Merge pull request #646 from PlasmaControl/rc/cleanup

Fix spelling errors, rename abstract base classes
PlasmaControl · Aug 31, 2023 · c6a2c34 · c6a2c34
2 parents 9680907 + edfe4c7
commit c6a2c34
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Showing 50 changed files with 348 additions and 370 deletions.
diff --git a/desc/_version.py b/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"]:

diff --git a/desc/basis.py b/desc/basis.py
@@ -21,7 +21,7 @@
 ]
 
 
-class Basis(IOAble, ABC):
+class _Basis(IOAble, ABC):
     """Basis is an abstract base class for spectral basis sets."""
 
     _io_attrs_ = [
@@ -223,7 +223,7 @@ def __repr__(self):
         )
 
 
-class PowerSeries(Basis):
+class PowerSeries(_Basis):
     """1D basis set for flux surface quantities.
 
     Power series in the radial coordinate.
@@ -333,7 +333,7 @@ def change_resolution(self, L):
             self._set_up()
 
 
-class FourierSeries(Basis):
+class FourierSeries(_Basis):
     """1D basis set for use with the magnetic axis.
 
     Fourier series in the toroidal coordinate.
@@ -453,7 +453,7 @@ def change_resolution(self, N, NFP=None, sym=None):
             self._set_up()
 
 
-class DoubleFourierSeries(Basis):
+class DoubleFourierSeries(_Basis):
     """2D basis set for use on a single flux surface.
 
     Fourier series in both the poloidal and toroidal coordinates.
@@ -600,7 +600,7 @@ def change_resolution(self, M, N, NFP=None, sym=None):
             self._set_up()
 
 
-class ZernikePolynomial(Basis):
+class ZernikePolynomial(_Basis):
     """2D basis set for analytic functions in a unit disc.
 
     Parameters
@@ -810,7 +810,7 @@ def change_resolution(self, L, M, sym=None):
             self._set_up()
 
 
-class ChebyshevDoubleFourierBasis(Basis):
+class ChebyshevDoubleFourierBasis(_Basis):
     """3D basis: tensor product of Chebyshev polynomials and two Fourier series.
 
     Fourier series in both the poloidal and toroidal coordinates.
@@ -943,7 +943,7 @@ def change_resolution(self, L, M, N, NFP=None, sym=None):
             self._set_up()
 
 
-class FourierZernikeBasis(Basis):
+class FourierZernikeBasis(_Basis):
     """3D basis set for analytic functions in a toroidal volume.
 
     Zernike polynomials in the radial & poloidal coordinates, and a Fourier
@@ -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
     -----

diff --git a/desc/coils.py b/desc/coils.py
@@ -14,12 +14,11 @@
     FourierXYZCurve,
     SplineXYZCurve,
 )
-from desc.grid import Grid
-from desc.magnetic_fields import MagneticField, biot_savart
+from desc.magnetic_fields import _MagneticField, biot_savart
 from desc.utils import flatten_list
 
 
-class Coil(MagneticField, ABC):
+class _Coil(_MagneticField, ABC):
     """Base class representing a magnetic field coil.
 
     Represents coils as a combination of a Curve and current
@@ -37,7 +36,7 @@ class Coil(MagneticField, ABC):
         current passing through the coil, in Amperes
     """
 
-    _io_attrs_ = MagneticField._io_attrs_ + ["_current"]
+    _io_attrs_ = _MagneticField._io_attrs_ + ["_current"]
 
     def __init__(self, current, *args, **kwargs):
         self._current = current
@@ -77,7 +76,7 @@ def compute_magnetic_field(self, coords, params=None, basis="rpz", grid=None):
             magnetic field at specified points, in either rpz or xyz coordinates
         """
         assert basis.lower() in ["rpz", "xyz"]
-        if isinstance(coords, Grid):
+        if hasattr(coords, "nodes"):
             coords = coords.nodes
         coords = jnp.atleast_2d(coords)
         if basis == "rpz":
@@ -102,7 +101,7 @@ def __repr__(self):
         )
 
 
-class FourierRZCoil(Coil, FourierRZCurve):
+class FourierRZCoil(_Coil, FourierRZCurve):
     """Coil parameterized by fourier series for R,Z in terms of toroidal angle phi.
 
     Parameters
@@ -154,7 +153,7 @@ class FourierRZCoil(Coil, FourierRZCurve):
 
     """
 
-    _io_attrs_ = Coil._io_attrs_ + FourierRZCurve._io_attrs_
+    _io_attrs_ = _Coil._io_attrs_ + FourierRZCurve._io_attrs_
 
     def __init__(
         self,
@@ -170,7 +169,7 @@ def __init__(
         super().__init__(current, R_n, Z_n, modes_R, modes_Z, NFP, sym, name)
 
 
-class FourierXYZCoil(Coil, FourierXYZCurve):
+class FourierXYZCoil(_Coil, FourierXYZCurve):
     """Coil parameterized by fourier series for X,Y,Z in terms of arbitrary angle phi.
 
     Parameters
@@ -219,7 +218,7 @@ class FourierXYZCoil(Coil, FourierXYZCurve):
 
     """
 
-    _io_attrs_ = Coil._io_attrs_ + FourierXYZCurve._io_attrs_
+    _io_attrs_ = _Coil._io_attrs_ + FourierXYZCurve._io_attrs_
 
     def __init__(
         self,
@@ -233,7 +232,7 @@ def __init__(
         super().__init__(current, X_n, Y_n, Z_n, modes, name)
 
 
-class FourierPlanarCoil(Coil, FourierPlanarCurve):
+class FourierPlanarCoil(_Coil, FourierPlanarCurve):
     """Coil that lines in a plane.
 
     Parameterized by a point (the center of the coil), a vector (normal to the plane),
@@ -290,7 +289,7 @@ class FourierPlanarCoil(Coil, FourierPlanarCurve):
 
     """
 
-    _io_attrs_ = Coil._io_attrs_ + FourierPlanarCurve._io_attrs_
+    _io_attrs_ = _Coil._io_attrs_ + FourierPlanarCurve._io_attrs_
 
     def __init__(
         self,
@@ -304,7 +303,7 @@ def __init__(
         super().__init__(current, center, normal, r_n, modes, name)
 
 
-class SplineXYZCoil(Coil, SplineXYZCurve):
+class SplineXYZCoil(_Coil, SplineXYZCurve):
     """Coil parameterized by spline points in X,Y,Z.
 
     Parameters
@@ -338,7 +337,7 @@ class SplineXYZCoil(Coil, SplineXYZCurve):
 
     """
 
-    _io_attrs_ = Coil._io_attrs_ + SplineXYZCurve._io_attrs_
+    _io_attrs_ = _Coil._io_attrs_ + SplineXYZCurve._io_attrs_
 
     def __init__(
         self,
@@ -353,7 +352,7 @@ def __init__(
         super().__init__(current, X, Y, Z, knots, method, name)
 
 
-class CoilSet(Coil, MutableSequence):
+class CoilSet(_Coil, MutableSequence):
     """Set of coils of different geometry.
 
     Parameters
@@ -367,11 +366,11 @@ class CoilSet(Coil, MutableSequence):
 
     """
 
-    _io_attrs_ = Coil._io_attrs_ + ["_coils"]
+    _io_attrs_ = _Coil._io_attrs_ + ["_coils"]
 
     def __init__(self, *coils, name=""):
         coils = flatten_list(coils, flatten_tuple=True)
-        assert all([isinstance(coil, (Coil)) for coil in coils])
+        assert all([isinstance(coil, (_Coil)) for coil in coils])
         self._coils = list(coils)
         self._name = str(name)
 
@@ -525,7 +524,7 @@ def linspaced_angular(
         endpoint : bool
             whether to include a coil at final angle
         """
-        assert isinstance(coil, Coil)
+        assert isinstance(coil, _Coil)
         if current is None:
             current = coil.current
         currents = jnp.broadcast_to(current, (n,))
@@ -557,7 +556,7 @@ def linspaced_linear(
         endpoint : bool
             whether to include a coil at final point
         """
-        assert isinstance(coil, Coil)
+        assert isinstance(coil, _Coil)
         if current is None:
             current = coil.current
         currents = jnp.broadcast_to(current, (n,))
@@ -762,7 +761,7 @@ def flatten_coils(coilset):
         coil_end_inds = []  # indices where the coils end, need to track these
         # to place the coilgroup number and name later, which MAKEGRID expects
         # at the end of each individual coil
-        if isinstance(grid, Grid):
+        if hasattr(grid, "endpoint"):
             endpoint = grid.endpoint
         elif isinstance(grid, numbers.Integral):
             endpoint = True  # if int, will create a grid w/ endpoint=True in compute
@@ -830,7 +829,7 @@ def __getitem__(self, i):
         return self.coils[i]
 
     def __setitem__(self, i, new_item):
-        if not isinstance(new_item, Coil):
+        if not isinstance(new_item, _Coil):
             raise TypeError("Members of CoilSet must be of type Coil.")
         self._coils[i] = new_item
 
@@ -842,7 +841,7 @@ def __len__(self):
 
     def insert(self, i, new_item):
         """Insert a new coil into the coilset at position i."""
-        if not isinstance(new_item, Coil):
+        if not isinstance(new_item, _Coil):
             raise TypeError("Members of CoilSet must be of type Coil.")
         self._coils.insert(i, new_item)
 

diff --git a/desc/compute/_core.py b/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"],

diff --git a/desc/compute/data_index.py b/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

diff --git a/desc/compute/utils.py b/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",
+}