From fcbbc0ab29039b9452b974552c5240f1dd50b6f5 Mon Sep 17 00:00:00 2001 From: Jessy Barrette <30420025+JessyBarrette@users.noreply.github.com> Date: Tue, 13 Aug 2024 11:44:56 -0400 Subject: [PATCH] use ruff for linter testing (#106) * update dependancies * update action * run all ruff tests and report any failure right after * fix nafc ruff check issues * fix seabird imports --- .github/workflows/test-package.yaml | 39 +- CHANGELOG.md | 6 + ocean_data_parser/batch/utils.py | 4 +- ocean_data_parser/parsers/amundsen.py | 6 +- .../parsers/dfo/ios_source/IosObsFile.py | 6 +- ocean_data_parser/parsers/dfo/nafc.py | 10 +- .../parsers/dfo/odf_source/flags.py | 12 +- .../parsers/dfo/odf_source/process.py | 6 +- ocean_data_parser/parsers/pme.py | 6 +- ocean_data_parser/parsers/seabird.py | 14 +- poetry.lock | 2534 +++++++++-------- pyproject.toml | 6 +- tests/test_batch.py | 19 +- tests/test_file_registry.py | 6 +- tests/test_reference_netcdf.py | 7 +- tests/test_vocabularies.py | 16 +- 16 files changed, 1369 insertions(+), 1328 deletions(-) diff --git a/.github/workflows/test-package.yaml b/.github/workflows/test-package.yaml index db76d3e08..a95d9a3f0 100644 --- a/.github/workflows/test-package.yaml +++ b/.github/workflows/test-package.yaml @@ -26,8 +26,8 @@ jobs: testing: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 with: python-version: '3.10' - name: Install dependencies @@ -35,16 +35,31 @@ jobs: python -m pip install --upgrade pip pip install poetry poetry install --with dev,geo - - name: Lint with flake8 - run: | - # stop the build if there are Python syntax errors or undefined names - poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - - name: Run ruff + - name: ruff check + id: ruff_check run: poetry run ruff check --output-format=github . + continue-on-error: true + - name: ruff import sorting check + id: ruff_imports + run: poetry run ruff check --select I --output-format=github . + continue-on-error: true + - name: ruff format + id: ruff_format + run: poetry run ruff format --check . + continue-on-error: true + - name: Check for ruff issues + if: steps.ruff_check.outcome == 'failure' || steps.ruff_imports.outcome == 'failure' || steps.ruff_format.outcome == 'failure' + run: | + echo "Some ruff steps failed. Please check the logs for more information.\n" + echo "Some of the issues can be fixed by running the following commands:\n" + echo " poetry run ruff check --fix . # for fixing all default issues" + echo " poetry run ruff check --fix --select I . # for fixing import sorting issues" + echo " poetry run ruff format . # for formatting the code" + exit 1 + - name: Review if metadata is updated uses: dorny/paths-filter@v3 + continue-on-error: true id: changes with: filters: | @@ -62,7 +77,9 @@ jobs: run: poetry run pytest -W error::UserWarning -k "not test_metadata" -n auto - name: Run benchmark run: poetry run pytest tests/run_benchmark.py --benchmark-json output.json - - name: Update CHANGELOG + - name: CHANGELOG updated check if: steps.changes.outputs.changelog == 'false' - run: exit 1 + run: | + echo "CHANGELOG.md update is required." + exit 1 \ No newline at end of file diff --git a/CHANGELOG.md b/CHANGELOG.md index e2e4ac298..afdd12dc5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Add odpy convert `input_table` input through config file, which gives the ability to list multiple file glob expression and associated metadata. - Add Onset.csv timestamp format: "\d+\/\d+\/\d\d\d\d\s+\d+\:\d+\:\d+" = "%m/%d/%Y %H:%M:%S" +- Rely on ruff for format and linter testing + +### Fixed + +- seabird parsers module import sorting +- nafc ruff check issues ## `0.5.2` - 2024-06-22 diff --git a/ocean_data_parser/batch/utils.py b/ocean_data_parser/batch/utils.py index c2fcf5194..4272d5bad 100644 --- a/ocean_data_parser/batch/utils.py +++ b/ocean_data_parser/batch/utils.py @@ -98,9 +98,7 @@ def generate_output_path( if "." in file_name and not output_format: file_name, output_format = file_name.rsplit(".", 1) - assert ( - output_format - ), "Unknown output file format extension: define the format through the path or output_format inputs" + assert output_format, "Unknown output file format extension: define the format through the path or output_format inputs" # Generate path return Path(output_path) / ( diff --git a/ocean_data_parser/parsers/amundsen.py b/ocean_data_parser/parsers/amundsen.py index 8c588b76e..8c874be63 100644 --- a/ocean_data_parser/parsers/amundsen.py +++ b/ocean_data_parser/parsers/amundsen.py @@ -118,9 +118,9 @@ def int_format( elif line == "% In situ density TEOS10 ((s, t, p) - 1000) [kg/m^3]": metadata["D_CT"] = "In situ density TEOS10 ((s, t, p) - 1000) [kg/m^3]" elif line == "% Potential density TEOS10 ((s, t, 0) - 1000) [kg/m^3]": - metadata[ - "D0CT" - ] = "Potential density TEOS10 ((s, t, 0) - 1000) [kg/m^3]" + metadata["D0CT"] = ( + "Potential density TEOS10 ((s, t, 0) - 1000) [kg/m^3]" + ) elif line == "% Potential density TEOS10 (s, t, 0) [kg/m^3]": metadata["D0CT"] = "Potential density TEOS10 (s, t, 0) [kg/m^3]" elif re.match(r"% .* \[.+\]", line): diff --git a/ocean_data_parser/parsers/dfo/ios_source/IosObsFile.py b/ocean_data_parser/parsers/dfo/ios_source/IosObsFile.py index 2f63b113c..03588e7c1 100644 --- a/ocean_data_parser/parsers/dfo/ios_source/IosObsFile.py +++ b/ocean_data_parser/parsers/dfo/ios_source/IosObsFile.py @@ -458,9 +458,9 @@ def add_to_history(self, input): self.history = {} if "ios_transform_history" not in self.history: self.history["ios_transform_history"] = "IOS Transform History:\n" - self.history[ - "ios_transform_history" - ] += f"{datetime.now().isoformat()} - {input}\n" + self.history["ios_transform_history"] += ( + f"{datetime.now().isoformat()} - {input}\n" + ) def get_data(self, formatline=None): # reads data using the information in FORMAT diff --git a/ocean_data_parser/parsers/dfo/nafc.py b/ocean_data_parser/parsers/dfo/nafc.py index 68ac55f14..a8489ee52 100644 --- a/ocean_data_parser/parsers/dfo/nafc.py +++ b/ocean_data_parser/parsers/dfo/nafc.py @@ -266,7 +266,7 @@ def _get_range(attrs: dict) -> tuple: dtype = _get_dtype(attrs["name"]) # Use int(float(x)) method because the integers have decimals - func = (lambda x: int(float(x))) if dtype == int else float + func = (lambda x: int(float(x))) if dtype is int else float return tuple( map( func, @@ -463,7 +463,7 @@ def _parse_ship_trip_stn(): logger.error("No data found in file") # Review datatypes - if any([dtype == object for _, dtype in ds.dtypes.items()]): + if any([dtype is object for _, dtype in ds.dtypes.items()]): logger.warning( "Some columns dtype=object suggest the file data wasn't correctely parsed." ) @@ -561,9 +561,9 @@ def _parse_ship_trip_stn(): if apply_func not in (None, np.nan) else var ) - ds.attrs[ - "history" - ] += f"\n{pd.Timestamp.now()} - Generated variable {name} = {apply_func}" + ds.attrs["history"] += ( + f"\n{pd.Timestamp.now()} - Generated variable {name} = {apply_func}" + ) attrs["source"] = f"Generated variable {name} = {apply_func}" ds[name] = (var.dims, new_data.data, {**var.attrs, **attrs}) diff --git a/ocean_data_parser/parsers/dfo/odf_source/flags.py b/ocean_data_parser/parsers/dfo/odf_source/flags.py index 3c46b01f3..9db96348f 100644 --- a/ocean_data_parser/parsers/dfo/odf_source/flags.py +++ b/ocean_data_parser/parsers/dfo/odf_source/flags.py @@ -73,9 +73,9 @@ def add_flag_attributes(dataset): """ def _add_ancillary(ancillary, variable): - dataset[variable].attrs[ - "ancillary_variables" - ] = f"{dataset[variable].attrs.get('ancillary_variables','')} {ancillary}".strip() + dataset[variable].attrs["ancillary_variables"] = ( + f"{dataset[variable].attrs.get('ancillary_variables','')} {ancillary}".strip() + ) return dataset[variable] # Add ancillary_variable attribute @@ -88,9 +88,9 @@ def _add_ancillary(ancillary, variable): _add_ancillary(variable, var) elif variable.startswith("Q") and variable[1:] in dataset: dataset[variable[1:]] = _add_ancillary(variable, variable[1:]) - dataset[variable].attrs[ - "long_name" - ] = f"Quality Flag for Parameter: {dataset[variable[1:]].attrs['long_name']}" + dataset[variable].attrs["long_name"] = ( + f"Quality Flag for Parameter: {dataset[variable[1:]].attrs['long_name']}" + ) else: # ignore normal variables continue diff --git a/ocean_data_parser/parsers/dfo/odf_source/process.py b/ocean_data_parser/parsers/dfo/odf_source/process.py index e4c91b33f..e343a3329 100644 --- a/ocean_data_parser/parsers/dfo/odf_source/process.py +++ b/ocean_data_parser/parsers/dfo/odf_source/process.py @@ -86,9 +86,9 @@ def parse_odf( "source": odf_path, } dataset = attributes.global_attributes_from_header(dataset, metadata) - dataset.attrs[ - "history" - ] += f"# Convert ODF to NetCDF with ocean_data_parser V {__version__}\n" + dataset.attrs["history"] += ( + f"# Convert ODF to NetCDF with ocean_data_parser V {__version__}\n" + ) # Handle ODF flag variables dataset = flags.rename_qqqq_flags(dataset) diff --git a/ocean_data_parser/parsers/pme.py b/ocean_data_parser/parsers/pme.py index f2a023e1c..6eec784e9 100644 --- a/ocean_data_parser/parsers/pme.py +++ b/ocean_data_parser/parsers/pme.py @@ -160,9 +160,9 @@ def _append_to_history(msg): if rename_variables: ds = ds.rename_vars(VARIABLE_RENAMING_MAPPING) - ds.attrs[ - "history" - ] += f"\n{pd.Timestamp.now().isoformat()} Rename variables: {VARIABLE_RENAMING_MAPPING}" + ds.attrs["history"] += ( + f"\n{pd.Timestamp.now().isoformat()} Rename variables: {VARIABLE_RENAMING_MAPPING}" + ) ds = standardize_dataset(ds) return ds diff --git a/ocean_data_parser/parsers/seabird.py b/ocean_data_parser/parsers/seabird.py index ba650bf6d..9effd8d1b 100644 --- a/ocean_data_parser/parsers/seabird.py +++ b/ocean_data_parser/parsers/seabird.py @@ -9,11 +9,11 @@ import logging import re from datetime import datetime +from pyexpat import ExpatError import pandas as pd import xarray import xmltodict -from pyexpat import ExpatError from ocean_data_parser.parsers.utils import convert_datetime_str, standardize_dataset from ocean_data_parser.vocabularies.load import seabird_vocabulary @@ -217,14 +217,14 @@ def btl( # Add cell_method attribute for var in ds: if var.endswith("_sdev") and var[:-5] in ds: - ds[var].attrs[ - "cell_method" - ] = f"scan: standard_deviation (previous {n_scan_per_bottle} scans)" + ds[var].attrs["cell_method"] = ( + f"scan: standard_deviation (previous {n_scan_per_bottle} scans)" + ) # TODO confirm that seabird uses the previous records from this timestamp elif var not in ["time", "bottle"]: - ds[var].attrs[ - "cell_method" - ] = f"scan: mean (previous {n_scan_per_bottle} scans)" + ds[var].attrs["cell_method"] = ( + f"scan: mean (previous {n_scan_per_bottle} scans)" + ) if not save_orginal_header: ds.attrs.pop("seabird_header") diff --git a/poetry.lock b/poetry.lock index 723fb6654..3d784d558 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,14 +1,14 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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"jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] +doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.13" -content-hash = "c57b22b15fe26a677787bbfc912f947d5cf5f5fad288e422354c7eb7564c271c" +content-hash = "6a3266caa4d08fc2c4b6a40bf6acb2d6cd0fb616a75d198b8dd097ee5048ce8f" diff --git a/pyproject.toml b/pyproject.toml index 41504016f..362e0892f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -73,13 +73,12 @@ optional = true [tool.poetry.group.dev.dependencies] pytest = "^7.4.2" -black = "^23.10.0" ioos-qc = "^2.1.0" pytest-benchmark = "^4.0.0" flake8 = "^6.1.0" -ruff = "^0.3.4" toml = "^0.10.2" pytest-xdist = "^3.6.1" +ruff = "^0.5.7" [tool.poetry.scripts] odpy = 'ocean_data_parser.cli:main' @@ -87,6 +86,3 @@ odpy = 'ocean_data_parser.cli:main' [build-system] requires = ["poetry-core"] build-backend = "poetry.core.masonry.api" - -[tool.isort] -profile = "black" \ No newline at end of file diff --git a/tests/test_batch.py b/tests/test_batch.py index dd7fa6597..030726a34 100644 --- a/tests/test_batch.py +++ b/tests/test_batch.py @@ -8,9 +8,12 @@ from loguru import logger from ocean_data_parser.batch.config import glob -from ocean_data_parser.batch.convert import BatchConversion, FileConversionRegistry +from ocean_data_parser.batch.convert import ( + BatchConversion, + FileConversionRegistry, + load_config, +) from ocean_data_parser.batch.convert import cli as convert_cli -from ocean_data_parser.batch.convert import load_config from ocean_data_parser.batch.utils import generate_output_path from ocean_data_parser.read import file @@ -197,7 +200,10 @@ def test_batch_failed_cli_conversion_with_no_matching_inputs(self, caplog): with caplog.at_level("ERROR"): result = self._run_cli_batch_process("-i", "*.csv") assert result.exit_code == 1 - assert any( "No files detected with *.csv" in record.message for record in caplog.records) + assert any( + "No files detected with *.csv" in record.message + for record in caplog.records + ) def test_batch_failed_cli_conversion_with_argument_inputs(self): result = self._run_cli_batch_process("*.csv") @@ -548,7 +554,9 @@ def test_get_files_with_file_column_prefix(self, config): files, attrs = batch.get_source_files_from_input_table() assert files assert len(files) > 0 - assert all(str(file).startswith("tests/parsers_test_files/onset/") for file in files) + assert all( + str(file).startswith("tests/parsers_test_files/onset/") for file in files + ) def test_get_files_with_file_column_suffix(self, config): config["input_table"]["file_column_suffix"] = "**/*.csv" @@ -566,7 +574,8 @@ def test_get_files_with_file_column_prefix_and_suffix(self, config): assert files assert len(files) > 0 assert all( - str(file).startswith("tests/parsers_test_files/onset/") and file.suffix == ".csv" + str(file).startswith("tests/parsers_test_files/onset/") + and file.suffix == ".csv" for file in files ) diff --git a/tests/test_file_registry.py b/tests/test_file_registry.py index a150239b9..89c1f8739 100644 --- a/tests/test_file_registry.py +++ b/tests/test_file_registry.py @@ -278,9 +278,9 @@ def test_get_source_base(self): assert file_registry.data.loc[ file_registry._is_new_file() ].empty, f" {file_registry._is_new_file()} didn't return an empty list of files" - assert file_registry.data.loc[ - file_registry._is_different_hash() - ].empty, f" {file_registry._is_different_hash()} didn't return an empty list of files" + assert ( + file_registry.data.loc[file_registry._is_different_hash()].empty + ), f" {file_registry._is_different_hash()} didn't return an empty list of files" assert file_registry.data.loc[ file_registry._is_new_file() | file_registry._is_different_hash() ].empty diff --git a/tests/test_reference_netcdf.py b/tests/test_reference_netcdf.py index 3f7fff7d6..8850f3ebc 100644 --- a/tests/test_reference_netcdf.py +++ b/tests/test_reference_netcdf.py @@ -33,10 +33,9 @@ def test_compare_test_to_reference_netcdf(reference_file): # Load test file and reference file ref = xr.open_dataset(reference_file) difference_detected = compare_test_to_reference_netcdf(ref, test) - assert ( - not difference_detected - ), f"Converted file {source_file} is different than the reference: " + "\n".join( - difference_detected + assert not difference_detected, ( + f"Converted file {source_file} is different than the reference: " + + "\n".join(difference_detected) ) diff --git a/tests/test_vocabularies.py b/tests/test_vocabularies.py index 84803df7f..b8cd971b7 100644 --- a/tests/test_vocabularies.py +++ b/tests/test_vocabularies.py @@ -46,31 +46,23 @@ def test_platform_unique_idendifiers(self, column): duplicated = platforms_vocab.query( f"{column}.notna() and {column}.duplicated(keep=False)" ) - assert ( - duplicated.empty - ), f"{len(duplicated)} duplicated {column=} found in platform vocabulary: {duplicated[['platform_name',column]]}" + assert duplicated.empty, f"{len(duplicated)} duplicated {column=} found in platform vocabulary: {duplicated[['platform_name',column]]}" def test_sdn_urm_prefix(self): sdn_prefix = platforms_vocab.query( "sdn_platform_urn.str.startswith('SDN:C17::') == False and sdn_platform_urn.notna()" ) - assert ( - sdn_prefix.empty - ), f"SDN URN prefix not found in platform vocabulary: {sdn_prefix[['platform_name','sdn_platform_urn']]}" + assert sdn_prefix.empty, f"SDN URN prefix not found in platform vocabulary: {sdn_prefix[['platform_name','sdn_platform_urn']]}" def test_matching_id_ices_sdn_codes(self): mismatched_codes = platforms_vocab.query( "ices_platform_code != platform_id and (ices_platform_code.notna() or platform_id.notna())" ) - assert ( - mismatched_codes.empty - ), f"mismatched codes found: {mismatched_codes[['platform_name','platform_id','ices_platform_code','sdn_platform_urn']]}" + assert mismatched_codes.empty, f"mismatched codes found: {mismatched_codes[['platform_name','platform_id','ices_platform_code','sdn_platform_urn']]}" mismatched_codes = platforms_vocab.query( "sdn_platform_urn.str.replace('SDN:C17::','') != platform_id and (sdn_platform_urn.notna() or platform_id.notna())" ) - assert ( - mismatched_codes.empty - ), f"mismatched codes found: {mismatched_codes[['platform_name','platform_id','ices_platform_code','sdn_platform_urn']]}" + assert mismatched_codes.empty, f"mismatched codes found: {mismatched_codes[['platform_name','platform_id','ices_platform_code','sdn_platform_urn']]}" @nerc_vocabulary_test @pytest.mark.parametrize(