diff --git a/.editorconfig b/.editorconfig index 569193b..b6494e0 100644 --- a/.editorconfig +++ b/.editorconfig @@ -7,12 +7,28 @@ insert_final_newline = true trim_trailing_whitespace = true charset = utf-8 -[*.py] +[*.{css,pcss}] +indent_size = 2 + +[*.html] +indent_size = 2 + +[*.ini] indent_size = 4 + +[*.{js,ts,vue}] +indent_size = 2 max_line_length = 100 -[{*.yml,*.yaml}] +[*.{json,jsonc,json5}] indent_size = 2 -[*.ini] +[*.py] indent_size = 4 +max_line_length = 100 + +[*.toml] +indent_size = 2 + +[*.{yml,yaml}] +indent_size = 2 diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..74055c8 --- /dev/null +++ b/.gitattributes @@ -0,0 +1 @@ +uv.lock linguist-generated=true diff --git a/.github/renovate.json5 b/.github/renovate.json5 new file mode 100644 index 0000000..2a2cc4d --- /dev/null +++ b/.github/renovate.json5 @@ -0,0 +1,6 @@ +{ + $schema: 'https://docs.renovatebot.com/renovate-schema.json', + extends: [ + 'github>kitware-resonant/.github:renovate-library.json5', + ], +} diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f452ef6..1988765 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -4,24 +4,24 @@ on: push: branches: - master - schedule: - - cron: "0 0 * * *" +permissions: + contents: read jobs: test: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.10", "3.11", "3.12", "3.13"] + python-version: ["3.12", "3.13", "3.14"] steps: - - uses: actions/checkout@v2 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + - name: Checkout repository + uses: actions/checkout@v6 + with: + # Tags are needed to compute the current version number + fetch-depth: 0 + - name: Install uv + uses: astral-sh/setup-uv@v7 with: python-version: ${{ matrix.python-version }} - - name: Install tox - run: | - pip install --upgrade pip - pip install tox - name: Run tests run: | - tox + uv run tox diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 6f16e2b..384cc5d 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -5,23 +5,21 @@ on: jobs: publish: runs-on: ubuntu-latest + environment: release + permissions: + contents: read + id-token: write steps: - - uses: actions/checkout@v2 + - name: Checkout repository + uses: actions/checkout@v6 with: # Tags are needed to compute the current version number fetch-depth: 0 - - name: Set up Python - uses: actions/setup-python@v2 - with: - python-version: "3.x" - - name: Install tox + - name: Install uv + uses: astral-sh/setup-uv@v7 + - name: Build the Python distribution run: | - pip install --upgrade pip - pip install tox - - name: Publish to PyPI - env: - TWINE_USERNAME: "__token__" - TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }} - TWINE_NON_INTERACTIVE: "true" + uv build + - name: Publish the Python distributions to PyPI run: | - tox -e release + uv publish --trusted-publishing=always diff --git a/.gitignore b/.gitignore index b6e4761..c1f993a 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,22 @@ -# Byte-compiled / optimized / DLL files +# Created by https://www.toptal.com/developers/gitignore/api/django +# Edit at https://www.toptal.com/developers/gitignore?templates=django + +### Django ### +*.log +*.pot +*.pyc __pycache__/ +local_settings.py +db.sqlite3 +db.sqlite3-journal +media + +# If your build process includes running collectstatic, then you probably don't need or want to include staticfiles/ +# in your Git repository. Update and uncomment the following line accordingly. +# /staticfiles/ + +### Django.Python Stack ### +# Byte-compiled / optimized / DLL files *.py[cod] *$py.class @@ -20,7 +37,6 @@ parts/ sdist/ var/ wheels/ -pip-wheel-metadata/ share/python-wheels/ *.egg-info/ .installed.cfg @@ -50,16 +66,12 @@ coverage.xml *.py,cover .hypothesis/ .pytest_cache/ +cover/ # Translations *.mo -*.pot # Django stuff: -*.log -local_settings.py -db.sqlite3 -db.sqlite3-journal # Flask stuff: instance/ @@ -72,6 +84,7 @@ instance/ docs/_build/ # PyBuilder +.pybuilder/ target/ # Jupyter Notebook @@ -82,7 +95,9 @@ profile_default/ ipython_config.py # pyenv -.python-version +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version # pipenv # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. @@ -91,7 +106,22 @@ ipython_config.py # install all needed dependencies. #Pipfile.lock -# PEP 582; used by e.g. github.com/David-OConnor/pyflow +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm __pypackages__/ # Celery stuff @@ -127,3 +157,18 @@ dmypy.json # Pyre type checker .pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +#.idea/ + +# End of https://www.toptal.com/developers/gitignore/api/django diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..e4fba21 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.12 diff --git a/NOTICE b/NOTICE new file mode 100644 index 0000000..f3ff753 --- /dev/null +++ b/NOTICE @@ -0,0 +1,13 @@ +Copyright 2022 Kitware, Inc. + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +See accompanying LICENSE file. You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. diff --git a/isic_metadata/__init__.py b/isic_metadata/__init__.py index 2f770bd..55c3ace 100644 --- a/isic_metadata/__init__.py +++ b/isic_metadata/__init__.py @@ -1,213 +1,49 @@ from __future__ import annotations -import contextlib -from dataclasses import dataclass -from importlib.metadata import PackageNotFoundError, version -from typing import Any, Literal - -with contextlib.suppress(PackageNotFoundError): - __version__ = version("isic-metadata") - - -@dataclass() -class SearchConfig: - key: str - es_property: dict[str, Any] - es_facet: dict[str, Any] - - -@dataclass() -class Field: - search: SearchConfig | None = None - label: str | None = None - type: Literal["acquisition", "clinical"] | None = None - - -FIELD_REGISTRY: dict[str, Field] = {} - -for field in [ - "blurry", - "hairy", - "marker_pen", - "personal_hx_mm", - "family_hx_mm", - "melanocytic", - "mel_ulcer", - "concomitant_biopsy", -]: - FIELD_REGISTRY[field] = Field( - search=SearchConfig( - key=field, - es_property={"type": "boolean"}, - es_facet={"terms": {"field": field}}, - ) - ) - - -for field in [ - "sex", - "diagnosis_confirm_type", - "image_type", - "dermoscopic_type", - "tbp_tile_type", - "mel_mitotic_index", - "anatom_site_general", - "anatom_site_special", - "color_tint", - "patient_id", - "lesion_id", - "rcm_case_id", - "image_manipulation", -]: - FIELD_REGISTRY[field] = Field( - search=SearchConfig( - key=field, - es_property={"type": "keyword"}, - es_facet={"terms": {"field": field}}, - ) - ) - - -FIELD_REGISTRY.update( - { - "fitzpatrick_skin_type": Field( - search=SearchConfig( - key="fitzpatrick_skin_type", - es_property={"type": "keyword"}, - es_facet={ - "terms": { - "field": "fitzpatrick_skin_type", - "order": {"_key": "asc"}, - } - }, - ) - ), - "clin_size_long_diam_mm": Field( - search=SearchConfig( - key="clin_size_long_diam_mm", - es_property={"type": "float"}, - es_facet={ - "histogram": { - "field": "clin_size_long_diam_mm", - "interval": 10, - "extended_bounds": {"min": 0, "max": 100}, - } - }, - ) - ), - "acquisition_day": Field(), - "diagnosis_1": Field( - search=SearchConfig( - key="diagnosis_1", - es_property={"type": "keyword"}, - es_facet={"terms": {"field": "diagnosis_1", "size": 100}}, - ) - ), - "diagnosis_2": Field( - search=SearchConfig( - key="diagnosis_2", - es_property={"type": "keyword"}, - es_facet={"terms": {"field": "diagnosis_2", "size": 100}}, - ) - ), - "diagnosis_3": Field( - search=SearchConfig( - key="diagnosis_3", - es_property={"type": "keyword"}, - es_facet={"terms": {"field": "diagnosis_3", "size": 100}}, - ) - ), - "diagnosis_4": Field( - search=SearchConfig( - key="diagnosis_4", - es_property={"type": "keyword"}, - es_facet={"terms": {"field": "diagnosis_4", "size": 100}}, - ) - ), - "diagnosis_5": Field( - search=SearchConfig( - key="diagnosis_5", - es_property={"type": "keyword"}, - es_facet={"terms": {"field": "diagnosis_5", "size": 100}}, - ) - ), - "anatom_site_1": Field( - search=SearchConfig( - key="anatom_site_1", - es_property={"type": "keyword"}, - es_facet={"terms": {"field": "anatom_site_1", "size": 100}}, - ) - ), - "anatom_site_2": Field( - search=SearchConfig( - key="anatom_site_2", - es_property={"type": "keyword"}, - es_facet={"terms": {"field": "anatom_site_2", "size": 100}}, - ) - ), - "anatom_site_3": Field( - search=SearchConfig( - key="anatom_site_3", - es_property={"type": "keyword"}, - es_facet={"terms": {"field": "anatom_site_3", "size": 100}}, - ) - ), - "anatom_site_4": Field( - search=SearchConfig( - key="anatom_site_4", - es_property={"type": "keyword"}, - es_facet={"terms": {"field": "anatom_site_4", "size": 100}}, - ) - ), - "anatom_site_5": Field( - search=SearchConfig( - key="anatom_site_5", - es_property={"type": "keyword"}, - es_facet={"terms": {"field": "anatom_site_5", "size": 100}}, - ) - ), - "mel_thick_mm": Field( - search=SearchConfig( - key="mel_thick_mm", - es_property={"type": "float"}, - es_facet={ - "range": { - "field": "mel_thick_mm", - "ranges": [ - {"from": 0.0, "to": 0.5}, - {"from": 0.5, "to": 1.0}, - {"from": 1.0, "to": 1.5}, - {"from": 1.5, "to": 2.0}, - {"from": 2.0, "to": 2.5}, - {"from": 2.5, "to": 3.0}, - {"from": 3.0, "to": 3.5}, - {"from": 3.5, "to": 4.0}, - {"from": 4.0, "to": 4.5}, - {"from": 4.5, "to": 5.0}, - {"from": 5.0}, - ], - } - }, - ) - ), - } +from isic_metadata.anatom_site_hierarchical import AnatomSiteEnum +from isic_metadata.diagnosis_hierarchical import DiagnosisEnum +from isic_metadata.fields import ( + Age, + AnatomSiteGeneralEnum, + AnatomSiteSpecialEnum, + ClinSizeLongDiamMm, + ColorTintEnum, + DermoscopicTypeEnum, + DiagnosisConfirmTypeEnum, + FitzpatrickSkinType, + ImageManipulationEnum, + ImageTypeEnum, + LegacyDxEnum, + MelMitoticIndexEnum, + MelThickMm, + TBPTileTypeEnum, ) - -for field in FIELD_REGISTRY: # noqa: PLC0206 - if field in [ - "blurry", - "color_tint", - "dermoscopic_type", - "hairy", - "image_type", - "marker_pen", - "image_manipulation", - ]: - FIELD_REGISTRY[field].type = "acquisition" - else: - FIELD_REGISTRY[field].type = "clinical" - -for field, label in [ - ("anatom_site_general", "Anatomic Site"), -]: - FIELD_REGISTRY[field].label = label +from isic_metadata.metadata import MetadataBatch, MetadataRow, convert_errors +from isic_metadata.registry import FIELD_REGISTRY, Field, SearchConfig +from isic_metadata.utils import get_unstructured_columns + +__all__ = [ + "FIELD_REGISTRY", + "Age", + "AnatomSiteEnum", + "AnatomSiteGeneralEnum", + "AnatomSiteSpecialEnum", + "ClinSizeLongDiamMm", + "ColorTintEnum", + "DermoscopicTypeEnum", + "DiagnosisConfirmTypeEnum", + "DiagnosisEnum", + "Field", + "FitzpatrickSkinType", + "ImageManipulationEnum", + "ImageTypeEnum", + "LegacyDxEnum", + "MelMitoticIndexEnum", + "MelThickMm", + "MetadataBatch", + "MetadataRow", + "SearchConfig", + "TBPTileTypeEnum", + "convert_errors", + "get_unstructured_columns", +] diff --git a/isic_metadata/anatom_site_hierarchical.py b/isic_metadata/anatom_site_hierarchical.py index c6e554a..1aff114 100644 --- a/isic_metadata/anatom_site_hierarchical.py +++ b/isic_metadata/anatom_site_hierarchical.py @@ -1,13 +1,11 @@ from __future__ import annotations -from enum import Enum +from enum import StrEnum from functools import cache -from typing import Any +from typing import Self -# ruff: noqa: E501 - -class AnatomSiteEnum(str, Enum): +class AnatomSiteEnum(StrEnum): head_and_neck = "Head and neck" trunk = "Trunk" upper_extremity = "Upper extremity" @@ -355,8 +353,7 @@ class AnatomSiteEnum(str, Enum): @cache def levels(value: str) -> list[str | None]: levels_list = value.split(":") - levels_list += [None] * (5 - len(levels_list)) - return levels_list + return levels_list + [None] * (5 - len(levels_list)) @staticmethod @cache @@ -371,20 +368,21 @@ def as_dict(value: str) -> dict[str, str | None]: @classmethod @cache - def reverse_ordered_hierarchy(cls) -> list[str]: - return sorted(cls, key=lambda x: x.value.count(":"), reverse=True) + def reverse_ordered_hierarchy(cls) -> list[Self]: + return sorted(cls, key=lambda x: x.count(":"), reverse=True) @classmethod @cache - def accept_terminal_values(cls, value: Any) -> Any: + def accept_terminal_values(cls, value: str) -> str: """ Allow the user to specify any terminal value of the hierarchy to obtain the relevant value. - e.g. "Scalp" can be used to obtain "Head and neck:Head:Scalp", or "Head" for "Head and neck:Head". + e.g. "Scalp" can be used to obtain "Head and neck:Head:Scalp", + or "Head" for "Head and neck:Head". """ if ":" not in value: for member in cls.reverse_ordered_hierarchy(): - if value == member.value.split(":")[-1]: - return member.value + if value == member.split(":")[-1]: + return member return value diff --git a/isic_metadata/diagnosis_hierarchical.py b/isic_metadata/diagnosis_hierarchical.py index cbb451a..9f0963e 100644 --- a/isic_metadata/diagnosis_hierarchical.py +++ b/isic_metadata/diagnosis_hierarchical.py @@ -1,13 +1,12 @@ from __future__ import annotations -from enum import Enum +from enum import StrEnum from functools import cache -from typing import Any +from typing import Self -# ruff: noqa: E501 - -class DiagnosisEnum(str, Enum): +class DiagnosisEnum(StrEnum): + # ruff: disable[E501] benign = "Benign" indeterminate = "Indeterminate" malignant = "Malignant" @@ -872,13 +871,13 @@ class DiagnosisEnum(str, Enum): malignant_malignant_melanocytic_proliferations_melanoma_melanoma_invasive_melanoma_invasive_blue_nevus_like_melanoma_invasive_resembling_blue_nevus = "Malignant:Malignant melanocytic proliferations (Melanoma):Melanoma Invasive:Melanoma Invasive, Blue nevus-like:Melanoma Invasive, resembling blue nevus" malignant_malignant_melanocytic_proliferations_melanoma_melanoma_invasive_melanoma_invasive_blue_nevus_like_melanoma_invasive_originating_from_blue_nevus = "Malignant:Malignant melanocytic proliferations (Melanoma):Melanoma Invasive:Melanoma Invasive, Blue nevus-like:Melanoma Invasive, originating from blue nevus" malignant_malignant_melanocytic_proliferations_melanoma_melanoma_invasive_melanoma_invasive_heavily_pigmented_melanoma_invasive_heavily_pigmented_resembling_epithelioid_blue_nevus_or_melanoma_developing_in_animals = "Malignant:Malignant melanocytic proliferations (Melanoma):Melanoma Invasive:Melanoma Invasive, Heavily pigmented:Melanoma Invasive, Heavily pigmented, resembling epithelioid blue nevus or melanoma developing in animals" + # ruff: enable[E501] @staticmethod @cache def levels(value: str) -> list[str | None]: levels_list = value.split(":") - levels_list += [None] * (5 - len(levels_list)) - return levels_list + return levels_list + [None] * (5 - len(levels_list)) @staticmethod @cache @@ -893,12 +892,12 @@ def as_dict(value: str) -> dict[str, str | None]: @classmethod @cache - def reverse_ordered_hierarchy(cls) -> list[str]: - return sorted(cls, key=lambda x: x.value.count(":"), reverse=True) + def reverse_ordered_hierarchy(cls) -> list[Self]: + return sorted(cls, key=lambda x: x.count(":"), reverse=True) @classmethod @cache - def accept_terminal_values(cls, value: Any) -> Any: + def accept_terminal_values(cls, value: str) -> str: """ Allow the user to specify any terminal value of the hierarchy to obtain the relevant value. @@ -906,14 +905,14 @@ def accept_terminal_values(cls, value: Any) -> Any: """ if ":" not in value: for member in cls.reverse_ordered_hierarchy(): - if value == member.value.split(":")[-1]: - return member.value + if value == member.split(":")[-1]: + return member return value @classmethod @cache - def _melanoma_diagnoses(cls): + def _melanoma_diagnoses(cls) -> list[Self]: return [ diagnosis for diagnosis in cls diff --git a/isic_metadata/fields.py b/isic_metadata/fields.py index 3a95adf..585f828 100644 --- a/isic_metadata/fields.py +++ b/isic_metadata/fields.py @@ -1,16 +1,12 @@ from __future__ import annotations -from enum import Enum +from enum import StrEnum import re -from typing import Any - -from isic_metadata.anatom_site_hierarchical import AnatomSiteEnum # noqa: F401 -from isic_metadata.diagnosis_hierarchical import DiagnosisEnum # noqa: F401 class ClinSizeLongDiamMm: @classmethod - def parse_measurement_str(cls, value: Any) -> Any: + def parse_measurement_str[T](cls, value: T) -> T | float: if isinstance(value, str): match = re.match(r"(.+)(um|mm|cm)$", value) @@ -33,7 +29,7 @@ def parse_measurement_str(cls, value: Any) -> Any: class Age: @classmethod - def handle_85plus(cls, value: Any) -> Any: + def handle_85plus[T](cls, value: T) -> T | int: if value == "85+": return 85 @@ -44,7 +40,7 @@ def clamp_upper_bound(value: int) -> int: return min(value, 85) -class DiagnosisConfirmTypeEnum(str, Enum): +class DiagnosisConfirmTypeEnum(StrEnum): histopathology = "histopathology" serial_imaging_showing_no_change = "serial imaging showing no change" single_image_expert_consensus = "single image expert consensus" @@ -52,7 +48,7 @@ class DiagnosisConfirmTypeEnum(str, Enum): single_contributor_clinical_assessment = "single contributor clinical assessment" -class LegacyDxEnum(str, Enum): +class LegacyDxEnum(StrEnum): actinic_keratosis = "actinic keratosis" adnexal_tumor = "adnexal tumor" aimp = "AIMP" @@ -91,7 +87,7 @@ class LegacyDxEnum(str, Enum): other = "other" -class ImageTypeEnum(str, Enum): +class ImageTypeEnum(StrEnum): dermoscopic = "dermoscopic" clinical_overview = "clinical: overview" clinical_close_up = "clinical: close-up" @@ -103,13 +99,13 @@ class ImageTypeEnum(str, Enum): rcm_mosaic = "RCM: mosaic" -class DermoscopicTypeEnum(str, Enum): +class DermoscopicTypeEnum(StrEnum): contact_polarized = "contact polarized" contact_non_polarized = "contact non-polarized" non_contact_polarized = "non-contact polarized" -class TBPTileTypeEnum(str, Enum): +class TBPTileTypeEnum(StrEnum): tbp_3d_white = "3D: white" tbp_3d_xp = "3D: XP" tbp_2d = "2D" @@ -119,21 +115,19 @@ class MelThickMm: _regex = re.compile(r"^([\d.]+)(\s+)?(mm)?$") @classmethod - def parse_measurement_str(cls, value: Any) -> Any: + def parse_measurement_str[T](cls, value: T) -> T | float: if isinstance(value, str): result = re.match(MelThickMm._regex, value) if not result: return value - value = result.group(1) - - return float(value) + return float(result.group(1)) return value -class MelMitoticIndexEnum(str, Enum): +class MelMitoticIndexEnum(StrEnum): zero = "0/mm^2" lt_one = "<1/mm^2" one = "1/mm^2" @@ -143,7 +137,7 @@ class MelMitoticIndexEnum(str, Enum): gt_4 = ">4/mm^2" -class AnatomSiteGeneralEnum(str, Enum): +class AnatomSiteGeneralEnum(StrEnum): head_neck = "head/neck" upper_extremity = "upper extremity" lower_extremity = "lower extremity" @@ -154,7 +148,7 @@ class AnatomSiteGeneralEnum(str, Enum): oral_genital = "oral/genital" -class AnatomSiteSpecialEnum(str, Enum): +class AnatomSiteSpecialEnum(StrEnum): acral_nos = "acral NOS" nail_nos = "nail NOS" fingernail = "fingernail" @@ -163,13 +157,13 @@ class AnatomSiteSpecialEnum(str, Enum): oral_genital = "oral or genital" -class ColorTintEnum(str, Enum): +class ColorTintEnum(StrEnum): blue = "blue" pink = "pink" none = "none" -class FitzpatrickSkinType(str, Enum): +class FitzpatrickSkinType(StrEnum): type_i = "I" type_ii = "II" type_iii = "III" @@ -178,7 +172,7 @@ class FitzpatrickSkinType(str, Enum): type_vi = "VI" -class ImageManipulationEnum(str, Enum): +class ImageManipulationEnum(StrEnum): instrument_only = "instrument only" altered = "altered" synthetic = "synthetic" diff --git a/isic_metadata/metadata.py b/isic_metadata/metadata.py index 0e76b09..e3023e2 100644 --- a/isic_metadata/metadata.py +++ b/isic_metadata/metadata.py @@ -2,7 +2,7 @@ from collections import defaultdict from decimal import Decimal -from typing import Annotated, Any, Literal +from typing import Annotated, Any, Literal, cast from annotated_types import Ge from pydantic import ( @@ -18,16 +18,16 @@ ) from pydantic_core import ErrorDetails, PydanticCustomError +from isic_metadata.anatom_site_hierarchical import AnatomSiteEnum +from isic_metadata.diagnosis_hierarchical import DiagnosisEnum from isic_metadata.fields import ( Age, - AnatomSiteEnum, AnatomSiteGeneralEnum, AnatomSiteSpecialEnum, ClinSizeLongDiamMm, ColorTintEnum, DermoscopicTypeEnum, DiagnosisConfirmTypeEnum, - DiagnosisEnum, FitzpatrickSkinType, ImageManipulationEnum, ImageTypeEnum, @@ -36,16 +36,7 @@ TBPTileTypeEnum, ) -""" -IGNORE_RCM_MODEL_CHECKS is a special attribute that allows disabling RCM model checks. It's -provided to allow batch checks to be performed on a set of metadata rows, some of which may -not be valid on a row level. e.g. if a batch of metadata rows contains RCM case ids that are -inconsistent with lesion ids, that ought to be validated even if the row with an RCM case id -has a missing image_type for instance. -""" -IGNORE_RCM_MODEL_CHECKS = "_ignore_rcm_model_checks" - -CUSTOM_MESSAGES = { +_CUSTOM_MESSAGES = { "enum": "Unsupported value for {loc}: '{value}'.", "int_parsing": "Unable to parse value as an integer.", "bool_parsing": "Unable to parse value as a boolean.", @@ -57,7 +48,7 @@ def convert_errors(e: ValidationError) -> list[ErrorDetails]: new_errors: list[ErrorDetails] = [] for error in e.errors(): - custom_message = CUSTOM_MESSAGES.get(error["type"]) + custom_message = _CUSTOM_MESSAGES.get(error["type"]) if custom_message: ctx = error.get("ctx") loc = {"loc": error.get("loc")[0]} @@ -70,7 +61,7 @@ def convert_errors(e: ValidationError) -> list[ErrorDetails]: return new_errors -def error_incompatible_fields( +def _error_incompatible_fields( field1: str, field2: str, field1_value: str | None = None, field2_value: str | None = None ) -> PydanticCustomError: message = ( @@ -93,7 +84,7 @@ def error_incompatible_fields( ) -def error_missing_field( +def _error_missing_field( field1: str, field2: str, field1_value: str | None = None, field2_value: str | None = None ) -> PydanticCustomError: message = ( @@ -265,55 +256,72 @@ class MetadataRow(BaseModel): blurry: bool | None = None color_tint: ColorTintEnum | None = None - @computed_field + @computed_field # type: ignore[prop-decorator] + @property def diagnosis_1(self) -> str | None: return DiagnosisEnum.levels(self.diagnosis)[0] if self.diagnosis else None - @computed_field + @computed_field # type: ignore[prop-decorator] + @property def diagnosis_2(self) -> str | None: return DiagnosisEnum.levels(self.diagnosis)[1] if self.diagnosis else None - @computed_field + @computed_field # type: ignore[prop-decorator] + @property def diagnosis_3(self) -> str | None: return DiagnosisEnum.levels(self.diagnosis)[2] if self.diagnosis else None - @computed_field + @computed_field # type: ignore[prop-decorator] + @property def diagnosis_4(self) -> str | None: return DiagnosisEnum.levels(self.diagnosis)[3] if self.diagnosis else None - @computed_field + @computed_field # type: ignore[prop-decorator] + @property def diagnosis_5(self) -> str | None: return DiagnosisEnum.levels(self.diagnosis)[4] if self.diagnosis else None - @computed_field + @computed_field # type: ignore[prop-decorator] + @property def anatom_site_1(self) -> str | None: return AnatomSiteEnum.levels(self.anatom_site)[0] if self.anatom_site else None - @computed_field + @computed_field # type: ignore[prop-decorator] + @property def anatom_site_2(self) -> str | None: return AnatomSiteEnum.levels(self.anatom_site)[1] if self.anatom_site else None - @computed_field + @computed_field # type: ignore[prop-decorator] + @property def anatom_site_3(self) -> str | None: return AnatomSiteEnum.levels(self.anatom_site)[2] if self.anatom_site else None - @computed_field + @computed_field # type: ignore[prop-decorator] + @property def anatom_site_4(self) -> str | None: return AnatomSiteEnum.levels(self.anatom_site)[3] if self.anatom_site else None - @computed_field + @computed_field # type: ignore[prop-decorator] + @property def anatom_site_5(self) -> str | None: return AnatomSiteEnum.levels(self.anatom_site)[4] if self.anatom_site else None - __slots__ = (IGNORE_RCM_MODEL_CHECKS,) + __slots__ = ("_ignore_rcm_model_checks",) + _ignore_rcm_model_checks: bool # see https://github.com/pydantic/pydantic/issues/655#issuecomment-570312649 for details on # implementing a private property to be used internally. - def __init__(self, **kwargs) -> None: - object.__setattr__(self, IGNORE_RCM_MODEL_CHECKS, False) + def __init__(self, *, _ignore_rcm_model_checks: bool = False, **kwargs: Any) -> None: + """ + Create a MetadataRow instance. - if IGNORE_RCM_MODEL_CHECKS in kwargs: - object.__setattr__(self, IGNORE_RCM_MODEL_CHECKS, kwargs.pop(IGNORE_RCM_MODEL_CHECKS)) + _ignore_rcm_model_checks is a special attribute that allows disabling RCM model checks. It's + provided to allow batch checks to be performed on a set of metadata rows, some of which may + not be valid on a row level. e.g. if a batch of metadata rows contains RCM case ids that are + inconsistent with lesion ids, that ought to be validated even if the row with an RCM case id + has a missing image_type for instance. + """ + object.__setattr__(self, "_ignore_rcm_model_checks", _ignore_rcm_model_checks) super().__init__(**kwargs) @@ -357,10 +365,10 @@ def handle_hierarchical_modes_and_unstructured_fields( @field_validator("*", mode="before") @classmethod - def strip(cls, v: Any) -> Any: + def strip[T](cls, v: T) -> T | None: # str_strip_whitespace doesn't seem to work for Literal values as it does for str and enum if isinstance(v, str): - v = v.strip() + v = cast("T", v.strip()) # drop empty strings as though they were never passed return None if v == "" else v @@ -375,9 +383,9 @@ def strip(cls, v: Any) -> Any: mode="before", ) @classmethod - def lower(cls, v: Any) -> Any: + def lower[T](cls, v: T) -> T: if isinstance(v, str): - v = v.lower() + v = cast("T", v.lower()) return v @model_validator(mode="after") @@ -393,10 +401,10 @@ def validate_melanoma_fields(self) -> MetadataRow: continue if not self.diagnosis: - raise error_missing_field(field, "diagnosis", field2_value=self.diagnosis) + raise _error_missing_field(field, "diagnosis", field2_value=self.diagnosis) if not DiagnosisEnum.is_melanoma(self.diagnosis): - raise error_incompatible_fields( + raise _error_incompatible_fields( field, "diagnosis", field2_value=self.diagnosis.value ) @@ -404,21 +412,21 @@ def validate_melanoma_fields(self) -> MetadataRow: @model_validator(mode="after") def validate_rcm_fields(self) -> MetadataRow: - if getattr(self, IGNORE_RCM_MODEL_CHECKS): + if self._ignore_rcm_model_checks: return self if not self.rcm_case_id: return self if not self.image_type: - raise error_missing_field("rcm_case_id", "image_type") + raise _error_missing_field("rcm_case_id", "image_type") if self.image_type not in [ ImageTypeEnum.rcm_macroscopic, ImageTypeEnum.rcm_tile, ImageTypeEnum.rcm_mosaic, ]: - raise error_incompatible_fields( + raise _error_incompatible_fields( "rcm_case_id", "image_type", field2_value=ImageTypeEnum.rcm_macroscopic ) @@ -430,10 +438,10 @@ def validate_dermoscopic_fields(self) -> MetadataRow: return self if not self.image_type: - raise error_missing_field("dermoscopic_type", "image_type") + raise _error_missing_field("dermoscopic_type", "image_type") if self.image_type != ImageTypeEnum.dermoscopic: - raise error_incompatible_fields( + raise _error_incompatible_fields( "dermoscopic_type", "image_type", field2_value="dermoscopic" ) @@ -445,7 +453,7 @@ def validate_anatom_site_special(self) -> MetadataRow: return self if not self.anatom_site_general: - raise error_missing_field("anatom_site_special", "anatom_site_general") + raise _error_missing_field("anatom_site_special", "anatom_site_general") valid_combinations = { AnatomSiteSpecialEnum.acral_nos: [ @@ -480,11 +488,11 @@ def validate_anatom_site_special(self) -> MetadataRow: ], } - if self.anatom_site_special.value not in valid_combinations: + if self.anatom_site_special not in valid_combinations: return self - if self.anatom_site_general.value not in valid_combinations[self.anatom_site_special.value]: - raise error_incompatible_fields( + if self.anatom_site_general not in valid_combinations[self.anatom_site_special]: + raise _error_incompatible_fields( "anatom_site_special", "anatom_site_general", self.anatom_site_special.value, @@ -499,13 +507,13 @@ def validate_tbp_tile_fields(self) -> MetadataRow: return self if not self.image_type: - raise error_missing_field("tbp_tile_type", "image_type") + raise _error_missing_field("tbp_tile_type", "image_type") if self.image_type not in [ ImageTypeEnum.tbp_tile_close_up, ImageTypeEnum.tbp_tile_overview, ]: - raise error_incompatible_fields( + raise _error_incompatible_fields( "tbp_tile_type", "image_type", field2_value=self.image_type.value ) @@ -516,7 +524,7 @@ def validate_concomitant_biopsy(self) -> MetadataRow: if self.concomitant_biopsy and ( not self.diagnosis_confirm_type or self.diagnosis_confirm_type != "histopathology" ): - raise error_missing_field( + raise _error_missing_field( "concomitant_biopsy", "diagnosis_confirm_type", field2_value="histopathology" ) diff --git a/isic_metadata/registry.py b/isic_metadata/registry.py new file mode 100644 index 0000000..490373f --- /dev/null +++ b/isic_metadata/registry.py @@ -0,0 +1,208 @@ +from __future__ import annotations + +from dataclasses import dataclass +from typing import Any, Literal + + +@dataclass() +class SearchConfig: + key: str + es_property: dict[str, Any] + es_facet: dict[str, Any] + + +@dataclass() +class Field: + search: SearchConfig | None = None + label: str | None = None + type: Literal["acquisition", "clinical"] | None = None + + +FIELD_REGISTRY: dict[str, Field] = {} + +for field in [ + "blurry", + "hairy", + "marker_pen", + "personal_hx_mm", + "family_hx_mm", + "melanocytic", + "mel_ulcer", + "concomitant_biopsy", +]: + FIELD_REGISTRY[field] = Field( + search=SearchConfig( + key=field, + es_property={"type": "boolean"}, + es_facet={"terms": {"field": field}}, + ) + ) + + +for field in [ + "sex", + "diagnosis_confirm_type", + "image_type", + "dermoscopic_type", + "tbp_tile_type", + "mel_mitotic_index", + "anatom_site_general", + "anatom_site_special", + "color_tint", + "patient_id", + "lesion_id", + "rcm_case_id", + "image_manipulation", +]: + FIELD_REGISTRY[field] = Field( + search=SearchConfig( + key=field, + es_property={"type": "keyword"}, + es_facet={"terms": {"field": field}}, + ) + ) + + +FIELD_REGISTRY.update( + { + "fitzpatrick_skin_type": Field( + search=SearchConfig( + key="fitzpatrick_skin_type", + es_property={"type": "keyword"}, + es_facet={ + "terms": { + "field": "fitzpatrick_skin_type", + "order": {"_key": "asc"}, + } + }, + ) + ), + "clin_size_long_diam_mm": Field( + search=SearchConfig( + key="clin_size_long_diam_mm", + es_property={"type": "float"}, + es_facet={ + "histogram": { + "field": "clin_size_long_diam_mm", + "interval": 10, + "extended_bounds": {"min": 0, "max": 100}, + } + }, + ) + ), + "acquisition_day": Field(), + "diagnosis_1": Field( + search=SearchConfig( + key="diagnosis_1", + es_property={"type": "keyword"}, + es_facet={"terms": {"field": "diagnosis_1", "size": 100}}, + ) + ), + "diagnosis_2": Field( + search=SearchConfig( + key="diagnosis_2", + es_property={"type": "keyword"}, + es_facet={"terms": {"field": "diagnosis_2", "size": 100}}, + ) + ), + "diagnosis_3": Field( + search=SearchConfig( + key="diagnosis_3", + es_property={"type": "keyword"}, + es_facet={"terms": {"field": "diagnosis_3", "size": 100}}, + ) + ), + "diagnosis_4": Field( + search=SearchConfig( + key="diagnosis_4", + es_property={"type": "keyword"}, + es_facet={"terms": {"field": "diagnosis_4", "size": 100}}, + ) + ), + "diagnosis_5": Field( + search=SearchConfig( + key="diagnosis_5", + es_property={"type": "keyword"}, + es_facet={"terms": {"field": "diagnosis_5", "size": 100}}, + ) + ), + "anatom_site_1": Field( + search=SearchConfig( + key="anatom_site_1", + es_property={"type": "keyword"}, + es_facet={"terms": {"field": "anatom_site_1", "size": 100}}, + ) + ), + "anatom_site_2": Field( + search=SearchConfig( + key="anatom_site_2", + es_property={"type": "keyword"}, + es_facet={"terms": {"field": "anatom_site_2", "size": 100}}, + ) + ), + "anatom_site_3": Field( + search=SearchConfig( + key="anatom_site_3", + es_property={"type": "keyword"}, + es_facet={"terms": {"field": "anatom_site_3", "size": 100}}, + ) + ), + "anatom_site_4": Field( + search=SearchConfig( + key="anatom_site_4", + es_property={"type": "keyword"}, + es_facet={"terms": {"field": "anatom_site_4", "size": 100}}, + ) + ), + "anatom_site_5": Field( + search=SearchConfig( + key="anatom_site_5", + es_property={"type": "keyword"}, + es_facet={"terms": {"field": "anatom_site_5", "size": 100}}, + ) + ), + "mel_thick_mm": Field( + search=SearchConfig( + key="mel_thick_mm", + es_property={"type": "float"}, + es_facet={ + "range": { + "field": "mel_thick_mm", + "ranges": [ + {"from": 0.0, "to": 0.5}, + {"from": 0.5, "to": 1.0}, + {"from": 1.0, "to": 1.5}, + {"from": 1.5, "to": 2.0}, + {"from": 2.0, "to": 2.5}, + {"from": 2.5, "to": 3.0}, + {"from": 3.0, "to": 3.5}, + {"from": 3.5, "to": 4.0}, + {"from": 4.0, "to": 4.5}, + {"from": 4.5, "to": 5.0}, + {"from": 5.0}, + ], + } + }, + ) + ), + } +) + +for field in FIELD_REGISTRY: # noqa: PLC0206 + if field in [ + "blurry", + "color_tint", + "dermoscopic_type", + "hairy", + "image_type", + "marker_pen", + "image_manipulation", + ]: + FIELD_REGISTRY[field].type = "acquisition" + else: + FIELD_REGISTRY[field].type = "clinical" + +for field, label in [ + ("anatom_site_general", "Anatomic Site"), +]: + FIELD_REGISTRY[field].label = label diff --git a/isic_metadata/utils.py b/isic_metadata/utils.py index c25249a..05d5477 100644 --- a/isic_metadata/utils.py +++ b/isic_metadata/utils.py @@ -1,7 +1,12 @@ -from collections.abc import Sequence +from __future__ import annotations + +from typing import TYPE_CHECKING from isic_metadata.metadata import MetadataRow +if TYPE_CHECKING: + from collections.abc import Sequence + def get_unstructured_columns(column_names: Sequence[str]) -> list[str]: reserved_columns = {"filename", "isic_id"} diff --git a/pyproject.toml b/pyproject.toml index d4a4f2c..fce6bf4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,13 +1,67 @@ [build-system] -requires = ["setuptools >= 42", "wheel", "setuptools-scm[toml]>=3.4"] -build-backend = "setuptools.build_meta" +requires = ["hatchling>=1,<2", "hatch-vcs>=0.4,<1"] +build-backend = "hatchling.build" -[tool.setuptools_scm] +[project] +name = "isic-metadata" +description = "" +readme = "README.md" +requires-python = ">=3.12" +license = "Apache-2.0" +license-files = ["LICENSE", "NOTICE"] +maintainers = [{ name = "Kitware, Inc.", email = "kitware@kitware.com" }] +keywords = [ + "isic", + "isic-archive", +] +classifiers = [ + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Developers", + "Operating System :: OS Independent", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", +] +dependencies = [ + "pydantic>=2.4", +] +dynamic = ["version"] + +[project.urls] +Repository = "https://github.com/ImageMarkup/isic-metadata" +"Bug Reports" = "https://github.com/ImageMarkup/isic-metadata/issues" + +[dependency-groups] +dev = [ + "tox==4.49.1", + "tox-uv==1.33.2", +] +lint = [ + "ruff==0.15.5", +] +type = [ + "mypy==1.19.1", +] +test = [ + "hypothesis==6.151.9", + "pydantic-to-pyarrow==0.1.6", + "pytest==9.0.2", + "pytest-cov==7.0.0", + "pytest-mock==3.15.1", +] + +[tool.hatch.build] +only-include = [ + "isic_metadata", +] + +[tool.hatch.version] +source = "vcs" [tool.ruff] line-length = 100 -target-version = "py310" -extend-exclude = ["typings"] [tool.ruff.lint] select = ["ALL"] @@ -16,7 +70,7 @@ ignore = [ # https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules "COM812", # missing-trailing-comma "COM819", # prohibited-trailing-comma - "D206", # indent-with-spaces + "D206", # docstring-tab-indentation "D300", # triple-single-quotes "E111", # indentation-with-invalid-multiple "E114", # indentation-with-invalid-multiple-comment @@ -26,41 +80,105 @@ ignore = [ "Q", # flake8-quotes "W191", # tab-indentation - "A003", # Class attribute is shadowing a Python builtin + # Incompatible with Django + "A003", # builtin-attribute-shadowing + "ARG001", # unused-function-argument + "ARG002", # unused-method-argument + "RUF012", # mutable-class-default + + # Overly burdensome "ANN", # flake8-annotations - "ARG001", # Unused function argument - "ARG002", # Unused method argument - "D1", # Missing docstring - "EM101", # Exception must not use a string literal, assign to variable first - "EM102", # Exception must not use an f-string literal, assign to variable first - "ERA001", # Found commented-out code + "D1", # undocumented-* + "EM", # flake8-errmsg + "ERA001", # commented-out-code "FIX", # flake8-fixme - "TD002", # Missing author in TODO - "TD003", # Missing issue link on the line following this TODO - "TRY003", # Avoid specifying long messages outside the exception class - - # Excessive - "RET503", # implict return - "PLR2004", # magic value used in comparison - - "TC003", # type checking blocks + "RET505", # superfluous-else-return + "RET506", # superfluous-else-raise + "RET507", # superfluous-else-continue + "RET508", # superfluous-else-break + "TD002", # missing-todo-author + "TD003", # missing-todo-link + "TRY003", # raise-vanilla-args + # Project-specific ] [tool.ruff.lint.per-file-ignores] -"tests/**" = [ - "PLR0913", # Too many arguments to function call - "PLR2004", # Magic value used in comparison +"**/tests/**" = [ + "DJ007", # django-all-with-model-form + "DJ008", # django-model-without-dunder-str + "INP001", # implicit-namespace-package + "PLR0913", # too-many-arguments + "PLR2004", # magic-value-comparison "S", # flake8-bandit - "SLF001", # Private member accessed + "SLF001", # private-member-access ] -[tool.ruff.format] -quote-style = "double" +[tool.ruff.lint.flake8-boolean-trap] +extend-allowed-calls = ["pydantic.Field", "django.db.models.Value"] + +[tool.ruff.lint.flake8-bugbear] +extend-immutable-calls = ["ninja.Query"] + +[tool.ruff.lint.flake8-self] +extend-ignore-names = ["_base_manager", "_default_manager", "_meta"] + +[tool.ruff.lint.flake8-type-checking] +runtime-evaluated-base-classes = ["pydantic.BaseModel"] +runtime-evaluated-decorators = ["pydantic.validate_call"] [tool.ruff.lint.isort] # Sort by name, don't cluster "from" vs "import" force-sort-within-sections = true +# Deferred annotations allows TC* rules to move more imports into TYPE_CHECKING blocks +required-imports = ["from __future__ import annotations"] [tool.ruff.lint.pydocstyle] convention = "pep257" + +[tool.mypy] +files = [ + "isic_metadata", + "tests", +] +check_untyped_defs = true +show_error_codes = true +strict = true +warn_redundant_casts = true +warn_unused_configs = true +warn_unused_ignores = true +mypy_path = [ + # Use the same pythonpath for MyPy as for Pytest + "tests", +] + +[[tool.mypy.overrides]] +module = [ +] +ignore_missing_imports = true + +[tool.pytest.ini_options] +testpaths = ["tests"] +# Allow test utility modules to be imported without adding the root directory to the pythonpath, +# which would cause the local "isic_metadata" module to shadow the install. +pythonpath = ["tests"] +addopts = [ + # Use the Pytest-recommended "importlib" mode + "--import-mode=importlib", + "--strict-config", + "--strict-markers", + "--showlocals", + "--verbose", + "--cov", +] +filterwarnings = [ + "error", + # pytest often causes unclosed socket warnings + 'ignore:unclosed =2.4"], - extras_require={ - "test": [ - "coverage[toml]", - "hypothesis", - "pydantic-to-pyarrow", - "pytest", - "pytest-mock", - "pytest-cov", - ], - }, - packages=find_packages(), - # needed to py.typed - include_package_data=True, -) diff --git a/tests/test_batch.py b/tests/test_batch.py index b99846c..75607af 100644 --- a/tests/test_batch.py +++ b/tests/test_batch.py @@ -1,10 +1,12 @@ +from __future__ import annotations + from pydantic import ValidationError import pytest from isic_metadata.metadata import MetadataBatch, MetadataRow -def test_batch(): +def test_batch() -> None: MetadataBatch( items=[ MetadataRow.model_validate({"sex": "male"}), @@ -13,7 +15,7 @@ def test_batch(): ) -def test_lesions_belong_to_same_patient(): +def test_lesions_belong_to_same_patient() -> None: with pytest.raises(ValidationError) as excinfo: MetadataBatch( items=[ @@ -25,7 +27,7 @@ def test_lesions_belong_to_same_patient(): assert "belong to multiple patients" in excinfo.value.errors()[0]["msg"] -def test_blank_lesions_dont_belong_to_same_patient(): +def test_blank_lesions_dont_belong_to_same_patient() -> None: MetadataBatch( items=[ MetadataRow(lesion_id="", patient_id="foopatient"), @@ -34,7 +36,7 @@ def test_blank_lesions_dont_belong_to_same_patient(): ) -def test_rcm_case_has_at_most_one_macroscopic_image(): +def test_rcm_case_has_at_most_one_macroscopic_image() -> None: with pytest.raises(ValidationError) as excinfo: MetadataBatch( items=[ @@ -53,7 +55,7 @@ def test_rcm_case_has_at_most_one_macroscopic_image(): ) -def test_rcm_cases_belong_to_same_lesion(): +def test_rcm_cases_belong_to_same_lesion() -> None: with pytest.raises(ValidationError) as excinfo: MetadataBatch( items=[ @@ -69,7 +71,7 @@ def test_rcm_cases_belong_to_same_lesion(): assert "belong to multiple lesions" in excinfo.value.errors()[0]["msg"] -def test_blank_rcm_cases_dont_belong_to_same_lesion(): +def test_blank_rcm_cases_dont_belong_to_same_lesion() -> None: MetadataBatch( items=[ MetadataRow(rcm_case_id="", lesion_id="foolesion"), diff --git a/tests/test_dependent_fields.py b/tests/test_dependent_fields.py index e4205a4..10a4ee6 100644 --- a/tests/test_dependent_fields.py +++ b/tests/test_dependent_fields.py @@ -1,3 +1,5 @@ +from __future__ import annotations + from typing import Any from pydantic import ValidationError @@ -17,7 +19,7 @@ ) def test_melanoma_fields_require_melanoma_diagnosis( diagnosis: str | None, field_name: str, field_value: Any -): +) -> None: with pytest.raises(ValidationError) as excinfo: MetadataRow.model_validate({field_name: field_value, "diagnosis": diagnosis}) assert len(excinfo.value.errors()) == 1 @@ -27,7 +29,7 @@ def test_melanoma_fields_require_melanoma_diagnosis( @pytest.mark.skip("TODO: https://github.com/ImageMarkup/tracker/issues/141") -def test_diagnosis_confirm_type_requires_diagnosis(): +def test_diagnosis_confirm_type_requires_diagnosis() -> None: with pytest.raises(ValidationError) as excinfo: MetadataRow.model_validate({"diagnosis_confirm_type": "histopathology"}) assert len(excinfo.value.errors()) == 1 @@ -38,7 +40,7 @@ def test_diagnosis_confirm_type_requires_diagnosis(): ) -def test_dermoscopic_type_requires_image_type_dermoscopic(): +def test_dermoscopic_type_requires_image_type_dermoscopic() -> None: with pytest.raises(ValidationError) as excinfo: MetadataRow.model_validate({"dermoscopic_type": "contact polarized"}) assert len(excinfo.value.errors()) == 1 @@ -49,7 +51,7 @@ def test_dermoscopic_type_requires_image_type_dermoscopic(): ) -def test_dermoscopic_type_requires_dermoscopic_image_type(): +def test_dermoscopic_type_requires_dermoscopic_image_type() -> None: with pytest.raises(ValidationError) as excinfo: MetadataRow.model_validate( {"dermoscopic_type": "contact polarized", "image_type": "clinical: overview"} @@ -58,7 +60,7 @@ def test_dermoscopic_type_requires_dermoscopic_image_type(): assert "dermoscopic_type is incompatible with image_type" in excinfo.value.errors()[0]["msg"] -def test_rcm_case_id_requires_rcm_image_type(): +def test_rcm_case_id_requires_rcm_image_type() -> None: with pytest.raises(ValidationError) as excinfo: MetadataRow.model_validate({"rcm_case_id": "12345"}) assert len(excinfo.value.errors()) == 1 @@ -67,7 +69,7 @@ def test_rcm_case_id_requires_rcm_image_type(): MetadataRow.model_validate({"rcm_case_id": "12345", "image_type": "RCM: tile"}) -def test_rcm_model_checks_disabling(): +def test_rcm_model_checks_disabling() -> None: with pytest.raises(ValidationError) as excinfo: MetadataRow(rcm_case_id="12345") assert len(excinfo.value.errors()) == 1 @@ -76,7 +78,7 @@ def test_rcm_model_checks_disabling(): MetadataRow(rcm_case_id="12345", _ignore_rcm_model_checks=True) -def test_tbp_tile_type_requires_image_type_tbp_tile(): +def test_tbp_tile_type_requires_image_type_tbp_tile() -> None: with pytest.raises(ValidationError) as excinfo: MetadataRow.model_validate({"tbp_tile_type": "2D"}) assert len(excinfo.value.errors()) == 1 @@ -86,7 +88,7 @@ def test_tbp_tile_type_requires_image_type_tbp_tile(): MetadataRow.model_validate({"tbp_tile_type": "2D", "image_type": "TBP tile: overview"}) -def test_tbp_tile_type_requires_tbp_tile_image_type(): +def test_tbp_tile_type_requires_tbp_tile_image_type() -> None: with pytest.raises(ValidationError) as excinfo: MetadataRow.model_validate({"tbp_tile_type": "2D", "image_type": "clinical: overview"}) assert len(excinfo.value.errors()) == 1 @@ -96,7 +98,7 @@ def test_tbp_tile_type_requires_tbp_tile_image_type(): MetadataRow.model_validate({"tbp_tile_type": "2D", "image_type": "TBP tile: overview"}) -def test_concomitant_biopsy_requires_histopathology(): +def test_concomitant_biopsy_requires_histopathology() -> None: with pytest.raises(ValidationError) as excinfo: MetadataRow.model_validate( {"concomitant_biopsy": True, "diagnosis_confirm_type": "single image expert consensus"} diff --git a/tests/test_fields.py b/tests/test_fields.py index ecf15ce..03dd45e 100644 --- a/tests/test_fields.py +++ b/tests/test_fields.py @@ -1,3 +1,5 @@ +from __future__ import annotations + from decimal import Decimal from typing import Any @@ -28,7 +30,7 @@ ) def test_non_str_types( field: str, str_value: str, parsed_value: Any, dependent_fields: dict[str, Any] -): +) -> None: as_str = MetadataRow.model_validate({field: str_value, **dependent_fields}) as_real = MetadataRow.model_validate({field: parsed_value, **dependent_fields}) @@ -36,20 +38,20 @@ def test_non_str_types( @pytest.mark.parametrize(("emptyish_value"), ["", " ", "\t", None]) -def test_empty_fields_are_omitted(emptyish_value: Any): +def test_empty_fields_are_omitted(emptyish_value: Any) -> None: metadata = MetadataRow.model_validate({"diagnosis": "Benign", "mel_ulcer": emptyish_value}) assert metadata.diagnosis == "Benign" assert metadata.mel_thick_mm is None -def test_unstructured_fields(): +def test_unstructured_fields() -> None: metadata = MetadataRow.model_validate({"diagnosis": "Benign", "hello": "world"}) assert metadata.diagnosis == "Benign" assert metadata.unstructured["hello"] == "world" @pytest.mark.parametrize(("melanoma_diagnosis"), DiagnosisEnum._melanoma_diagnoses()) -def test_melanoma_fields(melanoma_diagnosis: str): +def test_melanoma_fields(melanoma_diagnosis: str) -> None: with pytest.raises(ValidationError) as excinfo: # mel_ulcer can only be set if diagnosis is melanoma MetadataRow.model_validate({"diagnosis": "Benign", "mel_ulcer": True}) @@ -61,17 +63,17 @@ def test_melanoma_fields(melanoma_diagnosis: str): @given(age=st.integers(min_value=0).map(str)) -def test_age_ceiling(age: str): +def test_age_ceiling(age: str) -> None: metadata = MetadataRow.model_validate({"age": age}) assert metadata.age is not None assert metadata.age <= 85 -def test_age_special_case(): +def test_age_special_case() -> None: assert MetadataRow.model_validate({"age": "85+"}).age == 85 -def test_fitzpatrick_skin_type(): +def test_fitzpatrick_skin_type() -> None: MetadataRow.model_validate({"fitzpatrick_skin_type": "I"}) @@ -85,12 +87,12 @@ def test_fitzpatrick_skin_type(): ("3.25", Decimal("3.25")), ], ) -def test_mel_thick_mm(raw: str, parsed: float): +def test_mel_thick_mm(raw: str, parsed: float) -> None: metadata = MetadataRow.model_validate({"diagnosis": "Melanoma Invasive", "mel_thick_mm": raw}) assert metadata.mel_thick_mm == parsed -def test_mel_thick_mm_invalid(): +def test_mel_thick_mm_invalid() -> None: with pytest.raises(ValidationError) as excinfo: MetadataRow.model_validate({"mel_thick_mm": "foo"}) assert len(excinfo.value.errors()) == 1 @@ -105,13 +107,13 @@ def test_mel_thick_mm_invalid(): st.integers(min_value=1, max_value=9999), ).map(lambda x: f"{x} mm") ) -def test_clin_size_long_diam_mm_always_rounded(clin_size: str): +def test_clin_size_long_diam_mm_always_rounded(clin_size: str) -> None: metadata = MetadataRow.model_validate({"clin_size_long_diam_mm": clin_size}) assert isinstance(metadata.clin_size_long_diam_mm, Decimal) assert metadata.clin_size_long_diam_mm == round(metadata.clin_size_long_diam_mm, ndigits=1) -def test_clin_size_long_diam_mm_invalid(): +def test_clin_size_long_diam_mm_invalid() -> None: with pytest.raises(ValidationError) as excinfo: MetadataRow.model_validate({"clin_size_long_diam_mm": "foo"}) assert len(excinfo.value.errors()) == 1 @@ -132,7 +134,9 @@ def test_clin_size_long_diam_mm_invalid(): ), ], ) -def test_anatom_site_special(anatom_site_special: str, anatom_site_general_values: list[str]): +def test_anatom_site_special( + anatom_site_special: str, anatom_site_general_values: list[str] +) -> None: for anatom_site_general_value in anatom_site_general_values: metadata = MetadataRow.model_validate( { @@ -156,7 +160,7 @@ def test_anatom_site_special(anatom_site_special: str, anatom_site_general_value assert "is incompatible with anatom_site_general" in excinfo.value.errors()[0]["msg"] -def test_anatom_site_special_requires_anatom_site_general(): +def test_anatom_site_special_requires_anatom_site_general() -> None: with pytest.raises(ValidationError) as excinfo: MetadataRow.model_validate({"anatom_site_special": "acral NOS"}) assert len(excinfo.value.errors()) == 1 diff --git a/tests/test_hierarchical_anatom_site.py b/tests/test_hierarchical_anatom_site.py index 95bddb0..8ee11e7 100644 --- a/tests/test_hierarchical_anatom_site.py +++ b/tests/test_hierarchical_anatom_site.py @@ -1,3 +1,5 @@ +from __future__ import annotations + from pydantic import ValidationError import pytest @@ -21,11 +23,11 @@ ), ], ) -def test_levels_at_each_depth(value, expected): +def test_levels_at_each_depth(value: str, expected: list[str | None]) -> None: assert AnatomSiteEnum.levels(value) == expected -def test_accept_terminal_values_resolves_leaf(): +def test_accept_terminal_values_resolves_leaf() -> None: assert AnatomSiteEnum.accept_terminal_values("Scalp") == "Head and neck:Head:Scalp" assert ( AnatomSiteEnum.accept_terminal_values("Helix of pinna") @@ -33,12 +35,12 @@ def test_accept_terminal_values_resolves_leaf(): ) -def test_accept_terminal_values_passes_through_qualified(): +def test_accept_terminal_values_passes_through_qualified() -> None: qualified = "Head and neck:Head:Scalp" assert AnatomSiteEnum.accept_terminal_values(qualified) == qualified -def test_accept_terminal_values_has_unique_terminals(): +def test_accept_terminal_values_has_unique_terminals() -> None: terminal_nodes = [member.value.split(":")[-1] for member in AnatomSiteEnum] assert len(terminal_nodes) == len(set(terminal_nodes)) @@ -59,20 +61,20 @@ def test_accept_terminal_values_has_unique_terminals(): ), ], ) -def test_metadata_row_accepts_hierarchical_anatom_site(raw, parsed): +def test_metadata_row_accepts_hierarchical_anatom_site(raw: str, parsed: list[str]) -> None: metadata = MetadataRow.model_validate({"anatom_site": raw}) for i, value in enumerate(parsed, start=1): assert getattr(metadata, f"anatom_site_{i}") == value -def test_top_level_anatom_site_is_never_exported(): +def test_top_level_anatom_site_is_never_exported() -> None: metadata = MetadataRow.model_validate({"anatom_site": "Head and neck"}) dumped = metadata.model_dump() assert "anatom_site" not in dumped assert dumped["anatom_site_1"] == "Head and neck" -def test_metadata_row_reassembles_individual_levels(): +def test_metadata_row_reassembles_individual_levels() -> None: metadata = MetadataRow.model_validate( { "anatom_site_1": "Head and neck", @@ -87,7 +89,7 @@ def test_metadata_row_reassembles_individual_levels(): assert metadata.anatom_site_5 is None -def test_single_value_anatom_site_is_favored_over_levels(): +def test_single_value_anatom_site_is_favored_over_levels() -> None: metadata = MetadataRow.model_validate( { "anatom_site": "Lower extremity:Foot:Toes", @@ -100,7 +102,7 @@ def test_single_value_anatom_site_is_favored_over_levels(): assert metadata.anatom_site_3 == "Toes" -def test_anatom_site_validation_is_idempotent(): +def test_anatom_site_validation_is_idempotent() -> None: metadata = MetadataRow.model_validate({"anatom_site": "Scalp"}) metadata_2 = MetadataRow.model_validate( metadata.model_dump(exclude_unset=True, exclude_none=True, exclude={"unstructured"}) @@ -108,29 +110,29 @@ def test_anatom_site_validation_is_idempotent(): assert metadata == metadata_2 -def test_anatom_site_general_and_special_unaffected(): +def test_anatom_site_general_and_special_unaffected() -> None: metadata = MetadataRow.model_validate( { "anatom_site_general": "head/neck", "anatom_site_special": "oral or genital", } ) - assert metadata.anatom_site_general.value == "head/neck" - assert metadata.anatom_site_special.value == "oral or genital" + assert metadata.anatom_site_general == "head/neck" + assert metadata.anatom_site_special == "oral or genital" -def test_anatom_site_general_coexists_with_hierarchical(): +def test_anatom_site_general_coexists_with_hierarchical() -> None: metadata = MetadataRow.model_validate( { "anatom_site_general": "head/neck", "anatom_site": "Head and neck:Head:Scalp", } ) - assert metadata.anatom_site_general.value == "head/neck" + assert metadata.anatom_site_general == "head/neck" assert metadata.anatom_site_1 == "Head and neck" assert metadata.anatom_site_3 == "Scalp" -def test_invalid_anatom_site_raises_error(): +def test_invalid_anatom_site_raises_error() -> None: with pytest.raises(ValidationError): MetadataRow.model_validate({"anatom_site": "Not a real site"}) diff --git a/tests/test_hierarchical_diagnosis.py b/tests/test_hierarchical_diagnosis.py index 18be21c..42e81db 100644 --- a/tests/test_hierarchical_diagnosis.py +++ b/tests/test_hierarchical_diagnosis.py @@ -1,3 +1,5 @@ +from __future__ import annotations + from pydantic import ValidationError import pytest @@ -27,25 +29,25 @@ ), ], ) -def test_diagnosis(raw, parsed): +def test_diagnosis(raw: str, parsed: list[str]) -> None: metadata = MetadataRow.model_validate({"diagnosis": raw}) for i, diagnosis in enumerate(parsed, start=1): assert getattr(metadata, f"diagnosis_{i}") == diagnosis -def test_top_level_diagnosis_is_never_exported(): +def test_top_level_diagnosis_is_never_exported() -> None: metadata = MetadataRow.model_validate({"diagnosis": "Benign"}) assert "diagnosis" not in metadata.model_dump() assert metadata.diagnosis_1 == "Benign" -def test_diagnosis_enum_has_unique_terminal_values(): +def test_diagnosis_enum_has_unique_terminal_values() -> None: terminal_nodes = [member.value.split(":")[-1] for member in DiagnosisEnum] assert len(terminal_nodes) == len(set(terminal_nodes)) -def test_single_value_diagnosis_is_favored(): +def test_single_value_diagnosis_is_favored() -> None: # test that passing in a single diagnosis value is favored over multiple values. used # for when data is coming from the database and potentially contains an existing # 1..5 diagnosis and a newly updated single diagnosis. @@ -63,7 +65,7 @@ def test_single_value_diagnosis_is_favored(): assert "Setting mel_ulcer is incompatible with diagnosis" in excinfo.value.errors()[0]["msg"] -def test_diagnosis_multiple_levels_is_coerced(): +def test_diagnosis_multiple_levels_is_coerced() -> None: # test that passing in diagnosis_1..5 is coerced into a single diagnosis field to handle # cross field input validation metadata = MetadataRow.model_validate({"diagnosis_1": "Benign"}) @@ -74,7 +76,7 @@ def test_diagnosis_multiple_levels_is_coerced(): assert metadata.diagnosis_5 is None -def test_diagnosis_validation_is_idempotent(): +def test_diagnosis_validation_is_idempotent() -> None: # test that running model_validate on a MetadataRow multiple times does not change the # output metadata = MetadataRow.model_validate({"diagnosis": "Melanoma Invasive"}) diff --git a/tests/test_utils.py b/tests/test_utils.py index f3001cf..7aef821 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -1,16 +1,18 @@ +from __future__ import annotations + from pydantic_to_pyarrow import get_pyarrow_schema from isic_metadata.metadata import MetadataRow from isic_metadata.utils import get_unstructured_columns -def test_get_unstructured_columns(): +def test_get_unstructured_columns() -> None: assert get_unstructured_columns(["age", "foo", "bar"]) == ["bar", "foo"] -def test_get_unstructured_columns_ignore_filename(): +def test_get_unstructured_columns_ignore_filename() -> None: assert get_unstructured_columns(["age", "foo", "bar", "filename"]) == ["bar", "foo"] -def test_pyarrow_schema(): +def test_pyarrow_schema() -> None: get_pyarrow_schema(MetadataRow, exclude_fields=True) diff --git a/tox.ini b/tox.ini index 76f5671..384b989 100644 --- a/tox.ini +++ b/tox.ini @@ -1,55 +1,40 @@ [tox] -# Build in an environment which respects PEP 518 -isolated_build = true -envlist = - lint, - test, +min_version = 4.22 +requires = + tox-uv +env_list = + lint + type + test + +[testenv] +runner = uv-venv-lock-runner [testenv:lint] -skipsdist 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