Merge branch 'main' into T201_adjust

PaulJonasJost · PaulJonasJost · commit e0f3453c9cda · 2026-03-24T17:14:12.000+01:00
# Conflicts:
#	pyproject.toml
diff --git a/pyproject.toml b/pyproject.toml
@@ -88,7 +88,6 @@ lint.ignore = [
     "D101",  # Ignore missing docstring in public classes
     "F401",
     # FIXME: those are ignored for now, should be fixed eventually
-    "ERA001", # Found commented-out code
     "SIM105",  # Use `contextlib.suppress`
     "S110",  # `try`-`except`-`pass` detected, consider logging the exception
 ]
diff --git a/src/petab_gui/controllers/simulation_controller.py b/src/petab_gui/controllers/simulation_controller.py
@@ -103,7 +103,6 @@ def simulate(self):
                     model=petab_problem.model,
                 )
 
-        # import petabsimualtor
         import basico
         from basico.petab import PetabSimulator
 
diff --git a/src/petab_gui/views/simple_plot_view.py b/src/petab_gui/views/simple_plot_view.py
@@ -424,7 +424,6 @@ def plot_residuals(self):
             simulations_df,
             ax=axes_fit,
         )
-        # fig_fit.tight_layout()
         create_plot_tab(fig_fit, self, "Goodness of Fit")
 
     def disable_plotting(self, disable: bool):

Original file line number	Diff line number	Diff line change
`@@ -88,7 +88,6 @@ lint.ignore = [`
`88`	`88`	`"D101", # Ignore missing docstring in public classes`
`89`	`89`	`"F401",`
`90`	`90`	`# FIXME: those are ignored for now, should be fixed eventually`
`91`		`- "ERA001", # Found commented-out code`
`92`	`91`	"SIM105", # Use `contextlib.suppress`
`93`	`92`	"S110", # `try`-`except`-`pass` detected, consider logging the exception
`94`	`93`	`]`
Original file line number	Diff line number	Diff line change
`@@ -103,7 +103,6 @@ def simulate(self):`
`103`	`103`	`model=petab_problem.model,`
`104`	`104`	`)`
`105`	`105`
`106`		`- # import petabsimualtor`
`107`	`106`	`import basico`
`108`	`107`	`from basico.petab import PetabSimulator`
`109`	`108`
Original file line number	Diff line number	Diff line change
`@@ -424,7 +424,6 @@ def plot_residuals(self):`
`424`	`424`	`simulations_df,`
`425`	`425`	`ax=axes_fit,`
`426`	`426`	`)`
`427`		`- # fig_fit.tight_layout()`
`428`	`427`	`create_plot_tab(fig_fit, self, "Goodness of Fit")`
`429`	`428`
`430`	`429`	`def disable_plotting(self, disable: bool):`