From 088b11fd98a2eefc0b0824856245b35f0d5733f2 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Mon, 17 Jun 2024 16:03:03 -0400 Subject: [PATCH 1/9] roll up dependabot updates into single PR --- .github/dependabot.yml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index d42179e..1dc05b4 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -9,6 +9,10 @@ updates: directory: "/" schedule: interval: "monthly" + groups: + pip-dependencies: + patterns: + - "*" # Raise pull requests for version updates # to pip against the `develop` branch target-branch: "develop" @@ -17,6 +21,10 @@ updates: schedule: # Check for updates to GitHub Actions every week interval: "monthly" + groups: + gha-dependencies: + patterns: + - "*" # Raise pull requests for version updates # to pip against the `develop` branch target-branch: "develop" From 486b01fbf8f1544f40e4471d5801bbd7d950be98 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Mon, 17 Jun 2024 16:03:44 -0400 Subject: [PATCH 2/9] update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5b710a0..9a461b6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added - [Issue #229](https://github.com/nasa/ncompare/issues/229): Added Journal of Open Source Software (JOSS) info to README and CITATION docs. ### Changed +- [Issue #233](https://github.com/nasa/ncompare/issues/233): Group dependabot updates into fewer PRs. ### Deprecated ### Removed ### Fixed From 81e6f9e2e87c869d0da503f6014ac09cfcf3c299 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Mon, 17 Jun 2024 16:04:10 -0400 Subject: [PATCH 3/9] autoupdate pre-commit hooks --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 295e3dc..d1e0c31 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -3,7 +3,7 @@ default_language_version: repos: - repo: https://github.com/asottile/pyupgrade - rev: v3.15.2 + rev: v3.16.0 hooks: - id: pyupgrade args: [ "--py39-plus" ] @@ -24,7 +24,7 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: 'v0.4.6' + rev: 'v0.4.9' hooks: - id: ruff args: [ "--fix" ] From 0d2f05178cbeb6f9cc1c2e02d5c7e6541453ce73 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Mon, 17 Jun 2024 16:05:29 -0400 Subject: [PATCH 4/9] update poetry lock --- poetry.lock | 1033 +++++++++++++++++++++++++-------------------------- 1 file changed, 505 insertions(+), 528 deletions(-) diff --git a/poetry.lock b/poetry.lock index 58c80db..5183138 100644 --- a/poetry.lock +++ b/poetry.lock @@ -50,13 +50,13 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p [[package]] name = "babel" -version = "2.14.0" +version = "2.15.0" description = "Internationalization 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[metadata] lock-version = "2.0" From 65126d053788a4877e7449f4cee6436dd4230b84 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Mon, 17 Jun 2024 16:10:42 -0400 Subject: [PATCH 5/9] update dataset attribute to avoid FutureWarning Prevents: tests/test_core.py::test_no_error_compare_0to1group :894: FutureWarning: The return type of `Dataset.dims` will be changed to return a set of dimension names in future, in order to be more consistent with `DataArray.dims`. To access a mapping from dimension names to lengths, please use `Dataset.sizes`. --- ncompare/core.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ncompare/core.py b/ncompare/core.py index 113efa9..8b8d040 100644 --- a/ncompare/core.py +++ b/ncompare/core.py @@ -636,7 +636,7 @@ def _get_groups(nc_filepath: Union[str, Path]) -> list: def _get_dims(nc_filepath: Union[str, Path]) -> list: def __get_dim_list(decode_times=True): with xr.open_dataset(nc_filepath, decode_times=decode_times) as dataset: - return list(dataset.dims.items()) + return list(dataset.sizes.items()) try: dims_list = __get_dim_list() From 95b9e8d099a1374cbf72c45d9877e0d154b03be3 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Mon, 17 Jun 2024 16:34:36 -0400 Subject: [PATCH 6/9] minor cleanup of unused test lines --- tests/test_complete_file_output.py | 9 --------- tests/test_core.py | 10 ++-------- 2 files changed, 2 insertions(+), 17 deletions(-) diff --git a/tests/test_complete_file_output.py b/tests/test_complete_file_output.py index e24cbc8..d989733 100644 --- a/tests/test_complete_file_output.py +++ b/tests/test_complete_file_output.py @@ -94,13 +94,4 @@ def test_full_run_to_xlsx_output(temp_data_dir): difference = df1[df1 != df2] rows_with_differences = [(idx, row) for idx, row in difference.notnull().iterrows() if any(row)] - if len(rows_with_differences) != 0: - print( - f"Test will fail because of differences in <{len(rows_with_differences)}> rows. " - f"Differences identified (Row index ----> row contents):" - ) - for idx, row in rows_with_differences: - diff = difference.loc[idx] - print(f" {idx} ----> {diff}") - assert len(rows_with_differences) == 0 diff --git a/tests/test_core.py b/tests/test_core.py index e4d5890..77df53b 100644 --- a/tests/test_core.py +++ b/tests/test_core.py @@ -137,10 +137,7 @@ def test_comparison_group_no_error_for_duplicate_dataset( if "Variables within specified group :" in line: found_expected = True - if found_expected: - assert True - else: - assert False + assert found_expected def test_comparison_var_no_error_for_duplicate_dataset( @@ -160,10 +157,7 @@ def test_comparison_var_no_error_for_duplicate_dataset( if "Sample values within specified variable :" in line: found_expected = True - if found_expected: - assert True - else: - assert False + assert found_expected def test_get_vars_with_group(ds_3dims_3vars_4coords_1group): From cb75046a893a6b05251e29ee76b2f532edb07344 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Mon, 17 Jun 2024 16:48:06 -0400 Subject: [PATCH 7/9] add test for value matching when NaNs are present --- tests/conftest.py | 28 ++++++++++++++++++++++++++++ tests/test_core.py | 30 ++++++++++++++++++++++++++++++ 2 files changed, 58 insertions(+) diff --git a/tests/conftest.py b/tests/conftest.py index 838a2b0..1e33e03 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -74,6 +74,34 @@ def ds_3dims_2vars_4coords(temp_data_dir) -> Path: return filepath +@pytest.fixture(scope="session") +def ds_1dim_1var_1coord(temp_data_dir) -> Path: + ds = Dataset( + data_vars=dict(z1=(["y"], np.array([5, 6]))), + coords=dict( + y=range(2), + ), + ) + filepath = temp_data_dir / "test_1dim_1var_1coord.nc" + ds.to_netcdf(path=filepath) + + return filepath + + +@pytest.fixture(scope="session") +def ds_1dim_1var_allnan_1coord(temp_data_dir) -> Path: + ds = Dataset( + data_vars=dict(z1=(["y"], np.array([np.nan, np.nan]))), + coords=dict( + y=range(2), + ), + ) + filepath = temp_data_dir / "test_1dim_1var_allnan_1coord.nc" + ds.to_netcdf(path=filepath) + + return filepath + + @pytest.fixture(scope="session") def ds_4dims_3vars_5coords(temp_data_dir): ds = Dataset( diff --git a/tests/test_core.py b/tests/test_core.py index 77df53b..e106274 100644 --- a/tests/test_core.py +++ b/tests/test_core.py @@ -72,10 +72,14 @@ def test_matching_random_values( ds_3dims_2vars_4coords, ds_4dims_3vars_5coords, ds_3dims_3vars_4coords_1group, + ds_1dim_1var_1coord, + ds_1dim_1var_allnan_1coord, outputter_to_console, ): variable_array_1 = xr.open_dataset(ds_3dims_2vars_4coords).variables['z1'] variable_array_2 = xr.open_dataset(ds_4dims_3vars_5coords).variables['z1'] + variable_array_3 = xr.open_dataset(ds_1dim_1var_1coord).variables['z1'] + variable_array_allnan = xr.open_dataset(ds_1dim_1var_allnan_1coord).variables['z1'] assert ( _match_random_value( @@ -93,6 +97,32 @@ def test_matching_random_values( ) is False ) + assert ( + _match_random_value( + outputter_to_console, + variable_array_3, + variable_array_3, + ) + is True + ) + # NaN to non-NaN is NOT considered a match + assert ( + _match_random_value( + outputter_to_console, + variable_array_3, + variable_array_allnan, + ) + is None + ) + # NaN to NaN is considered a match + assert ( + _match_random_value( + outputter_to_console, + variable_array_allnan, + variable_array_allnan, + ) + is True + ) def test_print_values_runs_with_no_error(ds_3dims_3vars_4coords_1group, outputter_to_console): From 08ed650d583b185c0887a5ecdb9d47ceedff586e Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Mon, 17 Jun 2024 17:02:20 -0400 Subject: [PATCH 8/9] extract private function to streamline utils --- ncompare/utils.py | 42 ++++++++++++++++-------------------------- 1 file changed, 16 insertions(+), 26 deletions(-) diff --git a/ncompare/utils.py b/ncompare/utils.py index 160120d..0c03149 100644 --- a/ncompare/utils.py +++ b/ncompare/utils.py @@ -29,36 +29,16 @@ def ensure_valid_path_exists(should_be_path: Union[str, Path]) -> Path: - """Convert input to a pathlib.Path and check that the resulting filepath exists.""" - fails_to_exist_msg = "Expected file does not exist: " - wrong_type_msg = "Unexpected type for something that should be convertable to a Path: " - - if isinstance(should_be_path, str): - # Convert to a Path object - path_obj = Path(should_be_path) - if path_obj.exists(): - return path_obj - raise FileNotFoundError(fails_to_exist_msg + str(should_be_path)) - - if isinstance(should_be_path, Path): - if should_be_path.exists(): - return should_be_path - raise FileNotFoundError(fails_to_exist_msg + str(should_be_path)) - - raise TypeError(wrong_type_msg + str(type(should_be_path))) + """Coerce input to a pathlib.Path and check that the resulting filepath exists.""" + path_obj = _coerce_str_or_path_to_path(should_be_path) + if path_obj.exists(): + return path_obj + raise FileNotFoundError("Expected file does not exist: " + str(should_be_path)) def ensure_valid_path_with_suffix(should_be_path: Union[str, Path], suffix: str) -> Path: """Coerce input to a pathlib.Path with given suffix.""" - wrong_type_msg = "Unexpected type for something that should be convertable to a Path: " - - if isinstance(should_be_path, str): - path_obj = Path(should_be_path) - elif isinstance(should_be_path, Path): - path_obj = should_be_path - else: - raise TypeError(wrong_type_msg + str(type(should_be_path))) - + path_obj = _coerce_str_or_path_to_path(should_be_path) return path_obj.with_suffix(suffix) @@ -72,3 +52,13 @@ def coerce_to_str(some_object: Union[str, int, tuple]): return str(some_object) raise TypeError(f"Unable to coerce value to str. Unexpected type <{type(some_object)}>.") + + +def _coerce_str_or_path_to_path(should_be_path: Union[Path, str]) -> Path: + wrong_type_msg = "Unexpected type for something that should be convertable to a Path: " + if isinstance(should_be_path, str): + return Path(should_be_path) + elif isinstance(should_be_path, Path): + return should_be_path + else: + raise TypeError(wrong_type_msg + str(type(should_be_path))) From 9ec5b8d9fcbbd6b6974000420d2cbc8ff4051932 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Mon, 17 Jun 2024 17:02:48 -0400 Subject: [PATCH 9/9] add trivial tests that check errors raised from two utility functions --- tests/test_utils.py | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/tests/test_utils.py b/tests/test_utils.py index 182d9fa..fe800e0 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -50,9 +50,19 @@ def test_make_valid_path_from_Path_in_repo(): assert isinstance(returnval, Path) +def test_error_from_wrong_path_type(): + with pytest.raises(TypeError): + ensure_valid_path_exists((0, 1)) + + def test_coerce_int_to_str(): assert coerce_to_str(5) == "5" def test_coerce_tuple_to_str(): assert coerce_to_str(('step', 123)) == "('step', 123)" + + +def test_error_from_not_able_to_coerce_to_str(): + with pytest.raises(TypeError): + coerce_to_str(list[5, 6, 7])