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update assert np.allclose to numpy.testing.assert_allclose in tests #1904

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51 changes: 26 additions & 25 deletions tests/test_advection.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
import numpy as np
import pytest
import xarray as xr
from numpy.testing import assert_allclose

from parcels import (
AdvectionAnalytical,
Expand Down Expand Up @@ -98,7 +99,7 @@ def test_advection_meridional(lon, lat):
pset = ParticleSet(fieldset, pclass=Particle, lon=np.linspace(-60, 60, npart), lat=np.linspace(0, 30, npart))
delta_lat = np.diff(pset.lat)
pset.execute(AdvectionRK4, runtime=timedelta(hours=2), dt=timedelta(seconds=30))
assert np.allclose(np.diff(pset.lat), delta_lat, rtol=1.0e-4)
assert_allclose(np.diff(pset.lat), delta_lat, rtol=1.0e-4)


def test_advection_3D():
Expand All @@ -119,7 +120,7 @@ def test_advection_3D():
)
time = timedelta(hours=2).total_seconds()
pset.execute(AdvectionRK4, runtime=time, dt=timedelta(seconds=30))
assert np.allclose(pset.depth * pset.time, pset.lon, atol=1.0e-1)
assert_allclose(pset.depth * pset.time, pset.lon, atol=1.0e-1)


@pytest.mark.parametrize("direction", ["up", "down"])
Expand Down Expand Up @@ -161,8 +162,8 @@ def SubmergeParticle(particle, fieldset, time): # pragma: no cover
pset.execute(kernels, runtime=11.0, dt=1)

if direction == "up" and wErrorThroughSurface:
assert np.allclose(pset.lon[0], 0.6)
assert np.allclose(pset.depth[0], 0)
assert_allclose(pset.lon[0], 0.6)
assert_allclose(pset.depth[0], 0)
else:
assert len(pset) == 0

Expand Down Expand Up @@ -227,7 +228,7 @@ def test_conversion_3DCROCO():
for zi, z in enumerate(z_xroms):
sigma[zi] = _croco_from_z_to_sigma_scipy(fieldset, 0, z, lat, lon, None)

assert np.allclose(sigma, s_xroms, atol=1e-3)
assert_allclose(sigma, s_xroms, atol=1e-3)


@pytest.mark.v4alpha
Expand All @@ -246,8 +247,8 @@ def SampleW(particle, fieldset, time): # pragma: no cover
particle.w = fieldset.W[time, particle.depth, particle.lat, particle.lon]

pset.execute([AdvectionRK4_3D, SampleW], runtime=runtime, dt=100)
assert np.allclose(pset.depth, Z.flatten(), atol=5) # TODO lower this atol
assert np.allclose(pset.lon_nextloop, [x + runtime for x in X.flatten()], atol=1e-3)
assert_allclose(pset.depth, Z.flatten(), atol=5) # TODO lower this atol
assert_allclose(pset.lon_nextloop, [x + runtime for x in X.flatten()], atol=1e-3)


@pytest.mark.v4alpha
Expand All @@ -262,8 +263,8 @@ def test_advection_2DCROCO():
pset = ParticleSet(fieldset=fieldset, pclass=Particle, lon=X, lat=Y, depth=Z)

pset.execute([AdvectionRK4], runtime=runtime, dt=100)
assert np.allclose(pset.depth, Z.flatten(), atol=1e-3)
assert np.allclose(pset.lon_nextloop, [x + runtime for x in X], atol=1e-3)
assert_allclose(pset.depth, Z.flatten(), atol=1e-3)
assert_allclose(pset.lon_nextloop, [x + runtime for x in X], atol=1e-3)


def create_periodic_fieldset(xdim, ydim, uvel, vvel):
Expand Down Expand Up @@ -315,8 +316,8 @@ def test_advection_periodic_zonal_meridional():
fieldset.add_periodic_halo(zonal=True, meridional=True)
assert len(fieldset.U.lat) == ydim + 10 # default halo size is 5 grid points
assert len(fieldset.U.lon) == xdim + 10 # default halo size is 5 grid points
assert np.allclose(np.diff(fieldset.U.lat), fieldset.U.lat[1] - fieldset.U.lat[0], rtol=0.001)
assert np.allclose(np.diff(fieldset.U.lon), fieldset.U.lon[1] - fieldset.U.lon[0], rtol=0.001)
assert_allclose(np.diff(fieldset.U.lat), fieldset.U.lat[1] - fieldset.U.lat[0], rtol=0.001)
assert_allclose(np.diff(fieldset.U.lon), fieldset.U.lon[1] - fieldset.U.lon[0], rtol=0.001)

pset = ParticleSet(fieldset, pclass=Particle, lon=[0.4], lat=[0.5])
pset.execute(AdvectionRK4 + pset.Kernel(periodicBC), runtime=timedelta(hours=20), dt=timedelta(seconds=30))
Expand Down Expand Up @@ -431,8 +432,8 @@ def test_stationary_eddy(fieldset_stationary, method, rtol, diffField):

exp_lon = [truth_stationary(x, y, pset[0].time)[0] for x, y in zip(lon, lat, strict=True)]
exp_lat = [truth_stationary(x, y, pset[0].time)[1] for x, y in zip(lon, lat, strict=True)]
assert np.allclose(pset.lon, exp_lon, rtol=rtol)
assert np.allclose(pset.lat, exp_lat, rtol=rtol)
assert_allclose(pset.lon, exp_lon, rtol=rtol)
assert_allclose(pset.lat, exp_lat, rtol=rtol)


def test_stationary_eddy_vertical():
Expand Down Expand Up @@ -460,9 +461,9 @@ def test_stationary_eddy_vertical():
exp_lon = [truth_stationary(x, z, pset[0].time)[0] for x, z in zip(lon, depth, strict=True)]
exp_depth = [truth_stationary(x, z, pset[0].time)[1] for x, z in zip(lon, depth, strict=True)]
print(pset, exp_lon)
assert np.allclose(pset.lon, exp_lon, rtol=1e-5)
assert np.allclose(pset.lat, lat, rtol=1e-5)
assert np.allclose(pset.depth, exp_depth, rtol=1e-5)
assert_allclose(pset.lon, exp_lon, rtol=1e-5)
assert_allclose(pset.lat, lat, rtol=1e-5)
assert_allclose(pset.depth, exp_depth, rtol=1e-5)

data = {"U": fldzero, "V": fld2, "W": fld1}
fieldset = FieldSet.from_data(data, dimensions, mesh="flat")
Expand All @@ -471,9 +472,9 @@ def test_stationary_eddy_vertical():
pset.execute(AdvectionRK4_3D, dt=dt, endtime=endtime)
exp_depth = [truth_stationary(z, y, pset[0].time)[0] for z, y in zip(depth, lat, strict=True)]
exp_lat = [truth_stationary(z, y, pset[0].time)[1] for z, y in zip(depth, lat, strict=True)]
assert np.allclose(pset.lon, lon, rtol=1e-5)
assert np.allclose(pset.lat, exp_lat, rtol=1e-5)
assert np.allclose(pset.depth, exp_depth, rtol=1e-5)
assert_allclose(pset.lon, lon, rtol=1e-5)
assert_allclose(pset.lat, exp_lat, rtol=1e-5)
assert_allclose(pset.depth, exp_depth, rtol=1e-5)


def truth_moving(x_0, y_0, t):
Expand Down Expand Up @@ -536,8 +537,8 @@ def test_moving_eddy(fieldset_moving, method, rtol, diffField):

exp_lon = [truth_moving(x, y, t)[0] for x, y, t in zip(lon, lat, pset.time, strict=True)]
exp_lat = [truth_moving(x, y, t)[1] for x, y, t in zip(lon, lat, pset.time, strict=True)]
assert np.allclose(pset.lon, exp_lon, rtol=rtol)
assert np.allclose(pset.lat, exp_lat, rtol=rtol)
assert_allclose(pset.lon, exp_lon, rtol=rtol)
assert_allclose(pset.lat, exp_lat, rtol=rtol)


def truth_decaying(x_0, y_0, t):
Expand Down Expand Up @@ -619,8 +620,8 @@ def test_decaying_eddy(fieldset_decaying, method, rtol, diffField):

exp_lon = [truth_decaying(x, y, t)[0] for x, y, t in zip(lon, lat, pset.time, strict=True)]
exp_lat = [truth_decaying(x, y, t)[1] for x, y, t in zip(lon, lat, pset.time, strict=True)]
assert np.allclose(pset.lon, exp_lon, rtol=rtol)
assert np.allclose(pset.lat, exp_lat, rtol=rtol)
assert_allclose(pset.lon, exp_lon, rtol=rtol)
assert_allclose(pset.lat, exp_lat, rtol=rtol)


def test_analyticalAgrid():
Expand Down Expand Up @@ -669,6 +670,6 @@ def test_uniform_analytical(u, v, w, direction, tmp_zarrfile):
ds = xr.open_zarr(tmp_zarrfile)
times = (direction * ds["time"][:]).values.astype("timedelta64[s]")[0]
timeref = np.arange(1, 5).astype("timedelta64[s]")
assert np.allclose(times, timeref, atol=np.timedelta64(1, "ms"))
assert_allclose(times, timeref, atol=np.timedelta64(1, "ms"))
lons = ds["lon"][:].values
assert np.allclose(lons, x0 + direction * u * np.arange(1, 5))
assert_allclose(lons, x0 + direction * u * np.arange(1, 5))
21 changes: 11 additions & 10 deletions tests/test_diffusion.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@

import numpy as np
import pytest
from numpy.testing import assert_allclose
from scipy import stats

from parcels import (
Expand Down Expand Up @@ -44,10 +45,10 @@ def test_fieldKh_Brownian(mesh):
lons = pset.lon

tol = 500 * mesh_conversion # effectively 500 m errors
assert np.allclose(np.std(lats), expected_std_lat, atol=tol)
assert np.allclose(np.std(lons), expected_std_lon, atol=tol)
assert np.allclose(np.mean(lons), 0, atol=tol)
assert np.allclose(np.mean(lats), 0, atol=tol)
assert_allclose(np.std(lats), expected_std_lat, atol=tol)
assert_allclose(np.std(lons), expected_std_lon, atol=tol)
assert_allclose(np.mean(lons), 0, atol=tol)
assert_allclose(np.mean(lats), 0, atol=tol)


@pytest.mark.parametrize("mesh", ["spherical", "flat"])
Expand Down Expand Up @@ -78,8 +79,8 @@ def test_fieldKh_SpatiallyVaryingDiffusion(mesh, kernel):
lats = pset.lat
lons = pset.lon
tol = 2000 * mesh_conversion # effectively 2000 m errors (because of low numbers of particles)
assert np.allclose(np.mean(lons), 0, atol=tol)
assert np.allclose(np.mean(lats), 0, atol=tol)
assert_allclose(np.mean(lons), 0, atol=tol)
assert_allclose(np.mean(lats), 0, atol=tol)
assert stats.skew(lons) > stats.skew(lats)


Expand All @@ -106,7 +107,7 @@ def vertical_randomexponential(particle, fieldset, time): # pragma: no cover

depth = pset.depth
expected_mean = 1.0 / fieldset.lambd
assert np.allclose(np.mean(depth), expected_mean, rtol=0.1)
assert_allclose(np.mean(depth), expected_mean, rtol=0.1)


@pytest.mark.parametrize("mu", [0.8 * np.pi, np.pi])
Expand Down Expand Up @@ -134,8 +135,8 @@ def vonmises(particle, fieldset, time): # pragma: no cover

angles = np.array([p.angle for p in pset])

assert np.allclose(np.mean(angles), mu, atol=0.1)
assert_allclose(np.mean(angles), mu, atol=0.1)
vonmises_mean = stats.vonmises.mean(kappa=kappa, loc=mu)
assert np.allclose(np.mean(angles), vonmises_mean, atol=0.1)
assert_allclose(np.mean(angles), vonmises_mean, atol=0.1)
vonmises_var = stats.vonmises.var(kappa=kappa, loc=mu)
assert np.allclose(np.var(angles), vonmises_var, atol=0.1)
assert_allclose(np.var(angles), vonmises_var, atol=0.1)
5 changes: 3 additions & 2 deletions tests/test_field.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
import numpy as np
import pytest
import xarray as xr
from numpy.testing import assert_allclose

from parcels import Field
from parcels.tools.converters import (
Expand All @@ -22,8 +23,8 @@ def test_field_from_netcdf_variables():
variable = {"U": "vozocrtx"}
f3 = Field.from_netcdf(filename, variable, dims)

assert np.allclose(f1.data, f2.data, atol=1e-12)
assert np.allclose(f1.data, f3.data, atol=1e-12)
assert_allclose(f1.data, f2.data, atol=1e-12)
assert_allclose(f1.data, f3.data, atol=1e-12)

with pytest.raises(AssertionError):
variable = {"U": "vozocrtx", "nav_lat": "nav_lat"} # multiple variables will fail
Expand Down
47 changes: 24 additions & 23 deletions tests/test_fieldset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
import numpy as np
import pytest
import xarray as xr
from numpy.testing import assert_allclose

from parcels import (
AdvectionRK4,
Expand Down Expand Up @@ -89,8 +90,8 @@ def test_fieldset_from_data(xdim, ydim):
assert fieldset.U._creation_log == "from_data"
assert len(fieldset.U.data.shape) == 3
assert len(fieldset.V.data.shape) == 3
assert np.allclose(fieldset.U.data[0, :], data["U"], rtol=1e-12)
assert np.allclose(fieldset.V.data[0, :], data["V"], rtol=1e-12)
assert_allclose(fieldset.U.data[0, :], data["U"], rtol=1e-12)
assert_allclose(fieldset.V.data[0, :], data["V"], rtol=1e-12)


def test_fieldset_extra_syntax():
Expand Down Expand Up @@ -147,9 +148,9 @@ def test_fieldset_from_data_different_dimensions(xdim, ydim):
assert len(fieldset.V.data.shape) == 3
assert len(fieldset.P.data.shape) == 4
assert fieldset.P.data.shape == (tdim, zdim, ydim / 2, xdim / 2)
assert np.allclose(fieldset.U.data, 0.0, rtol=1e-12)
assert np.allclose(fieldset.V.data, 1.0, rtol=1e-12)
assert np.allclose(fieldset.P.data, 2.0, rtol=1e-12)
assert_allclose(fieldset.U.data, 0.0, rtol=1e-12)
assert_allclose(fieldset.V.data, 1.0, rtol=1e-12)
assert_allclose(fieldset.P.data, 2.0, rtol=1e-12)


@pytest.mark.parametrize("xdim", [100, 200])
Expand All @@ -163,8 +164,8 @@ def test_fieldset_from_parcels(xdim, ydim, tmpdir):
fieldset = FieldSet.from_parcels(filepath)
assert len(fieldset.U.data.shape) == 3 # Will be 4 once we use depth
assert len(fieldset.V.data.shape) == 3
assert np.allclose(fieldset.U.data[0, :], data["U"], rtol=1e-12)
assert np.allclose(fieldset.V.data[0, :], data["V"], rtol=1e-12)
assert_allclose(fieldset.U.data[0, :], data["U"], rtol=1e-12)
assert_allclose(fieldset.V.data[0, :], data["V"], rtol=1e-12)


def test_fieldset_from_modulefile():
Expand Down Expand Up @@ -392,7 +393,7 @@ def test_fieldset_write_curvilinear(tmpdir):
assert fieldset2.dx._creation_log == "from_netcdf"

for var in ["lon", "lat", "data"]:
assert np.allclose(getattr(fieldset2.dx, var), getattr(fieldset.dx, var))
assert_allclose(getattr(fieldset2.dx, var), getattr(fieldset.dx, var))


def addConst(particle, fieldset, time): # pragma: no cover
Expand Down Expand Up @@ -490,7 +491,7 @@ def UpdateU(particle, fieldset, time): # pragma: no cover
assert fieldset.U.data[0, 1, 0] == 11

da = xr.open_dataset(str(tmp_zarrfile).replace(".zarr", "_0005U.nc"))
assert np.allclose(fieldset.U.data, da["U"].values, atol=1.0)
assert_allclose(fieldset.U.data, da["U"].values, atol=1.0)


@pytest.mark.v4remove
Expand All @@ -517,12 +518,12 @@ def test_timestamps(datetype, tmpdir):
fieldset3 = FieldSet.from_parcels(tmpdir.join("file*"))
timestamps = [dims1["time"], dims2["time"]]
fieldset4 = FieldSet.from_parcels(tmpdir.join("file*"), timestamps=timestamps)
assert np.allclose(fieldset3.U.grid.time_full, fieldset4.U.grid.time_full)
assert_allclose(fieldset3.U.grid.time_full, fieldset4.U.grid.time_full)

for d in [0, 8, 10, 12]:
fieldset3.computeTimeChunk(d * 86400.0, 1.0)
fieldset4.computeTimeChunk(d * 86400.0, 1.0)
assert np.allclose(fieldset3.U.data, fieldset4.U.data)
assert_allclose(fieldset3.U.data, fieldset4.U.data)


@pytest.mark.v4remove
Expand Down Expand Up @@ -610,10 +611,10 @@ def sampleTemp(particle, fieldset, time): # pragma: no cover
temp_theo = temp_vec[-1]
elif dt_sign == -1:
temp_theo = temp_vec[0]
assert np.allclose(temp_theo, pset.temp[0], atol=1e-5)
assert np.allclose(pset.u1[0], pset.u2[0])
assert np.allclose(pset.v1[0], pset.v2[0])
assert np.allclose(pset.d[0], 1.0)
assert_allclose(temp_theo, pset.temp[0], atol=1e-5)
assert_allclose(pset.u1[0], pset.u2[0])
assert_allclose(pset.v1[0], pset.v2[0])
assert_allclose(pset.d[0], 1.0)


@pytest.mark.parametrize("tdim", [10, None])
Expand Down Expand Up @@ -654,9 +655,9 @@ def generate_dataset(xdim, ydim, zdim=1, tdim=1):

pset.execute(AdvectionRK4, dt=1, runtime=10)
if tdim == 10:
assert np.allclose(pset.lon_nextloop[0], 4.5) and np.allclose(pset.lat_nextloop[0], 10)
assert_allclose(pset.lon_nextloop[0], 4.5) and np.allclose(pset.lat_nextloop[0], 10)
else:
assert np.allclose(pset.lon_nextloop[0], 5.0) and np.allclose(pset.lat_nextloop[0], 10)
assert_allclose(pset.lon_nextloop[0], 5.0) and np.allclose(pset.lat_nextloop[0], 10)


@pytest.mark.v4alpha
Expand Down Expand Up @@ -695,16 +696,16 @@ def test_fieldset_from_data_gridtypes():
plon = pset.lon
plat = pset.lat
# sol of dx/dt = (init_depth+1)*x+0.1; x(0)=0
assert np.allclose(plon, [0.17173462592827032, 0.2177736932123214])
assert np.allclose(plat, [1, 1])
assert_allclose(plon, [0.17173462592827032, 0.2177736932123214])
assert_allclose(plat, [1, 1])

# Rectilinear S grid
dimensions["depth"] = depth_s
fieldset = FieldSet.from_data(data, dimensions, mesh="flat")
pset = ParticleSet(fieldset, Particle, [0, 0], [0, 0], [0, 0.4])
pset.execute(AdvectionRK4, runtime=1.5, dt=0.5)
assert np.allclose(plon, pset.lon)
assert np.allclose(plat, pset.lat)
assert_allclose(plon, pset.lon)
assert_allclose(plat, pset.lat)

# Curvilinear Z grid
dimensions["lon"] = lonm
Expand All @@ -713,8 +714,8 @@ def test_fieldset_from_data_gridtypes():
fieldset = FieldSet.from_data(data, dimensions, mesh="flat")
pset = ParticleSet(fieldset, Particle, [0, 0], [0, 0], [0, 0.4])
pset.execute(AdvectionRK4, runtime=1.5, dt=0.5)
assert np.allclose(plon, pset.lon)
assert np.allclose(plat, pset.lat)
assert_allclose(plon, pset.lon)
assert_allclose(plat, pset.lat)

# Curvilinear S grid
dimensions["depth"] = depth_s
Expand Down
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