Merge pull request #135 from ocefpaf/future_proof

Future proof pocean core by fixing all warnings and future deprecations

.github/workflows/tests.yml

@@ -40,4 +40,4 @@ jobs:
     - name: Tests
       run: >
         python pocean/tests/download_test_data.py
-        && python -m pytest --disable-warnings
+        && python -m pytest --pyargs pocean

pocean/cf.py

@@ -1,13 +1,15 @@
 #!python
+import datetime
 import itertools
 import os
 import re
-from datetime import datetime
 
 from . import logger
 from .dataset import EnhancedDataset
 from .utils import all_subclasses, is_url
 
+datetime.UTC = datetime.timezone.utc
+
 
 class CFDataset(EnhancedDataset):
     default_fill_value = False
@@ -182,7 +184,7 @@ def nc_attributes(self):
         return {
             "global": {
                 "Conventions": "CF-1.6",
-                "date_created": datetime.utcnow().strftime("%Y-%m-%dT%H:%M:00Z"),
+                "date_created": datetime.datetime.now(datetime.UTC).strftime("%Y-%m-%dT%H:%M:00Z"),
             }
         }
 

pocean/dsg/profile/om.py

@@ -1,4 +1,3 @@
-#!python
 from collections import OrderedDict
 from copy import copy
 

pocean/dsg/utils.py

@@ -1,6 +1,4 @@
-#!python
-
-from datetime import datetime
+import datetime
 
 import pandas as pd
 from shapely.geometry import (
@@ -14,6 +12,8 @@
 from pocean import logger as L  # noqa
 from pocean.utils import dict_update, get_default_axes, unique_justseen
 
+datetime.UTC = datetime.timezone.utc
+
 
 def get_calculated_attributes(df, axes=None, history=None):
     """Functions to automate netCDF attribute generation from the data itself
@@ -187,7 +187,7 @@ def get_creation_attributes(history=None):
     :param history: text initializing audit trail for modifications to the original data (optional, string)
     :return: dictionary of global attributes
     """
-    nc_create_ts = datetime.utcnow().strftime("%Y-%m-%dT%H:%M:%SZ")
+    nc_create_ts = datetime.datetime.now(datetime.UTC).strftime("%Y-%m-%dT%H:%M:%SZ")
 
     attrs = {
         "attributes": {

pocean/tests/download_test_data.py

@@ -6,11 +6,11 @@
 
 def download_test_data():
     url = "https://github.com/pyoceans/pocean-core/releases/download"
-    version = "2024.04"
+    version = "2025.01"
 
     fname = pooch.retrieve(
         url=f"{url}/{version}/test_data.zip",
-        known_hash="sha256:28be36e8e0ec90a8faf5ee3f4d52638bdeb2cbcbeac8c823de680cf84aa34940",
+        known_hash="sha256:41180c6bc6017de935250c9e8c1bbb407507049baebd767692c4f74fb8d662a8",
     )
 
     here = Path(__file__).resolve().parent

pocean/tests/dsg/profile/test_profile_om.py

@@ -1,4 +1,3 @@
-#!python
 import logging
 import os
 import tempfile

pocean/tests/dsg/test_utils.py

@@ -1,16 +1,22 @@
 #!python
+import datetime
 import os
 import unittest
-from datetime import datetime, timedelta
 
 import pandas as pd
+import pytest
 import pytz
 from dateutil.parser import parse as dtparse
 
 from pocean import logger as L  # noqa
 from pocean.cf import CFDataset
 from pocean.dsg import utils
 
+datetime.UTC = datetime.timezone.utc
+
+# RuntimeWarning: invalid value encountered in cast is fine here.
+ignore_invalid_value_cast = pytest.mark.filterwarnings("ignore::RuntimeWarning")
+
 
 class TestDsgUtils(unittest.TestCase):
     geo = pd.DataFrame({"x": [-1, -2, -3, -4], "y": [1, 2, 3, 4]})
@@ -139,13 +145,14 @@ def test_get_temporal_meta_from_times(self):
     def test_get_creation(self):
         meta = utils.get_creation_attributes(history="DID THINGS")
 
-        now = datetime.utcnow().replace(tzinfo=pytz.utc)
+        now = datetime.datetime.now(datetime.UTC).replace(tzinfo=pytz.utc)
 
-        assert (now - dtparse(meta["attributes"]["date_created"])) < timedelta(minutes=1)
-        assert (now - dtparse(meta["attributes"]["date_issued"])) < timedelta(minutes=1)
-        assert (now - dtparse(meta["attributes"]["date_modified"])) < timedelta(minutes=1)
+        assert (now - dtparse(meta["attributes"]["date_created"])) < datetime.timedelta(minutes=1)
+        assert (now - dtparse(meta["attributes"]["date_issued"])) < datetime.timedelta(minutes=1)
+        assert (now - dtparse(meta["attributes"]["date_modified"])) < datetime.timedelta(minutes=1)
         assert "DID THINGS" in meta["attributes"]["history"]
 
+    @ignore_invalid_value_cast
     def test_wrap_dateline(self):
         ncfile = os.path.join(
             os.path.dirname(os.path.dirname(__file__)), "resources/wrapping_dateline.nc"

pocean/tests/dsg/timeseries/test_timeseries_om.py

@@ -5,11 +5,15 @@
 import unittest
 
 import numpy as np
+import pytest
 
 from pocean import logger
 from pocean.dsg import OrthogonalMultidimensionalTimeseries
 from pocean.tests.dsg.test_new import test_is_mine
 
+# RuntimeWarning: invalid value encountered in cast is fine here.
+ignore_invalid_value_cast = pytest.mark.filterwarnings("ignore::RuntimeWarning")
+
 logger.level = logging.INFO
 logger.handlers = [logging.StreamHandler()]
 
@@ -51,6 +55,7 @@ def test_omp_load(self):
         OrthogonalMultidimensionalTimeseries(self.single).close()
         OrthogonalMultidimensionalTimeseries(self.multi).close()
 
+    @ignore_invalid_value_cast
     def test_timeseries_omt_dataframe_single(self):
         fid, single_tmp = tempfile.mkstemp(suffix=".nc")
         with OrthogonalMultidimensionalTimeseries(self.single) as s:
@@ -76,6 +81,7 @@ def test_timeseries_omt_dataframe_multi(self):
         os.close(fid)
         os.remove(single_tmp)
 
+    @ignore_invalid_value_cast
     def test_timeseries_omt_dataframe_unique_dims(self):
         fid, single_tmp = tempfile.mkstemp(suffix=".nc")
         with OrthogonalMultidimensionalTimeseries(self.single) as s:
@@ -89,6 +95,7 @@ def test_timeseries_omt_dataframe_unique_dims(self):
         os.close(fid)
         os.remove(single_tmp)
 
+    @ignore_invalid_value_cast
     def test_timeseries_omt_reduce_dims(self):
         fid, single_tmp = tempfile.mkstemp(suffix=".nc")
         with OrthogonalMultidimensionalTimeseries(self.single) as s:
@@ -102,6 +109,7 @@ def test_timeseries_omt_reduce_dims(self):
         os.close(fid)
         os.remove(single_tmp)
 
+    @ignore_invalid_value_cast
     def test_timeseries_omt_no_z(self):
         fid, single_tmp = tempfile.mkstemp(suffix=".nc")
         with OrthogonalMultidimensionalTimeseries(self.single) as s:
@@ -120,6 +128,7 @@ def test_timeseries_omt_no_z(self):
         os.close(fid)
         os.remove(single_tmp)
 
+    @ignore_invalid_value_cast
     def test_timeseries_omt_no_z_no_station(self):
         fid, single_tmp = tempfile.mkstemp(suffix=".nc")
         with OrthogonalMultidimensionalTimeseries(self.single) as s:
@@ -136,6 +145,7 @@ def test_timeseries_omt_no_z_no_station(self):
         os.close(fid)
         os.remove(single_tmp)
 
+    @ignore_invalid_value_cast
     def test_supplying_attributes(self):
         fid, single_tmp = tempfile.mkstemp(suffix=".nc")
 

pocean/tests/dsg/timeseriesProfile/test_timeseriesProfile_om.py

@@ -6,6 +6,7 @@
 
 import numpy as np
 import pandas as pd
+import pytest
 
 from pocean import logger
 from pocean.dsg import OrthogonalMultidimensionalTimeseriesProfile
@@ -14,6 +15,9 @@
 logger.level = logging.INFO
 logger.handlers = [logging.StreamHandler()]
 
+# RuntimeWarning: invalid value encountered in cast is fine here.
+ignore_invalid_value_cast = pytest.mark.filterwarnings("ignore::RuntimeWarning")
+
 
 class TestOrthogonalMultidimensionalTimeseriesProfile(unittest.TestCase):
     def test_omtp_multi(self):
@@ -237,6 +241,7 @@ def test_detach_z_with_station(self):
         os.close(fid)
         os.remove(tmpfile)
 
+    @ignore_invalid_value_cast
     def test_detach_z_no_station(self):
         df = pd.DataFrame(
             {

pocean/tests/dsg/timeseriesProfile/test_timeseriesProfile_r.py

@@ -1,4 +1,3 @@
-#!python
 import logging
 import os
 import tempfile
@@ -7,6 +6,7 @@
 
 import netCDF4 as nc4
 import pandas as pd
+import pytest
 from numpy.testing import assert_array_equal as npeq
 
 from pocean import logger
@@ -17,6 +17,9 @@
 logger.level = logging.INFO
 logger.handlers = [logging.StreamHandler()]
 
+# RuntimeWarning: invalid value encountered in cast is fine here.
+ignore_invalid_value_cast = pytest.mark.filterwarnings("ignore::RuntimeWarning")
+
 
 class TestRaggedTimeseriesProfile(unittest.TestCase):
     def test_csv_to_nc_single(self):
@@ -179,6 +182,7 @@ def test_csv_to_nc_single_reduce(self):
         os.close(fid)
         os.remove(tmpfile)
 
+    @ignore_invalid_value_cast
     def test_rtp_single(self):
         filepath = os.path.join(os.path.dirname(__file__), "resources", "r-ctd-single.nc")
 

pocean/tests/dsg/trajectory/test_trajectory_cr.py

@@ -15,6 +15,9 @@
 logger.level = logging.INFO
 logger.handlers = [logging.StreamHandler()]
 
+# RuntimeWarning: invalid value encountered in cast is fine here.
+ignore_invalid_value_cast = pytest.mark.filterwarnings("ignore::RuntimeWarning")
+
 
 @pytest.mark.parametrize(
     "fp",
@@ -89,6 +92,7 @@ def test_crt_dataframe_unlimited_dim(self):
         os.close(fid)
         os.remove(tmpnc)
 
+    @ignore_invalid_value_cast
     def test_crt_dataframe_oot_A(self):
         axes = {"t": "time", "x": "lon", "y": "lat", "z": "depth", "sample": "sample"}
         fid, tmpnc = tempfile.mkstemp(suffix=".nc")
@@ -113,6 +117,7 @@ def test_crt_dataframe_oot_A(self):
         os.close(fid)
         os.remove(tmpnc)
 
+    @ignore_invalid_value_cast
     def test_crt_dataframe_oot_B(self):
         axes = {
             "t": "time",

pocean/tests/dsg/trajectory/test_trajectory_im.py

@@ -5,6 +5,7 @@
 import unittest
 
 import numpy as np
+import pytest
 from dateutil.parser import parse as dtparse
 
 from pocean import logger
@@ -15,8 +16,12 @@
 logger.level = logging.INFO
 logger.handlers = [logging.StreamHandler()]
 
+# RuntimeWarning: invalid value encountered in cast is fine here.
+ignore_invalid_value_cast = pytest.mark.filterwarnings("ignore::RuntimeWarning")
+
 
 class TestIncompleteMultidimensionalTrajectory(unittest.TestCase):
+    @ignore_invalid_value_cast
     def test_im_single_row(self):
         filepath = os.path.join(os.path.dirname(__file__), "resources", "im-singlerow.nc")
 
@@ -75,6 +80,7 @@ def test_imt_multi(self):
             os.close(fid)
             os.remove(tmpfile)
 
+    @ignore_invalid_value_cast
     def test_imt_multi_not_string(self):
         filepath = os.path.join(os.path.dirname(__file__), "resources", "im-multiple-nonstring.nc")
 

pocean/tests/dsg/trajectoryProfile/test_trajectoryProfile_cr.py

@@ -5,6 +5,7 @@
 import unittest
 
 import numpy as np
+import pytest
 from dateutil.parser import parse as dtparse
 from shapely.wkt import loads as wktloads
 
@@ -15,6 +16,9 @@
 L.level = logging.INFO
 L.handlers = [logging.StreamHandler()]
 
+# RuntimeWarning: invalid value encountered in cast is fine here.
+ignore_invalid_value_cast = pytest.mark.filterwarnings("ignore::RuntimeWarning")
+
 
 class TestContinousRaggedTrajectoryProfile(unittest.TestCase):
     def setUp(self):
@@ -32,6 +36,7 @@ def test_crtp_load(self):
         ContiguousRaggedTrajectoryProfile(self.multi).close()
         ContiguousRaggedTrajectoryProfile(self.missing_time).close()
 
+    @ignore_invalid_value_cast
     def test_crtp_dataframe_single(self):
         axes = {
             "t": "time",
@@ -51,6 +56,7 @@ def test_crtp_dataframe_single(self):
         os.close(fid)
         os.remove(tmpnc)
 
+    @ignore_invalid_value_cast
     def test_crtp_dataframe_single_unique_dims(self):
         axes = {
             "t": "time",
@@ -89,6 +95,7 @@ def test_crtp_dataframe_multi(self):
         os.close(fid)
         os.remove(tmpnc)
 
+    @ignore_invalid_value_cast
     def test_crtp_dataframe_missing_time(self):
         axes = {
             "t": "precise_time",
@@ -108,6 +115,7 @@ def test_crtp_dataframe_missing_time(self):
         os.close(fid)
         os.remove(tmpnc)
 
+    @ignore_invalid_value_cast
     def test_crtp_calculated_metadata_single(self):
         axes = {
             "t": "time",
@@ -173,6 +181,7 @@ def test_crtp_calculated_metadata_multi(self):
             assert traj4.profiles[19].x == -44
             assert traj4.profiles[19].y == 47
 
+    @ignore_invalid_value_cast
     def test_crtp_calculated_metadata_missing_time(self):
         axes = {
             "t": "time",
@@ -199,6 +208,7 @@ def test_crtp_calculated_metadata_missing_time(self):
             assert np.isclose(first_loc[1], 43.5022166666667)
             assert len(traj.profiles) == 13
 
+    @ignore_invalid_value_cast
     def test_crtp_just_missing_time(self):
         axes = {
             "t": "time",
@@ -224,6 +234,7 @@ def test_crtp_just_missing_time(self):
             assert np.isclose(first_loc[1], 43.5022166666667)
             assert len(traj.profiles) == 13
 
+    @ignore_invalid_value_cast
     def test_crtp_just_missing_locations(self):
         axes = {
             "t": "time",