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use small datasets #88

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use small datasets #88

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d9e6e79
modify all paths
cosunae Oct 7, 2023
f8d4289
formatting
cosunae Oct 7, 2023
7356aa4
formatting
cosunae Oct 7, 2023
c3dd8d2
use mamba
cosunae Oct 7, 2023
5c73dd1
undo mamba
cosunae Oct 7, 2023
baa490c
debug
cosunae Oct 7, 2023
6347b94
remove unused variable
cosunae Oct 13, 2023
cc3145d
typo
cosunae Oct 14, 2023
344fce7
Merge branch 'main' into crop
cosunae Oct 26, 2023
8adff67
tighten threshold again
cosunae Oct 26, 2023
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2 changes: 0 additions & 2 deletions jenkins/Jenkinsfile
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Expand Up @@ -47,14 +47,12 @@ pipeline {
source $WORKSPACE/miniconda/etc/profile.d/conda.sh
conda activate no-deps
cd ${WORKSPACE}
export INPUT_DATA_DIR=/project/s83c/rz+/icon_data_processing_incubator/data/SWISS
pytest -m "not ifs" tests
'''
sh '''#!/usr/bin/env bash
source $WORKSPACE/miniconda/etc/profile.d/conda.sh
conda activate no-deps
cd ${WORKSPACE}
export INPUT_DATA_DIR=/project/s83c/rz+/icon_data_processing_incubator/data/SWISS
pytest -m ifs tests
'''
}
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10 changes: 0 additions & 10 deletions src/idpi/system_definition.py
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Expand Up @@ -10,16 +10,6 @@
print("The FIELDEXTRA_PATH is not set, exiting")
raise

try:
input_data_directory = os.environ["INPUT_DATA_DIR"]
except KeyError:
input_data_directory = str(
pathlib.Path(__file__).parent.parent.parent.resolve() / "test_data"
)
print(f"The INPUT_DATA_DIR is not set, setting it to {input_data_directory}")


FX_BINARY = fieldextra_executable
INPUT_DATA_DIR = input_data_directory

root_dir = (pathlib.Path(os.path.dirname(os.path.abspath(__file__))) / "..").resolve()
39 changes: 21 additions & 18 deletions tests/test_idpi/conftest.py
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@@ -1,7 +1,6 @@
"""Test configuration."""
# Standard library
import subprocess
from collections.abc import Iterable
from pathlib import Path

# Third-party
Expand All @@ -13,7 +12,9 @@
@pytest.fixture
def data_dir():
"""Base data dir."""
return Path("/project/s83c/rz+/icon_data_processing_incubator/data/SWISS")
return Path(
"/project/s83c/rz+/icon_data_processing_incubator/datasets/32_39x45_51/"
)


@pytest.fixture
Expand All @@ -34,25 +35,27 @@ def template_env():
def fieldextra(tmp_path, data_dir, template_env, fieldextra_executable):
"""Run fieldextra on a given field."""

def f(field_name, hh: int | Iterable[int] | None = 0, **ctx):
default_conf_files = {
"inputi": data_dir / "lfff<DDHH>0000.ch",
"inputc": data_dir / "lfff00000000c.ch",
"output": f"<HH>_{field_name}.nc",
}
conf_files = ctx.pop("conf_files", default_conf_files)
template = template_env.get_template(f"test_{field_name}.nl")
nl_path = tmp_path / f"test_{field_name}.nl"
def f(
product: str,
conf_files: dict[str, str] | None = None,
load_output: str | list[str] = "00_outfile.nc",
**ctx,
):
if not conf_files:
conf_files = {
"inputi": data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000",
"inputc": data_dir / "COSMO-1E/1h/const/000/lfff00000000c",
"output": "<HH>_outfile.nc",
}

template = template_env.get_template(f"test_{product}.nl")
nl_path = tmp_path / f"test_{product}.nl"
nl_path.write_text(template.render(file=conf_files, **ctx))

subprocess.run([fieldextra_executable, str(nl_path)], check=True, cwd=tmp_path)

if isinstance(hh, int):
return xr.open_dataset(tmp_path / f"{hh:02d}_{field_name}.nc")
if isinstance(hh, Iterable):
return [xr.open_dataset(tmp_path / f"{h:02d}_{field_name}.nc") for h in hh]
if hh is None:
return xr.open_dataset(tmp_path / f"{field_name}.nc")
raise TypeError("Unknown type for param hh")
if isinstance(load_output, str):
return xr.open_dataset(tmp_path / load_output)
return [xr.open_dataset(tmp_path / foutput) for foutput in load_output]

return f
4 changes: 2 additions & 2 deletions tests/test_idpi/test_brn.py
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Expand Up @@ -7,8 +7,8 @@


def test_brn(data_dir, fieldextra):
datafile = data_dir / "lfff00000000.ch"
cdatafile = data_dir / "lfff00000000c.ch"
datafile = data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000"
cdatafile = data_dir / "COSMO-1E/1h/const/000/lfff00000000c"

reader = GribReader([cdatafile, datafile])
ds = reader.load_cosmo_data(["P", "T", "QV", "U", "V", "HHL", "HSURF"])
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4 changes: 2 additions & 2 deletions tests/test_idpi/test_curl.py
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Expand Up @@ -10,8 +10,8 @@


def test_curl(data_dir):
datafile = data_dir / "lfff00000000.ch"
cdatafile = data_dir / "lfff00000000c.ch"
datafile = data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000"
cdatafile = data_dir / "COSMO-1E/1h/const/000/lfff00000000c"

reader = GribReader([cdatafile, datafile])
ds = reader.load_cosmo_data(["U", "V", "W", "HHL"])
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4 changes: 2 additions & 2 deletions tests/test_idpi/test_destagger.py
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Expand Up @@ -7,8 +7,8 @@


def test_destagger(data_dir, fieldextra):
datafile = data_dir / "lfff00000000.ch"
cdatafile = data_dir / "lfff00000000c.ch"
datafile = data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000"
cdatafile = data_dir / "COSMO-1E/1h/const/000/lfff00000000c"

reader = GribReader([cdatafile, datafile])
ds = reader.load_cosmo_data(
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6 changes: 2 additions & 4 deletions tests/test_idpi/test_diff.py
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Expand Up @@ -9,8 +9,7 @@


def test_masspoint_field(data_dir):
datafile = data_dir / "lfff00000000.ch"

datafile = data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000"
reader = GribReader([datafile], ref_param="P")

ds = reader.load_cosmo_data(["P", "T"])
Expand All @@ -33,8 +32,7 @@ def test_masspoint_field(data_dir):


def test_staggered_field(data_dir):
datafile = data_dir / "lfff00000000.ch"

datafile = data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000"
reader = GribReader([datafile], ref_param="W")

ds = reader.load_cosmo_data(["W"])
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6 changes: 5 additions & 1 deletion tests/test_idpi/test_flexpart.py
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Expand Up @@ -51,7 +51,11 @@ def test_flexpart(data_dir, fieldextra):
"output": "<HH>_flexpart.nc",
}

fs_ds, *fs_ds_h = fieldextra("flexpart", hh=(0, 3, 6), conf_files=conf_files)
fs_ds, *fs_ds_h = fieldextra(
"flexpart",
load_output=[f"{i:02d}_flexpart.nc" for i in (0, 3, 6)],
conf_files=conf_files,
)
fs_ds_o = {}
for f in ("FIS", "FR_LAND", "SDOR"):
fs_ds_o[f] = fs_ds[f].isel(y_1=slice(None, None, -1))
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3 changes: 1 addition & 2 deletions tests/test_idpi/test_gis.py
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Expand Up @@ -42,8 +42,7 @@ def test_geolatlon2swiss(coords):


def test_vref_rot2geolatlon(data_dir, fieldextra):
datafile = data_dir / "lfff00000000.ch"

datafile = data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000"
reader = grib_decoder.GribReader([datafile], ref_param="T")
ds = reader.load_cosmo_data(["U_10M", "V_10M"])

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4 changes: 2 additions & 2 deletions tests/test_idpi/test_hzerocl.py
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Expand Up @@ -9,8 +9,8 @@

@pytest.mark.parametrize("extrapolate", [True, False])
def test_hzerocl(data_dir, fieldextra, extrapolate):
datafile = data_dir / "lfff00000000.ch"
cdatafile = data_dir / "lfff00000000c.ch"
datafile = data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000"
cdatafile = data_dir / "COSMO-1E/1h/const/000/lfff00000000c"

reader = GribReader([cdatafile, datafile])
ds = reader.load_cosmo_data(
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4 changes: 2 additions & 2 deletions tests/test_idpi/test_integ_sfc2z.py
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Expand Up @@ -14,8 +14,8 @@
[("integral", "integ", 1e-4, 1e-6), ("normed_integral", "norm_integ", 1e-5, 1e-6)],
)
def test_integ_sfc2z(field, k_max, operator, fx_op, atol, rtol, data_dir, fieldextra):
datafile = data_dir / "lfff00000000.ch"
cdatafile = data_dir / "lfff00000000c.ch"
datafile = data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000"
cdatafile = data_dir / "COSMO-1E/1h/const/000/lfff00000000c"

# modes
mode = "z2z"
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4 changes: 2 additions & 2 deletions tests/test_idpi/test_integ_z2z.py
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Expand Up @@ -22,8 +22,8 @@ def test_integ_z2z(field, k_max, operator, fx_op, data_dir, fieldextra):
k_top = 60

# input data
datafile = data_dir / "lfff00000000.ch"
cdatafile = data_dir / "lfff00000000c.ch"
datafile = data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000"
cdatafile = data_dir / "COSMO-1E/1h/const/000/lfff00000000c"

# load input data set
reader = GribReader([cdatafile, datafile])
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4 changes: 2 additions & 2 deletions tests/test_idpi/test_intpl_hk2p.py
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Expand Up @@ -23,8 +23,8 @@ def test_intpl_hk2p(mode, fx_mode, rtol, data_dir, fieldextra):
tc_units = "hPa"

# input data
datafile = data_dir / "lfff00000000.ch"
cdatafile = data_dir / "lfff00000000c.ch"
datafile = data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000"
cdatafile = data_dir / "COSMO-1E/1h/const/000/lfff00000000c"

# load input data set
reader = GribReader([cdatafile, datafile])
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2 changes: 1 addition & 1 deletion tests/test_idpi/test_intpl_k2p.py
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Expand Up @@ -22,7 +22,7 @@ def test_intpl_k2p(mode, fx_mode, atol, rtol, data_dir, fieldextra):
tc_units = "hPa"

# input data
datafile = data_dir / "lfff00000000.ch"
datafile = data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000"

# load input data set
reader = GribReader([datafile], ref_param="P")
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4 changes: 2 additions & 2 deletions tests/test_idpi/test_intpl_k2theta.py
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Expand Up @@ -18,8 +18,8 @@ def test_intpl_k2theta(mode, data_dir, fieldextra):
tc_units = "K"

# input data
datafile = data_dir / "lfff00000000.ch"
cdatafile = data_dir / "lfff00000000c.ch"
datafile = data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000"
cdatafile = data_dir / "COSMO-1E/1h/const/000/lfff00000000c"

# load input data set
reader = GribReader([cdatafile, datafile])
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16 changes: 12 additions & 4 deletions tests/test_idpi/test_lat_ops.py
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@@ -1,3 +1,6 @@
# Standard library
from pathlib import Path

# Third-party
import numpy as np
import pytest
Expand All @@ -9,9 +12,14 @@
from idpi.operators.hzerocl import fhzerocl


@pytest.fixture
def data_dir():
return Path("/project/s83c/rz+/icon_data_processing_incubator/datasets/original/")


def test_fill_undef(data_dir, fieldextra):
datafile = data_dir / "lfff00000000.ch"
cdatafile = data_dir / "lfff00000000c.ch"
datafile = data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000"
cdatafile = data_dir / "COSMO-1E/1h/const/000/lfff00000000c"

reader = GribReader([cdatafile, datafile])
ds = reader.load_cosmo_data(["T", "HHL"])
Expand All @@ -27,8 +35,8 @@ def test_fill_undef(data_dir, fieldextra):


def test_disk_avg(data_dir, fieldextra):
datafile = data_dir / "lfff00000000.ch"
cdatafile = data_dir / "lfff00000000c.ch"
datafile = data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000"
cdatafile = data_dir / "COSMO-1E/1h/const/000/lfff00000000c"

reader = GribReader([cdatafile, datafile])

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4 changes: 2 additions & 2 deletions tests/test_idpi/test_minmax_z2z.py
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Expand Up @@ -19,8 +19,8 @@ def test_minmax_z2z(operator, fx_op, field, layer, data_dir, fieldextra):
k_top = 60

# input data
datafile = data_dir / "lfff00000000.ch"
cdatafile = data_dir / "lfff00000000c.ch"
datafile = data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000"
cdatafile = data_dir / "COSMO-1E/1h/const/000/lfff00000000c"

# load input data set
reader = GribReader([cdatafile, datafile])
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8 changes: 4 additions & 4 deletions tests/test_idpi/test_ninjo_k2th.py
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Expand Up @@ -7,8 +7,8 @@


def test_ninjo_k2th(data_dir, fieldextra):
datafile = data_dir / "lfff00000000.ch"
cdatafile = data_dir / "lfff00000000c.ch"
datafile = data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000"
cdatafile = data_dir / "COSMO-1E/1h/const/000/lfff00000000c"

reader = GribReader([cdatafile, datafile])

Expand Down Expand Up @@ -36,7 +36,7 @@ def test_ninjo_k2th(data_dir, fieldextra):
assert_allclose(
fs_ds["POT_VORTIC_AT_THETA"],
observed_at_theta["pot_vortic"],
atol=1e-9,
atol=1e-5,
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why do we need to decrease the absolute tolerance here?

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I'm not sure why this was necessary. Especially that 1e-5 is at the order of magnitude of the observable signal in the pot vortic field.

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Could be maybe an edge effect due to the differential operators and the reduced computational domain.

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I do not know either, but I think a different location of boundaries can affect the differential operators, (since the stencil applied is different at the boundaries), even if the data is the same in the cropped domain.
I checked again and could increase this threshold again until 1e-8. But still the one below (1e-4) fails if I try to relax it.
However I still think that 1e-4 is still in the "ok" range, provide we do not really know how these operators propagate errors.

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Considering that the expected values are in the 1e-5 range, it doesn't really make sense to me to put in an absolute tolerance of 1e-5. That would be comparable to setting an atol of 1e5 for the pressure field. The value for the rtol is fine in my opinion.

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I just realised that fieldextra is probably applying the same stencils on the same data so the argument about the edge effects does not hold.

rtol=1e-5,
)

Expand All @@ -50,7 +50,7 @@ def test_ninjo_k2th(data_dir, fieldextra):
assert_allclose(
fs_ds["U"],
observed_at_theta["u"],
atol=1e-9,
atol=1e-4,
rtol=1e-5,
)

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4 changes: 2 additions & 2 deletions tests/test_idpi/test_potvortic.py
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Expand Up @@ -11,8 +11,8 @@


def test_pv(data_dir, fieldextra):
datafile = data_dir / "lfff00000000.ch"
cdatafile = data_dir / "lfff00000000c.ch"
datafile = data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000"
cdatafile = data_dir / "COSMO-1E/1h/const/000/lfff00000000c"

reader = GribReader([cdatafile, datafile])
ds = reader.load_cosmo_data(["U", "V", "W", "P", "T", "QV", "QC", "QI", "HHL"])
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7 changes: 5 additions & 2 deletions tests/test_idpi/test_radiation.py
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Expand Up @@ -14,7 +14,10 @@

@pytest.fixture
def data_dir():
return Path("/project/s83c/rz+/icon_data_processing_incubator/data/temporal")
return Path(
"/project/s83c/rz+/icon_data_processing_incubator/datasets/"
"32_39x45_51/COSMO-1E_time/"
)


def test_athd_s(data_dir, fieldextra):
Expand All @@ -30,7 +33,7 @@ def test_athd_s(data_dir, fieldextra):

conf_files = {
"inputi": data_dir / "lfff<DDHH>0000",
"output": "athd_s.nc",
"output": "00_outfile.nc",
}
fx_ds = fieldextra("athd_s", conf_files=conf_files, hh=None)
expected = fx_ds["ATHD_S_TG"].transpose("epsd_1", "time", ...)
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13 changes: 11 additions & 2 deletions tests/test_idpi/test_regrid.py
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@@ -1,4 +1,8 @@
# Standard library
from pathlib import Path

# Third-party
import pytest
from numpy.testing import assert_allclose

# First-party
Expand All @@ -7,9 +11,14 @@
from idpi.operators.hzerocl import fhzerocl


@pytest.fixture
def data_dir():
return Path("/project/s83c/rz+/icon_data_processing_incubator/datasets/original/")


def test_regrid(data_dir, fieldextra):
datafile = data_dir / "lfff00000000.ch"
cdatafile = data_dir / "lfff00000000c.ch"
datafile = data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000"
cdatafile = data_dir / "COSMO-1E/1h/const/000/lfff00000000c"

reader = grib_decoder.GribReader([cdatafile, datafile])
ds = reader.load_cosmo_data(["T", "HHL"])
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4 changes: 2 additions & 2 deletions tests/test_idpi/test_relhum.py
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Expand Up @@ -7,8 +7,8 @@


def test_relhum(data_dir, fieldextra):
datafile = data_dir / "lfff00000000.ch"
cdatafile = data_dir / "lfff00000000c.ch"
datafile = data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000"
cdatafile = data_dir / "COSMO-1E/1h/const/000/lfff00000000c"

reader = GribReader([cdatafile, datafile], ref_param="P")
ds = reader.load_cosmo_data(["P", "T", "QV"])
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3 changes: 1 addition & 2 deletions tests/test_idpi/test_theta.py
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Expand Up @@ -7,8 +7,7 @@


def test_theta(data_dir, fieldextra):
datafile = data_dir / "lfff00000000.ch"

datafile = data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000"
reader = GribReader([datafile], ref_param="P")

ds = reader.load_cosmo_data(["P", "T"])
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3 changes: 1 addition & 2 deletions tests/test_idpi/test_thetav.py
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Expand Up @@ -7,8 +7,7 @@


def test_thetav(data_dir, fieldextra):
datafile = data_dir / "lfff00000000.ch"

datafile = data_dir / "COSMO-1E/1h/ml_sl/000/lfff00000000"
reader = GribReader([datafile], ref_param="P")

ds = reader.load_cosmo_data(["P", "T", "QV"])
Expand Down
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