fre.cmor: replace nccmp subprocess calls with netCDF4 in cmor run subtool tests

fre/cmor/tests/test_cmor_run_subtool.py

@@ -9,6 +9,8 @@
 import subprocess
 import shutil
 
+import netCDF4
+import numpy as np
 import pytest
 
 from fre.cmor import cmor_run_subtool
@@ -57,6 +59,57 @@ def test_setup_cmor_cmip_table_repo():
 FULL_OUTPUTFILE = \
 f"{FULL_OUTPUTDIR}/sos_Omon_PCMDI-test-1-0_piControl-withism_r3i1p1f1_{GRID_LABEL}_{DATETIMES_INPUTFILE}.nc"
 
+# CMIP6-required global attributes that must be present in CMOR output
+CMIP6_REQUIRED_GLOBAL_ATTRS = [
+    'variable_id', 'mip_era', 'table_id',
+    'experiment_id', 'institution_id', 'source_id'
+]
+
+
+def _assert_data_matches(ds_in, ds_out):
+    '''
+    helper: assert that science variable data, coordinate data, and shapes
+    are preserved between input and CMOR output datasets.
+    '''
+    # the science variable data must be preserved exactly
+    assert np.array_equal(ds_in.variables['sos'][:], ds_out.variables['sos'][:]), \
+        "sos data values differ between input and CMOR output"
+
+    # coordinate data must be preserved
+    assert np.allclose(ds_in.variables['lat'][:], ds_out.variables['lat'][:]), \
+        "latitude data differs between input and CMOR output"
+    assert np.allclose(ds_in.variables['lon'][:], ds_out.variables['lon'][:]), \
+        "longitude data differs between input and CMOR output"
+    assert np.allclose(ds_in.variables['time'][:], ds_out.variables['time'][:]), \
+        "time data differs between input and CMOR output"
+
+    # variable shapes must be preserved
+    assert ds_in.variables['sos'][:].shape == ds_out.variables['sos'][:].shape, \
+        "sos data shape differs between input and CMOR output"
+
+
+def _assert_metadata_matches(ds_in, ds_out):
+    '''
+    helper: assert that CMIP6-required global attributes are present and that
+    key variable-level metadata is preserved between input and CMOR output datasets.
+    '''
+    # CMOR output must contain CMIP6-required global attributes
+    for required_attr in CMIP6_REQUIRED_GLOBAL_ATTRS:
+        assert required_attr in ds_out.ncattrs(), \
+            f"CMOR output missing required global attribute '{required_attr}'"
+
+    # science variable standard_name and long_name must be preserved
+    assert ds_in.variables['sos'].standard_name == ds_out.variables['sos'].standard_name, \
+        "sos standard_name differs between input and CMOR output"
+    assert ds_in.variables['sos'].long_name == ds_out.variables['sos'].long_name, \
+        "sos long_name differs between input and CMOR output"
+
+    # _FillValue and missing_value must be preserved
+    assert ds_in.variables['sos']._FillValue == ds_out.variables['sos']._FillValue, \
+        "sos _FillValue differs between input and CMOR output"
+    assert ds_in.variables['sos'].missing_value == ds_out.variables['sos'].missing_value, \
+        "sos missing_value differs between input and CMOR output"
+
 
 def test_setup_fre_cmor_run_subtool(capfd):
     '''
@@ -124,41 +177,27 @@ def test_fre_cmor_run_subtool_case1_output_compare_data(capfd):
     print(f'FULL_OUTPUTFILE={FULL_OUTPUTFILE}')
     print(f'FULL_INPUTFILE={FULL_INPUTFILE}')
 
-    nccmp_cmd= [ "nccmp", "-f", "-d",
-                 f"{FULL_INPUTFILE}",
-                 f"{FULL_OUTPUTFILE}"    ]
-    print(f"via subprocess, running {' '.join(nccmp_cmd)}")
-    result = subprocess.run( ' '.join(nccmp_cmd),
-                             shell=True,
-                             check=False,
-                             capture_output=True
-    )
+    with netCDF4.Dataset(FULL_INPUTFILE) as ds_in, \
+         netCDF4.Dataset(FULL_OUTPUTFILE) as ds_out:
+        # file formats should differ: CMOR converts input to NETCDF4_CLASSIC
+        assert ds_in.file_format != ds_out.file_format, \
+            f"expected file formats to differ, got input={ds_in.file_format}, output={ds_out.file_format}"
 
-    # err_list has length two if end in newline
-    err_list = result.stderr.decode().split('\n')
-    expected_err = \
-        "DIFFER : FILE FORMATS : NC_FORMAT_NETCDF4 <> NC_FORMAT_NETCDF4_CLASSIC"
-    assert all( [result.returncode == 1,
-                 len(err_list)==2,
-                 '' in err_list,
-                 expected_err in err_list ] )
+        _assert_data_matches(ds_in, ds_out)
     _out, _err = capfd.readouterr()
 
 def test_fre_cmor_run_subtool_case1_output_compare_metadata(capfd):
     ''' I/O metadata-only comparison of test case1 '''
     print(f'FULL_OUTPUTFILE={FULL_OUTPUTFILE}')
     print(f'FULL_INPUTFILE={FULL_INPUTFILE}')
 
-    nccmp_cmd= [ "nccmp", "-f", "-m", "-g",
-                 f"{FULL_INPUTFILE}",
-                 f"{FULL_OUTPUTFILE}"    ]
-    print(f"via subprocess, running {' '.join(nccmp_cmd)}")
-    result = subprocess.run( ' '.join(nccmp_cmd),
-                             shell=True,
-                             check=False
-                          )
+    with netCDF4.Dataset(FULL_INPUTFILE) as ds_in, \
+         netCDF4.Dataset(FULL_OUTPUTFILE) as ds_out:
+        # CMOR processing should add/change global attributes
+        assert set(ds_in.ncattrs()) != set(ds_out.ncattrs()), \
+            "expected global attributes to differ between input and CMOR output"
 
-    assert result.returncode == 1
+        _assert_metadata_matches(ds_in, ds_out)
     _out, _err = capfd.readouterr()
 
 
@@ -253,39 +292,27 @@ def test_fre_cmor_run_subtool_case2_output_compare_data(capfd):
     print(f'FULL_OUTPUTFILE={FULL_OUTPUTFILE}')
     print(f'FULL_INPUTFILE_DIFF={FULL_INPUTFILE_DIFF}')
 
-    nccmp_cmd= [ "nccmp", "-f", "-d",
-                 f"{FULL_INPUTFILE_DIFF}",
-                 f"{FULL_OUTPUTFILE}"    ]
-    print(f"via subprocess, running {' '.join(nccmp_cmd)}")
-    result = subprocess.run( ' '.join(nccmp_cmd),
-                             shell=True,
-                             check=False,
-                             capture_output=True
-                          )
-
-    err_list = result.stderr.decode().split('\n')#length two if end in newline
-    expected_err="DIFFER : FILE FORMATS : NC_FORMAT_NETCDF4 <> NC_FORMAT_NETCDF4_CLASSIC"
-    assert all( [result.returncode == 1,
-                 len(err_list)==2,
-                 '' in err_list,
-                 expected_err in err_list ] )
+    with netCDF4.Dataset(FULL_INPUTFILE_DIFF) as ds_in, \
+         netCDF4.Dataset(FULL_OUTPUTFILE) as ds_out:
+        # file formats should differ: CMOR converts input to NETCDF4_CLASSIC
+        assert ds_in.file_format != ds_out.file_format, \
+            f"expected file formats to differ, got input={ds_in.file_format}, output={ds_out.file_format}"
+
+        _assert_data_matches(ds_in, ds_out)
     _out, _err = capfd.readouterr()
 
 def test_fre_cmor_run_subtool_case2_output_compare_metadata(capfd):
     ''' I/O metadata-only comparison of test case2 '''
     print(f'FULL_OUTPUTFILE={FULL_OUTPUTFILE}')
     print(f'FULL_INPUTFILE_DIFF={FULL_INPUTFILE_DIFF}')
 
-    nccmp_cmd= [ "nccmp", "-f", "-m", "-g",
-                 f"{FULL_INPUTFILE_DIFF}",
-                 f"{FULL_OUTPUTFILE}"    ]
-    print(f"via subprocess, running {' '.join(nccmp_cmd)}")
-    result = subprocess.run( ' '.join(nccmp_cmd),
-                             shell=True,
-                             check=False
-                          )
+    with netCDF4.Dataset(FULL_INPUTFILE_DIFF) as ds_in, \
+         netCDF4.Dataset(FULL_OUTPUTFILE) as ds_out:
+        # CMOR processing should add/change global attributes
+        assert set(ds_in.ncattrs()) != set(ds_out.ncattrs()), \
+            "expected global attributes to differ between input and CMOR output"
 
-    assert result.returncode == 1
+        _assert_metadata_matches(ds_in, ds_out)
     _out, _err = capfd.readouterr()
 
 def test_git_cleanup():

fre/tests/test_files/CMOR_input_example.json

@@ -44,4 +44,4 @@
     "#output_path_template": "Template for output path directory using tables keys or global attributes, these should follow the relevant data reference syntax",
     "output_path_template": "<mip_era><activity_id><institution_id><source_id><experiment_id><_member_id><table><variable_id><grid_label><version>",
     "output_file_template": "<variable_id><table><source_id><experiment_id><_member_id><grid_label>"
-}
+}