Convert docstrings with Doxygen equations to "raw" strings to avoid p…

…ytest warnings

src/python/OpenFUSIONToolkit/TokaMaker.py

@@ -15,7 +15,7 @@
 
 # Settings STRUCT
 class tokamaker_settings_struct(c_struct):
-    '''! TokaMaker settings structure
+    r'''! TokaMaker settings structure
 
      - `pm` Print 'performance' information (eg. iteration count) during run?
      - `free_boundary` Perform free-boundary calculation?
@@ -204,7 +204,7 @@ def tokamaker_default_settings():
     return settings
 
 def create_isoflux(npts, r0, z0, a, kappa, delta, kappaL=None, deltaL=None):
-    '''! Create isoflux points using simple analytic form
+    r'''! Create isoflux points using simple analytic form
 
     @param npts Number of points to sample (evenly spaced in \f$\theta\f$)
     @param r0 Major radial position for magnetic axis
@@ -475,7 +475,7 @@ def setup_regions(self,coil_file='none',cond_dict={}):
         tokamaker_setup_regions(cstring,eta_vals)
 
     def eval_green(self,x,xc):
-        '''! Evaluate Green's function for a toroidal filament
+        r'''! Evaluate Green's function for a toroidal filament
 
         @param x Observation point [2]
         @param xc Coil location [2]
@@ -490,7 +490,7 @@ def eval_green(self,x,xc):
         return vals*mu0
 
     def setup(self,order=2,F0=0.0,full_domain=False):
-        '''! Setup G-S solver
+        r'''! Setup G-S solver
 
         @param order Order of FE representation to use
         @param F0 Vacuum \f$F(\psi)\f$ value (B0*R0)
@@ -630,7 +630,7 @@ def set_coil_vsc(self,coil_gains):
         tokamaker_set_coil_vsc(coil_gains)
 
     def init_psi(self, r0=-1.0, z0=0.0, a=0.0, kappa=0.0, delta=0.0):
-        '''! Initialize \f$\psi\f$ using uniform current distributions
+        r'''! Initialize \f$\psi\f$ using uniform current distributions
 
         If r0>0 then a uniform current density inside a surface bounded by
         a curve of the form defined in @ref oftpy.create_isoflux is used.
@@ -647,7 +647,7 @@ def init_psi(self, r0=-1.0, z0=0.0, a=0.0, kappa=0.0, delta=0.0):
         return error_flag.value
 
     def load_profiles(self, f_file='f_prof.in', foffset=None, p_file='p_prof.in'):
-        '''! Load flux function profiles (\f$F*F'\f$ and \f$P'\f$) from files
+        r'''! Load flux function profiles (\f$F*F'\f$ and \f$P'\f$) from files
 
         @param f_file File containing \f$F*F'\f$ (or \f$F'\f$ if `mode=0`) definition
         @param foffset Value of \f$F0=R0*B0\f$
@@ -658,7 +658,7 @@ def load_profiles(self, f_file='f_prof.in', foffset=None, p_file='p_prof.in'):
         tokamaker_load_profiles(c_char_p(f_file.encode()),c_double(self._F0),c_char_p(p_file.encode()))
 
     def set_profiles(self, ffp_prof=None, foffset=None, pp_prof=None):
-        '''! Set flux function profiles (\f$F*F'\f$ and \f$P'\f$) using a piecewise linear definition
+        r'''! Set flux function profiles (\f$F*F'\f$ and \f$P'\f$) using a piecewise linear definition
 
         Arrays should have the form array[i,:] = (\f$\hat{\psi}_i\f$, \f$f(\hat{\psi}_i)\f$) and span
         \f$\hat{\psi}_i = [0,1]\f$.
@@ -790,7 +790,7 @@ def print_info(self,lcfs_pad=0.01):
         print("  l_i                     =   {0:7.4F}".format(eq_stats['l_i']))
 
     def set_isoflux(self,isoflux,weights=None,grad_wt_lim=-1.0):
-        '''! Set isoflux constraint points (all points lie on a flux surface)
+        r'''! Set isoflux constraint points (all points lie on a flux surface)
 
         To constraint points more uniformly in space additional weighting based on
         the gradient of $\psi$ at each point can also be included by setting
@@ -826,7 +826,7 @@ def set_saddles(self,saddles,weights=None):
             self._saddles = saddles.copy()
 
     def set_targets(self,Ip=None,Ip_ratio=None,pax=None,estore=None,R0=None,V0=None,retain_previous=False):
-        '''! Set global target values
+        r'''! Set global target values
 
         Once set, values are retained until they are explicitly set to their respective disabled
         values (see below). By default, all targets are disabled so this function should be called
@@ -866,7 +866,7 @@ def set_targets(self,Ip=None,Ip_ratio=None,pax=None,estore=None,R0=None,V0=None,
         tokamaker_set_targets(self._Ip_target,self._Ip_ratio_target,self._pax_target,self._estore_target,self._R0_target,self._V0_target)
 
     def get_psi(self,normalized=True):
-        '''! Get poloidal flux values on node points
+        r'''! Get poloidal flux values on node points
 
         @param normalized Normalize (and offset) poloidal flux
         @result \f$\hat{\psi} = \frac{\psi-\psi_0}{\psi_a-\psi_0} \f$ or \f$\psi\f$
@@ -907,7 +907,7 @@ def get_coil_currents(self):
         return currents, coil_map
 
     def get_coil_Lmat(self):
-        '''! Get mutual inductance matrix between coils
+        r'''! Get mutual inductance matrix between coils
 
         @note This is the inductance in terms of A-turns. To get in terms of
         current in a single of the \f$n\f$ windings you must multiply by \f$n_i*n_j\f$.
@@ -919,7 +919,7 @@ def get_coil_Lmat(self):
         return Lmat
 
     def trace_surf(self,psi):
-        '''! Trace surface for a given poloidal flux
+        r'''! Trace surface for a given poloidal flux
 
         @param psi Flux surface to trace \f$\hat{\psi}\f$
         @result \f$r(\hat{\psi})\f$
@@ -935,7 +935,7 @@ def trace_surf(self,psi):
             return None
 
     def get_q(self,psi=None,psi_pad=0.02,npsi=50):
-        '''! Get q-profile at specified or uniformly spaced points
+        r'''! Get q-profile at specified or uniformly spaced points
 
         @param psi Explicit sampling locations in \f$\hat{\psi}\f$
         @param psi_pad End padding (axis and edge) for uniform sampling (ignored if `psi` is not None)
@@ -964,7 +964,7 @@ def get_q(self,psi=None,psi_pad=0.02,npsi=50):
             return psi,qvals,ravgs,dl.value,rbounds,zbounds
 
     def sauter_fc(self,psi=None,psi_pad=0.02,npsi=50):
-        '''! Evaluate Sauter trapped particle fractions at specified or uniformly spaced points
+        r'''! Evaluate Sauter trapped particle fractions at specified or uniformly spaced points
 
         @param psi Explicit sampling locations in \f$\hat{\psi}\f$
         @param psi_pad End padding (axis and edge) for uniform sampling (ignored if `psi` is not None)
@@ -990,7 +990,7 @@ def sauter_fc(self,psi=None,psi_pad=0.02,npsi=50):
             return psi,fc,r_avgs,modb_avgs
 
     def get_globals(self):
-        '''! Get global plasma parameters
+        r'''! Get global plasma parameters
 
         @result Ip, [R_Ip, Z_Ip], \f$\int dV\f$, \f$\int P dV\f$, diamagnetic flux,
         enclosed toroidal flux
@@ -1007,7 +1007,7 @@ def get_globals(self):
         return Ip.value, centroid, vol.value, pvol.value, dflux.value, tflux.value, Li.value
 
     def get_profiles(self,psi=None,psi_pad=1.E-8,npsi=50):
-        '''! Get G-S source profiles
+        r'''! Get G-S source profiles
 
         @param psi Explicit sampling locations in \f$\hat{\psi}\f$
         @param psi_pad End padding (axis and edge) for uniform sampling (ignored if `psi` is not None)
@@ -1126,7 +1126,7 @@ def plot_constraints(self,fig,ax,isoflux_color='tab:red',isoflux_marker='+',sadd
     def plot_psi(self,fig,ax,psi=None,normalized=True,plasma_color=None,plasma_nlevels=8,plasma_levels=None,plasma_colormap=None,
                  vacuum_color='darkgray',vacuum_nlevels=8,vacuum_levels=None,vacuum_colormap=None,
                  xpoint_color='k',xpoint_marker='x',opoint_color='k',opoint_marker='*'):
-        '''! Plot contours of \f$\hat{\psi}\f$
+        r'''! Plot contours of \f$\hat{\psi}\f$
 
         @param fig Figure to add to
         @param ax Axis to add to
@@ -1194,7 +1194,7 @@ def plot_psi(self,fig,ax,psi=None,normalized=True,plasma_color=None,plasma_nleve
         ax.set_aspect('equal','box')
 
     def plot_eddy(self,fig,ax,dpsi_dt=None,nlevels=40,colormap='jet',clabel=r'$J_w$ [$A/m^2$]'):
-        '''! Plot contours of \f$\hat{\psi}\f$
+        r'''! Plot contours of \f$\hat{\psi}\f$
 
         @param fig Figure to add to
         @param ax Axis to add to