DAS-2389 - Update python version to 3.12

.pre-commit-config.yaml

@@ -19,4 +19,4 @@ repos:
     hooks:
       - id: black-jupyter
         args: ["--skip-string-normalization"]
-        language_version: python3.11
+        language_version: python3.12

.snyk

@@ -0,0 +1,4 @@
+# Snyk (https://snyk.io) policy file, patches or ignores known vulnerabilities.
+version: v1.25.0
+language-settings:
+  python: "3.12"

CHANGELOG.md

@@ -1,5 +1,11 @@
+## v1.2.0
+### 2025-08-21
+
+This version of HOSS updates the consa environment to support Python 3.12. This also updates the
+dependent packages to their latest supportable versions. Also updates harmony library version.
+
 ## v1.1.9
-### 2025-08-013
+### 2025-08-13
 
 This version of HOSS updates fixes invalid output extents in cases where the
 requested bounding area (bbox, shape) extends beyond valid locations for the native

conda_requirements.txt

@@ -1,2 +1,2 @@
 # This file should contain any requirements installed via Conda
-hdf5==1.12.0
+hdf5==1.14.6

docker/service.Dockerfile

@@ -24,9 +24,8 @@ WORKDIR "/home"
 COPY ./conda_requirements.txt conda_requirements.txt
 
 # Create Conda environment
-RUN conda create -y --name hoss --file conda_requirements.txt python=3.11 -q \
-	--channel conda-forge \
-	--override-channels
+RUN conda config --remove channels defaults
+RUN conda create -y --name hoss --file conda_requirements.txt python=3.12 -q --channel conda-forge --override-channels
 
 # Copy additional Pip dependencies into the container
 COPY ./pip_requirements.txt pip_requirements.txt

docker/service_version.txt

@@ -1 +1 @@
-1.1.9
+1.2.0

hoss/__main__.py

@@ -3,7 +3,7 @@
 from argparse import ArgumentParser
 from sys import argv
 
-from harmony import is_harmony_cli, run_cli, setup_cli
+from harmony_service_lib import is_harmony_cli, run_cli, setup_cli
 
 from hoss.adapter import HossAdapter
 

hoss/adapter.py

@@ -28,9 +28,9 @@
 import shutil
 from tempfile import mkdtemp
 
-from harmony import BaseHarmonyAdapter
-from harmony.message import Source
-from harmony.util import HarmonyException, generate_output_filename, stage
+from harmony_service_lib import BaseHarmonyAdapter
+from harmony_service_lib.message import Source
+from harmony_service_lib.util import HarmonyException, generate_output_filename, stage
 from pystac import Asset, Item
 
 from hoss.dimension_utilities import is_index_subset

hoss/bbox_utilities.py

@@ -20,8 +20,8 @@
 from typing import Dict, List, Optional, Tuple, Union
 
 import numpy as np
-from harmony.message import Message
-from harmony.util import Config, download
+from harmony_service_lib.message import Message
+from harmony_service_lib.util import Config, download
 
 from hoss.exceptions import InvalidInputGeoJSON, UnsupportedShapeFileFormat
 

hoss/dimension_utilities.py

@@ -15,9 +15,9 @@
 from typing import Dict, Set, Tuple
 
 import numpy as np
-from harmony.message import Message
-from harmony.message_utility import rgetattr
-from harmony.util import Config
+from harmony_service_lib.message import Message
+from harmony_service_lib.message_utility import rgetattr
+from harmony_service_lib.util import Config
 from netCDF4 import Dataset
 from numpy.ma.core import MaskedArray
 from varinfo import VariableFromDmr, VarInfoFromDmr

hoss/spatial.py

@@ -24,7 +24,7 @@
 
 from typing import List, Set
 
-from harmony.message import Message
+from harmony_service_lib.message import Message
 from netCDF4 import Dataset
 from numpy.ma.core import MaskedArray
 from varinfo import VariableFromDmr, VarInfoFromDmr

hoss/subset.py

@@ -8,10 +8,10 @@
 from logging import Logger
 from typing import List, Set
 
-from harmony.message import Message, Source
-from harmony.message import Variable as HarmonyVariable
-from harmony.message_utility import rgetattr
-from harmony.util import Config
+from harmony_service_lib.message import Message, Source
+from harmony_service_lib.message import Variable as HarmonyVariable
+from harmony_service_lib.message_utility import rgetattr
+from harmony_service_lib.util import Config
 from netCDF4 import Dataset
 from numpy.ma import masked
 from varinfo import VarInfoFromDmr

hoss/temporal.py

@@ -12,7 +12,7 @@
 from typing import List, Set
 
 from dateutil.parser import parse as parse_datetime
-from harmony.message import Message
+from harmony_service_lib.message import Message
 from netCDF4 import Dataset
 from varinfo import VarInfoFromDmr
 

hoss/utilities.py

@@ -13,9 +13,9 @@
 from urllib.parse import quote
 from uuid import uuid4
 
-from harmony.exceptions import ForbiddenException, ServerException
-from harmony.util import Config
-from harmony.util import download as util_download
+from harmony_service_lib.exceptions import ForbiddenException, ServerException
+from harmony_service_lib.util import Config
+from harmony_service_lib.util import download as util_download
 
 from hoss.exceptions import UrlAccessFailed
 

pip_requirements.txt

@@ -1,8 +1,8 @@
 # This file should contain requirements to be installed via Pip.
 # Open source packages available from PyPI
-earthdata-varinfo ~= 3.0.1
-harmony-service-lib ~= 1.0.25
-netCDF4 ~= 1.6.4
-numpy ~= 1.24.2
-pyproj ~= 3.6.1
-shapely ~= 2.0.1
+earthdata-varinfo ~= 3.1.0
+harmony-service-lib ~= 2.7.0
+netCDF4 ~= 1.7.2
+numpy ~= 2.2.6
+pyproj ~= 3.7.1
+shapely ~= 2.1.1

tests/pip_test_requirements.txt

@@ -1,5 +1,6 @@
-coverage~=7.2.2
-pre-commit~=3.7.0
-pycodestyle~=2.10.0
-pylint~=2.17.2
+coverage~=7.9.2
+pre-commit~=4.2.0
+pycodestyle~=2.14.0
+pylint ~= 3.3.7
+astroid ~= 3.3.10
 unittest-xml-reporting~=3.2.0

tests/test_adapter.py

@@ -12,8 +12,8 @@
 from unittest import TestCase
 from unittest.mock import ANY, Mock, call, patch
 
-from harmony.message import Message
-from harmony.util import HarmonyException, config
+from harmony_service_lib.message import Message
+from harmony_service_lib.util import HarmonyException, config
 from netCDF4 import Dataset
 from numpy.testing import assert_array_equal
 from pystac import Catalog

tests/unit/test_adapter.py

@@ -3,8 +3,8 @@
 from unittest import TestCase
 from unittest.mock import ANY, patch
 
-from harmony.message import Message
-from harmony.util import config
+from harmony_service_lib.message import Message
+from harmony_service_lib.util import config
 
 from hoss.adapter import HossAdapter
 from hoss.bbox_utilities import BBox

tests/unit/test_bbox_utilities.py

@@ -13,8 +13,8 @@
 from unittest import TestCase
 from unittest.mock import patch
 
-from harmony.message import Message
-from harmony.util import config
+from harmony_service_lib.message import Message
+from harmony_service_lib.util import config
 
 from hoss.bbox_utilities import (
     BBox,

tests/unit/test_coordinate_utilities.py

@@ -4,7 +4,7 @@
 from unittest.mock import ANY, patch
 
 import numpy as np
-from harmony.util import config
+from harmony_service_lib.util import config
 from netCDF4 import Dataset
 from numpy.testing import assert_array_equal
 from pyproj import CRS

tests/unit/test_dimension_utilities.py

@@ -6,8 +6,8 @@
 from unittest.mock import ANY, patch
 
 import numpy as np
-from harmony.message import Message
-from harmony.util import config
+from harmony_service_lib.message import Message
+from harmony_service_lib.util import config
 from netCDF4 import Dataset
 from numpy.ma import masked_array
 from numpy.testing import assert_array_equal
@@ -148,7 +148,7 @@ def test_get_dimension_index_range(self, mock_get_indices_from_values):
             get_dimension_index_range(
                 self.ascending_dimension, requested_min_value, requested_max_value
             )
-            mock_get_indices_from_values.called_once_with(
+            mock_get_indices_from_values.assert_called_once_with(
                 self.ascending_dimension, requested_min_value, requested_max_value
             )
             mock_get_indices_from_values.reset_mock()
@@ -157,7 +157,7 @@ def test_get_dimension_index_range(self, mock_get_indices_from_values):
             get_dimension_index_range(
                 self.ascending_dimension, requested_min_value, None
             )
-            mock_get_indices_from_values.called_once_with(
+            mock_get_indices_from_values.assert_called_once_with(
                 self.ascending_dimension,
                 requested_min_value,
                 self.ascending_dimension[:][-1],
@@ -168,7 +168,7 @@ def test_get_dimension_index_range(self, mock_get_indices_from_values):
             get_dimension_index_range(
                 self.ascending_dimension, None, requested_max_value
             )
-            mock_get_indices_from_values.called_once_with(
+            mock_get_indices_from_values.assert_called_once_with(
                 self.ascending_dimension,
                 self.ascending_dimension[:][0],
                 requested_max_value,
@@ -179,7 +179,7 @@ def test_get_dimension_index_range(self, mock_get_indices_from_values):
             get_dimension_index_range(
                 self.descending_dimension, requested_min_value, requested_max_value
             )
-            mock_get_indices_from_values.called_once_with(
+            mock_get_indices_from_values.assert_called_once_with(
                 self.descending_dimension, requested_max_value, requested_min_value
             )
             mock_get_indices_from_values.reset_mock()
@@ -188,7 +188,7 @@ def test_get_dimension_index_range(self, mock_get_indices_from_values):
             get_dimension_index_range(
                 self.descending_dimension, requested_min_value, None
             )
-            mock_get_indices_from_values.called_once_with(
+            mock_get_indices_from_values.assert_called_once_with(
                 self.descending_dimension,
                 self.descending_dimension[:][0],
                 requested_min_value,
@@ -199,7 +199,7 @@ def test_get_dimension_index_range(self, mock_get_indices_from_values):
             get_dimension_index_range(
                 self.descending_dimension, None, requested_max_value
             )
-            mock_get_indices_from_values.called_once_with(
+            mock_get_indices_from_values.assert_called_once_with(
                 self.descending_dimension,
                 requested_max_value,
                 self.descending_dimension[:][-1],

tests/unit/test_spatial.py

@@ -4,7 +4,7 @@
 from unittest.mock import ANY, call, patch
 
 import numpy as np
-from harmony.message import Message
+from harmony_service_lib.message import Message
 from netCDF4 import Dataset
 from numpy.testing import assert_array_equal
 from pyproj import CRS

tests/unit/test_subset.py

@@ -5,9 +5,9 @@
 from unittest.mock import call, patch
 
 import numpy as np
-from harmony.message import Message, Source
-from harmony.message import Variable as HarmonyVariable
-from harmony.util import config
+from harmony_service_lib.message import Message, Source
+from harmony_service_lib.message import Variable as HarmonyVariable
+from harmony_service_lib.util import config
 from netCDF4 import Dataset
 from varinfo import VarInfoFromDmr
 

tests/unit/test_temporal.py

@@ -5,7 +5,7 @@
 from unittest.mock import ANY, patch
 
 import numpy as np
-from harmony.message import Message
+from harmony_service_lib.message import Message
 from netCDF4 import Dataset
 from numpy.testing import assert_array_equal
 from varinfo import VarInfoFromDmr

tests/unit/test_utilities.py

@@ -2,8 +2,8 @@
 from unittest import TestCase
 from unittest.mock import Mock, patch
 
-from harmony.exceptions import ForbiddenException, ServerException
-from harmony.util import config
+from harmony_service_lib.exceptions import ForbiddenException, ServerException
+from harmony_service_lib.util import config
 
 from hoss.exceptions import UrlAccessFailed
 from hoss.utilities import (

tests/utilities.py

@@ -5,7 +5,7 @@
 from typing import List
 from unittest.mock import MagicMock
 
-from harmony.util import bbox_to_geometry
+from harmony_service_lib.util import bbox_to_geometry
 from pystac import Asset, Catalog, Item
 
 Granule = namedtuple('Granule', ['url', 'media_type', 'roles'])