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Better test skipping and basic project linting #643

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2 changes: 1 addition & 1 deletion autotest/autotest_notebooks.py
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@briochh briochh Dec 15, 2025

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I think this notebook wrapper is no longer hit -- at some point, we should check and remove,

Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@


def get_notebooks():
return [f for f in os.listdir(nbdir) if f.endswith('.ipynb') and not "notest" in f]
return [f for f in os.listdir(nbdir) if f.endswith('.ipynb') and "notest" not in f]

def run_notebook(fn):
#pth = os.path.join(nbdir, fn)
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12 changes: 10 additions & 2 deletions autotest/emulator_tests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,8 @@
mou_exe_path = get_exe_path("pestpp-mou")

def dsi_freyberg(tmp_d,transforms=None,tag=""):
if not ies_exe_path:
pytest.skip("missing ies_exe_path")
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@briochh briochh Dec 15, 2025

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assume we will throw a fail elsewhere in the CI if bins are missing -- might be worth checking this.


test_d = "ends_master"
test_d = setup_tmp(test_d, tmp_d)
Expand Down Expand Up @@ -92,6 +94,8 @@ def test_dsi_mixed(tmp_path):

# @pytest.mark.timeout(method="thread", timeout=1000)
def test_dsivc(tmp_path):
if not mou_exe_path:
pytest.skip("missing mou_exe_path")
# basic quick as so can re-run here
dsi_freyberg(tmp_path, transforms=None)
# now test dsicv
Expand Down Expand Up @@ -205,6 +209,7 @@ def plot_freyberg_dsi():


def lpfa_freyberg(tmp_d="temp",transforms=None):
pytest.importorskip("sklearn")

test_d = "ends_master"
test_d = setup_tmp(test_d, tmp_d)
Expand Down Expand Up @@ -331,6 +336,8 @@ def test_lpfa_std(tmp_path):


def gpr_compare_invest():
if not mou_exe_path:
pytest.skip("missing mou_exe_path")
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@briochh briochh Dec 15, 2025

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These "invest" funcs shouldn't be collected by pytest in the first place, so the "skip" probs ineffective.

import numpy as np
from sklearn.gaussian_process import GaussianProcessRegressor
case = "zdt1"
Expand Down Expand Up @@ -492,6 +499,8 @@ def gpr_compare_invest():


def gpr_constr_invest():
if not mou_exe_path:
pytest.skip("missing mou_exe_path")
import numpy as np
from sklearn.gaussian_process import GaussianProcessRegressor
case = "constr"
Expand Down Expand Up @@ -812,14 +821,13 @@ def gpr_zdt1_test():
gpr_t_d = os.path.join(case + "_gpr_template")

data, input_names, output_names = collate_training_data(pst,m_d,case)
from pyemu.emulators.gpr import GPR
gpr = GPR(data=data.copy(),
input_names=input_names,
output_names=output_names,
#transforms=transforms,
#kernel=gp_kernel,
n_restarts_optimizer=20,
);
)
gpr.fit()
gpr.prepare_pestpp(m_d,case,gpr_t_d=gpr_t_d)

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5 changes: 2 additions & 3 deletions autotest/en_tests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -349,7 +349,6 @@ def from_parfiles_test(tmp_path):

def triangular_draw_test():
import os
import matplotlib.pyplot as plt
import pyemu

pst = pyemu.Pst(os.path.join("pst","pest.pst"))
Expand Down Expand Up @@ -577,7 +576,6 @@ def emp_cov_draw_test():

def mixed_par_draw_test():
import os
import matplotlib.pyplot as plt
import pandas as pd
import pyemu

Expand All @@ -591,6 +589,7 @@ def mixed_par_draw_test():
pe2 = pyemu.ParameterEnsemble.from_mixed_draws(pst, {},default="uniform",num_reals=num_reals)
pe3 = pyemu.ParameterEnsemble.from_mixed_draws(pst, {}, default="triangular", num_reals=num_reals)

# import matplotlib.pyplot as plt
# ax = plt.subplot(111)
# pe1.loc[:,pname].hist(ax=ax,alpha=0.5,bins=25)
# pe2.loc[:, pname].hist(ax=ax,alpha=0.5,bins=25)
Expand Down Expand Up @@ -697,7 +696,6 @@ def binary_test(tmp_path):

def mixed_par_draw_2_test():
import os
import matplotlib.pyplot as plt
import pandas as pd
import pyemu

Expand All @@ -711,6 +709,7 @@ def mixed_par_draw_2_test():
pe2 = pyemu.ParameterEnsemble.from_mixed_draws(pst, {},default="uniform",num_reals=num_reals)
pe3 = pyemu.ParameterEnsemble.from_mixed_draws(pst, {}, default="triangular", num_reals=num_reals)

# import matplotlib.pyplot as plt
# ax = plt.subplot(111)
# pe1.loc[:,pname].hist(ax=ax,alpha=0.5,bins=25)
# pe2.loc[:, pname].hist(ax=ax,alpha=0.5,bins=25)
Expand Down
6 changes: 3 additions & 3 deletions autotest/full_meal_deal_tests_ignore.py
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@briochh briochh Dec 15, 2025

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I think this is also mostly legacy func testing -- at some point we should check and remove

Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ def _get_port():
def freyberg_spinup(tmp_path):
try:
import flopy
except Exception as e:
except Exception:
return
import pyemu

Expand Down Expand Up @@ -248,7 +248,7 @@ def freyberg_kl_pp_compare():
import pandas as pd
try:
import flopy
except Exception as e:
except Exception:
return
import pyemu

Expand Down Expand Up @@ -319,7 +319,7 @@ def freyberg_diff_obs_test(tmp_path):
import pandas as pd
try:
import flopy
except Exception as e:
except Exception:
return
import pyemu

Expand Down
34 changes: 8 additions & 26 deletions autotest/plot_tests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,14 +3,11 @@
import numpy as np
import pandas as pd
import pyemu
import pytest


def plot_summary_test(tmp_path):

try:
import matplotlib.pyplot as plt
except:
return
plt = pytest.importorskip("matplotlib.pyplot")
par_df_fname = os.path.join("utils","freyberg_pp.par.usum.csv")
shutil.copy(par_df_fname, tmp_path)
par_df_fname = os.path.join(tmp_path, "freyberg_pp.par.usum.csv")
Expand Down Expand Up @@ -38,10 +35,7 @@ def plot_summary_test(tmp_path):


def pst_plot_test(tmp_path):
try:
import matplotlib.pyplot as plt
except:
return
plt = pytest.importorskip("matplotlib.pyplot")
pstfile = os.path.join("pst", "pest.pst")
shutil.copy(pstfile,
os.path.join(tmp_path, "pest.pst"))
Expand Down Expand Up @@ -98,10 +92,7 @@ def pst_plot_test(tmp_path):


def ensemble_plot_test(tmp_path):
try:
import matplotlib.pyplot as plt
except:
return
plt = pytest.importorskip("matplotlib.pyplot")
pstfile = os.path.join("pst", "pest.pst")
shutil.copy(pstfile,
os.path.join(tmp_path, "pest.pst"))
Expand Down Expand Up @@ -165,10 +156,7 @@ def ensemble_plot_test(tmp_path):


def ensemble_1to1_test(tmp_path):
try:
import matplotlib.pyplot as plt
except:
return
plt = pytest.importorskip("matplotlib.pyplot")
shutil.copy(os.path.join("pst","pest.pst"),
os.path.join(tmp_path, "pest.pst"))
shutil.copy(os.path.join("pst","pest.rei"),
Expand Down Expand Up @@ -259,10 +247,7 @@ def ensemble_1to1_test(tmp_path):


def ensemble_summary_test(tmp_path):
try:
import matplotlib.pyplot as plt
except:
return
plt = pytest.importorskip("matplotlib.pyplot")

shutil.copy(os.path.join("pst", "pest.pst"),
os.path.join(tmp_path, "pest.pst"))
Expand Down Expand Up @@ -295,10 +280,7 @@ def ensemble_summary_test(tmp_path):
)

# def cov_test():
# try:
# import matplotlib.pyplot as plt
# except:
# return
# plt = pytest.importorskip("matplotlib.pyplot")
#
# import os
# import numpy as np
Expand All @@ -323,7 +305,7 @@ def ensemble_summary_test(tmp_path):


def ensemble_change_test(tmp_path):
import matplotlib.pyplot as plt
plt = pytest.importorskip("matplotlib.pyplot")
os.chdir(tmp_path)
pst = pyemu.Pst.from_par_obs_names(par_names=["p1","p2"])
cov = pyemu.Cov(np.array([[1.0,0.0],[0.0,1.0]]),names=["p1","p2"])
Expand Down
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