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Merge pull request #207 from dstansby/optional-deps
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Make astropy/xarray optional
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@dstansby
dstansby committed Jun 1, 2023
2 parents 9da61ee + 8e33f4f commit 9703b12
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Showing 3 changed files with 57 additions and 67 deletions.
12 changes: 1 addition & 11 deletions cdflib/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,17 +4,7 @@
from . import cdfread, cdfwrite
from .epochs import CDFepoch as cdfepoch # noqa: F401

try:
# This is an optional dependency for astropy time conversions
from .epochs_astropy import CDFAstropy as cdfastropy
except BaseException:
pass

# Another optional dependency for XArray <-> cdf conversions
from .cdf_to_xarray import cdf_to_xarray
from .xarray_to_cdf import xarray_to_cdf

__all__ = ["CDF", "xarray_to_cdf", "cdf_to_xarray"]
__all__ = ["CDF"]
try:
from ._version import version as __version__
except Exception:
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7 changes: 7 additions & 0 deletions doc/changelog.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,13 @@
Changelog
=========

1.0.1
=====
To keep ``astropy`` and ``xarray`` as optional dependencies, ``cdfastropy``,
``cdf_to_xarray``, and ``xarray_to_cdf`` are no longer available under ``cdflib``.
Instead import them from ``cdflib.xarray_to_cdf``, ``cdflib.cdf_to_xarray``, or
``cdflib.epochs_astropy``.

1.0.0
=====
Version 1.0.0 is a new major version for ``cdflib``, and contains a number
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105 changes: 49 additions & 56 deletions tests/test_xarray_reader_writer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,8 @@
import pytest
import xarray as xr

import cdflib
from cdflib.cdf_to_xarray import cdf_to_xarray
from cdflib.xarray_to_cdf import xarray_to_cdf

# To run these tests use `pytest --remote-data`

Expand Down Expand Up @@ -42,18 +43,18 @@ def test_xarray_read_write(tmp_path, cdf_fname, nc_fname):
if not os.path.exists(cdf_fname):
urllib.request.urlretrieve(url, cdf_fname)

a = cdflib.cdf_to_xarray(cdf_fname, to_unixtime=True, fillval_to_nan=True)
a = cdf_to_xarray(cdf_fname, to_unixtime=True, fillval_to_nan=True)

cdflib.xarray_to_cdf(a, tmp_path / cdf_fname, from_unixtime=True)
b = cdflib.cdf_to_xarray(tmp_path / cdf_fname, to_unixtime=True, fillval_to_nan=True)
xarray_to_cdf(a, tmp_path / cdf_fname, from_unixtime=True)
b = cdf_to_xarray(tmp_path / cdf_fname, to_unixtime=True, fillval_to_nan=True)

url = f"https://lasp.colorado.edu/maven/sdc/public/data/sdc/web/cdflib_testing/{nc_fname}"
if not os.path.exists(nc_fname):
urllib.request.urlretrieve(url, nc_fname)

c = xr.load_dataset(nc_fname)
cdflib.xarray_to_cdf(c, tmp_path / ("nc_" + cdf_fname))
d = cdflib.cdf_to_xarray(tmp_path / ("nc_" + cdf_fname), to_unixtime=True, fillval_to_nan=True)
xarray_to_cdf(c, tmp_path / ("nc_" + cdf_fname))
d = cdf_to_xarray(tmp_path / ("nc_" + cdf_fname), to_unixtime=True, fillval_to_nan=True)


@pytest.mark.remote_data
Expand All @@ -71,8 +72,8 @@ def test_MGITM_model():
c["latitude"].attrs["VAR_TYPE"] = "support_data"
c["altitude"].attrs["VAR_TYPE"] = "support_data"

cdflib.xarray_to_cdf(c, "MGITM_LS180_F130_150615-created-from-netcdf-input.cdf")
d = cdflib.cdf_to_xarray("MGITM_LS180_F130_150615-created-from-netcdf-input.cdf", to_unixtime=True, fillval_to_nan=True)
xarray_to_cdf(c, "MGITM_LS180_F130_150615-created-from-netcdf-input.cdf")
d = cdf_to_xarray("MGITM_LS180_F130_150615-created-from-netcdf-input.cdf", to_unixtime=True, fillval_to_nan=True)
os.remove("MGITM_LS180_F130_150615-created-from-netcdf-input.cdf")
os.remove("MGITM_LS180_F130_150615.nc")

Expand All @@ -90,10 +91,8 @@ def test_goes_mag():
c["coordinate"].attrs["VAR_TYPE"] = "support_data"
c["time"].attrs["VAR_TYPE"] = "support_data"
c["time_orbit"].attrs["VAR_TYPE"] = "support_data"
cdflib.xarray_to_cdf(c, "dn_magn-l2-hires_g17_d20211219_v1-0-1-created-from-netcdf-input.cdf")
d = cdflib.cdf_to_xarray(
"dn_magn-l2-hires_g17_d20211219_v1-0-1-created-from-netcdf-input.cdf", to_unixtime=True, fillval_to_nan=True
)
xarray_to_cdf(c, "dn_magn-l2-hires_g17_d20211219_v1-0-1-created-from-netcdf-input.cdf")
d = cdf_to_xarray("dn_magn-l2-hires_g17_d20211219_v1-0-1-created-from-netcdf-input.cdf", to_unixtime=True, fillval_to_nan=True)
os.remove("dn_magn-l2-hires_g17_d20211219_v1-0-1-created-from-netcdf-input.cdf")
os.remove("dn_magn-l2-hires_g17_d20211219_v1-0-1.nc")

Expand All @@ -112,8 +111,8 @@ def test_saber():
c["sclatitude"].attrs["VAR_TYPE"] = "support_data"
c["sclongitude"].attrs["VAR_TYPE"] = "support_data"
c["scaltitude"].attrs["VAR_TYPE"] = "support_data"
cdflib.xarray_to_cdf(c, "SABER_L2B_2021020_103692_02.07-created-from-netcdf-input.cdf")
d = cdflib.cdf_to_xarray("SABER_L2B_2021020_103692_02.07-created-from-netcdf-input.cdf", to_unixtime=True, fillval_to_nan=True)
xarray_to_cdf(c, "SABER_L2B_2021020_103692_02.07-created-from-netcdf-input.cdf")
d = cdf_to_xarray("SABER_L2B_2021020_103692_02.07-created-from-netcdf-input.cdf", to_unixtime=True, fillval_to_nan=True)
os.remove("SABER_L2B_2021020_103692_02.07-created-from-netcdf-input.cdf")
os.remove("SABER_L2B_2021020_103692_02.07.nc")

Expand All @@ -125,9 +124,9 @@ def test_euv():
if not os.path.exists(fname):
urllib.request.urlretrieve(url, fname)

a = cdflib.cdf_to_xarray("mvn_euv_l3_minute_20201130_v14_r02.cdf", to_unixtime=True, fillval_to_nan=True)
cdflib.xarray_to_cdf(a, "mvn_euv_l3_minute_20201130_v14_r02-created-from-cdf-input.cdf", from_unixtime=True)
b = cdflib.cdf_to_xarray("mvn_euv_l3_minute_20201130_v14_r02-created-from-cdf-input.cdf", to_unixtime=True, fillval_to_nan=True)
a = cdf_to_xarray("mvn_euv_l3_minute_20201130_v14_r02.cdf", to_unixtime=True, fillval_to_nan=True)
xarray_to_cdf(a, "mvn_euv_l3_minute_20201130_v14_r02-created-from-cdf-input.cdf", from_unixtime=True)
b = cdf_to_xarray("mvn_euv_l3_minute_20201130_v14_r02-created-from-cdf-input.cdf", to_unixtime=True, fillval_to_nan=True)
os.remove("mvn_euv_l3_minute_20201130_v14_r02-created-from-cdf-input.cdf")
os.remove("mvn_euv_l3_minute_20201130_v14_r02.cdf")

Expand All @@ -139,9 +138,9 @@ def test_sep_anc():
if not os.path.exists(fname):
urllib.request.urlretrieve(url, fname)

a = cdflib.cdf_to_xarray("mvn_sep_l2_anc_20210501_v06_r00.cdf", to_unixtime=True, fillval_to_nan=True)
cdflib.xarray_to_cdf(a, "mvn_sep_l2_anc_20210501_v06_r00-created-from-cdf-input.cdf", from_unixtime=True)
a = cdflib.cdf_to_xarray("mvn_sep_l2_anc_20210501_v06_r00-created-from-cdf-input.cdf", to_unixtime=True, fillval_to_nan=True)
a = cdf_to_xarray("mvn_sep_l2_anc_20210501_v06_r00.cdf", to_unixtime=True, fillval_to_nan=True)
xarray_to_cdf(a, "mvn_sep_l2_anc_20210501_v06_r00-created-from-cdf-input.cdf", from_unixtime=True)
a = cdf_to_xarray("mvn_sep_l2_anc_20210501_v06_r00-created-from-cdf-input.cdf", to_unixtime=True, fillval_to_nan=True)
os.remove("mvn_sep_l2_anc_20210501_v06_r00-created-from-cdf-input.cdf")
os.remove("mvn_sep_l2_anc_20210501_v06_r00.cdf")

Expand All @@ -153,9 +152,9 @@ def test_sep_svy():
if not os.path.exists(fname):
urllib.request.urlretrieve(url, fname)

a = cdflib.cdf_to_xarray("mvn_sep_l2_s2-raw-svy-full_20191231_v04_r05.cdf", to_unixtime=True, fillval_to_nan=True)
cdflib.xarray_to_cdf(a, "mvn_sep_l2_s2-raw-svy-full_20191231_v04_r05-created-from-cdf-input.cdf", from_unixtime=True)
b = cdflib.cdf_to_xarray(
a = cdf_to_xarray("mvn_sep_l2_s2-raw-svy-full_20191231_v04_r05.cdf", to_unixtime=True, fillval_to_nan=True)
xarray_to_cdf(a, "mvn_sep_l2_s2-raw-svy-full_20191231_v04_r05-created-from-cdf-input.cdf", from_unixtime=True)
b = cdf_to_xarray(
"mvn_sep_l2_s2-raw-svy-full_20191231_v04_r05-created-from-cdf-input.cdf", to_unixtime=True, fillval_to_nan=True
)
os.remove("mvn_sep_l2_s2-raw-svy-full_20191231_v04_r05-created-from-cdf-input.cdf")
Expand All @@ -173,10 +172,10 @@ def test_sta():
if not os.path.exists(fname):
urllib.request.urlretrieve(url, fname)
a = cdflib.cdf_to_xarray("mvn_sta_l2_d1-32e4d16a8m_20201130_v02_r04.cdf", to_unixtime=True,
a = cdf_to_xarray("mvn_sta_l2_d1-32e4d16a8m_20201130_v02_r04.cdf", to_unixtime=True,
fillval_to_nan=True)
cdflib.xarray_to_cdf(a, 'mvn_sta_l2_d1-32e4d16a8m_20201130_v02_r04-created-from-cdf-input.cdf', from_unixtime=True)
b = cdflib.cdf_to_xarray('mvn_sta_l2_d1-32e4d16a8m_20201130_v02_r04-created-from-cdf-input.cdf', to_unixtime=True,
xarray_to_cdf(a, 'mvn_sta_l2_d1-32e4d16a8m_20201130_v02_r04-created-from-cdf-input.cdf', from_unixtime=True)
b = cdf_to_xarray('mvn_sta_l2_d1-32e4d16a8m_20201130_v02_r04-created-from-cdf-input.cdf', to_unixtime=True,
fillval_to_nan=True)
os.remove('mvn_sta_l2_d1-32e4d16a8m_20201130_v02_r04-created-from-cdf-input.cdf')
os.remove('mvn_sta_l2_d1-32e4d16a8m_20201130_v02_r04.cdf')
Expand All @@ -190,9 +189,9 @@ def test_swe_arc3d():
if not os.path.exists(fname):
urllib.request.urlretrieve(url, fname)

a = cdflib.cdf_to_xarray("mvn_swe_l2_arc3d_20180717_v04_r02.cdf", to_unixtime=True, fillval_to_nan=True)
cdflib.xarray_to_cdf(a, "mvn_swe_l2_arc3d_20180717_v04_r02-created-from-cdf-input.cdf", from_unixtime=True)
b = cdflib.cdf_to_xarray("mvn_swe_l2_arc3d_20180717_v04_r02-created-from-cdf-input.cdf", to_unixtime=True, fillval_to_nan=True)
a = cdf_to_xarray("mvn_swe_l2_arc3d_20180717_v04_r02.cdf", to_unixtime=True, fillval_to_nan=True)
xarray_to_cdf(a, "mvn_swe_l2_arc3d_20180717_v04_r02-created-from-cdf-input.cdf", from_unixtime=True)
b = cdf_to_xarray("mvn_swe_l2_arc3d_20180717_v04_r02-created-from-cdf-input.cdf", to_unixtime=True, fillval_to_nan=True)
os.remove("mvn_swe_l2_arc3d_20180717_v04_r02-created-from-cdf-input.cdf")
os.remove("mvn_swe_l2_arc3d_20180717_v04_r02.cdf")

Expand All @@ -202,10 +201,8 @@ def test_swe_arc3d():
urllib.request.urlretrieve(url, fname)

c = xr.load_dataset("mvn_swe_l2_arc3d_20180717_v04_r02.nc")
cdflib.xarray_to_cdf(c, "mvn_swe_l2_arc3d_20180717_v04_r02-created-from-netcdf-input.cdf")
d = cdflib.cdf_to_xarray(
"mvn_swe_l2_arc3d_20180717_v04_r02-created-from-netcdf-input.cdf", to_unixtime=True, fillval_to_nan=True
)
xarray_to_cdf(c, "mvn_swe_l2_arc3d_20180717_v04_r02-created-from-netcdf-input.cdf")
d = cdf_to_xarray("mvn_swe_l2_arc3d_20180717_v04_r02-created-from-netcdf-input.cdf", to_unixtime=True, fillval_to_nan=True)
os.remove("mvn_swe_l2_arc3d_20180717_v04_r02-created-from-netcdf-input.cdf")
os.remove("mvn_swe_l2_arc3d_20180717_v04_r02.nc")

Expand All @@ -217,11 +214,9 @@ def test_swe_svyspec():
if not os.path.exists(fname):
urllib.request.urlretrieve(url, fname)

a = cdflib.cdf_to_xarray("mvn_swe_l2_svyspec_20180718_v04_r04.cdf", to_unixtime=True, fillval_to_nan=True)
cdflib.xarray_to_cdf(a, "mvn_swe_l2_svyspec_20180718_v04_r04-created-from-cdf-input.cdf", from_unixtime=True)
b = cdflib.cdf_to_xarray(
"mvn_swe_l2_svyspec_20180718_v04_r04-created-from-cdf-input.cdf", to_unixtime=True, fillval_to_nan=True
)
a = cdf_to_xarray("mvn_swe_l2_svyspec_20180718_v04_r04.cdf", to_unixtime=True, fillval_to_nan=True)
xarray_to_cdf(a, "mvn_swe_l2_svyspec_20180718_v04_r04-created-from-cdf-input.cdf", from_unixtime=True)
b = cdf_to_xarray("mvn_swe_l2_svyspec_20180718_v04_r04-created-from-cdf-input.cdf", to_unixtime=True, fillval_to_nan=True)
os.remove("mvn_swe_l2_svyspec_20180718_v04_r04-created-from-cdf-input.cdf")
os.remove("mvn_swe_l2_svyspec_20180718_v04_r04.cdf")

Expand All @@ -231,10 +226,8 @@ def test_swe_svyspec():
urllib.request.urlretrieve(url, fname)

c = xr.load_dataset("mvn_swe_l2_svyspec_20180718_v04_r04.nc")
cdflib.xarray_to_cdf(c, "mvn_swe_l2_svyspec_20180718_v04_r04-created-from-netcdf-input.cdf")
d = cdflib.cdf_to_xarray(
"mvn_swe_l2_svyspec_20180718_v04_r04-created-from-netcdf-input.cdf", to_unixtime=True, fillval_to_nan=True
)
xarray_to_cdf(c, "mvn_swe_l2_svyspec_20180718_v04_r04-created-from-netcdf-input.cdf")
d = cdf_to_xarray("mvn_swe_l2_svyspec_20180718_v04_r04-created-from-netcdf-input.cdf", to_unixtime=True, fillval_to_nan=True)
os.remove("mvn_swe_l2_svyspec_20180718_v04_r04-created-from-netcdf-input.cdf")
os.remove("mvn_swe_l2_svyspec_20180718_v04_r04.nc")

Expand All @@ -247,8 +240,8 @@ def test_raids():
urllib.request.urlretrieve(url, fname)

c = xr.load_dataset("raids_nirs_20100823_v1.1.nc")
cdflib.xarray_to_cdf(c, "raids_nirs_20100823_v1.1-created-from-netcdf-input.cdf")
d = cdflib.cdf_to_xarray("raids_nirs_20100823_v1.1-created-from-netcdf-input.cdf", to_unixtime=True, fillval_to_nan=True)
xarray_to_cdf(c, "raids_nirs_20100823_v1.1-created-from-netcdf-input.cdf")
d = cdf_to_xarray("raids_nirs_20100823_v1.1-created-from-netcdf-input.cdf", to_unixtime=True, fillval_to_nan=True)
os.remove("raids_nirs_20100823_v1.1-created-from-netcdf-input.cdf")
os.remove("raids_nirs_20100823_v1.1.nc")

Expand All @@ -264,11 +257,11 @@ def test_rbsp():
if not os.path.exists(fname):
urllib.request.urlretrieve(url, fname)
a = cdflib.cdf_to_xarray("rbsp-a_magnetometer_1sec-gsm_emfisis-l3_20190122_v1.6.2.cdf",
a = cdf_to_xarray("rbsp-a_magnetometer_1sec-gsm_emfisis-l3_20190122_v1.6.2.cdf",
to_unixtime=True, fillval_to_nan=True)
cdflib.xarray_to_cdf(a, 'rbsp-a_magnetometer_1sec-gsm_emfisis-l3_20190122_v1.6.2-created-from-cdf-input.cdf',
xarray_to_cdf(a, 'rbsp-a_magnetometer_1sec-gsm_emfisis-l3_20190122_v1.6.2-created-from-cdf-input.cdf',
from_unixtime=True)
b = cdflib.cdf_to_xarray('rbsp-a_magnetometer_1sec-gsm_emfisis-l3_20190122_v1.6.2-created-from-cdf-input.cdf',
b = cdf_to_xarray('rbsp-a_magnetometer_1sec-gsm_emfisis-l3_20190122_v1.6.2-created-from-cdf-input.cdf',
to_unixtime=True, fillval_to_nan=True)
os.remove('rbsp-a_magnetometer_1sec-gsm_emfisis-l3_20190122_v1.6.2-created-from-cdf-input.cdf')
os.remove('rbsp-a_magnetometer_1sec-gsm_emfisis-l3_20190122_v1.6.2.cdf')
Expand All @@ -283,8 +276,8 @@ def test_see_l3():
urllib.request.urlretrieve(url, fname)

c = xr.load_dataset("see__L3_2021009_012_01.ncdf")
cdflib.xarray_to_cdf(c, "see__L3_2021009_012_01.ncdfhello2.cdf")
d = cdflib.cdf_to_xarray("see__L3_2021009_012_01.ncdfhello2.cdf", to_unixtime=True, fillval_to_nan=True)
xarray_to_cdf(c, "see__L3_2021009_012_01.ncdfhello2.cdf")
d = cdf_to_xarray("see__L3_2021009_012_01.ncdfhello2.cdf", to_unixtime=True, fillval_to_nan=True)
os.remove("see__L3_2021009_012_01.ncdfhello2.cdf")
os.remove("see__L3_2021009_012_01.ncdf")

Expand All @@ -297,8 +290,8 @@ def test_see_l2a():
urllib.request.urlretrieve(url, fname)

c = xr.load_dataset("see__xps_L2A_2021006_012_02.ncdf")
cdflib.xarray_to_cdf(c, "see__xps_L2A_2021006_012_02.ncdfhello2.cdf")
d = cdflib.cdf_to_xarray("see__xps_L2A_2021006_012_02.ncdfhello2.cdf", to_unixtime=True, fillval_to_nan=True)
xarray_to_cdf(c, "see__xps_L2A_2021006_012_02.ncdfhello2.cdf")
d = cdf_to_xarray("see__xps_L2A_2021006_012_02.ncdfhello2.cdf", to_unixtime=True, fillval_to_nan=True)
os.remove("see__xps_L2A_2021006_012_02.ncdfhello2.cdf")
os.remove("see__xps_L2A_2021006_012_02.ncdf")

Expand All @@ -311,8 +304,8 @@ def test_something():
urllib.request.urlretrieve(url, fname)

c = xr.load_dataset("sgpsondewnpnC1.nc")
cdflib.xarray_to_cdf(c, "sgpsondewnpnC1-created-from-netcdf-input.cdf")
d = cdflib.cdf_to_xarray("sgpsondewnpnC1-created-from-netcdf-input.cdf", to_unixtime=True, fillval_to_nan=True)
xarray_to_cdf(c, "sgpsondewnpnC1-created-from-netcdf-input.cdf")
d = cdf_to_xarray("sgpsondewnpnC1-created-from-netcdf-input.cdf", to_unixtime=True, fillval_to_nan=True)
os.remove("sgpsondewnpnC1-created-from-netcdf-input.cdf")
os.remove("sgpsondewnpnC1.nc")

Expand All @@ -326,7 +319,7 @@ def test_build_from_scratch():
epoch_dims = ["epoch"]
epoch = xr.Variable(epoch_dims, epoch_data) # type: ignore[no-untyped-call]
ds = xr.Dataset(data_vars={"data": data, "epoch": epoch})
cdflib.xarray_to_cdf(ds, "hello.cdf")
xarray_to_cdf(ds, "hello.cdf")
os.remove("hello.cdf")
global_attributes = {
"Project": "Hail Mary",
Expand All @@ -347,11 +340,11 @@ def test_build_from_scratch():
data = xr.Variable(var_dims, var_data) # type: ignore[no-untyped-call]
epoch = xr.Variable(epoch_dims, epoch_data) # type: ignore[no-untyped-call]
ds = xr.Dataset(data_vars={"data": data, "epoch": epoch}, attrs=global_attributes)
cdflib.xarray_to_cdf(ds, "hello.cdf")
xarray_to_cdf(ds, "hello.cdf")
os.remove("hello.cdf")
dir_data = [1, 2, 3]
dir_dims = ["direction"]
direction = xr.Variable(dir_dims, dir_data) # type: ignore[no-untyped-call]
ds = xr.Dataset(data_vars={"data": data, "epoch": epoch, "direction": direction}, attrs=global_attributes)
cdflib.xarray_to_cdf(ds, "hello.cdf")
xarray_to_cdf(ds, "hello.cdf")
os.remove("hello.cdf")

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