more fixes

Author: zingale

.codespell-ignore-words

@@ -0,0 +1,21 @@
+blocs
+bloc
+inout
+als
+truns
+pres
+dum
+fom
+fromm
+thi
+nd
+ue
+bion
+aas
+checkin
+indx
+ans
+precesses
+fpr
+bu
+delt

.codespellrc

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

.github/workflows/codespell.yml

@@ -0,0 +1,32 @@
+name: codespell
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  codespell:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Setup Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.14'
+
+      - name: Install codespell
+        run: pip install codespell jupyter nbconvert
+
+      - name: Preprocess notebooks
+        run: for i in $(find . -name "*.ipynb"); do jupyter nbconvert --clear-output --inplace $i; done
+
+      - name: Run codespell
+        run: |
+          codespell content
+

basic_numerics/FFT/fft_simple_examples.py

@@ -82,7 +82,7 @@ def plot_FFT(xx, xmax, f, outfile):
     fk_r = fk.real
     fk_i = fk.imag
 
-    # the fftfreq returns the postive and negative (and 0) frequencies
+    # the fftfreq returns the positive and negative (and 0) frequencies
     # the newer versions of numpy (>=1.8) have an rfftfreq() function
     # that really does what we want -- we'll use that here.
     k = np.fft.rfftfreq(npts)

burgers/burgers.py

@@ -29,7 +29,7 @@ def __init__(self, nx, ng, xmin=0.0, xmax=1.0, bc="outflow"):
 
         self.bc=bc
 
-        # python is zero-based.  Make easy intergers to know where the
+        # python is zero-based.  Make easy integers to know where the
         # real data lives
         self.ilo = ng
         self.ihi = ng+nx-1

compressible/MOL/Fortran/riemann.f90

@@ -33,7 +33,7 @@
 !   Fry:  Fryxell et al. 2000, ApJS, 131, 273.
 !
 !   Toro: Toro 1999, ``Riemann Solvers and Numerical Methods for Fluid
-!         Dynamcs: A Practical Introduction, 2nd Ed.'', Springer-Verlag
+!         Dynamics: A Practical Introduction, 2nd Ed.'', Springer-Verlag
 !
 
 module riemann_module
@@ -139,7 +139,7 @@ subroutine riemann(gamma, &
 
 
     ! begin the secant iteration -- see CG Eq. 17 for details.  We will
-    ! continue to interate for convergence until the error falls below
+    ! continue to iterate for convergence until the error falls below
     ! tol (in which case, things are good), or we hit nriem iterations
     ! (in which case we have a problem, and we spit out an error).
     has_converged = .false.
@@ -222,7 +222,7 @@ subroutine riemann(gamma, &
 
     ustar_sgn = sign(1.d0, ustar)
 
-    ! decide which state is located at the zone iterface based on
+    ! decide which state is located at the zone interface based on
     ! the values of the wave speeds.  This is just saying that if
     ! ustar > 0, then the state is U_L.  if ustar < 0, then the
     ! state on the axis is U_R.

compressible/MOL/python/riemann.py

@@ -34,7 +34,7 @@
    Fry:  Fryxell et al. 2000, ApJS, 131, 273.
 
    Toro: Toro 1999, ``Riemann Solvers and Numerical Methods for Fluid
-         Dynamcs: A Practical Introduction, 2nd Ed.'', Springer-Verlag
+         Dynamcis: A Practical Introduction, 2nd Ed.'', Springer-Verlag
 """
 
 import numpy as np
@@ -107,7 +107,7 @@ def riemann(q_l, q_r, gamma):
     pstar2 = max(smallp, pstar2)
 
     # begin the secant iteration -- see CG Eq. 17 for details.  We will
-    # continue to interate for convergence until the error falls below
+    # continue to iterate for convergence until the error falls below
     # tol (in which case, things are good), or we hit nriem iterations
     # (in which case we have a problem, and we spit out an error).
     has_converged = False
@@ -188,7 +188,7 @@ def riemann(q_l, q_r, gamma):
     else:
         ustar_sgn = 1.0
 
-    # decide which state is located at the zone iterface based on
+    # decide which state is located at the zone interface based on
     # the values of the wave speeds.  This is just saying that if
     # ustar > 0, then the state is U_L.  if ustar < 0, then the
     # state on the axis is U_R.

compressible/euler-generaleos.ipynb

@@ -288,7 +288,7 @@
    },
    "outputs": [],
    "source": [
-    "# we use the helper rountines above to find the orthogonal left and right eigenvectors\n",
+    "# we use the helper routines above to find the orthogonal left and right eigenvectors\n",
     "eigen = eigensystem(A)"
    ]
   },
@@ -488,7 +488,7 @@
    "source": [
     "## $\\beta$'s and final update\n",
     "\n",
-    "The final interface state is writen by projecting the jump in primitive variables, $\\Delta q$, into characteristic variables (as $l \\cdot \\Delta q$), and then adding up all the jumps that reach the interface.\n",
+    "The final interface state is written by projecting the jump in primitive variables, $\\Delta q$, into characteristic variables (as $l \\cdot \\Delta q$), and then adding up all the jumps that reach the interface.\n",
     "\n",
     "The convention is to write $\\beta^\\nu = l^\\nu \\cdot \\Delta q$, where the superscript identifies which eigenvalue (and corresponding eigenvectors) we are considering.  Note, that often a reference state is used, and the jump, $\\Delta q$, will be the difference with respect to this reference state.  For PPM, the $\\Delta q$ will take the form of the integral under the parabola over the range that each wave can reach.\n",
     "\n",
@@ -877,7 +877,7 @@
    },
    "outputs": [],
    "source": [
-    "# we use the helper rountines above to find the orthogonal left and right eigenvectors\n",
+    "# we use the helper routines above to find the orthogonal left and right eigenvectors\n",
     "eigen = eigensystem(A)"
    ]
   },
@@ -1544,7 +1544,7 @@
    },
    "outputs": [],
    "source": [
-    "# we use the helper rountines above to find the orthogonal left and right eigenvectors\n",
+    "# we use the helper routines above to find the orthogonal left and right eigenvectors\n",
     "eigen = eigensystem(A, suba=cg, subb=sqrt(cc))"
    ]
   },
@@ -2092,7 +2092,7 @@
    "source": [
     "# Gray FLD Radiation Euler Equations with $(\\gamma_e)$\n",
     "\n",
-    "We now look at the same system with a different auxillary thermodynamic variable (as we did with pure hydro), using $q = (\\tau, u, p, {\\gamma_e}_g, E_r)^\\intercal$:\n",
+    "We now look at the same system with a different auxiliary thermodynamic variable (as we did with pure hydro), using $q = (\\tau, u, p, {\\gamma_e}_g, E_r)^\\intercal$:\n",
     "\\begin{align}\n",
     "\\frac{\\partial \\tau}{\\partial t} &= -u\\frac{\\partial \\tau}{\\partial x}  + \\tau \\frac{\\partial u}{\\partial x} \\\\\n",
     "\\frac{\\partial u}{\\partial t} &= -u \\frac{\\partial u}{\\partial x} - \\tau \\frac{\\partial p}{\\partial x}\n",
@@ -2295,7 +2295,7 @@
    },
    "outputs": [],
    "source": [
-    "# we use the helper rountines above to find the orthogonal left and right eigenvectors\n",
+    "# we use the helper routines above to find the orthogonal left and right eigenvectors\n",
     "eigen = eigensystem(A, suba=cg, subb=sqrt(cc))"
    ]
   },