add codespell CI (#1176)

.codespell-ignore-words

@@ -0,0 +1,15 @@
+blocs
+bloc
+inout
+pres
+bion
+tye
+delt
+thi
+daa
+numer
+clen
+coul
+dum
+crate
+vie

.codespellrc

@@ -0,0 +1,5 @@
+[codespell]
+skip = .git,*.ipynb,*.bib,*.ps,*~
+ignore-words = .codespell-ignore-words
+
+

.github/workflows/codespell.yml

@@ -0,0 +1,41 @@
+name: codespell
+
+on:
+  push:
+    branches:
+      - development
+      - main
+  pull_request:
+    branches:
+      - development
+
+jobs:
+  codespell:
+    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: Install dependencies
+        run: pip install codespell
+
+      - name: Run codespell
+        run: |
+          codespell
+

CHANGES.md

@@ -66,7 +66,7 @@
 
 # 22.11
 
-  * use of the auxillary state to define composition is now enabled
+  * use of the auxiliary state to define composition is now enabled
     via USE_AUX_THERMO and the preprocessor variable AUX_THERMO
     (#1003)
 
@@ -175,7 +175,7 @@
     breakout reactions (#751)
 
   * Some fixes to the NSE bailout in aprox19 (#739, #753, #755) and
-    the relaxation check on the NSE critera (#754)
+    the relaxation check on the NSE criteria (#754)
 
   * Added a new unit test for single-zone SDC (burn_cell_sdc) (#744)
 
@@ -560,7 +560,7 @@
     corresponding inverse from the work of Deboer et al. 2017
     (https://journals.aps.org/rmp/abstract/10.1103/RevModPhys.89.035007).
     To use the new rate, user must set `use_c12ag_deboer17` to `true`.
-    This rate is only useable in the `aprox13`, `aprox19`, `aprox21`,
+    This rate is only usable in the `aprox13`, `aprox19`, `aprox21`,
     and `iso7` reaction rate networks. Closes issue #44.
 
   * a routine util/cj_detonation was added to compute the
@@ -582,7 +582,7 @@
 
    * we now disable some composition derivatives in the EOS
      by default, for performance and memory reasons.  They can
-     be reenabled by defining the preprocessor variable
+     be re-enabled by defining the preprocessor variable
      EXTRA_THERMO (PR #59)
 
 # 17.10

EOS/helmholtz/actual_eos.H

@@ -677,7 +677,7 @@ void apply_coulomb_corrections (T& state)
 
     // uniform background corrections only
     // from yakovlev & shalybkov 1989
-    // lami is the average ion seperation
+    // lami is the average ion separation
     // plasg is the plasma coupling parameter
 
     Real ytot1 = 1.0e0_rt / state.abar;

integration/VODE/actual_integrator.H

@@ -76,7 +76,7 @@ void actual_integrator (burn_t& state, Real dt)
     // this in case we failed in our burn here because we entered NSE
 
 #ifdef AUX_THERMO
-    // need to sync the auxilary data up with the new mass fractions
+    // need to sync the auxiliary data up with the new mass fractions
     set_aux_comp_from_X(state);
 #endif
 

integration/VODE/vode_type.H

@@ -17,7 +17,7 @@ typedef ArrayUtil::MathArray2D<1, VODE_NEQS, 1, VODE_NEQS> RArray2D;
 
 const amrex::Real UROUND = std::numeric_limits<amrex::Real>::epsilon();
 
-// CCMXJ  = Threshhold on DRC for updating the Jacobian
+// CCMXJ  = Threshold on DRC for updating the Jacobian
 const amrex::Real CCMXJ = 0.2e0_rt;
 
 const amrex::Real HMIN = 0.0_rt;

integration/integrator_rhs_strang.H

@@ -36,7 +36,7 @@ void rhs (const Real time, burn_t& state, T& int_state, RArray1D& ydot, [[maybe_
     // network
 
     // Fix the state as necessary -- this ensures that the mass
-    // fractions that enter are valud (and optionally normalized)
+    // fractions that enter are valid (and optionally normalized)
 
     clean_state(int_state);
 

integration/nse_update_strang.H

@@ -52,7 +52,7 @@ void nse_burn(burn_t& state, const Real dt) {
 
   // call the NSE table using the * state to get the t^{n+1}
   // source estimates.  The thermodynamnics here is specified
-  // in terms of the auxillary composition, Ye, abar, and B/A
+  // in terms of the auxiliary composition, Ye, abar, and B/A
 
   nse_interp(T_in, state.rho, state.aux[iye],
              abar_out, dq_out, dyedt, X);
@@ -61,7 +61,7 @@ void nse_burn(burn_t& state, const Real dt) {
 
   state.aux[iye] += dt * dyedt;
 
-  // now get the composition from the table using the upated Ye
+  // now get the composition from the table using the updated Ye
 
   nse_interp(T_in, state.rho, state.aux[iye],
              abar_out, dq_out, dyedt, X);

interfaces/burn_type.H

@@ -37,7 +37,7 @@ typedef amrex::Array1D<Real, 1, neqs> YdotNetArray1D;
 
 #if defined(SDC_EVOLVE_ENERGY)
 
-// these indicies represent the order that the conserved state comes
+// these indices represent the order that the conserved state comes
 // into the ODE integration from the hydro code.
 //
 // they also represent the order of the advective sources

networks/aprox19/README.md

@@ -23,7 +23,7 @@ from Stan:
 > Probably all the code needs for hydrodynamics and energy generation
 > is abar and Ye (given rho and T) so to follow explosions you can use
 > the smaller table. It also gives crude measures of nucleosyntheis in
-> n+p+helium, si-ca, fe group. Probaly good enough for NSE
+> n+p+helium, si-ca, fe group. Probably good enough for NSE
 >
 > If you are following bufk nucleosynthesis you can use the larger table
 > which gives 125 isotopes packaged into 19 (CASTRO used to use the 19
@@ -48,7 +48,7 @@ The mapping of the nuclei from the large network to the 19 we carry is:
 * 13: 44Ti
 * 14: 48Cr
 * 15: 52Fe
-* 16: all oher iron group except 56Ni
+* 16: all other iron group except 56Ni
 * 17: 56Ni
 * 18: neutrons
 * 19: protons
@@ -158,4 +158,4 @@ similar rate for beta decay and positron capture
 
 So if electron capture dominates wrate is positive
 
-The inference is that it is a positive term that is subtracted from Ye
+The inference is that it is a positive term that is subtracted from Ye

networks/general_null/breakout.net

@@ -4,6 +4,6 @@
 # name short-name aion zion
  X X        1.0 1.0
 
-# auxillary variables
+# auxiliary variables
 __aux_Ye
 __aux_invmu

networks/general_null/gammalaw_aux.net

@@ -4,5 +4,5 @@
 # name short-name aion zion
  X X        1.0 1.0
 
-# auxillary variables
+# auxiliary variables
 __aux_Ye

networks/general_null/network_param_file.py

@@ -1,4 +1,4 @@
-"""core functions for deailing with a network file"""
+"""core functions for dealing with a network file"""
 
 import sys
 
@@ -17,13 +17,13 @@ def __str__(self):
 
 
 class AuxVar:
-    """convenience class for an auxilliary variable"""
+    """convenience class for an auxiliary variable"""
     def __init__(self):
         self.name = ""
         self.preprocessor = None
 
     def __str__(self):
-        return f"auxillary variable {self.name}"
+        return f"auxiliary variable {self.name}"
 
 
 class UnusedVar:
@@ -151,15 +151,15 @@ def parse_network_object(fields, defines):
         ret = AuxVar()
         ret.name = fields[0][6:]
         # we can put a preprocessor variable after the aux name to
-        # require that it be set in order to define the auxillary
+        # require that it be set in order to define the auxiliary
         # variable
         try:
             ret.preprocessor = fields[1]
         except IndexError:
             ret.preprocessor = None
 
         # we can put a preprocessor variable after the aux name to
-        # require that it be set in order to define the auxillary
+        # require that it be set in order to define the auxiliary
         # variable
         try:
             ret.preprocessor = fields[1]
@@ -173,7 +173,7 @@ def parse_network_object(fields, defines):
                 ret = UnusedVar()
 
         # we can put a preprocessor variable after the aux name to
-        # require that it be set in order to define the auxillary
+        # require that it be set in order to define the auxiliary
         # variable
         try:
             ret.preprocessor = fields[1]

networks/rprox/README.md

@@ -5,7 +5,7 @@ essentially the network described in Appendix C of Wallace & Woosley,
 ApJS 45, 389 (1981) but with updated reaction rates from ReacLib.
 
 The default setup is for burning in a neutron star atmosphere.  If you
-want a setup at lower density, you need to change the Lweak paramter
+want a setup at lower density, you need to change the Lweak parameter
 in actual_rhs.f90.
 
 This network was used in:

neutrinos/sneut5.H

@@ -285,7 +285,7 @@ void sneut5(const Real temp, const Real den,
     // theta is sin**2(theta_weinberg) = 0.2319 plus/minus 0.00005 (1996)
     // xnufam is the number of neutrino flavors = 3.02 plus/minus 0.005 (1998)
     // change theta and xnufam if need be, and the changes will automatically
-    // propagate through the routine. cv and ca are the vektor and axial currents.
+    // propagate through the routine. cv and ca are the vector and axial currents.
 
     constexpr Real theta  = 0.2319e0_rt;
     constexpr Real xnufam = 3.0e0_rt;

nse_solver/nse_check.H

@@ -653,7 +653,7 @@ void nse_union(const int nuc_ind_a, const int nuc_ind_b, amrex::Array1D<int, 1,
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
 int get_pair_rate_index(const int& rate_index){
 
-  // This funciton finds the pair rate index given a rate.
+  // This function finds the pair rate index given a rate.
   // For example given forward rate index, return reverse rate index, vice versa
 
   int pair_rate_index = -1;
@@ -949,7 +949,7 @@ void nse_grouping(amrex::Array1D<int, 1, NumSpec>& group_ind, const burn_t& stat
     merge_indices(2) = -1;
     fastest_t = std::numeric_limits<amrex::Real>::max();
 
-    // Find the fastest time scale of the avaliable reaction
+    // Find the fastest time scale of the available reaction
 
     for (int n = 1; n <= Rates::NumRates; ++n){
 
@@ -1002,7 +1002,7 @@ bool in_nse(burn_t& current_state, bool skip_molar_check=false) {
   }
 
   // We can do a further approximation where we use the NSE mass fractions
-  // instead of the current mass fractions. This makes the check soley dependent on
+  // instead of the current mass fractions. This makes the check solely dependent on
   // the thermodynamic condition.
   // Note we only do this after the first check, which should tell us whether
   // our current mass fractions are in the ballpark of NSE mass fractions.
@@ -1067,7 +1067,7 @@ bool in_nse(burn_t& current_state, bool skip_molar_check=false) {
   ydot(NumSpec + 1) = enuc - sneut;
 
   // Now we look through the network and see if there are fast reaction cycles
-  // Need to separate forward and reverse rate and detemine each step is fast enough.
+  // Need to separate forward and reverse rate and determine each step is fast enough.
   // use vectors for now
 
   bool found_fast_reaction_cycle = false;

screening/screen.H

@@ -890,7 +890,7 @@ void chabrier1998 (const plasma_state_t& state,
   }
 
   // Now we add quantum correction terms discussed in Alastuey 1978.
-  // Notice in Alastuey 1978, they have a differnt classical term,
+  // Notice in Alastuey 1978, they have a different classical term,
   // which is implemented in the strong screening limit of our screen5 routine.
 
   // See Wallace1982, Eq. A13

sphinx_docs/source/integrators.rst

@@ -303,7 +303,7 @@ This involves an EOS call and is the default behavior of the integration.
 
 If desired, the EOS call can be skipped and the temperature kept
 frozen over the entire time interval of the integration.  This is done
-bu setting ``integrator.call_eos_in_rhs = 0``.
+by setting ``integrator.call_eos_in_rhs = 0``.
 
 Note also that for the Jacobian, we need the specific heat, :math:`c_v`, since we
 usually calculate derivatives with respect to temperature (as this is the form

unit_test/burn_cell_primordial_chem/README.md

@@ -15,7 +15,7 @@
   because our equations are very stiff (stiffness ratios are as high as 1e31)
   because y/ydot (natural timescale for a species abundance to vary) can be 
   very different (by factors ~ 1e30) for different species.
-  However, state.rho still conatins the density in g/cm^3, and state.e 
+  However, state.rho still contains the density in g/cm^3, and state.e 
   still contains the specific internal energy in erg/g/K.
 
 # continuous integration

unit_test/burn_cell_sdc/parse_integration_failure.py

@@ -40,10 +40,11 @@
 
 import sys
 
+
 def doit(string):
     """break down the SDC VODE integration failure message"""
 
-    # figure out if it is the VODE failre or burn_t that was provided
+    # figure out if it is the VODE failure or burn_t that was provided
 
     is_vode = False
     rhoe = None

unit_test/test_ase/make_table/README.md

@@ -1,6 +1,6 @@
 # NSE check tables
 
-This test is used to have a table that has a variety of differen rho,
+This test is used to have a table that has a variety of different rho,
 T, and Y_e, to test the valitidy of the function `in_nse`.
 
 We solve for the NSE state for variety of different conditions, and update

unit_test/test_conductivity/main.cpp

@@ -112,7 +112,7 @@ void main_main ()
     // time = starting time in the simulation
     Real time = 0.0;
 
-    // How Boxes are distrubuted among MPI processes
+    // How Boxes are distributed among MPI processes
     DistributionMapping dm(ba);
 
     // we allocate our main multifabs

unit_test/test_eos/main.cpp

@@ -104,7 +104,7 @@ void main_main ()
     // time = starting time in the simulation
     Real time = 0.0;
 
-    // How Boxes are distrubuted among MPI processes
+    // How Boxes are distributed among MPI processes
     DistributionMapping dm(ba);
 
     // we allocate our main multifabs

unit_test/test_jac/main.cpp

@@ -112,7 +112,7 @@ void main_main ()
     // time = starting time in the simulation
     Real time = 0.0;
 
-    // How Boxes are distrubuted among MPI processes
+    // How Boxes are distributed among MPI processes
     DistributionMapping dm(ba);
 
     // we allocate our main multifabs

unit_test/test_react/main.cpp

@@ -118,7 +118,7 @@ void main_main ()
     // time = starting time in the simulation
     Real time = 0.0;
 
-    // How Boxes are distrubuted among MPI processes
+    // How Boxes are distributed among MPI processes
     DistributionMapping dm(ba);
 
     // we allocate our main multifabs
@@ -165,7 +165,7 @@ void main_main ()
                         amrex::max(xn[n], 1.e-10_rt);
                 }
 
-                // initialize the auxillary state (in particular, for NSE)
+                // initialize the auxiliary state (in particular, for NSE)
 #ifdef AUX_THERMO
                 eos_t eos_state;
                 for (int n = 0; n < NumSpec; n++) {