Applied black

src/mitim_modules/freegsu/FREEGSUmain.py

@@ -236,17 +236,21 @@ def runFreeGS(self, dictDVs, plot=False, figs=None, onlyPrepare=False, debug=Fal
     out = FREEGStools.evaluator(
         dictDVs,
         CoilCurrents=self.function_parameters["CoilCurrents"],
-        CoilCurrents_lower=self.function_parameters["CoilCurrents_lower"]
-        if "CoilCurrents_lower" in self.function_parameters
-        else None,
+        CoilCurrents_lower=(
+            self.function_parameters["CoilCurrents_lower"]
+            if "CoilCurrents_lower" in self.function_parameters
+            else None
+        ),
         Constraints=self.function_parameters["Constraints"],
         optionsFREEGS=self.function_parameters["optionsFREEGS"],
         plot=plot,
         figs=figs,
         debug=debug,
-        ProblemExtras=self.function_parameters["params"]
-        if "params" in self.function_parameters
-        else None,
+        ProblemExtras=(
+            self.function_parameters["params"]
+            if "params" in self.function_parameters
+            else None
+        ),
         onlyPrepare=onlyPrepare,
     )
 

src/mitim_modules/portals/PORTALSmain.py

@@ -71,9 +71,9 @@ def default_namelist(Optim):
     Optim["surrogateOptions"]["ensureTrainingBounds"] = True
 
     # Acquisition
-    Optim[
-        "optimizers"
-    ] = "root_5-botorch-ga"  # Added root which is not a default bc it needs dimX=dimY
+    Optim["optimizers"] = (
+        "root_5-botorch-ga"  # Added root which is not a default bc it needs dimX=dimY
+    )
     Optim["acquisitionType"] = "posterior_mean"
 
     return Optim
@@ -300,7 +300,7 @@ def prep(
             hardGradientLimits=hardGradientLimits,
             dfT=self.dfT,
             seedInitial=seedInitial,
-            checkForSpecies=askQuestions
+            checkForSpecies=askQuestions,
         )
         print(">> PORTALS initalization module (END)", typeMsg="i")
 
@@ -487,13 +487,13 @@ def reuseTrainingTabular(
                 self_copy = copy.deepcopy(self)
                 if reevaluateTargets == 1:
                     self_copy.powerstate.TransportOptions["TypeTransport"] = None
-                    self_copy.powerstate.TransportOptions[
-                        "TypeTarget"
-                    ] = self_copy.powerstate.TargetCalc = "powerstate"
+                    self_copy.powerstate.TransportOptions["TypeTarget"] = (
+                        self_copy.powerstate.TargetCalc
+                    ) = "powerstate"
                 else:
-                    self_copy.powerstate.TransportOptions[
-                        "TypeTransport"
-                    ] = "tglf_neo_tgyro"
+                    self_copy.powerstate.TransportOptions["TypeTransport"] = (
+                        "tglf_neo_tgyro"
+                    )
 
                 results, tgyro, powerstate, dictOFs = runModelEvaluator(
                     self_copy,

src/mitim_modules/portals/aux/PORTALSanalysis.py

@@ -68,12 +68,17 @@ def from_folder(cls, folder, folderRemote=None, folderAnalysis=None):
                 return cls(opt_fun, folderAnalysis=folderAnalysis)
 
             except (FileNotFoundError, AttributeError) as e:
-                print("\t- Could not read optimization results due to error:", typeMsg="w")
+                print(
+                    "\t- Could not read optimization results due to error:", typeMsg="w"
+                )
                 print(e)
                 print("\t- Trying to read PORTALS initialization...", typeMsg="w")
                 return PORTALSinitializer(folder)
         else:
-            print("\t- Folder does not exist, are you sure you are on the right path?", typeMsg="w")
+            print(
+                "\t- Folder does not exist, are you sure you are on the right path?",
+                typeMsg="w",
+            )
 
     @classmethod
     def merge_instances(cls, instances, folderAnalysis=None, base_index=0):
@@ -408,7 +413,7 @@ def plotPORTALS(self):
         self.plotExpected(fig=fig)
 
         fig = self.fn.add_figure(label="PORTALS Simulation", tab_color=4)
-        _,_ = self.plotModelComparison(fig=fig)
+        _, _ = self.plotModelComparison(fig=fig)
 
     def plotMetrics(self, **kwargs):
         PORTALSplot.PORTALSanalyzer_plotMetrics(self, **kwargs)
@@ -666,9 +671,9 @@ def runTGLFfull(
         if not os.path.exists(folder):
             os.system(f"mkdir {folder}")
 
-        if onlyBest: 
+        if onlyBest:
             ranges = [self.ibest]
-        else: 
+        else:
             ranges = range(self.ilast + 1)
 
         for ev in ranges:
@@ -997,7 +1002,7 @@ def plotMetrics(self, extra_lab="", **kwargs):
                     lastRho=self.powerstates[0].plasma["rho"][-1, -1].item(),
                     lw=0.5,
                     ms=0,
-                    label=f'profile #{i}',
+                    label=f"profile #{i}",
                 )
 
             axs[0].legend(prop={"size": 8})

src/mitim_modules/portals/aux/PORTALSinit.py

@@ -108,11 +108,14 @@ def initializeProblem(
     if checkForSpecies:
         speciesNotFound = []
         for i in range(len(profiles.Species)):
-            c = TARGETStools.get_chebyshev_coeffs(profiles.Species[i]['N'])
-            if c[0]<=-1E10:
-                speciesNotFound.append(profiles.Species[i]['N'])
-        if len(speciesNotFound)>0:
-            a = print(f"\t- Species {speciesNotFound} not found, radiation will be zero in PORTALS. Make sure this is ok with your predictions", typeMsg="q")
+            c = TARGETStools.get_chebyshev_coeffs(profiles.Species[i]["N"])
+            if c[0] <= -1e10:
+                speciesNotFound.append(profiles.Species[i]["N"])
+        if len(speciesNotFound) > 0:
+            a = print(
+                f"\t- Species {speciesNotFound} not found, radiation will be zero in PORTALS. Make sure this is ok with your predictions",
+                typeMsg="q",
+            )
             if not a:
                 raise ValueError("Species not found")
     """
@@ -168,9 +171,9 @@ def initializeProblem(
     portals_fun.powerstate.calculateTargets()
 
     # Prepare powerstate for evaluations
-    portals_fun.powerstate.TransportOptions[
-        "TypeTransport"
-    ] = portals_fun.PORTALSparameters["model_used"]
+    portals_fun.powerstate.TransportOptions["TypeTransport"] = (
+        portals_fun.PORTALSparameters["model_used"]
+    )
     if ModelOptions is not None:
         portals_fun.powerstate.TransportOptions["ModelOptions"] = ModelOptions
     else:

src/mitim_modules/portals/aux/PORTALSplot.py

@@ -634,7 +634,9 @@ def PORTALSanalyzer_plotMetrics(
         ax.plot(
             self.evaluations, resChosen, "-o", lw=1.0, c=c, markersize=2, label=label
         )
-        indeces_plot, colors_plot, labels_plot, markers_plot = define_extra_iterators(self)
+        indeces_plot, colors_plot, labels_plot, markers_plot = define_extra_iterators(
+            self
+        )
 
         for cont, (indexUse, col, lab, mars) in enumerate(
             zip(
@@ -770,7 +772,9 @@ def PORTALSanalyzer_plotMetrics(
             markersize=2,
             label="$\\chi_R$",
         )
-        indeces_plot, colors_plot, labels_plot, markers_plot = define_extra_iterators(self)
+        indeces_plot, colors_plot, labels_plot, markers_plot = define_extra_iterators(
+            self
+        )
 
         for cont, (indexUse, col, lab, mars) in enumerate(
             zip(
@@ -970,7 +974,9 @@ def PORTALSanalyzer_plotMetrics(
             markersize=2,
             label="$P_{fus}$",
         )
-        indeces_plot, colors_plot, labels_plot, markers_plot = define_extra_iterators(self)
+        indeces_plot, colors_plot, labels_plot, markers_plot = define_extra_iterators(
+            self
+        )
 
         for cont, (indexUse, col, lab, mars) in enumerate(
             zip(
@@ -1034,22 +1040,21 @@ def define_extra_iterators(self):
         if self.ibest != self.evaluations[-2]:
             self.iextra = self.iextra + [self.evaluations[-2]]
 
-
     # Add extra points
     colors = GRAPHICStools.listColors()
-    colors = [color for color in colors if color not in ['r', 'b']]
+    colors = [color for color in colors if color not in ["r", "b"]]
     indeces_plot = indeces_plot + self.iextra
-    colors_plot = colors_plot+colors[:len(self.iextra)]
+    colors_plot = colors_plot + colors[: len(self.iextra)]
 
     for i in range(len(self.iextra)):
 
         if self.iextra[i] == -1 or self.iextra[i] == self.evaluations[-1]:
-            ll = 'Last'
+            ll = "Last"
         else:
-            ll = 'Extra'
+            ll = "Extra"
         labels_plot = labels_plot + [f"{ll} (#{self.evaluations[self.iextra[i]]})"]
 
-    markers_plot = GRAPHICStools.listmarkers()[:len(indeces_plot)]
+    markers_plot = GRAPHICStools.listmarkers()[: len(indeces_plot)]
 
     return indeces_plot, colors_plot, labels_plot, markers_plot
 
@@ -1977,7 +1982,7 @@ def PORTALSanalyzer_plotModelComparison(
     quantityX_stds = "QeGB_sim_turb_stds" if UseTGLFfull_x is None else None
     quantityY = "QeGB_sim_turb"
     quantityY_stds = "QeGB_sim_turb_stds"
-    metrics['Qe'] = plotModelComparison_quantity(
+    metrics["Qe"] = plotModelComparison_quantity(
         self,
         axs[0],
         quantityX=quantityX,
@@ -1999,7 +2004,7 @@ def PORTALSanalyzer_plotModelComparison(
     quantityX_stds = "QiGBIons_sim_turb_thr_stds" if UseTGLFfull_x is None else None
     quantityY = "QiGBIons_sim_turb_thr"
     quantityY_stds = "QiGBIons_sim_turb_thr_stds"
-    metrics['Qi'] = plotModelComparison_quantity(
+    metrics["Qi"] = plotModelComparison_quantity(
         self,
         axs[1],
         quantityX=quantityX,
@@ -2021,7 +2026,7 @@ def PORTALSanalyzer_plotModelComparison(
     quantityX_stds = "GeGB_sim_turb_stds" if UseTGLFfull_x is None else None
     quantityY = "GeGB_sim_turb"
     quantityY_stds = "GeGB_sim_turb_stds"
-    metrics['Ge'] = plotModelComparison_quantity(
+    metrics["Ge"] = plotModelComparison_quantity(
         self,
         axs[2],
         quantityX=quantityX,
@@ -2059,7 +2064,7 @@ def PORTALSanalyzer_plotModelComparison(
         quantityX_stds = "GiGB_sim_turb_stds" if UseTGLFfull_x is None else None
         quantityY = "GiGB_sim_turb"
         quantityY_stds = "GiGB_sim_turb_stds"
-        metrics['Gi'] = plotModelComparison_quantity(
+        metrics["Gi"] = plotModelComparison_quantity(
             self,
             axs[2 + cont],
             quantityX=quantityX,
@@ -2105,7 +2110,7 @@ def PORTALSanalyzer_plotModelComparison(
         quantityX_stds = "MtGB_sim_turb_stds"
         quantityY = "MtGB_sim_turb"
         quantityY_stds = "MtGB_sim_turb_stds"
-        metrics['Mt'] = plotModelComparison_quantity(
+        metrics["Mt"] = plotModelComparison_quantity(
             self,
             axs[2 + cont],
             quantityX=quantityX,
@@ -2142,7 +2147,7 @@ def PORTALSanalyzer_plotModelComparison(
         quantityX_stds = "EXeGB_sim_turb_stds"
         quantityY = "EXeGB_sim_turb"
         quantityY_stds = "EXeGB_sim_turb_stds"
-        metrics['EX'] = plotModelComparison_quantity(
+        metrics["EX"] = plotModelComparison_quantity(
             self,
             axs[2 + cont],
             quantityX=quantityX,
@@ -2171,7 +2176,7 @@ def PORTALSanalyzer_plotModelComparison(
 
         cont += 1
 
-    return axs,metrics
+    return axs, metrics
 
 
 def plotModelComparison_quantity(
@@ -2315,6 +2320,7 @@ def plotModelComparison_quantity(
 
     return metrics
 
+
 # ---------------------------------------------------------------------------------------------------------------------
 
 
@@ -3033,7 +3039,11 @@ def plotFluxComparison(
                     y = tBest.derived[var] * mult
                 if plotTargets:
                     ax.plot(
-                        tBest.profiles["rho(-)"] if not useRoa else tBest.derived["roa"],
+                        (
+                            tBest.profiles["rho(-)"]
+                            if not useRoa
+                            else tBest.derived["roa"]
+                        ),
                         y,
                         "-.",
                         lw=0.5,
@@ -3043,7 +3053,11 @@ def plotFluxComparison(
                     )
                 else:
                     ax.plot(
-                        tBest.profiles["rho(-)"] if not useRoa else tBest.derived["roa"],
+                        (
+                            tBest.profiles["rho(-)"]
+                            if not useRoa
+                            else tBest.derived["roa"]
+                        ),
                         y,
                         "--",
                         lw=2,

src/mitim_modules/portals/exe/runTGLF.py

@@ -24,9 +24,7 @@
 parser.add_argument(
     "--var", type=float, required=False, default=0.05
 )  # Variation in inputs (5% default)
-parser.add_argument(
-    "--num", type=int, required=False, default=10
-)
+parser.add_argument("--num", type=int, required=False, default=10)
 parser.add_argument(
     "--restart", "-r", required=False, default=False, action="store_true"
 )

src/mitim_modules/powertorch/aux/PARAMtools.py

@@ -60,7 +60,6 @@ def deparametrizer(x, y, printMessages=printDeviations):
             printMessages=printMessages,
         )
 
-
     """
 	Construct curve in a coarse grid
 	----------------------------------------------------------------------------------------------------
@@ -86,7 +85,6 @@ def deparametrizer_coarse_middle(x, y, printMessages=printDeviations):
             printMessages=printMessages,
         )
 
-
     return (
         dict_param["aLy_coarse"],
         deparametrizer,

src/mitim_modules/vitals/VITALSmain.py

@@ -17,9 +17,9 @@ def default_namelist(Optim):
     Optim["initialPoints"] = 8
     Optim["BOiterations"] = 20
     Optim["newPoints"] = 4
-    Optim[
-        "parallelCalls"
-    ] = 4  # each TGLF is run with 4 cores, so 16 total cores consumed with this default
+    Optim["parallelCalls"] = (
+        4  # each TGLF is run with 4 cores, so 16 total cores consumed with this default
+    )
     Optim["surrogateOptions"]["TypeMean"] = 2
     Optim["StrategyOptions"]["AllowedExcursions"] = [0.1, 0.1]
     Optim["StrategyOptions"]["HitBoundsIncrease"] = [1.1, 1.1]