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MAINT: backward compatibility for pysat #133

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merged 4 commits into from
Oct 5, 2023
Merged

MAINT: backward compatibility for pysat #133

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7aec080
MAINT: remove backwards compat for sami
jklenzing Oct 5, 2023
7fb3f43
MAINT: remove backward compat for tests
jklenzing Oct 5, 2023
c459a96
DOC: changelog
jklenzing Oct 5, 2023
6dac063
MAINT: update path for load_netcdf
jklenzing Oct 5, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@ This project adheres to [Semantic Versioning](https://semver.org/).
* Added manual test for pysatModels RC pip install
* Updated tests to new pysat and pytest standards
* Added a cap for pysatNASA
* Removed backwards-support for pysat pre-3.0.4 functions
* Documentation
* Added badges and instructions for PyPi and Zenodo

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21 changes: 4 additions & 17 deletions pysatModels/models/sami2py_sami2.py
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Expand Up @@ -23,7 +23,6 @@

import datetime as dt
import functools
from packaging import version as pack_version
import warnings
import xarray as xr

Expand Down Expand Up @@ -146,26 +145,14 @@ def load(fnames, tag='', inst_id='', **kwargs):
file_info['day']):
epochs.append(dt.datetime(year, month, day))

vstr = '3.0.2' # TODO(#112) Remove support for backwards compatibility
loaded_data = []
loaded_meta = []
for epoch, fname in zip(epochs, fnames):
# Load data
# TODO(#112) Remove backwards compatibility
if pack_version.Version(pysat.__version__) < pack_version.Version(vstr):
data, meta = pysat.utils.load_netcdf4([fname], pandas_format=False,
epoch_name='ut')
data = data.rename({"ut": "time"})

# Create datetimes from 'ut' variable
data['time'] = [epoch
+ dt.timedelta(seconds=int(val * 3600.0))
for val in data['time'].values]
else:
data, meta = pysat.utils.load_netcdf4([fname], pandas_format=False,
epoch_name='ut',
epoch_origin=epoch,
epoch_unit='h')
data, meta = pysat.utils.io.load_netcdf([fname], pandas_format=False,
epoch_name='ut',
epoch_origin=epoch,
epoch_unit='h')

# Store data/meta for each loop
loaded_data.append(data)
Expand Down
10 changes: 3 additions & 7 deletions pysatModels/models/ucar_tiegcm.py
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Expand Up @@ -185,13 +185,9 @@ def load(fnames, tag='', inst_id='', **kwargs):

"""

# TODO(#114): eventually remove support for multiple pysat versions
if hasattr(pysat.utils, 'io'):
data, meta = pysat.utils.io.load_netcdf(fnames, pandas_format=False,
epoch_name='time',
decode_times=True)
else:
data, meta = pysat.utils.load_netcdf4(fnames, pandas_format=False)
data, meta = pysat.utils.io.load_netcdf(fnames, pandas_format=False,
epoch_name='time',
decode_times=True)

# Move misc parameters from xarray to the Instrument object via Meta.
# Doing this after `meta` created ensures all metadata is still kept
Expand Down
77 changes: 0 additions & 77 deletions pysatModels/tests/test_models.py
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Expand Up @@ -8,8 +8,6 @@

import datetime as dt
import os
from packaging import version as pack_version
import pytest
import shutil
import sys
import tempfile
Expand All @@ -36,81 +34,6 @@ class TestModels(clslib.InstLibTests):
"""


class TestSAMIPysatVersion(object):
"""Test SAMI load code for pysat version differences across v3.0.2."""

def setup_class(self):
"""Initialize the testing setup once before all tests are run."""
# Make sure to use a temporary directory so that the user setup is not
# altered

# TODO(#100): remove if-statement when it is always triggered
tkwargs = {}
if sys.version_info.major >= 3 and sys.version_info.minor >= 10:
tkwargs = {"ignore_cleanup_errors": True}
self.tempdir = tempfile.TemporaryDirectory(**tkwargs)
self.saved_path = pysat.params['data_dirs']
self.saved_ver = pysat.__version__
pysat.params.data['data_dirs'] = [self.tempdir.name]

# Assign the location of the model Instrument sub-modules
self.inst_loc = pysatModels.models
return

def teardown_class(self):
"""Clean up downloaded files and parameters from tests."""

pysat.params.data['data_dirs'] = self.saved_path
pysat.__version__ = self.saved_ver

# Remove the temporary directory
# TODO(#100): Remove try/except when Python 3.10 is the lowest version
try:
self.tempdir.cleanup()
except Exception:
pass

del self.inst_loc, self.saved_path, self.tempdir, self.saved_ver
return

def test_load_failure(self):
"""Test for SAMI load failure when faking a different pysat version."""

if (pack_version.Version(pysat.__version__)
>= pack_version.Version('3.0.2')):
# Define target error variable label
label = 'ut'

# Replace reported version with one before 3.0.2
vlabel = '3.0.1'

# Expected error
error = ValueError
else:
# Define target error variable label
label = 'epoch_origin'

# Expected error
error = TypeError

# Replace reported version with one including 3.0.2
vlabel = '3.0.2'

# Update reported pysat version
pysat.__version__ = vlabel

with pytest.raises(error) as verr:
inst = pysat.Instrument(inst_module=self.inst_loc.sami2py_sami2,
tag='test')
inst.download(self.inst_loc.sami2py_sami2._test_dates['']['test'],
self.inst_loc.sami2py_sami2._test_dates['']['test'])
inst.load(date=self.inst_loc.sami2py_sami2._test_dates['']['test'])

assert str(verr).find(label) >= 0

return


class TestSAMILoadMultipleDays(object):
"""Test SAMI load code for multiple days."""

Expand Down
65 changes: 9 additions & 56 deletions pysatModels/tests/test_utils_extract.py
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Expand Up @@ -7,7 +7,6 @@

import logging
import numpy as np
from packaging import version as pack_version
import platform
import pytest

Expand All @@ -28,9 +27,7 @@ def setup_method(self):

# Load the data in the instruments
load_kwargs = {'date': pysat_testmodel._test_dates['']['']}
if(pack_version.Version(pysat.__version__)
> pack_version.Version('3.0.1')):
load_kwargs['use_header'] = True
load_kwargs['use_header'] = True

self.inst.load(**load_kwargs)
self.model.load(**load_kwargs)
Expand Down Expand Up @@ -198,10 +195,6 @@ def test_success_for_some_already_ran_data(self, caplog):
return


@pytest.mark.skipif(pack_version.Version(pysat.__version__)
<= pack_version.Version('3.0.1'),
reason=''.join(('Requires test model in pysat ',
' v3.0.2 or later.')))
class TestUtilsExtractModObs(TestUtilsExtractInstThroughMod):
"""Unit tests for `utils.extract.extract_modelled_observations`."""

Expand All @@ -213,9 +206,7 @@ def setup_method(self):

# Load the data in the instruments
load_kwargs = {'date': pysat_testmodel._test_dates['']['']}
if(pack_version.Version(pysat.__version__)
> pack_version.Version('3.0.1')):
load_kwargs['use_header'] = True
load_kwargs['use_header'] = True

self.inst.load(**load_kwargs)
self.model.load(**load_kwargs)
Expand Down Expand Up @@ -344,10 +335,6 @@ def test_success_for_some_already_ran_data(self, caplog):
return


@pytest.mark.skipif(pack_version.Version(pysat.__version__)
<= pack_version.Version('3.0.1'),
reason=''.join(('Requires test model in pysat ',
' v3.0.2 or later.')))
class TestUtilsExtractModObsXarray(TestUtilsExtractModObs):
"""Xarray unit tests for `utils.extract.extract_modelled_observations`."""

Expand All @@ -359,9 +346,7 @@ def setup_method(self):

# Load the data in the instruments
load_kwargs = {'date': pysat_testmodel._test_dates['']['']}
if(pack_version.Version(pysat.__version__)
> pack_version.Version('3.0.1')):
load_kwargs['use_header'] = True
load_kwargs['use_header'] = True

self.inst.load(**load_kwargs)
self.model.load(**load_kwargs)
Expand All @@ -386,10 +371,6 @@ def teardown_method(self):
return


@pytest.mark.skipif(pack_version.Version(pysat.__version__)
<= pack_version.Version('3.0.1'),
reason=''.join(('Requires test model in pysat ',
' v3.0.2 or later.')))
class TestUtilsExtractModObsXarray2D(TestUtilsExtractModObs):
"""Xarray unit tests for `utils.extract.extract_modelled_observations`."""

Expand All @@ -401,9 +382,7 @@ def setup_method(self):

# Load the data in the instruments
load_kwargs = {'date': pysat_testmodel._test_dates['']['']}
if(pack_version.Version(pysat.__version__)
> pack_version.Version('3.0.1')):
load_kwargs['use_header'] = True
load_kwargs['use_header'] = True

self.inst.load(**load_kwargs)
self.model.load(**load_kwargs)
Expand Down Expand Up @@ -439,9 +418,7 @@ def setup_method(self):

# Load the data in the instruments
load_kwargs = {'date': pysat_testmodel._test_dates['']['']}
if(pack_version.Version(pysat.__version__)
> pack_version.Version('3.0.1')):
load_kwargs['use_header'] = True
load_kwargs['use_header'] = True

self.inst.load(**load_kwargs)
self.model.load(**load_kwargs)
Expand Down Expand Up @@ -475,10 +452,6 @@ def teardown_method(self):
# TODO(#118): fix `instrument_altitude_to_model_pressure` for Windows env
@pytest.mark.skipif(platform.system() == "Windows",
reason="Broken on windows, see #118")
@pytest.mark.skipif(pack_version.Version(pysat.__version__)
<= pack_version.Version('3.0.1'),
reason=''.join(('Requires test model in pysat ',
' v3.0.2 or later.')))
class TestUtilsAltitudePressure(object):
"""Unit tests for `utils.extract.instrument_altitude_to_model_pressure`."""

Expand All @@ -491,9 +464,7 @@ def setup_method(self):

# Load the data in the instruments
load_kwargs = {'date': pysat_testmodel._test_dates['']['']}
if(pack_version.Version(pysat.__version__)
> pack_version.Version('3.0.1')):
load_kwargs['use_header'] = True
load_kwargs['use_header'] = True

self.inst.load(**load_kwargs)
self.model.load(**load_kwargs)
Expand Down Expand Up @@ -611,10 +582,6 @@ def test_alternate_output_names(self):
# TODO(#118): fix `instrument_altitude_to_model_pressure` for Windows env
@pytest.mark.skipif(platform.system() == "Windows",
reason="Broken on windows, see #118")
@pytest.mark.skipif(pack_version.Version(pysat.__version__)
<= pack_version.Version('3.0.1'),
reason=''.join(('Requires test model in pysat ',
' v3.0.2 or later.')))
class TestUtilsAltitudePressureXarray(TestUtilsAltitudePressure):
"""Xarray unit tests for `instrument_altitude_to_model_pressure`."""

Expand All @@ -627,9 +594,7 @@ def setup_method(self):

# Load the data in the instruments
load_kwargs = {'date': pysat_testmodel._test_dates['']['']}
if(pack_version.Version(pysat.__version__)
> pack_version.Version('3.0.1')):
load_kwargs['use_header'] = True
load_kwargs['use_header'] = True

self.inst.load(**load_kwargs)
self.model.load(**load_kwargs)
Expand All @@ -653,10 +618,6 @@ def teardown_method(self):
return


@pytest.mark.skipif(pack_version.Version(pysat.__version__)
<= pack_version.Version('3.0.1'),
reason=''.join(('Requires `max_latitude` test Instrument ',
'support in pysat v3.0.2 or later.')))
class TestUtilsExtractInstModIrregView(object):
"""Unit tests for `utils.extract.instrument_view_irregular_model`."""

Expand All @@ -671,9 +632,7 @@ def setup_method(self):

# Load the data in the instruments
load_kwargs = {'date': pysat_testmodel._test_dates['']['']}
if(pack_version.Version(pysat.__version__)
> pack_version.Version('3.0.1')):
load_kwargs['use_header'] = True
load_kwargs['use_header'] = True

self.inst.load(**load_kwargs)
self.model.load(**load_kwargs)
Expand Down Expand Up @@ -766,10 +725,6 @@ def test_bad_kwarg_input(self, bad_key, bad_val, err_msg):
return


@pytest.mark.skipif(pack_version.Version(pysat.__version__)
<= pack_version.Version('3.0.1'),
reason=''.join(('Requires `max_latitude` test Instrument ',
'support in pysat v3.0.2 or later.')))
class TestUtilsExtractInstModIrregViewXarray(TestUtilsExtractInstModIrregView):
"""Xarray unit tests for `instrument_view_irregular_model`."""

Expand All @@ -784,9 +739,7 @@ def setup_method(self):

# Load the data in the instruments
load_kwargs = {'date': pysat_testmodel._test_dates['']['']}
if(pack_version.Version(pysat.__version__)
> pack_version.Version('3.0.1')):
load_kwargs['use_header'] = True
load_kwargs['use_header'] = True

self.inst.load(**load_kwargs)
self.model.load(**load_kwargs)
Expand Down
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