Fix misspellings found with codespell (#173)

yut23 · web-flow · commit aa189b0cd8d3 · 2023-04-26T16:36:02.000-04:00
diff --git a/pyproject.toml b/pyproject.toml
@@ -42,3 +42,7 @@ defining-attr-methods = [
 
 [tool.pylint.FORMAT]
 max-line-length = 132
+
+[tool.codespell]
+skip = ".git,*docs/build"
+ignore-words-list = "pres"
diff --git a/pyro/compressible/interface.py b/pyro/compressible/interface.py
@@ -81,7 +81,7 @@ def states(idir, ng, dx, dt,
     qv : ndarray
         The primitive state vector
     dqv : ndarray
-        Spatial derivitive of the state vector
+        Spatial derivative of the state vector
 
     Returns
     -------
@@ -1121,7 +1121,7 @@ def consFlux(idir, gamma, idens, ixmom, iymom, iener, irhoX, nspec, U_state):
 def artificial_viscosity(ng, dx, dy,
                          cvisc, u, v):
     r"""
-    Compute the artifical viscosity.  Here, we compute edge-centered
+    Compute the artificial viscosity.  Here, we compute edge-centered
     approximations to the divergence of the velocity.  This follows
     directly Colella \ Woodward (1984) Eq. 4.5
 
diff --git a/pyro/compressible/problems/_ramp.defaults b/pyro/compressible/problems/_ramp.defaults
@@ -1,7 +1,7 @@
 # these defaults comes from the third test problem in 
 # Woodward and Colella. Journal of Computational Physics, 54, 115-174, 1984
 #
-# Also, the numbers is consitent with the ones in Castro
+# Also, the numbers is consistent with the ones in Castro
 #
 
 
diff --git a/pyro/compressible/problems/quad.py b/pyro/compressible/problems/quad.py
@@ -53,7 +53,7 @@ def init_data(my_data, rp):
 
     # there is probably an easier way to do this, but for now, we
     # will just do an explicit loop.  Also, we really want to set
-    # the pressue and get the internal energy from that, and then
+    # the pressure and get the internal energy from that, and then
     # compute the total energy (which is what we store).  For now
     # we will just fake this
 
diff --git a/pyro/compressible/problems/ramp.py b/pyro/compressible/problems/ramp.py
@@ -45,7 +45,7 @@ def init_data(my_data, rp):
 
     # there is probably an easier way to do this, but for now, we
     # will just do an explicit loop.  Also, we really want to set
-    # the pressue and get the internal energy from that, and then
+    # the pressure and get the internal energy from that, and then
     # compute the total energy (which is what we store).  For now
     # we will just fake this
 
diff --git a/pyro/compressible/problems/rt2.py b/pyro/compressible/problems/rt2.py
@@ -1,5 +1,5 @@
 """A RT problem with two distinct modes: short wave length on the
-left and long wavelenght on the right.  This allows one to see
+left and long wavelength on the right.  This allows one to see
 how the growth rate depends on wavenumber.
 """
 
diff --git a/pyro/compressible/simulation.py b/pyro/compressible/simulation.py
@@ -129,7 +129,7 @@ def initialize(self, extra_vars=None, ng=4):
             for v in extra_vars:
                 my_data.register_var(v, bc)
 
-        # store the EOS gamma as an auxillary quantity so we can have a
+        # store the EOS gamma as an auxiliary quantity so we can have a
         # self-contained object stored in output files to make plots.
         # store grav because we'll need that in some BCs
         my_data.set_aux("gamma", self.rp.get_param("eos.gamma"))
@@ -142,7 +142,7 @@ def initialize(self, extra_vars=None, ng=4):
         if self.rp.get_param("particles.do_particles") == 1:
             self.particles = particles.Particles(self.cc_data, bc, self.rp)
 
-        # some auxillary data that we'll need to fill GC in, but isn't
+        # some auxiliary data that we'll need to fill GC in, but isn't
         # really part of the main solution
         aux_data = self.data_class(my_grid)
         aux_data.register_var("ymom_src", bc_yodd)
diff --git a/pyro/compressible_react/TODO b/pyro/compressible_react/TODO
@@ -1,7 +1,7 @@
--- modify the main compressible init to allow for auxillary advected
+-- modify the main compressible init to allow for auxiliary advected
    quantities
 
--- modify the interface reconstruction to allow for auxillary advected
+-- modify the interface reconstruction to allow for auxiliary advected
    quantities
 
 -- create a burning module that can be imported
diff --git a/pyro/compressible_sr/interface.py b/pyro/compressible_sr/interface.py
@@ -81,7 +81,7 @@ def states(idir, ng, dx, dt,
     qv : ndarray
         The primitive state vector
     dqv : ndarray
-        Spatial derivitive of the state vector
+        Spatial derivative of the state vector
 
     Returns
     -------
@@ -1157,7 +1157,7 @@ def consFlux(idir, idens, ixmom, iymom, iener, irhoX, iu, iv, ip, nspec, U_state
 def artificial_viscosity(ng, dx, dy,
                          cvisc, u, v):
     r"""
-    Compute the artifical viscosity.  Here, we compute edge-centered
+    Compute the artificial viscosity.  Here, we compute edge-centered
     approximations to the divergence of the velocity.  This follows
     directly Colella \ Woodward (1984) Eq. 4.5
 
diff --git a/pyro/compressible_sr/problems/quad.py b/pyro/compressible_sr/problems/quad.py
@@ -54,7 +54,7 @@ def init_data(my_data, rp):
 
     # there is probably an easier way to do this, but for now, we
     # will just do an explicit loop.  Also, we really want to set
-    # the pressue and get the internal energy from that, and then
+    # the pressure and get the internal energy from that, and then
     # compute the total energy (which is what we store).  For now
     # we will just fake this
 
diff --git a/pyro/compressible_sr/problems/rt2.py b/pyro/compressible_sr/problems/rt2.py
@@ -1,5 +1,5 @@
 """A RT problem with two distinct modes: short wave length on the
-left and long wavelenght on the right.  This allows one to see
+left and long wavelength on the right.  This allows one to see
 how the growth rate depends on wavenumber.
 """
 
diff --git a/pyro/compressible_sr/simulation.py b/pyro/compressible_sr/simulation.py
@@ -121,7 +121,7 @@ def initialize(self, extra_vars=None, ng=4):
             for v in extra_vars:
                 my_data.register_var(v, bc)
 
-        # store the EOS gamma as an auxillary quantity so we can have a
+        # store the EOS gamma as an auxiliary quantity so we can have a
         # self-contained object stored in output files to make plots.
         # store grav because we'll need that in some BCs
         my_data.set_aux("gamma", self.rp.get_param("eos.gamma"))
@@ -131,7 +131,7 @@ def initialize(self, extra_vars=None, ng=4):
 
         self.cc_data = my_data
 
-        # some auxillary data that we'll need to fill GC in, but isn't
+        # some auxiliary data that we'll need to fill GC in, but isn't
         # really part of the main solution
         aux_data = self.data_class(my_grid)
         aux_data.register_var("ymom_src", bc_yodd)
diff --git a/pyro/diffusion/problems/gaussian.py b/pyro/diffusion/problems/gaussian.py
@@ -45,7 +45,7 @@ def init_data(my_data, rp):
 
     phi[:, :] = phi_analytic(dist, 0.0, t_0, k, phi_0, phi_max)
 
-    # for later interpretation / analysis, store some auxillary data
+    # for later interpretation / analysis, store some auxiliary data
     my_data.set_aux("k", k)
     my_data.set_aux("t_0", t_0)
     my_data.set_aux("phi_0", phi_0)
diff --git a/pyro/incompressible/simulation.py b/pyro/incompressible/simulation.py
@@ -230,7 +230,7 @@ def evolve(self):
         v_MAC = ai.ArrayIndexer(d=_vm, grid=myg)
 
         # ---------------------------------------------------------------------
-        # do a MAC projection ot make the advective velocities divergence
+        # do a MAC projection to make the advective velocities divergence
         # free
         # ---------------------------------------------------------------------
 
diff --git a/pyro/lm_atm/simulation.py b/pyro/lm_atm/simulation.py
@@ -97,7 +97,7 @@ def initialize(self):
 
         self.cc_data = my_data
 
-        # some auxillary data that we'll need to fill GC in, but isn't
+        # some auxiliary data that we'll need to fill GC in, but isn't
         # really part of the main solution
         aux_data = patch.CellCenterData2d(myg)
 
@@ -198,7 +198,7 @@ def preevolve(self):
         # 1. do the initial projection.  This makes sure that our original
         # velocity field satisties div U = 0
 
-        # the coefficent for the elliptic equation is beta_0^2/rho
+        # the coefficient for the elliptic equation is beta_0^2/rho
         coeff = 1/rho
         beta0 = self.base["beta0"]
         coeff.v()[:, :] = coeff.v()*beta0.v2d()**2
diff --git a/pyro/mesh/integration.py b/pyro/mesh/integration.py
@@ -119,7 +119,7 @@ def get_stage_start(self, istage):
         return ytmp
 
     def compute_final_update(self):
-        """this constructs the final t + dt update, overwriting the inital data"""
+        """this constructs the final t + dt update, overwriting the initial data"""
         ytmp = self.start
         for n in range(ytmp.nvar):
             var = ytmp.get_var_by_index(n)
diff --git a/pyro/mesh/patch.py b/pyro/mesh/patch.py
@@ -204,7 +204,7 @@ class CellCenterData2d:
          my_data.register_var('x-momentum', BC)
          ...
 
-    * Register any auxillary data -- these are any parameters that are
+    * Register any auxiliary data -- these are any parameters that are
       needed to interpret the data outside of the simulation (for
       example, the gamma for the equation of state)::
 
@@ -280,7 +280,7 @@ def register_var(self, name, bc):
 
     def set_aux(self, keyword, value):
         """
-        Set any auxillary (scalar) data.  This data is simply carried
+        Set any auxiliary (scalar) data.  This data is simply carried
         along with the CellCenterData2d object
 
         Parameters
@@ -415,12 +415,12 @@ def get_vars(self):
 
     def get_aux(self, keyword):
         """
-        Get the auxillary data associated with keyword
+        Get the auxiliary data associated with keyword
 
         Parameters
         ----------
         keyword : str
-            The name of the auxillary data to access
+            The name of the auxiliary data to access
 
         Returns
         -------
@@ -628,7 +628,7 @@ def write_data(self, f):
 
         """
 
-        # auxillary data
+        # auxiliary data
         gaux = f.create_group("aux")
         for k, v in self.aux.items():
             gaux.attrs[k] = v
diff --git a/pyro/multigrid/examples/mg_test_general_alphabeta_only.py b/pyro/multigrid/examples/mg_test_general_alphabeta_only.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-"""Test the general MG solver with a variable coeffcient Helmholtz
+"""Test the general MG solver with a variable coefficient Helmholtz
 problem.  This ensures we didn't screw up the base functionality here.
 
 Here we solve::
diff --git a/pyro/multigrid/examples/mg_test_general_beta_only.py b/pyro/multigrid/examples/mg_test_general_beta_only.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-"""Test the general MG solver with a variable coeffcient Poisson
+"""Test the general MG solver with a variable coefficient Poisson
 problem (in essence, we are making this solver act like the
 variable_coefficient_MG.py solver).  This ensures we didn't
 screw up the base functionality here.
diff --git a/pyro/multigrid/general_MG.py b/pyro/multigrid/general_MG.py
@@ -58,7 +58,7 @@ def __init__(self, nx, ny, xmin=0.0, xmax=1.0, ymin=0.0, ymax=1.0,
         # scaled by 1/dx**2
         self.beta_edge = []
 
-        # initialize the MG object with the auxillary fields
+        # initialize the MG object with the auxiliary fields
         MG.CellCenterMG2d.__init__(self, nx, ny, ng=1,
                                    xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax,
                                    xl_BC_type=xl_BC_type, xr_BC_type=xr_BC_type,
@@ -74,7 +74,7 @@ def __init__(self, nx, ny, xmin=0.0, xmax=1.0, ymin=0.0, ymax=1.0,
                                    true_function=true_function, vis=vis,
                                    vis_title=vis_title)
 
-        # the coefficents come in a dictionary.  Set the coefficients
+        # the coefficients come in a dictionary.  Set the coefficients
         # and restrict them down the hierarchy we only need to do this
         # once.  We need to hold the original coeffs in our grid so we
         # can do a ghost cell fill.
diff --git a/pyro/multigrid/variable_coeff_MG.py b/pyro/multigrid/variable_coeff_MG.py
@@ -45,7 +45,7 @@ def __init__(self, nx, ny, xmin=0.0, xmax=1.0, ymin=0.0, ymax=1.0,
         # on each level -- note: this will already be scaled by 1/dx**2
         self.edge_coeffs = []
 
-        # initialize the MG object with the auxillary "coeffs" field
+        # initialize the MG object with the auxiliary "coeffs" field
         MG.CellCenterMG2d.__init__(self, nx, ny, ng=1,
                                    xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax,
                                    xl_BC_type=xl_BC_type, xr_BC_type=xr_BC_type,
@@ -88,7 +88,7 @@ def __init__(self, nx, ny, xmin=0.0, xmax=1.0, ymin=0.0, ymax=1.0,
             # put the coefficients on edges
             self.edge_coeffs.insert(0, self.edge_coeffs[0].restrict())  # _EdgeCoeffs(self.grids[n].grid, coeffs_c))
 
-            # if we are periodic, then we should force the edge coefficents
+            # if we are periodic, then we should force the edge coefficients
             # to be periodic
             # if self.grids[n].BCs["coeffs"].xlb == "periodic":
             #     self.edge_coeffs[0].x[self.grids[n].grid.ihi+1,:] = \
diff --git a/pyro/particles/tests/test_particles.py b/pyro/particles/tests/test_particles.py
@@ -27,7 +27,7 @@ def setup_test(n_particles=50, extra_rp_params=None):
     Function for setting up Particles tests. Would use unittest for this, but
     it doesn't seem to be possible/easy to pass in options to a setUp function.
 
-    Sets up runtime paramters, a blank simulation, fills it with a grid and sets
+    Sets up runtime parameters, a blank simulation, fills it with a grid and sets
     up the boundary conditions and simulation data.
 
     Parameters
diff --git a/pyro/swe/interface.py b/pyro/swe/interface.py
@@ -77,7 +77,7 @@ def states(idir, ng, dx, dt,
     qv : ndarray
         The primitive state vector
     dqv : ndarray
-        Spatial derivitive of the state vector
+        Spatial derivative of the state vector
 
     Returns
     -------
diff --git a/pyro/swe/problems/quad.py b/pyro/swe/problems/quad.py
@@ -47,7 +47,7 @@ def init_data(my_data, rp):
 
     # there is probably an easier way to do this, but for now, we
     # will just do an explicit loop.  Also, we really want to set
-    # the pressue and get the internal energy from that, and then
+    # the pressure and get the internal energy from that, and then
     # compute the total energy (which is what we store).  For now
     # we will just fake this
 
diff --git a/pyro/swe/simulation.py b/pyro/swe/simulation.py
@@ -119,7 +119,7 @@ def initialize(self, extra_vars=None, ng=4):
             for v in extra_vars:
                 my_data.register_var(v, bc)
 
-        # store the gravitational acceration g as an auxillary quantity
+        # store the gravitational acceration g as an auxiliary quantity
         # so we can have a
         # self-contained object stored in output files to make plots.
         # store grav because we'll need that in some BCs
@@ -134,7 +134,7 @@ def initialize(self, extra_vars=None, ng=4):
             particle_generator = self.rp.get_param("particles.particle_generator")
             self.particles = particles.Particles(self.cc_data, bc, n_particles, particle_generator)
 
-        # some auxillary data that we'll need to fill GC in, but isn't
+        # some auxiliary data that we'll need to fill GC in, but isn't
         # really part of the main solution
         aux_data = self.data_class(my_grid)
         aux_data.register_var("ymom_src", bc_yodd)
diff --git a/pyro/util/io_pyro.py b/pyro/util/io_pyro.py
@@ -83,7 +83,7 @@ def read(filename):
 
         myd.create()
 
-        # auxillary data
+        # auxiliary data
         for k in f["aux"].attrs:
             myd.set_aux(k, f["aux"].attrs[k])
 
diff --git a/pyro/util/runparams.py b/pyro/util/runparams.py
@@ -56,7 +56,7 @@
 
 
 def is_int(string):
-    """ is the given string an interger? """
+    """ is the given string an integer? """
     try:
         int(string)
     except ValueError:
@@ -108,7 +108,7 @@ def load_params(self, pfile, no_new=0):
         file : str
             The name of the file to parse
         no_new : int, optional
-            If no_new = 1, then we don't add any new paramters to the
+            If no_new = 1, then we don't add any new parameters to the
             dictionary of runtime parameters, but instead just override
             the values of existing ones.
 
@@ -190,7 +190,7 @@ def command_line_params(self, cmd_strings):
                 msg.warning("warning, key: %s not defined" % (key))
                 continue
 
-            # check in turn whether this is an interger, float, or string
+            # check in turn whether this is an integer, float, or string
             self.params[key] = _get_val(value)
 
     def get_param(self, key):

Original file line number	Diff line number	Diff line change
`@@ -1,7 +1,7 @@`
`1`	`1`	`# these defaults comes from the third test problem in`
`2`	`2`	`# Woodward and Colella. Journal of Computational Physics, 54, 115-174, 1984`
`3`	`3`	`#`
`4`		`-# Also, the numbers is consitent with the ones in Castro`
	`4`	`+# Also, the numbers is consistent with the ones in Castro`
`5`	`5`	`#`
`6`	`6`
`7`	`7`