Refactor test paths

tests/test_pyglider.py

@@ -1,28 +1,24 @@
-from pathlib import Path
-
 import numpy as np
 import pytest
 import xarray as xr
 import yaml
 
 import pyglider.seaexplorer as seaexplorer
-
-library_dir = Path(__file__).parent.parent.absolute()
-example_dir = library_dir / 'tests/example-data/'
+from tests.utils import EXAMPLE_DIR, LIBRARY_DIR
 
 # Create an L0 timeseries from seaexplorer data and test that the resulting netcdf
 # is identical to the test data
-rawdir = str(example_dir / 'example-seaexplorer/realtime_raw/') + '/'
-rawncdir = str(example_dir / 'example-seaexplorer/realtime_rawnc/') + '/'
-deploymentyaml = str(example_dir / 'example-seaexplorer/deploymentRealtime.yml')
-l0tsdir = str(example_dir / 'example-seaexplorer/L0-timeseries-test/') + '/'
+rawdir = str(EXAMPLE_DIR / 'example-seaexplorer/realtime_raw/') + '/'
+rawncdir = str(EXAMPLE_DIR / 'example-seaexplorer/realtime_rawnc/') + '/'
+deploymentyaml = str(EXAMPLE_DIR / 'example-seaexplorer/deploymentRealtime.yml')
+l0tsdir = str(EXAMPLE_DIR / 'example-seaexplorer/L0-timeseries-test/') + '/'
 seaexplorer.raw_to_rawnc(rawdir, rawncdir, deploymentyaml)
 seaexplorer.merge_parquet(rawncdir, rawncdir, deploymentyaml, kind='sub')
 outname = seaexplorer.raw_to_L0timeseries(rawncdir, l0tsdir, deploymentyaml, kind='sub')
 output = xr.open_dataset(outname)
 # Open test data file
 test_data = xr.open_dataset(
-    library_dir
+    LIBRARY_DIR
     / 'tests/expected/example-seaexplorer/L0-timeseries/dfo-eva035-20190718.nc'
 )
 variables = list(output.variables)
@@ -61,12 +57,12 @@ def test_example_seaexplorer_metadata():
 # Test that interpolation over nans does not change the output with nrt data
 with open(deploymentyaml) as fin:
     deployment = yaml.safe_load(fin)
-interp_yaml = str(example_dir / 'example-seaexplorer/deploymentRealtimeInterp.yml')
+interp_yaml = str(EXAMPLE_DIR / 'example-seaexplorer/deploymentRealtimeInterp.yml')
 deployment['netcdf_variables']['interpolate'] = True
 with open(interp_yaml, 'w') as fout:
     yaml.dump(deployment, fout)
 l0tsdir_interp = (
-    str(example_dir / 'example-seaexplorer/L0-timeseries-test-interp/') + '/'
+    str(EXAMPLE_DIR / 'example-seaexplorer/L0-timeseries-test-interp/') + '/'
 )
 
 outname_interp = seaexplorer.raw_to_L0timeseries(
@@ -91,10 +87,10 @@ def test_example_seaexplorer_interp_nrt(var):
 
 
 # Test raw (full resolution) seaexplorer data.
-rawdir = str(example_dir / 'example-seaexplorer-raw/delayed_raw/') + '/'
-rawncdir = str(example_dir / 'example-seaexplorer-raw/delayed_rawnc/') + '/'
-deploymentyaml_raw = str(example_dir / 'example-seaexplorer-raw/deployment.yml')
-l0tsdir = str(example_dir / 'example-seaexplorer-raw/L0-timeseries-test/') + '/'
+rawdir = str(EXAMPLE_DIR / 'example-seaexplorer-raw/delayed_raw/') + '/'
+rawncdir = str(EXAMPLE_DIR / 'example-seaexplorer-raw/delayed_rawnc/') + '/'
+deploymentyaml_raw = str(EXAMPLE_DIR / 'example-seaexplorer-raw/deployment.yml')
+l0tsdir = str(EXAMPLE_DIR / 'example-seaexplorer-raw/L0-timeseries-test/') + '/'
 seaexplorer.raw_to_rawnc(rawdir, rawncdir, deploymentyaml_raw)
 seaexplorer.merge_parquet(rawncdir, rawncdir, deploymentyaml_raw, kind='raw')
 outname_raw = seaexplorer.raw_to_L0timeseries(
@@ -103,7 +99,7 @@ def test_example_seaexplorer_interp_nrt(var):
 output_raw = xr.open_dataset(outname_raw)
 # Open test data file
 test_data_raw = xr.open_dataset(
-    library_dir
+    LIBRARY_DIR
     / 'tests/expected/example-seaexplorer-raw/L0-timeseries/dfo-bb046-20200908.nc'
 )
 
@@ -138,12 +134,12 @@ def test_example_seaexplorer_metadata_raw():
 # Test that interpolation over nans in raw data results in a greater or equal number of non-nan values
 with open(deploymentyaml_raw) as fin:
     deployment_raw = yaml.safe_load(fin)
-interp_yaml = str(example_dir / 'example-seaexplorer-raw/deploymentDelayedInterp.yml')
+interp_yaml = str(EXAMPLE_DIR / 'example-seaexplorer-raw/deploymentDelayedInterp.yml')
 deployment_raw['netcdf_variables']['interpolate'] = True
 with open(interp_yaml, 'w') as fout:
     yaml.dump(deployment_raw, fout)
 l0tsdir_interp_raw = (
-    str(example_dir / 'example-seaexplorer-raw/L0-timeseries-test-interp/') + '/'
+    str(EXAMPLE_DIR / 'example-seaexplorer-raw/L0-timeseries-test-interp/') + '/'
 )
 
 outname_interp_raw = seaexplorer.raw_to_L0timeseries(

tests/test_seaexplorer.py

@@ -1,16 +1,14 @@
 import os
-from pathlib import Path
 
 import numpy as np
 import polars as pl
 import pytest
 import yaml
 
 os.system('rm tests/data/realtime_rawnc/*')
-library_dir = Path(__file__).parent.parent.absolute()
-example_dir = library_dir / 'tests/example-data/'
 
 import pyglider.seaexplorer as seaexplorer
+from tests.utils import EXAMPLE_DIR
 
 
 def test__outputname():
@@ -67,13 +65,13 @@ def test_merge_rawnc():
     result_default = seaexplorer.merge_parquet(
         'tests/data/realtime_rawnc/',
         'tests/data/realtime_rawnc/',
-        str(example_dir / 'example-seaexplorer/deploymentRealtime.yml'),
+        str(EXAMPLE_DIR / 'example-seaexplorer/deploymentRealtime.yml'),
     )
 
     result_sub = seaexplorer.merge_parquet(
         'tests/data/realtime_rawnc/',
         'tests/data/realtime_rawnc/',
-        str(example_dir / 'example-seaexplorer/deploymentRealtime.yml'),
+        str(EXAMPLE_DIR / 'example-seaexplorer/deploymentRealtime.yml'),
         kind='sub',
     )
     assert result_default is False
@@ -107,12 +105,12 @@ def test_raw_to_timeseries():
         result_default = seaexplorer.raw_to_timeseries(
             'tests/data/realtime_rawnc/',
             'tests/data/l0-profiles/',
-            str(example_dir / 'example-seaexplorer/deploymentRealtime.yml'),
+            str(EXAMPLE_DIR / 'example-seaexplorer/deploymentRealtime.yml'),
         )
     result_sub = seaexplorer.raw_to_timeseries(
         'tests/data/realtime_rawnc/',
         'tests/data/l0-profiles/',
-        str(example_dir / 'example-seaexplorer/deploymentRealtime.yml'),
+        str(EXAMPLE_DIR / 'example-seaexplorer/deploymentRealtime.yml'),
         kind='sub',
     )
     assert 'No such file or directory' in str(missing_file_exc)
@@ -121,26 +119,26 @@ def test_raw_to_timeseries():
 
 def test_missing_bad_timebase():
     # Prepare yaml files with bad timebase and no timebase
-    with open(example_dir / 'example-seaexplorer/deploymentRealtime.yml') as fin:
+    with open(EXAMPLE_DIR / 'example-seaexplorer/deploymentRealtime.yml') as fin:
         deployment = yaml.safe_load(fin)
     deployment['netcdf_variables']['timebase']['source'] = 'non existing sensor'
-    with open(example_dir / 'example-seaexplorer/bad_timebase.yml', 'w') as fin:
+    with open(EXAMPLE_DIR / 'example-seaexplorer/bad_timebase.yml', 'w') as fin:
         yaml.dump(deployment, fin)
     deployment['netcdf_variables'].pop('timebase')
-    with open(example_dir / 'example-seaexplorer/no_timebase.yml', 'w') as fin:
+    with open(EXAMPLE_DIR / 'example-seaexplorer/no_timebase.yml', 'w') as fin:
         yaml.dump(deployment, fin)
     with pytest.raises(ValueError) as bad_timebase_exc:
         result_bad_timebase = seaexplorer.raw_to_timeseries(
             'tests/data/realtime_rawnc/',
             'tests/data/l0-profiles/',
-            str(example_dir / 'example-seaexplorer/bad_timebase.yml'),
+            str(EXAMPLE_DIR / 'example-seaexplorer/bad_timebase.yml'),
             kind='sub',
         )
     with pytest.raises(ValueError) as no_timebase_exc:
         result_no_timebase = seaexplorer.raw_to_timeseries(
             'tests/data/realtime_rawnc/',
             'tests/data/l0-profiles/',
-            str(example_dir / 'example-seaexplorer/no_timebase.yml'),
+            str(EXAMPLE_DIR / 'example-seaexplorer/no_timebase.yml'),
             kind='sub',
         )
     assert 'sensor not found in pld1 columns' in str(bad_timebase_exc)

tests/test_slocum.py

@@ -1,5 +1,4 @@
 import json
-from pathlib import Path
 
 import numpy as np
 import pytest
@@ -8,21 +7,19 @@
 
 import pyglider.ncprocess as ncprocess
 import pyglider.slocum as slocum
-
-library_dir = Path(__file__).parent.parent.absolute()
-example_dir = library_dir / 'tests/example-data/'
+from tests.utils import EXAMPLE_DIR, LIBRARY_DIR
 
 # Create an L0 timeseries from slocum data and test that the resulting netcdf is
 # identical to the test data
-cacdir = example_dir / 'example-slocum/cac/'
-sensorlist = str(example_dir / 'example-slocum/dfo-rosie713_sensors.txt')
-binarydir = str(example_dir / 'example-slocum/realtime_raw/') + '/'
-rawdir_slocum = str(example_dir / 'example-slocum/realtime_rawnc/') + '/'
-deploymentyaml_slocum = str(example_dir / 'example-slocum/deploymentRealtime.yml')
-tsdir = str(example_dir / 'example-slocum/L0-timeseries/') + '/'
+cacdir = EXAMPLE_DIR / 'example-slocum/cac/'
+sensorlist = str(EXAMPLE_DIR / 'example-slocum/dfo-rosie713_sensors.txt')
+binarydir = str(EXAMPLE_DIR / 'example-slocum/realtime_raw/') + '/'
+rawdir_slocum = str(EXAMPLE_DIR / 'example-slocum/realtime_rawnc/') + '/'
+deploymentyaml_slocum = str(EXAMPLE_DIR / 'example-slocum/deploymentRealtime.yml')
+tsdir = str(EXAMPLE_DIR / 'example-slocum/L0-timeseries/') + '/'
 scisuffix = 'tbd'
 glidersuffix = 'sbd'
-profiledir = str(example_dir / 'example-slocum/L0-profiles/')
+profiledir = str(EXAMPLE_DIR / 'example-slocum/L0-profiles/')
 do_direct = True
 
 # This needs to get run every time the tests are run, so do at top level:
@@ -45,7 +42,7 @@
 output_slocum = xr.open_dataset(outname_slocum)
 # Open test data file
 test_data_slocum = xr.open_dataset(
-    library_dir / 'tests/expected/example-slocum/L0-timeseries/dfo-rosie713-20190615.nc'
+    LIBRARY_DIR / 'tests/expected/example-slocum/L0-timeseries/dfo-rosie713-20190615.nc'
 )
 variables_slocum = list(output_slocum.variables)
 
@@ -95,7 +92,7 @@ def test_profiles_compliant():
     checker_names = ['gliderdac', 'cf:1.8']
     verbose = 0
     criteria = 'normal'
-    output_filename = example_dir / 'report.json'
+    output_filename = EXAMPLE_DIR / 'report.json'
     output_format = 'json'
     """
     Inputs to ComplianceChecker.run_checker
@@ -139,7 +136,7 @@ def test_timeseries_compliant():
     checker_names = ['cf:1.8']
     verbose = 0
     criteria = 'normal'
-    output_filename = example_dir / 'report.json'
+    output_filename = EXAMPLE_DIR / 'report.json'
     output_format = 'json'
     """
     Inputs to ComplianceChecker.run_checker

tests/test_utils.py

@@ -1,21 +1,17 @@
-from pathlib import Path
-
 import numpy as np
 import pytest
 import xarray as xr
 import yaml
 
 import pyglider.utils as utils
-
-library_dir = Path(__file__).parent.parent.absolute()
-example_dir = library_dir / 'tests/example-data/'
+from tests.utils import EXAMPLE_DIR, LIBRARY_DIR
 
 test_data = xr.open_dataset(
-    library_dir
+    LIBRARY_DIR
     / 'tests/expected/example-seaexplorer/L0-timeseries/dfo-eva035-20190718.nc'
 )
 deploymentyaml = (
-    example_dir / 'example-seaexplorer-legato-flntu-arod-ad2cp/deploymentRealtime.yml'
+    EXAMPLE_DIR / 'example-seaexplorer-legato-flntu-arod-ad2cp/deploymentRealtime.yml'
 )
 with open(deploymentyaml) as fin:
     deployment = yaml.safe_load(fin)

tests/utils.py

@@ -0,0 +1,6 @@
+"""Utilities specific to the test suite."""
+
+from pathlib import Path
+
+LIBRARY_DIR = Path(__file__).parent.parent.absolute()
+EXAMPLE_DIR = LIBRARY_DIR / 'tests/example-data/'