Swap cdf_to_xarray to accept CDF instances, rather than filenames

cdflib/xarray/cdf_to_xarray.py

@@ -99,12 +99,10 @@ def _convert_cdf_time_types(
 
 
 def _convert_cdf_to_dicts(
-    filename: Union[str, Path], to_datetime: bool = False, to_unixtime: bool = False
+    cdf_file: CDF, to_datetime: bool = False, to_unixtime: bool = False
 ) -> Tuple[Dict[str, List[Union[str, np.ndarray]]], Dict[str, Any], Dict[str, npt.NDArray], Dict[str, VDRInfo]]:
-    # Open the CDF file
     # Converts the entire CDF file into python dictionary objects
 
-    cdf_file = CDF(filename, string_encoding="latin-1")
     cdf_info = cdf_file.cdf_info()
     all_cdf_variables = cdf_info.rVariables + cdf_info.zVariables
 
@@ -685,12 +683,12 @@ def _verify_dimension_sizes(created_data_vars: Dict[str, xr.Variable], created_c
                     )
 
 
-def cdf_to_xarray(filename: str, to_datetime: bool = True, to_unixtime: bool = False, fillval_to_nan: bool = False) -> xr.Dataset:
+def cdf_to_xarray(cdf_file: CDF, to_datetime: bool = True, to_unixtime: bool = False, fillval_to_nan: bool = False) -> xr.Dataset:
     """
     This function converts CDF files into XArray Dataset Objects.
 
     Parameters:
-        filename (str):  The path to the CDF file to read
+        cdf_file (CDF):  The CDF file to convert
         to_datetime (bool, optional): Whether or not to convert CDF_EPOCH/EPOCH_16/TT2000 to datetime64, or leave them as is
         to_unixtime (bool, optional): Whether or not to convert CDF_EPOCH/EPOCH_16/TT2000 to unixtime, or leave them as is
         fillval_to_nan (bool, optional): If True, any data values that match the FILLVAL attribute for a variable will be set to NaN
@@ -767,7 +765,7 @@ def cdf_to_xarray(filename: str, to_datetime: bool = True, to_unixtime: bool = F
 
     # Convert the CDF file into a series of dicts, so we don't need to keep reading the file
     global_attributes, all_variable_attributes, all_variable_data, all_variable_properties = _convert_cdf_to_dicts(
-        filename, to_datetime=to_datetime, to_unixtime=to_unixtime
+        cdf_file, to_datetime=to_datetime, to_unixtime=to_unixtime
     )
 
     created_vars, depend_dimensions = _generate_xarray_data_variables(

tests/test_cdfwrite.py

@@ -4,7 +4,7 @@
 import numpy as np
 import pytest
 
-from cdflib import cdfread, cdfwrite
+from cdflib import cdfread, cdfwrite, CDF
 from cdflib.xarray import cdf_to_xarray
 
 R = Path(__file__).parent
@@ -660,7 +660,7 @@ def test_string_input_but_number_type(tmp_path):
     cdf.close()
 
     # Reading it back in would cause an error
-    cdf_to_xarray(tmp_path / "test.cdf")
+    cdf_to_xarray(CDF(tmp_path / "test.cdf"))
 
 
 def test_array_string_input_but_number_type(tmp_path):
@@ -681,4 +681,4 @@ def test_array_string_input_but_number_type(tmp_path):
     cdf.close()
 
     # Reading it back in would cause an error
-    cdf_to_xarray(tmp_path / "test.cdf")
+    cdf_to_xarray(CDF(tmp_path / "test.cdf"))

tests/test_xarray_reader_writer.py

@@ -5,6 +5,7 @@
 import pytest
 import xarray as xr
 
+from cdflib import CDF
 from cdflib.xarray import cdf_to_xarray, xarray_to_cdf
 
 # To run these tests use `pytest --remote-data`
@@ -43,18 +44,21 @@ 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 = cdf_to_xarray(cdf_fname, fillval_to_nan=True)
+    with CDF(cdf_fname) as cdf_file:
+        a = cdf_to_xarray(cdf_file, fillval_to_nan=True)
 
     xarray_to_cdf(a, tmp_path / cdf_fname)
-    b = cdf_to_xarray(tmp_path / cdf_fname, fillval_to_nan=True)
+    with CDF(tmp_path / cdf_fname) as cdf_file:
+        b = cdf_to_xarray(cdf_file, 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)
     xarray_to_cdf(c, tmp_path / ("nc_" + cdf_fname))
-    d = cdf_to_xarray(tmp_path / ("nc_" + cdf_fname), fillval_to_nan=True)
+    with CDF(tmp_path / ("nc_" + cdf_fname)) as cdf_file:
+        d = cdf_to_xarray(cdf_file, fillval_to_nan=True)
 
 
 @pytest.mark.remote_data
@@ -73,7 +77,8 @@ def test_MGITM_model():
     c["altitude"].attrs["VAR_TYPE"] = "support_data"
 
     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", fillval_to_nan=True)
+    with CDF("MGITM_LS180_F130_150615-created-from-netcdf-input.cdf") as cdf_file:
+        d = cdf_to_xarray(cdf_file, fillval_to_nan=True)
     os.remove("MGITM_LS180_F130_150615-created-from-netcdf-input.cdf")
     os.remove("MGITM_LS180_F130_150615.nc")
 
@@ -92,7 +97,8 @@ def test_goes_mag():
     c["time"].attrs["VAR_TYPE"] = "support_data"
     c["time_orbit"].attrs["VAR_TYPE"] = "support_data"
     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", fillval_to_nan=True)
+    with CDF("dn_magn-l2-hires_g17_d20211219_v1-0-1-created-from-netcdf-input.cdf") as cdf_file:
+        d = cdf_to_xarray(cdf_file, 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")
 
@@ -112,7 +118,8 @@ def test_saber():
     c["sclongitude"].attrs["VAR_TYPE"] = "support_data"
     c["scaltitude"].attrs["VAR_TYPE"] = "support_data"
     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", fillval_to_nan=True)
+    with CDF("SABER_L2B_2021020_103692_02.07-created-from-netcdf-input.cdf") as cdf_file:
+        d = cdf_to_xarray(cdf_file, 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")
 
@@ -124,9 +131,11 @@ def test_euv():
     if not os.path.exists(fname):
         urllib.request.urlretrieve(url, fname)
 
-    a = cdf_to_xarray("mvn_euv_l3_minute_20201130_v14_r02.cdf", fillval_to_nan=True)
+    with CDF("mvn_euv_l3_minute_20201130_v14_r02.cdf") as cdf_file:
+        a = cdf_to_xarray(cdf_file, fillval_to_nan=True)
     xarray_to_cdf(a, "mvn_euv_l3_minute_20201130_v14_r02-created-from-cdf-input.cdf")
-    b = cdf_to_xarray("mvn_euv_l3_minute_20201130_v14_r02-created-from-cdf-input.cdf", fillval_to_nan=True)
+    with CDF("mvn_euv_l3_minute_20201130_v14_r02-created-from-cdf-input.cdf") as cdf_file:
+        b = cdf_to_xarray(cdf_file, 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")
 
@@ -138,9 +147,11 @@ def test_sep_anc():
     if not os.path.exists(fname):
         urllib.request.urlretrieve(url, fname)
 
-    a = cdf_to_xarray("mvn_sep_l2_anc_20210501_v06_r00.cdf", fillval_to_nan=True)
+    with CDF("mvn_sep_l2_anc_20210501_v06_r00.cdf") as cdf_file:
+        a = cdf_to_xarray(cdf_file, fillval_to_nan=True)
     xarray_to_cdf(a, "mvn_sep_l2_anc_20210501_v06_r00-created-from-cdf-input.cdf")
-    a = cdf_to_xarray("mvn_sep_l2_anc_20210501_v06_r00-created-from-cdf-input.cdf", fillval_to_nan=True)
+    with CDF("mvn_sep_l2_anc_20210501_v06_r00-created-from-cdf-input.cdf") as cdf_file:
+        a = cdf_to_xarray(cdf_file, 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")
 
@@ -152,9 +163,11 @@ def test_sep_svy():
     if not os.path.exists(fname):
         urllib.request.urlretrieve(url, fname)
 
-    a = cdf_to_xarray("mvn_sep_l2_s2-raw-svy-full_20191231_v04_r05.cdf", fillval_to_nan=True)
+    with CDF("mvn_sep_l2_s2-raw-svy-full_20191231_v04_r05.cdf") as cdf_file:
+        a = cdf_to_xarray(cdf_file, fillval_to_nan=True)
     xarray_to_cdf(a, "mvn_sep_l2_s2-raw-svy-full_20191231_v04_r05-created-from-cdf-input.cdf")
-    b = cdf_to_xarray("mvn_sep_l2_s2-raw-svy-full_20191231_v04_r05-created-from-cdf-input.cdf", fillval_to_nan=True)
+    with CDF("mvn_sep_l2_s2-raw-svy-full_20191231_v04_r05-created-from-cdf-input.cdf") as cdf_file:
+        b = cdf_to_xarray(cdf_file, fillval_to_nan=True)
     os.remove("mvn_sep_l2_s2-raw-svy-full_20191231_v04_r05-created-from-cdf-input.cdf")
     os.remove("mvn_sep_l2_s2-raw-svy-full_20191231_v04_r05.cdf")
 
@@ -187,9 +200,11 @@ def test_swe_arc3d():
     if not os.path.exists(fname):
         urllib.request.urlretrieve(url, fname)
 
-    a = cdf_to_xarray("mvn_swe_l2_arc3d_20180717_v04_r02.cdf", fillval_to_nan=True)
+    with CDF("mvn_swe_l2_arc3d_20180717_v04_r02.cdf") as cdf_file:
+        a = cdf_to_xarray(cdf_file, fillval_to_nan=True)
     xarray_to_cdf(a, "mvn_swe_l2_arc3d_20180717_v04_r02-created-from-cdf-input.cdf")
-    b = cdf_to_xarray("mvn_swe_l2_arc3d_20180717_v04_r02-created-from-cdf-input.cdf", fillval_to_nan=True)
+    with CDF("mvn_swe_l2_arc3d_20180717_v04_r02-created-from-cdf-input.cdf") as cdf_file:
+        b = cdf_to_xarray(cdf_file, 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")
 
@@ -200,7 +215,8 @@ def test_swe_arc3d():
 
     c = xr.load_dataset("mvn_swe_l2_arc3d_20180717_v04_r02.nc")
     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", fillval_to_nan=True)
+    with CDF("mvn_swe_l2_arc3d_20180717_v04_r02-created-from-netcdf-input.cdf") as cdf_file:
+        d = cdf_to_xarray(cdf_file, 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")
 
@@ -212,9 +228,11 @@ def test_swe_svyspec():
     if not os.path.exists(fname):
         urllib.request.urlretrieve(url, fname)
 
-    a = cdf_to_xarray("mvn_swe_l2_svyspec_20180718_v04_r04.cdf", fillval_to_nan=True)
+    with CDF("mvn_swe_l2_svyspec_20180718_v04_r04.cdf") as cdf_file:
+        a = cdf_to_xarray(cdf_file, fillval_to_nan=True)
     xarray_to_cdf(a, "mvn_swe_l2_svyspec_20180718_v04_r04-created-from-cdf-input.cdf")
-    b = cdf_to_xarray("mvn_swe_l2_svyspec_20180718_v04_r04-created-from-cdf-input.cdf", fillval_to_nan=True)
+    with CDF("mvn_swe_l2_svyspec_20180718_v04_r04-created-from-cdf-input.cdf") as cdf_file:
+        b = cdf_to_xarray(cdf_file, 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")
 
@@ -225,7 +243,8 @@ def test_swe_svyspec():
 
     c = xr.load_dataset("mvn_swe_l2_svyspec_20180718_v04_r04.nc")
     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", fillval_to_nan=True)
+    with CDF("mvn_swe_l2_svyspec_20180718_v04_r04-created-from-netcdf-input.cdf") as cdf_file:
+        d = cdf_to_xarray(cdf_file, 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")
 
@@ -239,7 +258,8 @@ def test_raids():
 
     c = xr.load_dataset("raids_nirs_20100823_v1.1.nc")
     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", fillval_to_nan=True)
+    with CDF("raids_nirs_20100823_v1.1-created-from-netcdf-input.cdf") as cdf_file:
+        d = cdf_to_xarray(cdf_file, fillval_to_nan=True)
     os.remove("raids_nirs_20100823_v1.1-created-from-netcdf-input.cdf")
     os.remove("raids_nirs_20100823_v1.1.nc")
 
@@ -274,7 +294,8 @@ def test_see_l3():
 
     c = xr.load_dataset("see__L3_2021009_012_01.ncdf")
     xarray_to_cdf(c, "see__L3_2021009_012_01.ncdfhello2.cdf")
-    d = cdf_to_xarray("see__L3_2021009_012_01.ncdfhello2.cdf", fillval_to_nan=True)
+    with CDF("see__L3_2021009_012_01.ncdfhello2.cdf") as cdf_file:
+        d = cdf_to_xarray(cdf_file, fillval_to_nan=True)
     os.remove("see__L3_2021009_012_01.ncdfhello2.cdf")
     os.remove("see__L3_2021009_012_01.ncdf")
 
@@ -288,7 +309,8 @@ def test_see_l2a():
 
     c = xr.load_dataset("see__xps_L2A_2021006_012_02.ncdf")
     xarray_to_cdf(c, "see__xps_L2A_2021006_012_02.ncdfhello2.cdf")
-    d = cdf_to_xarray("see__xps_L2A_2021006_012_02.ncdfhello2.cdf", fillval_to_nan=True)
+    with CDF("see__xps_L2A_2021006_012_02.ncdfhello2.cdf") as cdf_file:
+        d = cdf_to_xarray(cdf_file, fillval_to_nan=True)
     os.remove("see__xps_L2A_2021006_012_02.ncdfhello2.cdf")
     os.remove("see__xps_L2A_2021006_012_02.ncdf")
 
@@ -302,7 +324,8 @@ def test_something():
 
     c = xr.load_dataset("sgpsondewnpnC1.nc")
     xarray_to_cdf(c, "sgpsondewnpnC1-created-from-netcdf-input.cdf")
-    d = cdf_to_xarray("sgpsondewnpnC1-created-from-netcdf-input.cdf", fillval_to_nan=True)
+    with CDF("sgpsondewnpnC1-created-from-netcdf-input.cdf") as cdf_file:
+        d = cdf_to_xarray(cdf_file, fillval_to_nan=True)
     os.remove("sgpsondewnpnC1-created-from-netcdf-input.cdf")
     os.remove("sgpsondewnpnC1.nc")
 
@@ -348,7 +371,8 @@ def test_build_from_scratch():
 
 
 def test_smoke(cdf_path, tmp_path):
-    a = cdf_to_xarray(cdf_path, fillval_to_nan=True)
+    with CDF(cdf_path) as cdf_file:
+        a = cdf_to_xarray(cdf_file, fillval_to_nan=True)
     xarray_to_cdf(a, tmp_path / cdf_path.name)
 
 
@@ -363,7 +387,8 @@ def test_datetime64_conversion():
     epoch = xr.Variable(epoch_dims, epoch_data)
     ds = xr.Dataset(data_vars={"data": data, "epoch": epoch})
     xarray_to_cdf(ds, "hello.cdf")
-    x = cdf_to_xarray("hello.cdf", to_datetime=True)
+    with CDF("hello.cdf") as cdf_file:
+        x = cdf_to_xarray(cdf_file, to_datetime=True)
     assert x["epoch"][0] == np.datetime64("1970-01-01T00:00:01")
     os.remove("hello.cdf")
 
@@ -380,7 +405,8 @@ def test_datetime64_conversion_odd_units():
     epoch = xr.Variable(epoch_dims, epoch_data)
     ds = xr.Dataset(data_vars={"data": data, "epoch": epoch})
     xarray_to_cdf(ds, "hello.cdf")
-    x = cdf_to_xarray("hello.cdf", to_datetime=True)
+    with CDF("hello.cdf") as cdf_file:
+        x = cdf_to_xarray(cdf_file, to_datetime=True)
     assert x["epoch"][1] == np.datetime64("2000-01-02")
     os.remove("hello.cdf")
 
@@ -397,6 +423,7 @@ def test_numpy_string_array():
     epoch = xr.Variable(epoch_dims, epoch_data)
     ds = xr.Dataset(data_vars={"data": data, "epoch": epoch})
     xarray_to_cdf(ds, "hello.cdf")
-    x = cdf_to_xarray("hello.cdf", to_datetime=True)
+    with CDF("hello.cdf") as cdf_file:
+        x = cdf_to_xarray(cdf_file, to_datetime=True)
     assert x["data"][2] == "c"
     os.remove("hello.cdf")