apply precommit

docs/conf.py

@@ -7,11 +7,12 @@
 import datetime
 import os
 
-# -- Project information -----------------------------------------------------
-
 # The full version, including alpha/beta/rc tags
 from ebtelplusplus import __version__
 
+# -- Project information -----------------------------------------------------
+
+
 release = __version__
 is_development = '.dev' in __version__
 
@@ -137,4 +138,3 @@
     'doc_module': ('ebtelplusplus',),
     'only_warn_on_example_error': True,
 }
-

docs/index.rst

@@ -19,7 +19,7 @@ EBTEL also calculates the differential emission measure (DEM) for both the trans
 Details regarding this formulation can be found in :cite:t:`klimchuk_highly_2008`.
 
 .. note::
-   
+
    If you are looking for the original IDL implementation,
    the repository for the original IDL code can be found `here <https://github.com/rice-solar-physics/EBTEL>`__.
 

ebtelplusplus/__init__.py

@@ -1,7 +1,7 @@
 """
 ebtelplusplus: Zero-dimensional hydrodynamics of coronal loops
 """
-from ebtelplusplus.high_level import run, build_configuration
+from ebtelplusplus.high_level import build_configuration, run
 
 try:
     from ebtelplusplus._version import __version__

ebtelplusplus/_low_level.py

@@ -3,4 +3,4 @@
 """
 from ._core import run
 
-__all__ = ["run"]
+__all__ = ["run"]

ebtelplusplus/extern/heater.cpp

@@ -1,6 +1,6 @@
 /*
 heater.cpp
-Class defnition for heater object
+Class definition for heater object
 */
 
 #include "heater.h"

ebtelplusplus/high_level.py

@@ -1,12 +1,13 @@
 """
 High level interface to running an ebtel++ simulation
 """
-from collections import namedtuple
-
 import astropy.units as u
+
 from astropy.utils.data import get_pkg_data_path
+from collections import namedtuple
 
 import ebtelplusplus._low_level
+
 from ebtelplusplus.models import DemModel, PhysicsModel, SolverModel
 
 __all__ = ["run", "build_configuration"]
@@ -54,7 +55,7 @@ def run(total_time: u.s, loop_length: u.cm, heating, physics=None, solver=None,
     solver_model: `~ebtelplusplus.models.SolverModel`, optional
         Configuration parameters related to the numerical solver
     dem_model: `~ebtelplusplus.models.DemModel`, optional
-        Configruation parameters related to the DEM calculation
+        Configuration parameters related to the DEM calculation
 
     Returns
     -------

ebtelplusplus/models.py

@@ -1,9 +1,8 @@
 """
 Models for configuring ebtel++ runs
 """
-import dataclasses
-
 import astropy.units as u
+import dataclasses
 
 __all__ = [
     'PhysicsModel',
@@ -50,14 +49,14 @@ class PhysicsModel:
         abundances), or "variable" (to vary the radiative loss function from
         coronal to photospheric as a function of density and temperature).
     loop_length_ratio_tr_total: `float`
-        Ratio between the length of the transition region and the total loop 
+        Ratio between the length of the transition region and the total loop
         length. For a transition region of finite length, a typical value of
         0.15 is used :cite:p:`cargill_static_2022`.
     area_ratio_tr_corona: `float`
-        Ratio between the cross-sectional area averaged over the transition 
+        Ratio between the cross-sectional area averaged over the transition
         region and averaged over the corona
     area_ratio_0_corona: `float`
-        Ratio between the cross-sectional area at the TR-corona boundary and 
+        Ratio between the cross-sectional area at the TR-corona boundary and
         the cross-sectional area averaged over the corona
     """
     saturation_limit: float = None
@@ -134,7 +133,7 @@ class DemModel:
     calculate_dem: `bool`
         If true, calculate the coronal and transition region DEM
     use_new_tr_method: `bool`
-        If true, the transition region DEM is calculated using the method 
+        If true, the transition region DEM is calculated using the method
         outlined in section 3 (the appendix) of :cite:t:`klimchuk_highly_2008`.
     temperature_bins: `int`
         Number of bins to use when calculating the DEM
@@ -259,7 +258,7 @@ class HeatingModel:
     ebtel++ input parameters for the time-dependent heating
 
     The ebtel++ time-dependent heating model is parameterized by a
-    series of discrete events (`HeatingEvent`) combined with a constant 
+    series of discrete events (`HeatingEvent`) combined with a constant
     background heating rate. Furthermore, this energy can be injected into
     either the electrons or the ions or some admixture of the two.
 

ebtelplusplus/tests/helpers.py

@@ -1,11 +1,11 @@
 """
 Helper functions for tests
 """
-import pathlib
-
 import astropy.units as u
 import h5py
 import numpy as np
+import pathlib
+
 from astropy.utils.data import get_pkg_data_path
 
 

ebtelplusplus/tests/test_compare_hydrad.py

@@ -3,9 +3,11 @@
 """
 import astropy.units as u
 import pytest
+
 from scipy.interpolate import interp1d
 
 import ebtelplusplus
+
 from ebtelplusplus.models import (
     HeatingModel,
     PhysicsModel,
@@ -53,7 +55,7 @@ def test_compare_hydrad_single_event_peak_values(tau, heating_type, solver_model
     # done in Barnes et al. (2016a)
     for name in ['electron_temperature', 'ion_temperature', 'density']:
         f_interp = interp1d(r_ebtel.time.to_value('s'),
-                            getattr(r_ebtel, name).to_value(r_hydrad[name].unit), 
+                            getattr(r_ebtel, name).to_value(r_hydrad[name].unit),
                             fill_value='extrapolate')
         x_ebtel_interp = u.Quantity(f_interp(r_hydrad['time'].to_value('s')), r_hydrad[name].unit)
         i_peak = r_hydrad[name].argmax()

ebtelplusplus/tests/test_compare_idl.py

@@ -5,6 +5,7 @@
 import pytest
 
 import ebtelplusplus
+
 from ebtelplusplus.models import (
     DemModel,
     HeatingModel,
@@ -73,7 +74,7 @@ def test_compare_idl_single_event(physics_model,
     assert u.allclose(r_cpp.ion_temperature, r_idl['temperature'], rtol=RTOL)
     assert u.allclose(r_cpp.density, r_idl['density'], rtol=RTOL)
     assert u.allclose(r_cpp.electron_pressure+r_cpp.ion_pressure,
-                      r_idl['pressure'], 
+                      r_idl['pressure'],
                       rtol=RTOL)
     assert u.allclose(r_cpp.velocity, r_idl['velocity'], rtol=RTOL)
 

ebtelplusplus/tests/test_rad_loss.py

@@ -5,6 +5,7 @@
 import pytest
 
 import ebtelplusplus
+
 from ebtelplusplus.models import HeatingModel, PhysicsModel, TriangularHeatingEvent
 
 

ebtelplusplus/tests/test_single_fluid.py

@@ -5,6 +5,7 @@
 import pytest
 
 import ebtelplusplus
+
 from ebtelplusplus.models import HeatingEvent, HeatingModel, PhysicsModel
 
 

ebtelplusplus/tests/test_solver.py

@@ -1,13 +1,13 @@
 """
 Compare results of adaptive and static solvers
 """
-import copy
 
 import astropy.units as u
 import numpy as np
 import pytest
 
 import ebtelplusplus
+
 from ebtelplusplus.models import (
     HeatingModel,
     PhysicsModel,
@@ -53,7 +53,7 @@ def adaptive_results(physics_model, adaptive_solver, heating_model):
                              40*u.Mm,
                              heating_model,
                              physics=physics_model,
-                             solver=adaptive_solver)    
+                             solver=adaptive_solver)
 
 
 @pytest.fixture()
@@ -62,7 +62,7 @@ def static_results(physics_model, static_solver, heating_model):
                              40*u.Mm,
                              heating_model,
                              physics=physics_model,
-                             solver=static_solver)    
+                             solver=static_solver)
 
 
 @pytest.mark.parametrize(('name', 'atol'), [

examples/electron_single_event.py

@@ -5,11 +5,13 @@
 and injecting 10 ergs per cubic centimeter into the loop plasma.
 """
 import astropy.units as u
-from astropy.visualization import quantity_support
 import matplotlib.pyplot as plt
 import numpy as np
 
+from astropy.visualization import quantity_support
+
 import ebtelplusplus
+
 from ebtelplusplus.models import DemModel, HeatingModel, TriangularHeatingEvent
 
 quantity_support()

examples/ion_multi_event.py

@@ -5,11 +5,13 @@
 200 seconds with heating rates chosen from a uniform distribution.
 """
 import astropy.units as u
-from astropy.visualization import quantity_support
 import matplotlib.pyplot as plt
 import numpy as np
 
+from astropy.visualization import quantity_support
+
 import ebtelplusplus
+
 from ebtelplusplus.models import DemModel, HeatingModel, SquareHeatingEvent
 
 quantity_support()

examples/single_trapezoid_event.py

@@ -5,12 +5,14 @@
 same temperature to illustrate the single fluid case.
 """
 import astropy.units as u
-from astropy.visualization import quantity_support
 import matplotlib.pyplot as plt
 import numpy as np
 
+from astropy.visualization import quantity_support
+
 import ebtelplusplus
-from ebtelplusplus.models import DemModel, HeatingModel, HeatingEvent, PhysicsModel
+
+from ebtelplusplus.models import DemModel, HeatingEvent, HeatingModel, PhysicsModel
 
 quantity_support()
 

pyproject.toml

@@ -127,7 +127,7 @@ lines_between_types = 1
 
 [tool.codespell]
 skip = "*.fts,*.fits,venv,*.pro,*.bib,*.asdf,*.json"
-ignore-words-list = ""
+#ignore-words-list = ""
 
 [tool.ruff]
 target-version = "py310"
@@ -177,4 +177,3 @@ lint.extend-ignore = [
 
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"
-