From c48fb4d6b837053366bcd25c5fe72433d009f645 Mon Sep 17 00:00:00 2001 From: Philipp Kats Date: Mon, 12 Aug 2024 22:16:42 -0400 Subject: [PATCH] 64 rename na limit (#70) * wip: pandas 2, pydantic 2 compatibility * fixed: tests with migration to pydantic v2 * fixed: generate_v2 write files * fixed: removed py3.7 from matrix, added py3.10, py3.11 * fixed: removed py3.7 from matrix, added py3.10, py3.11 * fixed: python 3.10 issue * fixed: formatted with black * adding tomli * fixed: added tomli as dev dependency * fixed: added tomli as dev dependency * fixed: added tomli as dev dependency * fixed: added tomli as dev dependency * fixed: added tomli as dev dependency --- .github/workflows/pre-release.yml | 12 +- .github/workflows/release.yml | 12 +- .github/workflows/test.yml | 4 +- .../typer_build_docs.yaml-deactivated-for-now | 2 +- changelog.md | 31 +- dfschema/__init__.py | 2 +- dfschema/core/column.py | 21 +- dfschema/core/core.py | 16 +- dfschema/core/dtype.py | 1 + dfschema/core/legacy/__init__.py | 2 +- dfschema/core/legacy/v1.py | 2 +- dfschema/core/metadata.py | 2 +- dfschema/core/shape.py | 2 +- poetry.lock | 4276 ++++++++++------- pyproject.toml | 10 +- tests/test_core.py | 2 +- tests/test_invalid.py | 2 +- .../test_schemas/v2/good/v2_predictions.json | 50 + .../test_schemas/v2/good/v2_predictions2.json | 51 + tests/test_str_patterns.py | 6 +- tests/test_v1.py | 3 +- tests/test_validate.py | 34 +- tests/test_version.py | 7 +- 23 files changed, 2684 insertions(+), 1866 deletions(-) create mode 100644 tests/test_schemas/v2/good/v2_predictions.json create mode 100644 tests/test_schemas/v2/good/v2_predictions2.json diff --git a/.github/workflows/pre-release.yml b/.github/workflows/pre-release.yml index 57e9f27..fbd1b70 100644 --- a/.github/workflows/pre-release.yml +++ b/.github/workflows/pre-release.yml @@ -11,8 +11,8 @@ jobs: strategy: matrix: - python-version: [3.7, 3.8, 3.9] - poetry-version: [1.2] + python-version: [3.8, 3.9, "3.10", 3.11] + poetry-version: [1.8] os: [ubuntu-latest, macos-latest, windows-latest] runs-on: ${{ matrix.os }} @@ -72,14 +72,14 @@ jobs: with: submodules: recursive - - name: Set up Python 3.7 + - name: Set up Python 3.8 uses: actions/setup-python@v2 with: - python-version: 3.7 - - name: Set up Poetry 1.2 + python-version: 3.8 + - name: Set up Poetry 1.8 uses: abatilo/actions-poetry@v2.1.6 with: - poetry-version: 1.2 + poetry-version: 1.8 - uses: actions/download-artifact@v2 with: diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 38bc620..d013c65 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -11,8 +11,8 @@ jobs: if: "!github.event.release.prerelease" strategy: matrix: - python-version: [3.7, 3.8, 3.9] - poetry-version: [1.2] + python-version: [3.8, 3.9, "3.10", 3.11] + poetry-version: [1.8] os: [ubuntu-latest, macos-latest, windows-latest] runs-on: ${{ matrix.os }} @@ -72,15 +72,15 @@ jobs: with: submodules: recursive - - name: Set up Python 3.7 + - name: Set up Python 3.8 uses: actions/setup-python@v2 with: - python-version: 3.7 + python-version: 3.8 - - name: Set up Poetry 1.2 + - name: Set up Poetry 1.8 uses: abatilo/actions-poetry@v2.1.6 with: - poetry-version: 1.2 + poetry-version: 1.8 - name: Set up cache uses: actions/cache@v1 diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index a42c582..858cfef 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -16,8 +16,8 @@ jobs: runs-on: macos-latest strategy: matrix: - python-version: [3.7, 3.8, 3.9] - poetry-version: [1.2] + python-version: [3.8, 3.9, "3.10", 3.11] + poetry-version: [1.8] # Steps represent a sequence of tasks that will be executed as part of the job steps: diff --git a/.github/workflows/typer_build_docs.yaml-deactivated-for-now b/.github/workflows/typer_build_docs.yaml-deactivated-for-now index 94950f4..4692c5d 100644 --- a/.github/workflows/typer_build_docs.yaml-deactivated-for-now +++ b/.github/workflows/typer_build_docs.yaml-deactivated-for-now @@ -23,7 +23,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v2 with: - python-version: "3.7" + python-version: "3.8" # Allow debugging with tmate - name: Setup tmate session uses: mxschmitt/action-tmate@v3 diff --git a/changelog.md b/changelog.md index 9071f6e..758f37a 100644 --- a/changelog.md +++ b/changelog.md @@ -1,20 +1,31 @@ # Changelog -v0.0.11: +### v0.0.12 + +Fixed: +- using `na_pct_below` +- `from_df` now includes metadata +Changed: +- bumped minimum python version to 3.8 +- Pydantic migrated to v2 +- Allows use of Pandas v2 + + +### v0.0.11: - Version in metadata - adds `dfschema` and `pandas` version in metadata upon generation (Later will worn if Schema is initialized from json, generated by later version) - Renamed `na_limit` to `na_pct_below` to make it unambiguous (with backward support) - Added `optional=True` flag for columns. If true, does not raise exception if column is not present - added `dfschema update {existing_schema} {output_schema}` command to upgrade schemas -v0.0.10: +### v0.0.10: - relaxed Pydantic requirement to `>=1.9` -v0.0.9: +### v0.0.9: - Pydantic bumped to `1.10` - Bug Fix: Categorical constraints (`exact_set`, `oneof`, `include`) now can keeo `int` and `float` values. That expands to legacy schemas as well. -v0.0.8: +### v0.0.8: Legacy Schema Aliases (support for legacy schemas): - `min_value` now also supports `min` alias - `max_value` now also supports `max` alias @@ -28,25 +39,27 @@ Testing: - pre-commit setup was updated -v0.0.7: +### v0.0.7: - rename `DfSchema.validate_df` to `DfSchema.validate` (UNDONE: `validate` is reserved by Pydantic object) - updated documentation -v0.0.6: +### v0.0.6: - `DfSchema.to_file`, `DfSchema.from_file` proper testing - CLI command help texts - added pre-commit install to the repo - Some benchmarking - renamed `dfs.validate_df` to `dfs.validate` -v0.0.5: fix column dtype generation/validation bug +### v0.0.5 +- fix column dtype generation/validation bug ## Pre-Publication -v1.3.0 + +### v1.3.0 - renamed strict_column_set to additionalColumns - renamed strict_column_order to exactColumnOrder -v1.2.0 +### v1.2.0 - Metadata SubObject - Summary Exception is now collected for specific DfSchema, not via Borg State - Supports SubSets diff --git a/dfschema/__init__.py b/dfschema/__init__.py index 002a58c..8d742a6 100644 --- a/dfschema/__init__.py +++ b/dfschema/__init__.py @@ -7,7 +7,7 @@ DataFrameSummaryError, ) -__version__ = "0.0.11" +__version__ = "0.0.12" __all__ = [ "validate", diff --git a/dfschema/core/column.py b/dfschema/core/column.py index 03cf3d0..c4de946 100644 --- a/dfschema/core/column.py +++ b/dfschema/core/column.py @@ -4,7 +4,7 @@ from warnings import warn import pandas as pd -from pydantic import BaseModel, Extra, Field # , validator +from pydantic.v1 import BaseModel, Extra, Field # , validator from .dtype import DtypeAliasPool, DtypeLiteral from .exceptions import DataFrameSchemaError, DataFrameValidationError @@ -52,6 +52,21 @@ def _validate_column_presence( raise DataFrameValidationError(text) +def _is_string(series: pd.Series, strict: bool = False) -> bool: + """Check if series is string-like + NOTE: Pandas 2 does not accept object dtype as string; + THis is a workaround. + TODO: explicitly check for object dtype and raise warning + """ + result = pd.api.types.is_string_dtype(series) or pd.isnull(series).all() + if strict: + return result + + object_like = pd.api.types.is_object_dtype(series) + + return result or object_like + + class ValueLimits(BaseModel): # type: ignore min: Union[float, date, datetime, str, None] = None max: Union[float, date, datetime, str, None] = None @@ -212,6 +227,7 @@ class ColSchema(BaseModel): lt=1.0, description="limit of missing values. If set to true, will raise if all values are empty. If set to a number, will raise if more than given perecnt of values are empty (Nan)", alias="na_limit", + alias_priority=2, ) value_limits: Optional[ValueLimits] = Field( @@ -234,6 +250,7 @@ class ColSchema(BaseModel): class Config: extra = Extra.forbid use_enum_values = True + allow_population_by_field_name = True def _map_dtype( self, dtype: Optional[str] = None, raise_error: bool = True @@ -252,7 +269,7 @@ def _map_dtype( "numeric": pd.api.types.is_numeric_dtype, "int": pd.api.types.is_integer_dtype, "float": pd.api.types.is_float_dtype, - "string": lambda s: (pd.api.types.is_string_dtype(s) or pd.isnull(s).all()), + "string": _is_string, "timedelta64[ns]": pd.api.types.is_timedelta64_dtype, } diff --git a/dfschema/core/core.py b/dfschema/core/core.py index 26b2ed1..72ab9cb 100644 --- a/dfschema/core/core.py +++ b/dfschema/core/core.py @@ -1,10 +1,10 @@ from typing import Callable, Optional, Union, List import json from pathlib import Path - +from datetime import datetime import pandas as pd -from pydantic import BaseModel, Extra, Field, PrivateAttr +from pydantic.v1 import BaseModel, Extra, Field, PrivateAttr from .column import ColSchema, _validate_column_presence from .exceptions import DataFrameSchemaError, DataFrameSummaryError, SubsetSummaryError @@ -30,7 +30,7 @@ class Config: arbitrary_types_allowed = True metadata: Optional[MetaData] = Field( - MetaData(), + MetaData, description="optional metadata, including version and protocol version", ) @@ -197,7 +197,7 @@ def from_file(cls, path: Union[str, Path]) -> "DfSchema": ) return cls.from_dict(schema) except Exception as e: - raise DataFrameSchemaError(f"Error loading schema from file {path}") from e + raise DataFrameSchemaError(f"Error loading schema from file {path}: {e}") def to_file(self, path: Union[str, Path]) -> None: """write chema to file @@ -233,7 +233,7 @@ def to_file(self, path: Union[str, Path]) -> None: ) except Exception as e: - raise DataFrameSchemaError(f"Error wriging schema to file {path}") from e + raise DataFrameSchemaError(f"Error wriging schema to file {path}: {e}") @classmethod def from_dict( @@ -282,10 +282,14 @@ def from_df( """ schema = generate_schema_dict_from_df(df) + schema["metadata"] = { + "protocol_version": 2.0, + "version": datetime.now().isoformat(), + } subset_schemas = [] if subset_predicates: for predicate in subset_predicates: - filtered = SubsetSchema.filter_df(df, predicate) + filtered = SubsetSchema._filter(df, predicate) subset_schema = generate_schema_dict_from_df(filtered) subset_schema["predicate"] = predicate diff --git a/dfschema/core/dtype.py b/dfschema/core/dtype.py index cce0c94..03db21a 100644 --- a/dfschema/core/dtype.py +++ b/dfschema/core/dtype.py @@ -3,6 +3,7 @@ mostly based on pandas.core.dtypes.dtypes. https://pandas.pydata.org/docs/user_guide/basics.html#basics-dtypes """ + import sys if sys.version_info >= (3, 8): diff --git a/dfschema/core/legacy/__init__.py b/dfschema/core/legacy/__init__.py index da90ccf..b244b3a 100644 --- a/dfschema/core/legacy/__init__.py +++ b/dfschema/core/legacy/__init__.py @@ -9,4 +9,4 @@ def infer_protocol_version(d: dict) -> float: if "metadata" not in d or "protocol_version" not in d["metadata"]: logging.info("Missing `protocol_version` in metadata. Assuming PV=1.0") - return d.get("metadata", {}).get("protocol_version", 1.0) + return d.get("metadata", dict()).get("protocol_version", 1.0) diff --git a/dfschema/core/legacy/v1.py b/dfschema/core/legacy/v1.py index cb4952a..559165c 100644 --- a/dfschema/core/legacy/v1.py +++ b/dfschema/core/legacy/v1.py @@ -1,4 +1,4 @@ -from pydantic import BaseModel, Extra, Field, PositiveInt +from pydantic.v1 import BaseModel, Extra, Field, PositiveInt # import json diff --git a/dfschema/core/metadata.py b/dfschema/core/metadata.py index 4a1dac9..387d305 100644 --- a/dfschema/core/metadata.py +++ b/dfschema/core/metadata.py @@ -2,7 +2,7 @@ from datetime import date from typing import Optional -from pydantic import BaseModel, Field +from pydantic.v1 import BaseModel, Field from .config import CURRENT_PROTOCOL_VERSION diff --git a/dfschema/core/shape.py b/dfschema/core/shape.py index 42160ac..a9b0b3f 100644 --- a/dfschema/core/shape.py +++ b/dfschema/core/shape.py @@ -1,6 +1,6 @@ from typing import Optional import pandas as pd -from pydantic import BaseModel, Field, PositiveInt, Extra +from pydantic.v1 import BaseModel, Field, PositiveInt, Extra from .exceptions import DataFrameValidationError from .collector import exception_collector diff --git a/poetry.lock b/poetry.lock index b0a6490..da83d55 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,53 +1,98 @@ +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. + +[[package]] +name = "annotated-types" +version = "0.7.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.8" +files = [ + {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, + {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, +] + [[package]] name = "anyio" -version = "3.6.2" +version = "4.4.0" description = "High level 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PyYAML = {version = "^6.0", optional = true} @@ -42,6 +42,8 @@ MarkupSafe = "2.0.1" jupyter = "^1.0.0" watermark = "^2.3.1" gitchangelog = "^3.0.4" +black = "^24.8.0" +tomli = {version = "^2.0.1", python = "<3.11"} [build-system] requires = ["poetry-core>=1.0.0"] diff --git a/tests/test_core.py b/tests/test_core.py index 24df42e..751110a 100644 --- a/tests/test_core.py +++ b/tests/test_core.py @@ -1,5 +1,5 @@ import pytest -from pydantic.error_wrappers import ValidationError +from pydantic.v1.error_wrappers import ValidationError def test_schema_objects(good_schema: dict): diff --git a/tests/test_invalid.py b/tests/test_invalid.py index faedf71..25dd33c 100644 --- a/tests/test_invalid.py +++ b/tests/test_invalid.py @@ -3,7 +3,7 @@ def test_df_validate_invalid_schema(df1, bad_schema: dict): from dfschema import validate - from pydantic import ValidationError + from pydantic.v1.error_wrappers import ValidationError with pytest.raises(ValidationError): validate(df1, bad_schema["schema"]) diff --git a/tests/test_schemas/v2/good/v2_predictions.json b/tests/test_schemas/v2/good/v2_predictions.json new file mode 100644 index 0000000..d8c3b76 --- /dev/null +++ b/tests/test_schemas/v2/good/v2_predictions.json @@ -0,0 +1,50 @@ +{ + "metadata": { + "protocol_version": 2.0, + "version": "2024-03-04" + }, + + "columns": [ + { + "name": "value", + "dtype": "number", + "na_pct_below": 0.01, + "value_limits": { + "min": 100000, + "max": 50000000 + } + }, + { + "name": "inferred_at", + "dtype": "datetime64[ns]", + "na_pct_below": 0.01 + }, + { + "name": "trained_at", + "dtype": "datetime64[ns]", + "na_pct_below": 0.01 + }, + { + "name": "model", + "dtype": "string", + "na_pct_below": 0.01, + "categorical": { + "value_set": [ + "main", + "certainty_low", + "certainty_hight", + "certainty_median" + ], + "mode": "exact_set" + } + }, + { + "name": "version", + "dtype": "string", + "na_pct_below": 0.01, + "str_pattern": "^\\d+\\.\\d+\\.\\d+.*$" + } + ], + "additionalColumns": false, + "exactColumnOrder": false +} diff --git a/tests/test_schemas/v2/good/v2_predictions2.json b/tests/test_schemas/v2/good/v2_predictions2.json new file mode 100644 index 0000000..8ca7442 --- /dev/null +++ b/tests/test_schemas/v2/good/v2_predictions2.json @@ -0,0 +1,51 @@ +{ + "metadata": { + "protocol_version": 2.0, + "version": "2024-03-04", + "generated_with": {} + }, + + "columns": [ + { + "name": "value", + "dtype": "number", + "na_limit": 0.01, + "value_limits": { + "min": 100000, + "max": 50000000 + } + }, + { + "name": "inferred_at", + "dtype": "datetime64[ns]", + "na_limit": 0.01 + }, + { + "name": "trained_at", + "dtype": "datetime64[ns]", + "na_limit": 0.01 + }, + { + "name": "model", + "dtype": "string", + "na_limit": 0.01, + "categorical": { + "value_set": [ + "main", + "certainty_low", + "certainty_hight", + "certainty_median" + ], + "mode": "exact_set" + } + }, + { + "name": "version", + "dtype": "string", + "na_limit": 0.01, + "str_pattern": "^\\d+\\.\\d+\\.\\d+.*$" + } + ], + "additionalColumns": false, + "exactColumnOrder": false +} diff --git a/tests/test_str_patterns.py b/tests/test_str_patterns.py index 3540eee..28aab6b 100644 --- a/tests/test_str_patterns.py +++ b/tests/test_str_patterns.py @@ -4,7 +4,7 @@ @pytest.fixture def str_df() -> pd.DataFrame: - return pd.DataFrame( + df = pd.DataFrame( { "x": ["A-1", "A-10", "Z-12", None], "y": ["A-1 APT", "A-10 PH", "Z-12 THS", None], @@ -12,6 +12,10 @@ def str_df() -> pd.DataFrame: } ) + for col in df.columns: + df[col] = df[col].astype("string") + return df + def test_string_matching(str_df): from dfschema.core.core import DfSchema diff --git a/tests/test_v1.py b/tests/test_v1.py index c8d86cd..ac86b0d 100644 --- a/tests/test_v1.py +++ b/tests/test_v1.py @@ -4,8 +4,9 @@ def test_validate_df_v1_invalid(bad_schema_v1): from dfschema.core.core import DfSchema + from pydantic.v1.error_wrappers import ValidationError as v1ValidationError - with pytest.raises((ValidationError, TypeError)): + with pytest.raises((v1ValidationError, ValidationError, TypeError)): DfSchema.from_dict(bad_schema_v1["schema"]) diff --git a/tests/test_validate.py b/tests/test_validate.py index 7529360..cc8c7e2 100644 --- a/tests/test_validate.py +++ b/tests/test_validate.py @@ -1,5 +1,5 @@ import pytest - +from pathlib import Path good_schemas = [ {"shape": {"rows": 4, "cols": 2}}, @@ -144,3 +144,35 @@ def test_validate_df3_raises(df3, schema): with pytest.raises(DataFrameValidationError): validate(df3, schema) + + +prediction_good_schemas = [ + Path(__file__).parent / "test_schemas/v2/good/v2_predictions.json", + Path(__file__).parent / "test_schemas/v2/good/v2_predictions2.json", +] + + +@pytest.fixture +def df4(): + import pandas as pd + + df = pd.DataFrame( + { + "value": [100000, 200000, 300000, 500000], + "inferred_at": ["2020-01-01", "2020-01-02", "2020-01-03", "2020-01-03"], + "trained_at": ["2020-01-01", "2020-01-02", "2020-01-03", "2020-01-03"], + "model": ["main", "certainty_low", "certainty_hight", "certainty_median"], + "version": ["1.0.0", "1.0.1", "1.0.2", "1.0.3"], + } + ) + for col in ["inferred_at", "trained_at"]: + df[col] = pd.to_datetime(df[col]) + return df + + +@pytest.mark.parametrize("schema", prediction_good_schemas) +def test_validate_df4(df4, schema): + from dfschema import DfSchema + + schema = DfSchema.from_file(schema) + schema.validate_df(df4) diff --git a/tests/test_version.py b/tests/test_version.py index f658524..1218757 100644 --- a/tests/test_version.py +++ b/tests/test_version.py @@ -1,4 +1,7 @@ -import toml +try: + import tomllib +except ImportError: + import tomli as tomllib from pathlib import Path import dfschema @@ -14,7 +17,7 @@ def test_versions_are_in_sync(): print(f"{item} - {'dir' if item.is_dir() else 'file'}") raise Exception(e) - pyproject = toml.loads(open(str(path)).read()) + pyproject = tomllib.loads(open(str(path)).read()) pyproject_version = pyproject["tool"]["poetry"]["version"] package_init_version = dfschema.__version__