diff --git a/.github/workflows/build-pipeline.yml b/.github/workflows/build-pipeline.yml index 23afb009..a885e0b8 100644 --- a/.github/workflows/build-pipeline.yml +++ b/.github/workflows/build-pipeline.yml @@ -24,11 +24,11 @@ jobs: - uses: actions/checkout@v2 - uses: actions/setup-python@v2 with: - python-version: 3.8 + python-version: 3.9 - name: Install Poetry uses: abatilo/actions-poetry@v2.0.0 with: - poetry-version: 1.1.8 + poetry-version: 1.3.2 - name: Get version id: get-version run: | @@ -99,7 +99,7 @@ jobs: -Dsonar.tests=tests/ -Dsonar.projectName=l2ss-py -Dsonar.projectVersion=${{ env.software_version }} - -Dsonar.python.version=3.7,3.8,3.9 + -Dsonar.python.version=3.8,3.9,3.10 - name: Run Snyk as a blocking step uses: snyk/actions/python-3.8@master env: diff --git a/.pylintrc b/.pylintrc index 3e1fb9b5..d67aacb1 100644 --- a/.pylintrc +++ b/.pylintrc @@ -484,5 +484,5 @@ min-public-methods=2 # Exceptions that will emit a warning when being caught. Defaults to # "BaseException, Exception". -overgeneral-exceptions=BaseException, - Exception +overgeneral-exceptions=builtins.BaseException, + builtins.Exception diff --git a/CHANGELOG.md b/CHANGELOG.md index 97f801be..308d73bb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Deprecated ### Removed ### Fixed +- [issue/153](https://github.com/podaac/l2ss-py/issues/153): Remove the asc_node_tai93 variable when blank in the SNDR collections for xarray.decode_times to decode ### Security diff --git a/podaac/subsetter/subset.py b/podaac/subsetter/subset.py index 08820111..d55f3578 100644 --- a/podaac/subsetter/subset.py +++ b/podaac/subsetter/subset.py @@ -1094,6 +1094,13 @@ def subset(file_to_subset: str, bbox: np.ndarray, output_file: str, 'mask_and_scale': False, 'decode_times': False } + # clean up time variable in SNDR before decode_times + # SNDR.AQUA files have ascending node time blank + if any('__asc_node_tai93' in i for i in list(nc_dataset.variables)): + asc_time_var = nc_dataset.variables['__asc_node_tai93'] + if not asc_time_var[:] > 0: + del nc_dataset.variables['__asc_node_tai93'] + if min_time or max_time: args['decode_times'] = True @@ -1159,7 +1166,7 @@ def subset(file_to_subset: str, bbox: np.ndarray, output_file: str, )) else: encoding = {} - compression = dict(zlib=True, complevel=5, _FillValue=None) + compression = {"zlib": True, "complevel": 5, "_FillValue": None} if (min_time or max_time) and not all( dim_size == 1 for dim_size in dataset.dims.values()): diff --git a/podaac/subsetter/subset_harmony.py b/podaac/subsetter/subset_harmony.py index 28602a75..d120f1cd 100644 --- a/podaac/subsetter/subset_harmony.py +++ b/podaac/subsetter/subset_harmony.py @@ -175,10 +175,10 @@ def filter_by_subtype(variables, subtype): # Stage the output file with a conventional filename mime = 'application/x-netcdf4' - operations = dict( - variable_subset=subset_params.get('variables'), - is_subsetted=bool(result_bbox is not None) - ) + operations = { + "variable_subset": subset_params.get('variables'), + "is_subsetted": bool(result_bbox is not None) + } staged_filename = generate_output_filename(asset.href, '.nc4', **operations) url = stage(subset_params['output_file'], diff --git a/poetry.lock b/poetry.lock index 22d4ddb2..70bb5d67 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,22 +1,32 @@ +# This file is automatically @generated by Poetry and should not be changed by hand. + [[package]] name = "alabaster" -version = "0.7.12" +version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" category = "dev" optional = false -python-versions = "*" +python-versions = ">=3.6" +files = [ + {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"}, + {file = "alabaster-0.7.13.tar.gz", hash = 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'podaac.subsetter.subset_worker:main' l2ss_harmony = 'podaac.subsetter.subset_harmony:main' l2ss-py = 'podaac.subsetter.run_subsetter:main' diff --git a/tests/data/SNDR/SNDR.AQUA.AIRS.20140110T0305.m06.g031.L2_CLIMCAPS_RET.std.v02_39.G.210131015806.nc b/tests/data/SNDR/SNDR.AQUA.AIRS.20140110T0305.m06.g031.L2_CLIMCAPS_RET.std.v02_39.G.210131015806.nc new file mode 100644 index 00000000..3984b78b Binary files /dev/null and b/tests/data/SNDR/SNDR.AQUA.AIRS.20140110T0305.m06.g031.L2_CLIMCAPS_RET.std.v02_39.G.210131015806.nc differ diff --git a/tests/test_subset.py b/tests/test_subset.py index 7a0c1605..9e8d7bc5 100644 --- a/tests/test_subset.py +++ b/tests/test_subset.py @@ -1270,6 +1270,34 @@ def test_subset_size(test_file, data_dir, subset_output_dir, request): assert subset_file_size < original_file_size +def test_cf_decode_times_sndr(data_dir, subset_output_dir, request): + """ + Check that SNDR ascending and descending granule types are able + to go through xarray cf_decode_times + """ + SNDR_dir = join(data_dir, 'SNDR') + sndr_files = ['SNDR.J1.CRIMSS.20210224T0100.m06.g011.L2_CLIMCAPS_RET.std.v02_28.G.210331064430.nc', + 'SNDR.AQUA.AIRS.20140110T0305.m06.g031.L2_CLIMCAPS_RET.std.v02_39.G.210131015806.nc', + 'SNDR.SNPP.CRIMSS.20200118T0024.m06.g005.L2_CLIMCAPS_RET.std.v02_28.G.200314032326_subset.nc'] + bbox = np.array(((-180, 180), (-90, 90))) + for sndr_file in sndr_files: + output_file = "{}_{}".format(request.node.name, sndr_file) + shutil.copyfile( + os.path.join(SNDR_dir, sndr_file), + os.path.join(subset_output_dir, sndr_file) + ) + + box_test = subset.subset( + file_to_subset=join(subset_output_dir, sndr_file), + bbox=bbox, + output_file=join(subset_output_dir, output_file), + min_time='2014-01-10T00:50:20Z', + max_time='2021-02-24T01:09:55Z' + ) + + if not isinstance(box_test, np.ndarray): + raise ValueError('Subset for SNDR not returned properly') + def test_duplicate_dims_sndr(data_dir, subset_output_dir, request): """