Remove _set_up method now that io save stuff was...

    determined to be cause of the bug. The transform matrices
    attribute is being assigned and is persistent. The error the
    previous commits were trying to isolate was just an issue with
    loosing the matrices attribute while saving to output.
    By calling .matrics property attribute everywhere we do not need
    a _set_up method.

desc/basis.py

@@ -39,6 +39,8 @@ def __init__(self):
 
     def _set_up(self):
         """Do things after loading or changing resolution."""
+        # Also recreates any attributes not in _io_attrs on load from input file.
+        # See IOAble class docstring for more info.
         self._enforce_symmetry()
         self._sort_modes()
         self._create_idx()

desc/transform.py

@@ -372,7 +372,7 @@ def build(self):
 
         if self.method == "direct1":
             for d in self.derivatives:
-                self._matrices["direct1"][d[0]][d[1]][d[2]] = self.basis.evaluate(
+                self.matrices["direct1"][d[0]][d[1]][d[2]] = self.basis.evaluate(
                     self.grid.nodes, d, unique=True
                 )
 
@@ -406,7 +406,7 @@ def build_pinv(self):
         rcond = None if self.rcond == "auto" else self.rcond
         if self.method == "direct1":
             A = self.basis.evaluate(self.grid.nodes, np.array([0, 0, 0]))
-            self._matrices["pinv"] = (
+            self.matrices["pinv"] = (
                 scipy.linalg.pinv(A, rcond=rcond) if A.size else np.zeros_like(A.T)
             )
         elif self.method == "direct2":
@@ -726,19 +726,14 @@ def change_derivatives(self, derivs, build=True):
         self._sort_derivatives()
 
         if len(derivs_to_add):
-            # if we actually added derivatives and didn't build them, then it's not built
+            # if we actually added derivatives and didn't build them, then it's not
+            # built
             self._built = False
         if build:
             # we don't update self._built here because it is still built from before,
             # but it still might have unbuilt matrices from new derivatives
             self.build()
 
-    def _set_up(self):
-        """Recreate attributes that were not saved to output files."""
-        # fixme: Make api for reloading attributes that are not saved better.
-        # See equilibrium_io.py for the logic that calls this function.
-        self._matrices = self.matrices
-
     @property
     def matrices(self):
         """dict: transform matrices such that x=A*c."""