultiFab or iMultiFab) usign the new BoxArray and
+        //! MultiFab or iMultiFab) using the new BoxArray and
         //! DistributionMapping. The boolean flag `regrid_ghost` switched
         //! between the SymmetricGhost and AsymmetricGhost copy functions.
         template<typename T>

Src/Base/AMReX_PODVector.H

@@ -422,7 +422,7 @@ namespace amrex
 
         iterator insert (const_iterator a_pos, T&& a_item)
         {
-            // This is *POD* vector afterall
+            // This is *POD* vector after all
             return insert(a_pos, 1, a_item);
         }
 

Src/Base/AMReX_ParReduce.H

@@ -14,7 +14,7 @@ namespace amrex {
  * the second MultiFab.
  \verbatim
      auto const& ma1 = mf1.const_arrays();
-     auot const& ma2 = mf2.const_arrays();
+     auto const& ma2 = mf2.const_arrays();
      GpuTuple<Real,Real> mm = ParReduce(TypeList<ReduceOpMin,ReduceOpMax>{},
                                         TypeList<Real,Real>{},
                                         mf1, mf1.nGrowVect(),
@@ -29,7 +29,7 @@ namespace amrex {
  *                ReduceOpLogicalAnd, and ReduceOpLogicalOr)
  * \tparam Ts...  data types (e.g., Real, int, etc.)
  * \tparam FAB    MultiFab/FabArray type
- * \tparam F      callable type like a lambda funcion
+ * \tparam F      callable type like a lambda function
  *
  * \param operation_list list of reduce operators
  * \param type_list      list of data types
@@ -79,7 +79,7 @@ ParReduce (TypeList<Ops...> operation_list, TypeList<Ts...> type_list,
  *             ReduceOpLogicalAnd, and ReduceOpLogicalOr)
  * \tparam T   data type (e.g., Real, int, etc.)
  * \tparam FAB MultiFab/FabArray type
- * \tparam F   callable type like a lambda funcion
+ * \tparam F   callable type like a lambda function
  *
  * \param operation_list a reduce operator stored in TypeList
  * \param type_list      a data type stored in TypeList
@@ -113,7 +113,7 @@ ParReduce (TypeList<Op> operation_list, TypeList<T> type_list,
  * and the maximum of the second MultiFab.
  \verbatim
      auto const& ma1 = mf1.const_arrays();
-     auot const& ma2 = mf2.const_arrays();
+     auto const& ma2 = mf2.const_arrays();
      GpuTuple<Real,Real> mm = ParReduce(TypeList<ReduceOpMin,ReduceOpMax>{},
                                         TypeList<Real,Real>{},
                                         mf1, mf1.nGrowVect(), mf1.nComp(),
@@ -128,7 +128,7 @@ ParReduce (TypeList<Op> operation_list, TypeList<T> type_list,
  *                ReduceOpLogicalAnd, and ReduceOpLogicalOr)
  * \tparam Ts...  data types (e.g., Real, int, etc.)
  * \tparam FAB    MultiFab/FabArray type
- * \tparam F      callable type like a lambda funcion
+ * \tparam F      callable type like a lambda function
  *
  * \param operation_list list of reduce operators
  * \param type_list      list of data types
@@ -175,7 +175,7 @@ ParReduce (TypeList<Ops...> operation_list, TypeList<Ts...> type_list,
  *             ReduceOpLogicalAnd, and ReduceOpLogicalOr)
  * \tparam T   data type (e.g., Real, int, etc.)
  * \tparam FAB MultiFab/FabArray type
- * \tparam F   callable type like a lambda funcion
+ * \tparam F   callable type like a lambda function
  *
  * \param operation_list a reduce operator stored in TypeList
  * \param type_list      a data type stored in TypeList
@@ -210,7 +210,7 @@ ParReduce (TypeList<Op> operation_list, TypeList<T> type_list,
  * the second MultiFab.
  \verbatim
      auto const& ma1 = mf1.const_arrays();
-     auot const& ma2 = mf2.const_arrays();
+     auto const& ma2 = mf2.const_arrays();
      GpuTuple<Real,Real> mm = ParReduce(TypeList<ReduceOpMin,ReduceOpMax>{},
                                         TypeList<Real,Real>{}, mf1,
      [=] AMREX_GPU_DEVICE (int box_no, int i, int j, int k) noexcept
@@ -224,7 +224,7 @@ ParReduce (TypeList<Op> operation_list, TypeList<T> type_list,
  *                ReduceOpLogicalAnd, and ReduceOpLogicalOr)
  * \tparam Ts...  data types (e.g., Real, int, etc.)
  * \tparam FAB    MultiFab/FabArray type
- * \tparam F      callable type like a lambda funcion
+ * \tparam F      callable type like a lambda function
  *
  * \param operation_list list of reduce operators
  * \param type_list      list of data types
@@ -268,7 +268,7 @@ ParReduce (TypeList<Ops...> operation_list, TypeList<Ts...> type_list,
  *             ReduceOpLogicalAnd, and ReduceOpLogicalOr)
  * \tparam T   data type (e.g., Real, int, etc.)
  * \tparam FAB MultiFab/FabArray type
- * \tparam F   callable type like a lambda funcion
+ * \tparam F   callable type like a lambda function
  *
  * \param operation_list a reduce operator stored in TypeList
  * \param type_list      a data type stored in TypeList