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Python: Errors & Linting #5124

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Aug 18, 2024
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Python: Errors & Linting #5124

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c476e0e
`__init__.py`: Intentionally Unused Imports
ax3l Aug 10, 2024
4e1d10c
Autofixes
ax3l Aug 10, 2024
108d2ba
Move Fixes ("Unsafe" - Checked & Edited)
ax3l Aug 10, 2024
b07d552
Errors & Their Manual Fixes
ax3l Aug 10, 2024
88025fc
Sphinx: Import has side-effect (keep)
ax3l Aug 10, 2024
5eef031
Remove unused var
ax3l Aug 10, 2024
19e8b3c
Add Used `dt` - Used in `eval` below
ax3l Aug 10, 2024
668aed6
Address Review Comments from Dave
ax3l Aug 10, 2024
1262ee6
Remove outdated perf tests
ax3l Aug 10, 2024
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2 changes: 1 addition & 1 deletion Docs/source/conf.py
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Expand Up @@ -31,7 +31,7 @@
import urllib.request

import pybtex.plugin
import sphinx_rtd_theme
import sphinx_rtd_theme # noqa
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from pybtex.style.formatting.unsrt import Style as UnsrtStyle

sys.path.insert(0, os.path.join(os.path.dirname(os.path.abspath(__file__)), '../../Regression/Checksum'))
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1 change: 0 additions & 1 deletion Docs/source/index.rst
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Expand Up @@ -140,7 +140,6 @@ Maintenance
:hidden:

maintenance/release
maintenance/performance_tests

Epilogue
--------
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135 changes: 0 additions & 135 deletions Docs/source/maintenance/performance_tests.rst
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2 changes: 1 addition & 1 deletion Docs/source/usage/workflows/ml_materials/train.py
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Expand Up @@ -85,7 +85,7 @@
train_loss_list = []
test_loss_list = []

model.to(device=device);
model.to(device=device)

########## train and test functions ####
# Manual: Train function START
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2 changes: 1 addition & 1 deletion Docs/source/usage/workflows/ml_materials/visualize.py
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Expand Up @@ -65,7 +65,7 @@
act = activation_type
)
model.load_state_dict(model_data['model_state_dict'])
model.to(device=device);
model.to(device=device)

###### load model data ###############
dataset_filename = f'dataset_{species}.pt'
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2 changes: 1 addition & 1 deletion Examples/Tests/AcceleratorLattice/analysis.py
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Expand Up @@ -42,7 +42,7 @@
# The simulation data is in the boosted frame.
# Transform the z position to the lab frame.
time = ds.current_time.value
zz_sim = gamma_boost*zz_sim + uz_boost*time;
zz_sim = gamma_boost*zz_sim + uz_boost*time

# Fetch the quadrupole lattice data
quad_starts = []
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2 changes: 1 addition & 1 deletion Examples/Tests/btd_rz/analysis_BTD_laser_antenna.py
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Expand Up @@ -38,7 +38,7 @@ def fit_function(z, z0_phase):

# The values must be consistent with the values provided in the simulation input
t_current = 80e-15 # Time of the snapshot1
c = 299792458;
c = 299792458
z0_antenna = -1.e-6 # position of laser
lambda0 = 0.8e-6 # wavelength of the signal
tau0 = 10e-15 # duration of the signal
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20 changes: 10 additions & 10 deletions Examples/Tests/collision/analysis_collision_1d.py
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Expand Up @@ -43,28 +43,28 @@

# Find the index 'Npmin' that separates macroparticles from group A and group B
Np = len(sorted_wp)
wpmin = sorted_wp.min();
wpmax = sorted_wp.max();
wpmin = sorted_wp.min()
wpmax = sorted_wp.max()
for i in range(len(sorted_wp)):
if sorted_wp[i] > wpmin:
Npmin = i
break

NpA = Npmin
wpA = wpmin;
wpA = wpmin
NpB = Np - Npmin
wpB = wpmax;
wpB = wpmax
NpAs = 0
NpAe = Npmin
NpBs = Npmin
NpBe = Np

#############

sorted_px_sum = np.abs(sorted_px).sum();
sorted_py_sum = np.abs(sorted_py).sum();
sorted_pz_sum = np.abs(sorted_pz).sum();
sorted_wp_sum = np.abs(sorted_wp).sum();
sorted_px_sum = np.abs(sorted_px).sum()
sorted_py_sum = np.abs(sorted_py).sum()
sorted_pz_sum = np.abs(sorted_pz).sum()
sorted_wp_sum = np.abs(sorted_wp).sum()

# compute mean velocities
wAtot = wpA*NpA
Expand Down Expand Up @@ -118,8 +118,8 @@
TApar_30ps_soln = 6.15e3 # TA parallel solution at t = 30 ps
error = np.abs(TApar-TApar_30ps_soln)/TApar_30ps_soln
tolerance = 0.02
print('TApar at 30ps error = ', error);
print('tolerance = ', tolerance);
print('TApar at 30ps error = ', error)
print('tolerance = ', tolerance)
assert error < tolerance

test_name = os.path.split(os.getcwd())[1]
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15 changes: 8 additions & 7 deletions Examples/Tests/electrostatic_sphere/analysis_electrostatic_sphere.py
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Expand Up @@ -84,14 +84,15 @@
# r(0) = r_0, r'(0) = 0, and a = q_e*q_tot/(4*pi*eps_0*m_e)
#
# The E was calculated at the end of the last time step
v_exact = lambda r: np.sqrt((q_e*q_tot)/(2*pi*m_e*eps_0)*(1/r_0-1/r))
t_exact = lambda r: np.sqrt(r_0**3*2*pi*m_e*eps_0/(q_e*q_tot)) \
* (np.sqrt(r/r_0-1)*np.sqrt(r/r_0) \
+ np.log(np.sqrt(r/r_0-1)+np.sqrt(r/r_0)))
func = lambda rho: t_exact(rho) - t_max #Objective function to find r(t_max)
def v_exact(r):
return np.sqrt(q_e * q_tot / (2 * pi * m_e * eps_0) * (1 / r_0 - 1 / r))
def t_exact(r):
return np.sqrt(r_0 ** 3 * 2 * pi * m_e * eps_0 / (q_e * q_tot)) * (np.sqrt(r / r_0 - 1) * np.sqrt(r / r_0) + np.log(np.sqrt(r / r_0 - 1) + np.sqrt(r / r_0)))
def func(rho):
return t_exact(rho) - t_max #Objective function to find r(t_max)
r_end = fsolve(func,r_0)[0] #Numerically solve for r(t_max)
E_exact = lambda r: np.sign(r)*(q_tot/(4*pi*eps_0*r**2)*(abs(r)>=r_end) \
+ q_tot*abs(r)/(4*pi*eps_0*r_end**3)*(abs(r)<r_end))
def E_exact(r):
return np.sign(r) * (q_tot / (4 * pi * eps_0 * r ** 2) * (abs(r) >= r_end) + q_tot * abs(r) / (4 * pi * eps_0 * r_end ** 3) * (abs(r) < r_end))

# Load data pertaining to fields
data = ds.covering_grid(level=0,
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2 changes: 1 addition & 1 deletion Examples/Tests/laser_injection_from_file/analysis_from_RZ_file.py
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Expand Up @@ -148,7 +148,7 @@ def launch_analysis(executable):
def main() :

from lasy.laser import Laser
from lasy.profiles import CombinedLongitudinalTransverseProfile, GaussianProfile
from lasy.profiles import CombinedLongitudinalTransverseProfile
from lasy.profiles.longitudinal import GaussianLongitudinalProfile
from lasy.profiles.transverse import LaguerreGaussianTransverseProfile

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2 changes: 1 addition & 1 deletion Examples/Tests/nci_fdtd_stability/analysis_ncicorr.py
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Expand Up @@ -22,7 +22,7 @@
import checksumAPI

fn = sys.argv[1]
use_MR = re.search( 'nci_correctorMR', fn ) != None
use_MR = re.search( 'nci_correctorMR', fn ) is not None

if use_MR:
energy_corrector_off = 5.e32
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48 changes: 25 additions & 23 deletions Examples/Tests/nuclear_fusion/analysis_two_product_fusion.py
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Expand Up @@ -243,30 +243,32 @@ def cross_section( E_keV ):
## Returns cross section in b, using the analytical fits given
## in H.-S. Bosch and G.M. Hale 1992 Nucl. Fusion 32 611
joule_to_keV = 1.e-3/scc.e
B_G = scc.pi * scc.alpha * np.sqrt( 2.*m_reduced * scc.c**2 * joule_to_keV );
B_G = scc.pi * scc.alpha * np.sqrt( 2.*m_reduced * scc.c**2 * joule_to_keV )
if reaction_type == 'DT':
A1 = 6.927e4;
A2 = 7.454e8;
A3 = 2.050e6;
A4 = 5.2002e4;
A5 = 0;
B1 = 6.38e1;
B2 = -9.95e-1;
B3 = 6.981e-5;
B4 = 1.728e-4;
A1 = 6.927e4
A2 = 7.454e8
A3 = 2.050e6
A4 = 5.2002e4
A5 = 0
B1 = 6.38e1
B2 = -9.95e-1
B3 = 6.981e-5
B4 = 1.728e-4
elif reaction_type == 'DD':
A1 = 5.3701e4;
A2 = 3.3027e2;
A3 = -1.2706e-1;
A4 = 2.9327e-5;
A5 = -2.5151e-9;
B1 = 0;
B2 = 0;
B3 = 0;
B4 = 0;

astrophysical_factor = (A1 + E_keV*(A2 + E_keV*(A3 + E_keV*(A4 + E_keV*A5)))) / (1 + E_keV*(B1 + E_keV*(B2 + E_keV*(B3 + E_keV*B4))));
millibarn_to_barn = 1.e-3;
A1 = 5.3701e4
A2 = 3.3027e2
A3 = -1.2706e-1
A4 = 2.9327e-5
A5 = -2.5151e-9
B1 = 0
B2 = 0
B3 = 0
B4 = 0
else:
raise RuntimeError(f"Reaction type '{reaction_type}' not implemented.")

astrophysical_factor = (A1 + E_keV*(A2 + E_keV*(A3 + E_keV*(A4 + E_keV*A5)))) / (1 + E_keV*(B1 + E_keV*(B2 + E_keV*(B3 + E_keV*B4))))
millibarn_to_barn = 1.e-3
return millibarn_to_barn * astrophysical_factor/E_keV * np.exp(-B_G/np.sqrt(E_keV))

def E_com_to_p_sq_com(m1, m2, E):
Expand Down Expand Up @@ -405,7 +407,7 @@ def main():
ds_start = yt.load(filename_start)
ad_end = ds_end.all_data()
ad_start = ds_start.all_data()
dt = float(ds_end.current_time - ds_start.current_time)
dt = float(ds_end.current_time - ds_start.current_time) # noqa

Check notice

Code scanning / CodeQL

Unused local variable Note

Variable dt is not used.
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@dpgrote wrote in #5123 (comment)

The eval below needs dt. The eval is kind of hacky anyway. Something like this would be better

if i == 1:
    specific_check1(data, dt)
elif i == 2:
    specific_check2(data, dt)

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@NeilZaim @RemiLehe can you quickly see how to remove the eval with a more explicit or handling in this function?

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A simple fix would be to do

eval("specific_check"+str(i))(data, dt)

But it would be better to remove the eval altogether.

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Yes, that looks very similar to me 😅

field_data_end = ds_end.covering_grid(level=0, left_edge=ds_end.domain_left_edge,
dims=ds_end.domain_dimensions)
field_data_start = ds_start.covering_grid(level=0, left_edge=ds_start.domain_left_edge,
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2 changes: 1 addition & 1 deletion Examples/Tests/ohm_solver_EM_modes/PICMI_inputs.py
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Expand Up @@ -93,7 +93,7 @@ def __init__(self, test, dim, B_dir, verbose):

# dump all the current attributes to a dill pickle file
if comm.rank == 0:
with open(f'sim_parameters.dpkl', 'wb') as f:
with open('sim_parameters.dpkl', 'wb') as f:
dill.dump(self, f)

# print out plasma parameters
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2 changes: 1 addition & 1 deletion Examples/Tests/ohm_solver_EM_modes/PICMI_inputs_rz.py
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Expand Up @@ -82,7 +82,7 @@ def __init__(self, test, verbose):

# dump all the current attributes to a dill pickle file
if comm.rank == 0:
with open(f'sim_parameters.dpkl', 'wb') as f:
with open('sim_parameters.dpkl', 'wb') as f:
dill.dump(self, f)

# print out plasma parameters
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2 changes: 1 addition & 1 deletion Examples/Tests/ohm_solver_EM_modes/analysis.py
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Expand Up @@ -14,7 +14,7 @@
matplotlib.rcParams.update({'font.size': 20})

# load simulation parameters
with open(f'sim_parameters.dpkl', 'rb') as f:
with open('sim_parameters.dpkl', 'rb') as f:
sim = dill.load(f)

if sim.B_dir == 'z':
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6 changes: 3 additions & 3 deletions Examples/Tests/ohm_solver_EM_modes/analysis_rz.py
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Expand Up @@ -16,7 +16,7 @@
constants = picmi.constants

# load simulation parameters
with open(f'sim_parameters.dpkl', 'rb') as f:
with open('sim_parameters.dpkl', 'rb') as f:
sim = dill.load(f)

diag_dir = "diags/field_diags"
Expand Down Expand Up @@ -124,8 +124,8 @@ def process(it):
omega_fast = sim.vA * np.sqrt(R2 + np.sqrt(R2**2 - P4))
omega_slow = sim.vA * np.sqrt(R2 - np.sqrt(R2**2 - P4))
# Upper right corner
ax.plot(k*sim.l_i, omega_fast/sim.w_ci, 'w--', label = f"$\omega_{{fast}}$")
ax.plot(k*sim.l_i, omega_slow/sim.w_ci, color='white', linestyle='--', label = f"$\omega_{{slow}}$")
ax.plot(k*sim.l_i, omega_fast/sim.w_ci, 'w--', label = "$\omega_{fast}$")
ax.plot(k*sim.l_i, omega_slow/sim.w_ci, color='white', linestyle='--', label = "$\omega_{slow}$")
# Thermal resonance
thermal_res = sim.w_ci + 3*sim.v_ti*k
ax.plot(k*sim.l_i, thermal_res/sim.w_ci, color='magenta', linestyle='--', label = "$\omega = \Omega_i + 3v_{th,i}k$")
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2 changes: 1 addition & 1 deletion Examples/Tests/ohm_solver_ion_Landau_damping/analysis.py
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Expand Up @@ -14,7 +14,7 @@
matplotlib.rcParams.update({'font.size': 20})

# load simulation parameters
with open(f'sim_parameters.dpkl', 'rb') as f:
with open('sim_parameters.dpkl', 'rb') as f:
sim = dill.load(f)

# theoretical damping rates were taken from Fig. 14b of Munoz et al.
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