CI: Add codespell (#112)

.codespell-ignore-words

@@ -0,0 +1,4 @@
+Blocs
+inout
+ptd
+recuse

.codespellrc

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

.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@v4
+
+      - 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

CODE_OF_CONDUCT.md

@@ -5,7 +5,7 @@
 We as members, contributors, and leaders pledge to make participation in our
 community a harassment-free experience for everyone, regardless of age, body
 size, visible or invisible disability, ethnicity, sex characteristics, gender
-identity and expression, level of experience, education, socio-economic status,
+identity and expression, level of experience, education, socioeconomic status,
 nationality, personal appearance, race, caste, color, religion, or sexual
 identity and orientation.
 

Docs/sphinx_documentation/source/EB.rst

@@ -21,7 +21,7 @@ incflo provides several options of embedded boundary geometries. The inputs para
 determines which geometry is selected by :cpp:`incflo::MakeEBGeometry()` within :cpp:`incflo/src/embedded_boundaries`.
 The procedure to create your own EB geometry is described in the AMReX documentation on :ref:`amrex:sec:EB:ebinit`.
 As discussed in the AMReX documentation, note that when constructing the EB, we must specify a
-maxium coarsening level (``max_crse_level``):
+maximum coarsening level (``max_crse_level``):
 
 .. highlight:: c++
 

Docs/sphinx_documentation/source/GettingStarted.rst

@@ -370,4 +370,4 @@ files are used for restarting the code. For more information see the AMReX Docum
 Visualizing the Results
 =======================
 
-Options for visualizing the data are discussed in the AMReX Documenation on :ref:`amrex:Chap:Visualization`.
+Options for visualizing the data are discussed in the AMReX Documentation on :ref:`amrex:Chap:Visualization`.

Docs/sphinx_documentation/source/InputsProblemDefinition.rst

@@ -65,10 +65,9 @@ Setting basic boundary conditions can be specified by inputs preceded by "xlo",
    The implementation requires that there is EB separating the inflow and outflow regions,
    and only currently treats constant viscosity (i.e. requires the inputs file contains  ``incflo.use_tensor_solve = false``).
    It does allow for non-constant scalar diffusivity. To create a new problem setup with mixed BCs, one must additionally
-   specify the Dirchlet and Neumann areas in ``prob/prob_bc.cpp`` In this file there are functions to set the needed BC info for the diffusion solver, the MAC projection, and with the same function, the nodal projection and advection. Comments in the code provide a detailed explaination for each instance. For addditional details on mixed BCs, also see AMReX-Hydro's documentation (:ref:`bcs`).
+   specify the Dirchlet and Neumann areas in ``prob/prob_bc.cpp`` In this file there are functions to set the needed BC info for the diffusion solver, the MAC projection, and with the same function, the nodal projection and advection. Comments in the code provide a detailed explanation for each instance. For additional details on mixed BCs, also see AMReX-Hydro's documentation (:ref:`bcs`).
 
 ..
    To create a new setup:
    initial conditions go in prob/prob_init_fluid.cpp
    inflow boundary conditions are set in prob/prob_bc.H -- the BCType for mixed bc is set at foextrap here to allow the outflow to get appropriately filled, which would already have happened before reaching these functions.
-

src/boundary_conditions/incflo_set_bcs.cpp

@@ -156,7 +156,7 @@ incflo::make_robinBC_MFs(int lev, MultiFab* state)
                 Array4<Real> const& f_arr     = robin_f.array(mfi);
 
                 if (state) {
-                    // state has filled boundry, so can use its ghost cells for the BC values
+                    // state has filled boundary, so can use its ghost cells for the BC values
                     Array4<Real const> const& bcv = state->const_array(mfi);
                     // Diffusion, solving for velocity, density, tracer
                     //

src/convection/incflo_compute_advection_term.cpp

@@ -224,7 +224,7 @@ incflo::compute_convective_term (Vector<MultiFab*> const& conv_u,
             {
                 //
                 // BDS needs umac on physical boundaries.
-                // Godunov handles physical boundaries interally, but needs periodic ghosts filled.
+                // Godunov handles physical boundaries internally, but needs periodic ghosts filled.
                 // MOL doesn't need any umac ghost cells, so it doesn't get here.
                 //
                 Real fake_time = 0.;

src/particles/ParticleData.H

@@ -210,7 +210,7 @@ class ParticleData
             return m_namelist_unalloc;
         }
 
-        /*! queries if containe has species of a certain name */
+        /*! queries if container has species of a certain name */
         inline bool contains ( const std::string& a_name ) const
         {
             BL_PROFILE("ParticleData::contains()");
@@ -238,4 +238,3 @@ class ParticleData
 
 #endif
 #endif
-

src/prob/prob_init_fluid.cpp

@@ -858,7 +858,7 @@ void incflo::init_periodic_tracer (Box const& vbx, Box const& /*gbx*/,
             tracer(i,j,k,1) = A *(std::sin(C*(y+z) - Real(0.00042)) + Real(1.0)) * std::exp(x);
         });
     } else {
-        Abort("Unknow periodic tracer probtype");
+        Abort("Unknown periodic tracer probtype");
     }
 }
 

src/setup/init.cpp

@@ -82,7 +82,7 @@ void incflo::ReadParameters ()
             m_redistribution_type != "StateRedist")
             amrex::Abort("redistribution type must be NoRedist, FluxRedist, or StateRedist");
 
-        if (m_advection_type == "Godunov" && m_godunov_ppm) amrex::Abort("Cant use PPM with EBGodunov");
+        if (m_advection_type == "Godunov" && m_godunov_ppm) amrex::Abort("Can't use PPM with EBGodunov");
         pp.query("write_geom_chk", m_write_geom_chk);
 #endif
 

test_2d/benchmark.rotated_planes_y

@@ -85,7 +85,7 @@ cylinder.center    =  0.0  0.0  0.0
 incflo.probtype         =   6
 
 # Note that with this prob_type, ic_u is used to mean the velocity
-# along the direction of the cylinder, irregardless of the direction
+# along the direction of the cylinder, regardless of the direction
 # of the cylinder
 incflo.ic_u             = -0.5          #
 incflo.ic_v             =  0.8660254038 #

test_bds_2d/inputs.circ_traceradvect

@@ -1,4 +1,4 @@
-amrex.fpe_trap_invalid=1                # hav a trap to catch a bug
+amrex.fpe_trap_invalid=1                # have a trap to catch a bug
 incflo.probtype         =  14
 #¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
 #            SIMULATION STOP            #

test_bds_2d/inputs.gaussian_traceradvect

@@ -1,4 +1,4 @@
-amrex.fpe_trap_invalid=1                # hav a trap to catch a bug
+amrex.fpe_trap_invalid=1                # have a trap to catch a bug
 incflo.probtype         =  15
 #¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
 #            SIMULATION STOP            #

test_bds_3d/inputs.circ_traceradvect

@@ -1,4 +1,4 @@
-amrex.fpe_trap_invalid=1                # hav a trap to catch a bug
+amrex.fpe_trap_invalid=1                # have a trap to catch a bug
 incflo.probtype         =  14
 #¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
 #            SIMULATION STOP            #

test_bds_3d/inputs.gaussian_traceradvect

@@ -1,4 +1,4 @@
-amrex.fpe_trap_invalid=1                # hav a trap to catch a bug
+amrex.fpe_trap_invalid=1                # have a trap to catch a bug
 incflo.probtype         =  15
 #¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨#
 #            SIMULATION STOP            #