Fix typos and spelling errors

desc/_version.py

@@ -1,5 +1,5 @@
 # This file helps to compute a version number in source trees obtained from
-# git-archive tarball (such as those provided by githubs download-from-tag
+# git-archive tarball (such as those provided by github's download-from-tag
 # feature). Distribution tarballs (built by setup.py sdist) and build
 # directories (produced by setup.py build) will contain a much shorter file
 # that just contains the computed version number.
@@ -292,7 +292,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
         # TAG-NUM-gHEX
         mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe)
         if not mo:
-            # unparseable. Maybe git-describe is misbehaving?
+            # unparsable. Maybe git-describe is misbehaving?
             pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out
             return pieces
 
@@ -409,7 +409,7 @@ def render_pep440_old(pieces):
 
     The ".dev0" means dirty.
 
-    Eexceptions:
+    Exceptions:
     1: no tags. 0.postDISTANCE[.dev0]
     """
     if pieces["closest-tag"]:

desc/basis.py

@@ -1318,7 +1318,7 @@ def zernike_radial_coeffs(l, m, exact=True):
     Returns
     -------
     coeffs : ndarray
-
+        Polynomial coefficients for Zernike polynomials, in descending powers of r.
 
     Notes
     -----

desc/compute/_core.py

@@ -175,7 +175,7 @@ def _R_rrt(params, transforms, profiles, data, **kwargs):
     label="\\partial_{\\rho \\rho \\theta \\theta} R",
     units="m",
     units_long="meters",
-    description="Major radius in lab frame, fouth derivative, wrt radius twice "
+    description="Major radius in lab frame, fourth derivative, wrt radius twice "
     "and poloidal angle twice",
     dim=1,
     params=["R_lmn"],

desc/compute/data_index.py

@@ -99,7 +99,7 @@ def _decorator(func):
     return _decorator
 
 
-# This allows us to handle subclasses whos data_index stuff should inherit
+# This allows us to handle subclasses whose data_index stuff should inherit
 # from parent classes.
 # This is the least bad solution I've found, since everything else requires
 # crazy circular imports

desc/compute/utils.py

@@ -12,35 +12,6 @@
 
 from .data_index import data_index
 
-# defines the order in which objective arguments get concatenated into the state vector
-arg_order = (
-    "R_lmn",
-    "Z_lmn",
-    "L_lmn",
-    "p_l",
-    "i_l",
-    "c_l",
-    "Psi",
-    "Te_l",
-    "ne_l",
-    "Ti_l",
-    "Zeff_l",
-    "Ra_n",
-    "Za_n",
-    "Rb_lmn",
-    "Zb_lmn",
-)
-# map from profile name to equilibrium parameter name
-profile_names = {
-    "pressure": "p_l",
-    "iota": "i_l",
-    "current": "c_l",
-    "electron_temperature": "Te_l",
-    "electron_density": "ne_l",
-    "ion_temperature": "Ti_l",
-    "atomic_number": "Zeff_l",
-}
-
 
 def _parse_parameterization(p):
     if isinstance(p, str):
@@ -1309,3 +1280,34 @@ def body(i, mins):
     # The above implementation was benchmarked to be more efficient than
     # alternatives without explicit loops in GitHub pull request #501.
     return grid.expand(mins, surface_label)
+
+
+# defines the order in which objective arguments get concatenated into the state vector
+arg_order = (
+    "R_lmn",
+    "Z_lmn",
+    "L_lmn",
+    "p_l",
+    "i_l",
+    "c_l",
+    "Psi",
+    "Te_l",
+    "ne_l",
+    "Ti_l",
+    "Zeff_l",
+    "Ra_n",
+    "Za_n",
+    "Rb_lmn",
+    "Zb_lmn",
+)
+
+# map from profile name to equilibrium parameter name
+profile_names = {
+    "pressure": "p_l",
+    "iota": "i_l",
+    "current": "c_l",
+    "electron_temperature": "Te_l",
+    "electron_density": "ne_l",
+    "ion_temperature": "Ti_l",
+    "atomic_number": "Zeff_l",
+}

desc/continuation.py

@@ -167,7 +167,7 @@ def _solve_axisym(
         if mres_step == MIN_MRES_STEP:
             raise RuntimeError(
                 "Automatic continuation failed with mres_step=1, "
-                + "something is probaby very wrong with your desired equilibrium."
+                + "something is probably very wrong with your desired equilibrium."
             )
         else:
             warnings.warn(
@@ -297,7 +297,7 @@ def _add_pressure(
         if pres_step <= MIN_PRES_STEP:
             raise RuntimeError(
                 "Automatic continuation failed with "
-                + f"pres_step={pres_step}, something is probaby very wrong with your "
+                + f"pres_step={pres_step}, something is probably very wrong with your "
                 + "desired equilibrium."
             )
         else:
@@ -430,7 +430,7 @@ def _add_shaping(
         if bdry_step <= MIN_BDRY_STEP:
             raise RuntimeError(
                 "Automatic continuation failed with "
-                + f"bdry_step={bdry_step}, something is probaby very wrong with your "
+                + f"bdry_step={bdry_step}, something is probably very wrong with your "
                 + "desired equilibrium."
             )
         else:
@@ -485,7 +485,7 @@ def solve_continuation_automatic(  # noqa: C901
         Unsolved Equilibrium with the final desired boundary, profiles, resolution.
     objective : {"force", "energy", "vacuum"}
         function to solve for equilibrium solution
-    optimizer : str or Optimzer (optional)
+    optimizer : str or Optimizer (optional)
         optimizer to use
     pert_order : int
         order of perturbations to use.
@@ -609,7 +609,7 @@ def solve_continuation(  # noqa: C901
 ):
     """Solve for an equilibrium by continuation method.
 
-    Steps through an EquilibriaFamily, solving each equilibrium, and uses pertubations
+    Steps through an EquilibriaFamily, solving each equilibrium, and uses perturbations
     to step between different profiles/boundaries.
 
     Uses the previous step as an initial guess for each solution.
@@ -620,7 +620,7 @@ def solve_continuation(  # noqa: C901
         Equilibria to solve for at each step.
     objective : {"force", "energy", "vacuum"}
         function to solve for equilibrium solution
-    optimizer : str or Optimzer (optional)
+    optimizer : str or Optimizer (optional)
         optimizer to use
     pert_order : int or array of int
         order of perturbations to use. If array-like, should be same length as eqfam

desc/derivatives.py

@@ -436,7 +436,6 @@ def _compute_grad_or_jac(self, *args, **kwargs):
         kwargs : dict
             keyword arguments passed to fun
 
-
         Returns
         -------
         J : ndarray of float, shape(len(f),len(x))
@@ -702,7 +701,4 @@ def compute(self, *args, **kwargs):
         return self._compute(*args, **kwargs)
 
 
-if use_jax:
-    Derivative = AutoDiffDerivative
-else:
-    Derivative = FiniteDiffDerivative
+Derivative = AutoDiffDerivative if use_jax else FiniteDiffDerivative

desc/equilibrium/equilibrium.py

@@ -1626,7 +1626,6 @@ def solve(
             ``message`` which describes the cause of the termination. See
             `OptimizeResult` for a description of other attributes.
 
-
         """
         if constraints is None:
             constraints = get_fixed_boundary_constraints(
@@ -2092,7 +2091,7 @@ def solve_continuation(
         """Solve for an equilibrium by continuation method.
 
         Steps through an EquilibriaFamily, solving each equilibrium, and uses
-        pertubations to step between different profiles/boundaries.
+        perturbations to step between different profiles/boundaries.
 
         Uses the previous step as an initial guess for each solution.
 
@@ -2102,7 +2101,7 @@ def solve_continuation(
             Equilibria to solve for at each step.
         objective : str or ObjectiveFunction (optional)
             function to solve for equilibrium solution
-        optimizer : str or Optimzer (optional)
+        optimizer : str or Optimizer (optional)
             optimizer to use
         pert_order : int or array of int
             order of perturbations to use. If array-like, should be same length as
@@ -2170,7 +2169,7 @@ def solve_continuation_automatic(
             Unsolved Equilibrium with the final desired boundary, profiles, resolution.
         objective : str or ObjectiveFunction (optional)
             function to solve for equilibrium solution
-        optimizer : str or Optimzer (optional)
+        optimizer : str or Optimizer (optional)
             optimizer to use
         pert_order : int
             order of perturbations to use.
@@ -2236,8 +2235,6 @@ def equilibria(self, equil):
             )
         self._equilibria = list(equil)
 
-    # dunder methods required by MutableSequence
-
     def __getitem__(self, i):
         return self._equilibria[i]
 

desc/geometry/core.py

@@ -69,7 +69,7 @@ def compute(
             Computed quantity and intermediate variables.
 
         """
-        # set a default numpts for the SplineXYZCurve
+        # set a default number of points for the SplineXYZCurve
         N = self.N if hasattr(self, "N") else self.X.size
         if isinstance(names, str):
             names = [names]

desc/geometry/curve.py

@@ -751,17 +751,18 @@ def from_values(cls, coords, knots=None, method="cubic", name="", basis="xyz"):
             If supplied, will be rescaled to lie in [0,2pi]
         method : str
             method of interpolation
+
             - `'nearest'`: nearest neighbor interpolation
             - `'linear'`: linear interpolation
             - `'cubic'`: C1 cubic splines (aka local splines)
             - `'cubic2'`: C2 cubic splines (aka natural splines)
             - `'catmull-rom'`: C1 cubic centripetal "tension" splines
+
         name : str
             name for this curve
         basis : {"rpz", "xyz"}
             basis for input coordinates. Defaults to "xyz"
 
-
         Returns
         -------
         SplineXYZCurve: SplineXYZCurve

desc/geometry/surface.py

@@ -371,7 +371,7 @@ class ZernikeRZToroidalSection(Surface):
         For L>0, the indexing scheme defines order of the basis functions:
 
         ``'ansi'``: ANSI indexing fills in the pyramid with triangles of
-        decreasing size, ending in a triagle shape. For L == M,
+        decreasing size, ending in a triangle shape. For L == M,
         the traditional ANSI pyramid indexing is recovered. For L>M, adds rows
         to the bottom of the pyramid, increasing L while keeping M constant,
         giving a "house" shape

desc/io/ascii_io.py

@@ -34,7 +34,7 @@ def write_ascii(fname, eq):
     file.write("NFP = {:3d}\n".format(int(eq.NFP)))
     file.write("Psi = {:16.8E}\n".format(eq.Psi))
 
-    # boundary paramters
+    # boundary parameters
     if eq.sym:
         nbdry = len(np.nonzero(eq.Rb_lmn)[0]) + len(np.nonzero(eq.Zb_lmn)[0])
         file.write("Nbdry = {:3d}\n".format(nbdry))

desc/io/core_io.py

@@ -11,7 +11,7 @@ def __init__(self):
         self.resolve_base()
 
     def __del__(self):
-        """Close file upon garbage colleciton or explicit deletion with del function."""
+        """Close file upon garbage collection or explicit deletion with del function."""
         self.close()
 
     def close(self):
@@ -53,7 +53,7 @@ def resolve_where(self, where):
         -------
         if where is None:
             base attribute
-        if where is file with type foundin _file_types_
+        if where is file with type found in _file_types_
             where
 
         """

desc/io/hdf5_io.py

@@ -115,7 +115,7 @@ def read_obj(self, obj, where=None):
         ----------
         obj : python object instance
             object must have _io_attrs_ attribute to have attributes read and loaded
-        where : None or file insance
+        where : None or file instance
             specifies where to read obj from
 
         """
@@ -217,7 +217,7 @@ def read_list(self, where=None):
         Parameters
         ----------
         where : None or file instance
-            specifies wehre to read dict from
+            specifies where to read dict from
 
         """
         thelist = []

desc/io/input_reader.py

@@ -566,7 +566,7 @@ def parse_inputs(self, fname=None):  # noqa: C901 - FIXME: simplify this
         if inputs["objective"] == "vacuum" and (pres_flag or iota_flag or curr_flag):
             warnings.warn(
                 "Vacuum objective does not use any profiles, "
-                + "ignoring presssure, iota, and current"
+                + "ignoring pressure, iota, and current"
             )
 
         # sort axis array
@@ -901,7 +901,7 @@ def descout_to_input(  # noqa: C901 - fxn too complex
         f.write("\n")
 
         f.write("\n# fixed-boundary surface shape\n")
-        # boundary paramters
+        # boundary parameters
         if eq0.sym:
             for k, (l, m, n) in enumerate(eq0.surface.R_basis.modes):
                 if abs(eq0.Rb_lmn[k]) > 1e-8:
@@ -1615,9 +1615,6 @@ def parse_vmec_inputs(vmec_fname, threshold=0):  # noqa: C901 - FIXME: simplify
         return inputs_arr
 
 
-# NOTE: this has to be outside the class to work with autodoc
-
-
 def get_parser():
     """Get parser for command line arguments.
 
@@ -1627,6 +1624,7 @@ def get_parser():
         argument parser
 
     """
+    # NOTE: this has to be outside the class to work with autodoc
     parser = argparse.ArgumentParser(
         prog="desc",
         allow_abbrev=True,

desc/io/pickle_io.py

@@ -57,7 +57,7 @@ def read_obj(self, obj=None, where=None):
         ----------
         obj : python object instance
             object must have _io_attrs_ attribute to have attributes read and loaded
-        where : None or file insance
+        where : None or file instance
             specifies where to read obj from
 
         """
@@ -107,7 +107,7 @@ def write_obj(self, obj, where=None):
         ----------
         obj : python object instance
             object must have _io_attrs_ attribute to have attributes read and loaded
-        where : None or file insance
+        where : None or file instance
             specifies where to write obj to
 
         """