From 7635f0363ea20673ff877801e7f513fbe868d627 Mon Sep 17 00:00:00 2001 From: Ryan Avery Date: Thu, 31 Oct 2024 13:53:05 -0400 Subject: [PATCH 01/22] convert poetry toml to uv toml using pdm build backend --- pyproject.toml | 151 +++--- uv.lock | 1347 ++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 1416 insertions(+), 82 deletions(-) create mode 100644 uv.lock diff --git a/pyproject.toml b/pyproject.toml index f76d9fe..546754d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,93 +1,84 @@ - -# Poetry pyproject.toml: https://python-poetry.org/docs/pyproject/ [build-system] -requires = ["poetry_core>=1.0.0"] -build-backend = "poetry.core.masonry.api" +requires = ["pdm-backend"] +build-backend = "pdm.backend" +[tool.pdm.build] +includes = [ + "stac_model", +] -[tool.poetry] +[project] +authors = [ + {name = "Ryan Avery", email = "ryan@wherobots.com"}, + {name = "Francis Charette-Migneault", email = "francis.charette-migneault@crim.ca"}, +] +license = {text = "Apache Software License 2.0"} +requires-python = "<4.0,>=3.10" +dependencies = [ + "typer[all]<1.0.0,>=0.9.0", + "rich<14.0.0,>=13.7.0", + "pydantic<3.0.0,>=2.6.3", + "pydantic-core<3,>=2", + "pystac<2.0.0,>=1.9.0", + "shapely<3,>=2", + "jsonschema<5.0.0,>=4.21.1", +] name = "stac-model" version = "0.2.0" description = "A PydanticV2 validation and serialization libary for the STAC ML Model Extension" readme = "README_STAC_MODEL.md" -authors = [ - "Ryan Avery ", - "Francis Charette-Migneault " -] -license = "Apache Software License 2.0" -repository = "https://github.com/crim-ca/mlm-extension" -homepage = "https://github.com/stac-extensions/mlm/blob/main/README_STAC_MODEL.md" -packages = [ - {include = "stac_model"} -] - - -# Keywords description https://python-poetry.org/docs/pyproject/#keywords -keywords = [] # UPDATEME with relevant keywords - - -# Pypi classifiers: https://pypi.org/classifiers/ +keywords = [] classifiers = [ - "Development Status :: 4 - Beta", - "Operating System :: OS 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Software License", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3 :: Only", + "Framework :: Pydantic", + "Framework :: Pydantic :: 2", + "Intended Audience :: Developers", + "Intended Audience :: Information Technology", + "Intended Audience :: Science/Research", + "Topic :: File Formats :: JSON :: JSON Schema", + "Topic :: Scientific/Engineering :: Artificial Intelligence", + "Topic :: Scientific/Engineering :: GIS", + "Topic :: Scientific/Engineering :: Image Processing", + "Topic :: Scientific/Engineering :: Image Recognition", ] +[tool.uv] +dev-dependencies = [ + "mypy<2.0.0,>=1.0.0", + "mypy-extensions<1.0.0,>=0.4.3", + "pre-commit<3.0.0,>=2.21.0", + "bandit<2.0.0,>=1.7.5", + "safety<3.0.0,>=2.3.4", + "pystac<2.0.0,>=1.10.0", + "pydocstyle[toml]<7.0.0,>=6.2.0", + "pydoclint<0.6,>=0.3", + "pytest<8.0.0,>=7.2.1", + 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-pydocstyle = {extras = ["toml"], version = "^6.2.0"} -pydoclint = ">=0.3,<0.6" +[project.urls] +homepage = "https://github.com/stac-extensions/mlm/blob/main/README_STAC_MODEL.md" +repository = "https://github.com/crim-ca/mlm-extension" -pytest = "^7.2.1" -pytest-cov = "^4.1.0" -pytest-mock = "^3.10.0" -pytest-timeout = "^2.2.0" -pytest-benchmark = "^4.0.0" -pytest-sugar = "^0.9.7" -pytest-click = "^1.1.0" -pytest-pikachu = "^1.0.0" -coverage = "^7.3.0" -ruff = "^0.2.2" -bump-my-version = ">=0.21,<0.27" +[project.scripts] +stac-model = "stac_model.__main__:app" [tool.bumpversion] # NOTE: @@ -262,7 +253,6 @@ plugins = [ "pydantic.mypy" ] - [tool.pydantic-mypy] init_forbid_extra = true init_typed = true @@ -314,12 +304,10 @@ addopts = [ "--pikachu" ] - [tool.coverage.run] source = ["tests"] branch = true - [tool.coverage.report] exclude_also = [ "def main", @@ -328,6 +316,5 @@ exclude_also = [ fail_under = 50 show_missing = true - [tool.coverage.paths] source = ["stac_model"] diff --git 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curl -sSL https://install.python-poetry.org | $(PYTHON) - --uninstall - -.PHONY: poetry-plugins -poetry-plugins: - $(POETRY) self add poetry-plugin-up - -.PHONY: poetry-env -poetry-env: - $(POETRY) config virtualenvs.in-project true +ACTIVEPYTHON = $(shell which python) + +#* UV +.PHONY: setup +setup: + @if ! command -v uv &> /dev/null; then \ + curl -LsSf https://astral.sh/uv/install.sh | sh; \ + else \ + echo "uv is already installed"; \ + fi + +.PHONY: remove +remove: + @read -p "Are you sure you want to remove uv and all its data? [y/N] " confirm && \ + if [ "$$confirm" = "y" ]; then \ + uv cache clean; \ + rm -r "$$(uv python dir)"; \ + rm -r "$$(uv tool dir)"; \ + rm ~/.cargo/bin/uv ~/.cargo/bin/uvx; \ + else \ + echo "Operation cancelled."; \ + fi .PHONY: publish publish: - $(POETRY) publish --build + uv publish --build #* Installation .PHONY: install -install: poetry-env - $(POETRY) lock -n && poetry export --without-hashes > requirements-lock.txt - $(POETRY) install -n - -poetry run mypy --install-types --non-interactive ./ +install: setup + uv export --format requirements-txt -o requirements.txt --no-dev + uv pip install --python $(ACTIVEPYTHON) -r requirements.txt .PHONY: install-dev -install-dev: poetry-env install - $(POETRY) install -n --with dev +install-dev: setup + uv export --format requirements-txt -o requirements-dev.txt + uv pip install --python $(ACTIVEPYTHON) -r requirements-dev.txt .PHONY: pre-commit-install -pre-commit-install: - $(POETRY) run pre-commit install - +pre-commit-install: setup + uv run --python $(ACTIVEPYTHON) pre-commit install #* Formatters .PHONY: codestyle -codestyle: - $(POETRY) run ruff format --config=pyproject.toml stac_model tests +codestyle: setup + uv run --python $(ACTIVEPYTHON) ruff format --config=pyproject.toml stac_model tests .PHONY: format format: codestyle #* Linting .PHONY: test -test: - PYTHONPATH=$(PYTHONPATH) poetry run pytest -c pyproject.toml --cov-report=html --cov=stac_model tests/ +test: setup + uv run --python $(ACTIVEPYTHON) pytest -c pyproject.toml --cov-report=html --cov=stac_model tests/ .PHONY: check check: check-examples check-markdown check-lint check-mypy check-safety check-citation @@ -61,8 +62,8 @@ check: check-examples check-markdown check-lint check-mypy check-safety check-ci check-all: check .PHONY: mypy -mypy: - $(POETRY) run mypy --config-file pyproject.toml ./ +mypy: setup + uv run --python $(ACTIVEPYTHON) mypy --config-file pyproject.toml ./ .PHONY: check-mypy check-mypy: mypy @@ -72,26 +73,25 @@ check-mypy: mypy # see https://github.com/citation-file-format/cffconvert/issues/292 .PHONY: check-citation check-citation: - docker run --rm -v $(PYTHONPATH)/CITATION.cff:/app/CITATION.cff citationcff/cffconvert --validate + docker run --rm -v $(ACTIVEPYTHON)/CITATION.cff:/app/CITATION.cff citationcff/cffconvert --validate .PHONY: check-safety -check-safety: - $(POETRY) check - $(POETRY) run safety check --full-report - $(POETRY) run bandit -ll --recursive stac_model tests +check-safety: setup + uv check + uv run --python $(ACTIVEPYTHON) safety check --full-report + uv run --python $(ACTIVEPYTHON) bandit -ll --recursive stac_model tests .PHONY: lint -lint: - $(POETRY) run ruff --config=pyproject.toml ./ - $(POETRY) run pydocstyle --count --config=pyproject.toml ./ - $(POETRY) run pydoclint --config=pyproject.toml ./ +lint: setup + uv run --python $(ACTIVEPYTHON) ruff check --fix --config=pyproject.toml ./ .PHONY: check-lint check-lint: lint +uv run --python $(ACTIVEPYTHON) ruff check --config=pyproject.toml ./ .PHONY: format-lint -format-lint: - $(POETRY) run ruff --config=pyproject.toml --fix ./ +format-lint: setup lint + ruff format --config=pyproject.toml ./ .PHONY: install-npm install-npm: @@ -120,8 +120,9 @@ $(addprefix fix-, $(FORMATTERS)): fix-%: format-% lint-all: lint mypy check-safety check-markdown .PHONY: update-dev-deps -update-dev-deps: - 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name: Run checks run: | make lint-all + npm list - name: Run tests run: | From 634bf2b81161ece7c3bb3e43fd01a1e4d68ca8d3 Mon Sep 17 00:00:00 2001 From: Ryan Avery Date: Fri, 1 Nov 2024 10:19:54 -0400 Subject: [PATCH 06/22] gitignore reqs generated from make --- .github/workflows/stac-model.yml | 1 - .github/workflows/test.yaml | 1 + .gitignore | 2 ++ Makefile | 2 +- 4 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/stac-model.yml b/.github/workflows/stac-model.yml index 4fb75b8..1881d7f 100644 --- a/.github/workflows/stac-model.yml +++ b/.github/workflows/stac-model.yml @@ -30,7 +30,6 @@ jobs: - name: Run checks run: | make lint-all - npm list - name: Run tests run: | diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 2260534..03169a5 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -12,3 +12,4 @@ jobs: - run: | npm install npm test + npm list diff --git a/.gitignore b/.gitignore index 4d99463..e82a7d8 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,5 @@ +requirements*.txt + ### ArchLinuxPackages ### *.tar *.tar.* diff --git a/Makefile b/Makefile index f890680..b3f4de7 100644 --- a/Makefile +++ b/Makefile @@ -87,7 +87,7 @@ lint: setup .PHONY: check-lint check-lint: lint -uv run --python $(ACTIVEPYTHON) ruff check --config=pyproject.toml ./ + uv run --python $(ACTIVEPYTHON) ruff check --config=pyproject.toml ./ .PHONY: format-lint format-lint: setup lint From 305e40cf2ef29b2a1a79f98298712427d4a9c497 Mon Sep 17 00:00:00 2001 From: Ryan Avery Date: Fri, 1 Nov 2024 10:22:43 -0400 Subject: [PATCH 07/22] poetry>uv in actions --- .github/workflows/publish.yaml | 8 ++++---- .github/workflows/stac-model.yml | 6 +++--- pyproject.toml | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml index 8b56119..ff89a22 100644 --- a/.github/workflows/publish.yaml +++ b/.github/workflows/publish.yaml @@ -25,9 +25,9 @@ jobs: uses: actions/setup-python@v5.2.0 with: python-version: "3.10" - - name: Install poetry - run: make poetry-install + - name: Install uv + run: make setup - name: Publish stac-model to PyPI run: | - poetry build - poetry publish --username __token__ --password ${{ secrets.PYPI_SECRET }} + uv build + uv publish --username __token__ --password ${{ secrets.PYPI_SECRET }} diff --git a/.github/workflows/stac-model.yml b/.github/workflows/stac-model.yml index 1881d7f..5d42720 100644 --- a/.github/workflows/stac-model.yml +++ b/.github/workflows/stac-model.yml @@ -16,14 +16,14 @@ jobs: with: python-version: ${{ matrix.python-version }} - - name: Install poetry - run: make poetry-install + - name: Install uv + run: make setup - name: Set up cache uses: actions/cache@v4.0.2 with: path: .venv - key: venv-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('poetry.lock') }} + key: venv-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('uv.lock') }} - name: Install dependencies run: make install-dev diff --git a/pyproject.toml b/pyproject.toml index 6bd1c10..7413902 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -86,7 +86,7 @@ stac-model = "stac_model.__main__:app" # NOTE: # Although these definitions are provided in this 'stac-model' project file, # they are actually intented for versioning the MLM specification itself. -# To version 'stac-model', use the 'poetry version' operations. +# To version 'stac-model', use the 'bumpversion bump' operation. # See also https://github.com/stac-extensions/mlm/blob/main/CONTRIBUTING.md#building-and-releasing current_version = "1.3.0" parse = "(?P\\d+)\\.(?P\\d+)\\.(?P\\d+)" From 6094b22b05afb4b7df203a630977dee2e7240e7c Mon Sep 17 00:00:00 2001 From: Ryan Avery Date: Fri, 1 Nov 2024 10:44:37 -0400 Subject: [PATCH 08/22] code linting with ruff, fix makefile command, ignore line length and type annotation rules --- Makefile | 1 - pyproject.toml | 1 + stac_model/base.py | 13 ++------ stac_model/examples.py | 2 +- stac_model/input.py | 67 +++++++++++++----------------------------- stac_model/output.py | 20 ++++++------- stac_model/runtime.py | 18 ++++++------ stac_model/schema.py | 23 +++++++-------- tests/conftest.py | 10 +++---- tests/test_schema.py | 18 ++++++------ 10 files changed, 69 insertions(+), 104 deletions(-) diff --git a/Makefile b/Makefile index b3f4de7..90cc310 100644 --- a/Makefile +++ b/Makefile @@ -77,7 +77,6 @@ check-citation: .PHONY: check-safety check-safety: setup - uv check uv run --python $(ACTIVEPYTHON) safety check --full-report uv run --python $(ACTIVEPYTHON) bandit -ll --recursive stac_model tests diff --git a/pyproject.toml b/pyproject.toml index 7413902..0bd5f97 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -185,6 +185,7 @@ search = "https://stac-extensions.github.io/mlm/v{current_version}/schema.json" replace = "https://stac-extensions.github.io/mlm/v{new_version}/schema.json" [tool.ruff] +ignore = ["UP007", "E501"] exclude = [ ".git", "__pycache__", diff --git a/stac_model/base.py b/stac_model/base.py index c5ff7c6..772cb12 100644 --- a/stac_model/base.py +++ b/stac_model/base.py @@ -1,18 +1,11 @@ from dataclasses import dataclass from enum import Enum -from typing import Any, Dict, List, Literal, TypeAlias, Union +from typing import Any, Literal, TypeAlias, Union from pydantic import BaseModel, ConfigDict, model_serializer -Number: TypeAlias = Union[int, float] -JSON: TypeAlias = Union[ - Dict[str, "JSON"], - List["JSON"], - Number, - bool, - str, - None, -] +Number: TypeAlias = int | float +JSON: TypeAlias = dict[str, "JSON"] | list["JSON"] | Number | bool | str | None @dataclass diff --git a/stac_model/examples.py b/stac_model/examples.py index d882623..dbd0657 100644 --- a/stac_model/examples.py +++ b/stac_model/examples.py @@ -68,7 +68,7 @@ def eurosat_resnet() -> ItemMLModelExtension: mean=mean, stddev=stddev, ) - for mean, stddev in zip(stats_mean, stats_stddev) + for mean, stddev in zip(stats_mean, stats_stddev, strict=False) ] model_input = ModelInput( name="13 Band Sentinel-2 Batch", diff --git a/stac_model/input.py b/stac_model/input.py index 22788d7..3001941 100644 --- a/stac_model/input.py +++ b/stac_model/input.py @@ -1,4 +1,5 @@ -from typing import Annotated, Any, List, Literal, Optional, Sequence, TypeAlias, Union +from collections.abc import Sequence +from typing import Annotated, Any, Literal, TypeAlias from typing_extensions import Self from pydantic import Field, model_validator @@ -7,8 +8,8 @@ class InputStructure(MLMBaseModel): - shape: List[Union[int, float]] = Field(min_items=1) - dim_order: List[str] = Field(min_items=1) + shape: list[int | float] = Field(min_items=1) + dim_order: list[str] = Field(min_items=1) data_type: DataType @model_validator(mode="after") @@ -19,43 +20,17 @@ def validate_dimensions(self) -> Self: class MLMStatistic(MLMBaseModel): # FIXME: add 'Statistics' dep from raster extension (cases required to be triggered) - minimum: Annotated[Optional[Number], OmitIfNone] = None - maximum: Annotated[Optional[Number], OmitIfNone] = None - mean: Annotated[Optional[Number], OmitIfNone] = None - stddev: Annotated[Optional[Number], OmitIfNone] = None - count: Annotated[Optional[int], OmitIfNone] = None - valid_percent: Annotated[Optional[Number], OmitIfNone] = None + minimum: Annotated[Number | None, OmitIfNone] = None + maximum: Annotated[Number | None, OmitIfNone] = None + mean: Annotated[Number | None, OmitIfNone] = None + stddev: Annotated[Number | None, OmitIfNone] = None + count: Annotated[int | None, OmitIfNone] = None + valid_percent: Annotated[Number | None, OmitIfNone] = None -NormalizeType: TypeAlias = Optional[ - Literal[ - "min-max", - "z-score", - "l1", - "l2", - "l2sqr", - "hamming", - "hamming2", - "type-mask", - "relative", - "inf", - ] -] +NormalizeType: TypeAlias = Literal["min-max", "z-score", "l1", "l2", "l2sqr", "hamming", "hamming2", "type-mask", "relative", "inf"] | None -ResizeType: TypeAlias = Optional[ - Literal[ - "crop", - "pad", - "interpolation-nearest", - "interpolation-linear", - "interpolation-cubic", - "interpolation-area", - "interpolation-lanczos4", - "interpolation-max", - "wrap-fill-outliers", - "wrap-inverse-map", - ] -] +ResizeType: TypeAlias = Literal["crop", "pad", "interpolation-nearest", "interpolation-linear", "interpolation-cubic", "interpolation-area", "interpolation-lanczos4", "interpolation-max", "wrap-fill-outliers", "wrap-inverse-map"] | None class ModelBand(MLMBaseModel): @@ -66,11 +41,11 @@ class ModelBand(MLMBaseModel): ) ) # similar to 'ProcessingExpression', but they can be omitted here - format: Annotated[Optional[str], OmitIfNone] = Field( + format: Annotated[str | None, OmitIfNone] = Field( default=None, description="", ) - expression: Annotated[Optional[Any], OmitIfNone] = Field( + expression: Annotated[Any | None, OmitIfNone] = Field( default=None, description="", ) @@ -88,7 +63,7 @@ def validate_expression(self) -> Self: class ModelInput(MLMBaseModel): name: str # order is critical here (same index as dim shape), allow duplicate if the model needs it somehow - bands: Sequence[Union[str, ModelBand]] = Field( + bands: Sequence[str | ModelBand] = Field( description=( "List of bands that compose the input. " "If a string is used, it is implied to correspond to a named-band. " @@ -107,9 +82,9 @@ class ModelInput(MLMBaseModel): ], ) input: InputStructure - norm_by_channel: Annotated[Optional[bool], OmitIfNone] = None - norm_type: Annotated[Optional[NormalizeType], OmitIfNone] = None - norm_clip: Annotated[Optional[List[Union[float, int]]], OmitIfNone] = None - resize_type: Annotated[Optional[ResizeType], OmitIfNone] = None - statistics: Annotated[Optional[List[MLMStatistic]], OmitIfNone] = None - pre_processing_function: Optional[ProcessingExpression] = None + norm_by_channel: Annotated[bool | None, OmitIfNone] = None + norm_type: Annotated[NormalizeType | None, OmitIfNone] = None + norm_clip: Annotated[list[float | int] | None, OmitIfNone] = None + resize_type: Annotated[ResizeType | None, OmitIfNone] = None + statistics: Annotated[list[MLMStatistic] | None, OmitIfNone] = None + pre_processing_function: ProcessingExpression | None = None diff --git a/stac_model/output.py b/stac_model/output.py index 0e25ec7..5b1d2ea 100644 --- a/stac_model/output.py +++ b/stac_model/output.py @@ -1,4 +1,4 @@ -from typing import Annotated, Any, Dict, List, Optional, Set, Union, cast +from typing import Annotated, Any, cast from pydantic import AliasChoices, ConfigDict, Field, model_serializer from pystac.extensions.classification import Classification @@ -7,8 +7,8 @@ class ModelResult(MLMBaseModel): - shape: List[Union[int, float]] = Field(..., min_items=1) - dim_order: List[str] = Field(..., min_items=1) + shape: list[int | float] = Field(..., min_items=1) + dim_order: list[str] = Field(..., min_items=1) data_type: DataType @@ -32,15 +32,15 @@ class ModelResult(MLMBaseModel): class MLMClassification(MLMBaseModel, Classification): @model_serializer() - def model_dump(self, *_: Any, **__: Any) -> Dict[str, Any]: + def model_dump(self, *_: Any, **__: Any) -> dict[str, Any]: return self.to_dict() # type: ignore[call-arg] def __init__( self, value: int, - description: Optional[str] = None, - name: Optional[str] = None, - color_hint: Optional[str] = None, + description: str | None = None, + name: str | None = None, + color_hint: str | None = None, ) -> None: Classification.__init__(self, {}) if not name and not description: @@ -78,7 +78,7 @@ def __setattr__(self, key: str, value: Any) -> None: class ModelOutput(MLMBaseModel): name: str - tasks: Set[ModelTask] + tasks: set[ModelTask] result: ModelResult # NOTE: @@ -86,11 +86,11 @@ class ModelOutput(MLMBaseModel): # it is more important to keep the order in this case, # which we would lose with 'Set'. # We also get some unhashable errors with 'Set', although 'MLMClassification' implements '__hash__'. - classes: Annotated[List[MLMClassification], OmitIfNone] = Field( + classes: Annotated[list[MLMClassification], OmitIfNone] = Field( alias="classification:classes", validation_alias=AliasChoices("classification:classes", "classification_classes", "classes"), ) - post_processing_function: Optional[ProcessingExpression] = None + post_processing_function: ProcessingExpression | None = None model_config = ConfigDict( populate_by_name=True, diff --git a/stac_model/runtime.py b/stac_model/runtime.py index 9104fa6..197f7b8 100644 --- a/stac_model/runtime.py +++ b/stac_model/runtime.py @@ -1,5 +1,5 @@ from enum import Enum -from typing import Annotated, Literal, Optional, Union +from typing import Annotated, Literal, Union from pydantic import AliasChoices, Field @@ -33,17 +33,17 @@ def __str__(self): class Runtime(MLMBaseModel): - framework: Annotated[Optional[str], OmitIfNone] = Field(default=None) - framework_version: Annotated[Optional[str], OmitIfNone] = Field(default=None) - file_size: Annotated[Optional[int], OmitIfNone] = Field( + framework: Annotated[str | None, OmitIfNone] = Field(default=None) + framework_version: Annotated[str | None, OmitIfNone] = Field(default=None) + file_size: Annotated[int | None, OmitIfNone] = Field( alias="file:size", validation_alias=AliasChoices("file_size", "file:size"), default=None, ) - memory_size: Annotated[Optional[int], OmitIfNone] = Field(default=None) - batch_size_suggestion: Annotated[Optional[int], OmitIfNone] = Field(default=None) + memory_size: Annotated[int | None, OmitIfNone] = Field(default=None) + batch_size_suggestion: Annotated[int | None, OmitIfNone] = Field(default=None) - accelerator: Optional[AcceleratorType] = Field(default=None) + accelerator: AcceleratorType | None = Field(default=None) accelerator_constrained: bool = Field(default=False) - accelerator_summary: Annotated[Optional[str], OmitIfNone] = Field(default=None) - accelerator_count: Annotated[Optional[int], OmitIfNone] = Field(default=None, minimum=1) + accelerator_summary: Annotated[str | None, OmitIfNone] = Field(default=None) + accelerator_count: Annotated[int | None, OmitIfNone] = Field(default=None, minimum=1) diff --git a/stac_model/schema.py b/stac_model/schema.py index 63310ba..aea1e41 100644 --- a/stac_model/schema.py +++ b/stac_model/schema.py @@ -1,13 +1,10 @@ import json +from collections.abc import Iterable from typing import ( Annotated, Any, Generic, - Iterable, - List, Literal, - Optional, - Set, TypeVar, Union, cast, @@ -48,13 +45,13 @@ def mlm_prefix_adder(field_name: str) -> str: class MLModelProperties(Runtime): name: str = Field(min_length=1) architecture: str = Field(min_length=1) - tasks: Set[ModelTask] - input: List[ModelInput] - output: List[ModelOutput] + tasks: set[ModelTask] + input: list[ModelInput] + output: list[ModelOutput] total_parameters: int - pretrained: Annotated[Optional[bool], OmitIfNone] = Field(default=True) - pretrained_source: Annotated[Optional[str], OmitIfNone] = None + pretrained: Annotated[bool | None, OmitIfNone] = Field(default=True) + pretrained_source: Annotated[str | None, OmitIfNone] = None model_config = ConfigDict(alias_generator=mlm_prefix_adder, populate_by_name=True, extra="ignore") @@ -80,7 +77,7 @@ def name(self) -> SchemaName: def apply( self, - properties: Union[MLModelProperties, dict[str, Any]], + properties: MLModelProperties | dict[str, Any], ) -> None: """ Applies Machine Learning Model Extension properties to the extended :mod:`~pystac` object. @@ -118,7 +115,7 @@ def ext(cls, obj: pystac.Collection, add_if_missing: bool = False) -> "Collectio @classmethod def ext( cls, - obj: Union[pystac.Collection, pystac.Item, pystac.Asset], # item_assets.AssetDefinition + obj: pystac.Collection | pystac.Item | pystac.Asset, # item_assets.AssetDefinition add_if_missing: bool = False, ) -> Union[ "CollectionMLModelExtension", @@ -186,7 +183,7 @@ def _validate_mlm_property(self, prop: str, summaries: list[Any]) -> None: for value in summaries: validator.validate_assignment(model, prop, value) - def get_mlm_property(self, prop: str) -> Optional[list[Any]]: + def get_mlm_property(self, prop: str) -> list[Any] | None: self._check_mlm_property(prop) return self.summaries.get_list(prop) @@ -251,7 +248,7 @@ class AssetMLModelExtension(MLModelExtension[pystac.Asset]): properties: dict[str, Any] """The :class:`~pystac.Asset` fields, including extension properties.""" - additional_read_properties: Optional[Iterable[dict[str, Any]]] = None + additional_read_properties: Iterable[dict[str, Any]] | None = None """If present, this will be a list containing 1 dictionary representing the properties of the owning :class:`~pystac.Item`.""" diff --git a/tests/conftest.py b/tests/conftest.py index 417a913..5688bd9 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,7 +1,7 @@ import glob import json import os -from typing import TYPE_CHECKING, Any, Dict, List, cast +from typing import TYPE_CHECKING, Any, cast import pystac import pytest @@ -18,7 +18,7 @@ JSON_SCHEMA_DIR = os.path.abspath(os.path.join(TEST_DIR, "../json-schema")) -def get_all_stac_item_examples() -> List[str]: +def get_all_stac_item_examples() -> list[str]: all_json = glob.glob("**/*.json", root_dir=EXAMPLES_DIR, recursive=True) all_geojson = glob.glob("**/*.geojson", root_dir=EXAMPLES_DIR, recursive=True) all_stac_items = [ @@ -39,7 +39,7 @@ def mlm_schema() -> JSON: @pytest.fixture(scope="session") def mlm_validator( request: "SubRequest", - mlm_schema: Dict[str, Any], + mlm_schema: dict[str, Any], ) -> pystac.validation.stac_validator.JsonSchemaSTACValidator: """ Update the :class:`pystac.validation.RegisteredValidator` with the local MLM JSON schema definition. @@ -58,10 +58,10 @@ def mlm_validator( @pytest.fixture -def mlm_example(request: "SubRequest") -> Dict[str, JSON]: +def mlm_example(request: "SubRequest") -> dict[str, JSON]: with open(os.path.join(EXAMPLES_DIR, request.param)) as example_file: data = json.load(example_file) - return cast(Dict[str, JSON], data) + return cast(dict[str, JSON], data) @pytest.fixture(name="eurosat_resnet") diff --git a/tests/test_schema.py b/tests/test_schema.py index 4755978..83cfe29 100644 --- a/tests/test_schema.py +++ b/tests/test_schema.py @@ -1,6 +1,6 @@ import copy import os -from typing import Any, Dict, List, cast +from typing import Any, cast import pystac import pytest @@ -19,9 +19,9 @@ ) def test_mlm_schema( mlm_validator: STACValidator, - mlm_example: Dict[str, JSON], + mlm_example: dict[str, JSON], ) -> None: - mlm_item = pystac.Item.from_dict(cast(Dict[str, Any], mlm_example)) + mlm_item = pystac.Item.from_dict(cast(dict[str, Any], mlm_example)) validated = pystac.validation.validate(mlm_item, validator=mlm_validator) assert len(validated) >= len(mlm_item.stac_extensions) # extra STAC core schemas assert SCHEMA_URI in validated @@ -34,7 +34,7 @@ def test_mlm_schema( ) def test_mlm_missing_bands_invalid_if_mlm_input_lists_bands( mlm_validator: STACValidator, - mlm_example: Dict[str, JSON], + mlm_example: dict[str, JSON], ) -> None: mlm_item = pystac.Item.from_dict(mlm_example) pystac.validation.validate(mlm_item, validator=mlm_validator) # ensure original is valid @@ -53,7 +53,7 @@ def test_mlm_missing_bands_invalid_if_mlm_input_lists_bands( ) def test_mlm_eo_bands_invalid_only_in_item_properties( mlm_validator: STACValidator, - mlm_example: Dict[str, JSON], + mlm_example: dict[str, JSON], ) -> None: mlm_item = pystac.Item.from_dict(mlm_example) pystac.validation.validate(mlm_item, validator=mlm_validator) # ensure original is valid @@ -72,7 +72,7 @@ def test_mlm_eo_bands_invalid_only_in_item_properties( ) def test_mlm_no_input_allowed_but_explicit_empty_array_required( mlm_validator: STACValidator, - mlm_example: Dict[str, JSON], + mlm_example: dict[str, JSON], ) -> None: mlm_data = copy.deepcopy(mlm_example) mlm_data["properties"]["mlm:input"] = [] # type: ignore @@ -92,7 +92,7 @@ def test_mlm_no_input_allowed_but_explicit_empty_array_required( ) def test_mlm_other_non_mlm_assets_allowed( mlm_validator: STACValidator, - mlm_example: Dict[str, JSON], + mlm_example: dict[str, JSON], ) -> None: mlm_data = copy.deepcopy(mlm_example) mlm_item = pystac.Item.from_dict(mlm_data) @@ -121,7 +121,7 @@ def test_mlm_other_non_mlm_assets_allowed( ) def test_mlm_at_least_one_asset_model( mlm_validator: STACValidator, - mlm_example: Dict[str, JSON], + mlm_example: dict[str, JSON], ) -> None: mlm_data = copy.deepcopy(mlm_example) mlm_item = pystac.Item.from_dict(mlm_data) @@ -163,7 +163,7 @@ def test_collection_include_all_items(mlm_example): """ This is only for self-validation, to make sure all examples are contained in the example STAC collection. """ - col_links: List[Dict[str, str]] = mlm_example["links"] + col_links: list[dict[str, str]] = mlm_example["links"] col_items = {os.path.basename(link["href"]) for link in col_links if link["rel"] == "item"} all_items = {os.path.basename(path) for path in get_all_stac_item_examples()} assert all_items == col_items, "Missing STAC Item examples in the example STAC Collection links." From fe169535d6fb098a16aa3d358a1fdffff916f21d Mon Sep 17 00:00:00 2001 From: Ryan Avery Date: Fri, 1 Nov 2024 10:52:23 -0400 Subject: [PATCH 09/22] update example to 1.0.0 --- examples/collection.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/collection.json b/examples/collection.json index aff632b..0c596b4 100644 --- a/examples/collection.json +++ b/examples/collection.json @@ -1,5 +1,5 @@ { - "stac_version": "1.0.0-rc.1", + "stac_version": "1.0.0", "stac_extensions": [ "https://stac-extensions.github.io/item-assets/v1.0.0/schema.json" ], From 5a849052a9f86cc2d0a58ecdf58f72ce6102ef8d Mon Sep 17 00:00:00 2001 From: Ryan Avery Date: Fri, 1 Nov 2024 11:00:01 -0400 Subject: [PATCH 10/22] remove docker, point to uv docs, uv badge --- .dockerignore | 39 ----------------------------------- .github/dependabot.yml | 10 --------- CONTRIBUTING.md | 19 +++++++++-------- Makefile | 7 ------- README_STAC_MODEL.md | 10 ++++----- docker/Dockerfile | 25 ---------------------- docker/README.md | 47 ------------------------------------------ 7 files changed, 15 insertions(+), 142 deletions(-) delete mode 100644 .dockerignore delete mode 100644 docker/Dockerfile delete mode 100644 docker/README.md diff --git a/.dockerignore b/.dockerignore deleted file mode 100644 index b6d76d3..0000000 --- a/.dockerignore +++ /dev/null @@ -1,39 +0,0 @@ -# Git -.git -.gitignore -.github - -# Docker -.dockerignore - -# IDE -.idea -.vscode - -# Byte-compiled / optimized / DLL files -__pycache__/ -**/__pycache__/ -*.pyc -*.pyo -*.pyd -.Python -*.py[cod] -*$py.class -.pytest_cache/ -..mypy_cache/ - -# poetry -.venv -requirements*.txt - -# C extensions -*.so - -# Virtual environment -.venv -venv - -.DS_Store -.AppleDouble -.LSOverride -._* diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 8f872f1..ff92d7a 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -23,13 +23,3 @@ updates: commit-message: prefix: ":arrow_up:" open-pull-requests-limit: 5 - - - package-ecosystem: "docker" - directory: "/docker" - schedule: - interval: "monthly" - allow: - - dependency-type: "all" - commit-message: - prefix: ":arrow_up:" - open-pull-requests-limit: 5 diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index a9adfdb..dc2ba61 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -2,23 +2,24 @@ ## Project setup -1. If you don't have `Poetry` installed run: +1. If you don't have `uv` installed run: ```bash -make poetry-install +make setup ``` -> This installs Poetry as a [standalone application][poetry-install].
-> For more details, see also the [Poetry Documentation][poetry-docs].
-> If you prefer, you can simply install it inside your virtual environment. +> This installs uv as a [standalone application][uv-install].
+> For more details, see also the [uv documentation][uv-docs].
-2. Initialize project dependencies with poetry and install `pre-commit` hooks: +2. Initialize project dependencies with uv and install `pre-commit` hooks: ```bash make install-dev make pre-commit-install ``` +This will install project dependencies into the currently active environment. If you would like to use uv's default behavior of managing a project-scoped environment, use uv commands directly to install dependencies. `uv sync` will install dependencies and dev dependencies in `.venv` and update the `uv.lock`. + ## PR submission Before submitting your code please do the following steps: @@ -85,7 +86,7 @@ git push -u origin your-branch ### Building a new version of `stac-model` - Apply any relevant changes and `CHANGELOG.md` entries in a PR that modifies `stac-model`. -- Bump the version with `poetry version `. +- Bump the version with `bumpversion bump `. - You can pass the new version explicitly, or a rule such as `major`, `minor`, or `patch`.
For more details, refer to the [Semantic Versions][semver] standard; - Once CI validation succeeded, merge the corresponding PR branch. @@ -110,6 +111,6 @@ You can also share how the ML Model extension does or does not serve your needs with us in the GitHub Discussions or raise Issues for bugs. -[poetry-install]: https://github.com/python-poetry/install.python-poetry.org -[poetry-docs]: https://python-poetry.org/docs/ +[uv-install]: https://docs.astral.sh/uv/getting-started/installation/ +[uv-docs]: https://docs.astral.sh/uv/ [semver]: https://semver.org/ diff --git a/Makefile b/Makefile index 90cc310..29f54cc 100644 --- a/Makefile +++ b/Makefile @@ -68,13 +68,6 @@ mypy: setup .PHONY: check-mypy check-mypy: mypy -# NOTE: -# purposely running with docker rather than python package due to conflicting dependencies -# see https://github.com/citation-file-format/cffconvert/issues/292 -.PHONY: check-citation -check-citation: - docker run --rm -v $(ACTIVEPYTHON)/CITATION.cff:/app/CITATION.cff citationcff/cffconvert --validate - .PHONY: check-safety check-safety: setup uv run --python $(ACTIVEPYTHON) safety check --full-report diff --git a/README_STAC_MODEL.md b/README_STAC_MODEL.md index 897f5cd..b60a37f 100644 --- a/README_STAC_MODEL.md +++ b/README_STAC_MODEL.md @@ -12,7 +12,7 @@ [![Contributions Welcome][bp8]][bp9] -[![Poetry][bp11]][bp12] +[![uv][bp11]][bp12] [![Pre-commit][bp15]][bp16] [![Semantic versions][blic3]][bp5] [![Pipelines][bscm6]][bscm7] @@ -30,10 +30,10 @@ _A PydanticV2 and PySTAC validation and serialization library for the STAC ML Mo pip install -U stac-model ``` -or install with `Poetry`: +or install with `uv`: ```shell -poetry add stac-model +uv add stac-model ``` Then you can run @@ -73,8 +73,8 @@ See [LICENSE][blic2] for more details. [bp7]: https://kutt.it/7fYqQl [bp8]: https://img.shields.io/static/v1.svg?label=Contributions&message=Welcome&color=0059b3&style=for-the-badge [bp9]: https://github.com/stac-extensions/mlm/blob/main/CONTRIBUTING.md -[bp11]: https://img.shields.io/endpoint?url=https://python-poetry.org/badge/v0.json&style=for-the-badge -[bp12]: https://python-poetry.org/ +[bp11]: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json +[bp12]: https://docs.astral.sh/uv/ [bp15]: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white&style=for-the-badge [bp16]: https://github.com/stac-extensions/mlm/blob/main/.pre-commit-config.yaml diff --git a/docker/Dockerfile b/docker/Dockerfile deleted file mode 100644 index 6972457..0000000 --- a/docker/Dockerfile +++ /dev/null @@ -1,25 +0,0 @@ -FROM python:3.11-slim-buster - -ENV LANG=C.UTF-8 \ - LC_ALL=C.UTF-8 \ - PATH="${PATH}:/root/.poetry/bin" - -RUN apt-get update && \ - apt-get install -y --no-install-recommends \ - curl \ - && rm -rf /var/lib/apt/lists/* - -COPY pyproject.toml ./ - -# Install Poetry -RUN curl -sSL https://install.python-poetry.org | POETRY_HOME=/opt/poetry python && \ - cd /usr/local/bin && \ - ln -s /opt/poetry/bin/poetry && \ - poetry config virtualenvs.create false - -# Allow installing dev dependencies to run tests -ARG INSTALL_DEV=false -RUN bash -c "if [ $INSTALL_DEV == 'true' ] ; then poetry install --no-root ; else poetry install --no-root --no-dev ; fi" - -CMD mkdir -p /workspace -WORKDIR /workspace diff --git a/docker/README.md b/docker/README.md deleted file mode 100644 index 614d5b4..0000000 --- a/docker/README.md +++ /dev/null @@ -1,47 +0,0 @@ -# Docker for stac-model - -## Installation - -To create Docker you need to run: - -```bash -make docker-build -``` - -which is equivalent to: - -```bash -make docker-build VERSION=latest -``` - -You may provide name and version for the image. -Default name is `IMAGE := stac_model`. -Default version is `VERSION := latest`. - -```bash -make docker-build IMAGE=some_name VERSION=0.1.0 -``` - -## Usage - -```bash -docker run -it --rm \ - -v $(pwd):/workspace \ - stac_model bash -``` - -## How to clean up - -To uninstall docker image run `make docker-remove` with `VERSION`: - -```bash -make docker-remove VERSION=0.1.0 -``` - -you may also choose the image name - -```bash -make docker-remove IMAGE=some_name VERSION=latest -``` - -If you want to clean all, including `build` and `pycache` run `make cleanup` From 15b7aae4320777f792ab54abf7cd617331244618 Mon Sep 17 00:00:00 2001 From: Ryan Avery Date: Fri, 1 Nov 2024 11:03:06 -0400 Subject: [PATCH 11/22] line length fix --- CONTRIBUTING.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index dc2ba61..d1a29ab 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -18,7 +18,9 @@ make install-dev make pre-commit-install ``` -This will install project dependencies into the currently active environment. If you would like to use uv's default behavior of managing a project-scoped environment, use uv commands directly to install dependencies. `uv sync` will install dependencies and dev dependencies in `.venv` and update the `uv.lock`. +This will install project dependencies into the currently active environment. If you would like to +use uv's default behavior of managing a project-scoped environment, use uv commands directly to +install dependencies. `uv sync` will install dependencies and dev dependencies in `.venv` and update the `uv.lock`. ## PR submission From a94aaa5711d9f12dd647a226f402ecbb954c9a81 Mon Sep 17 00:00:00 2001 From: Ryan Avery Date: Fri, 1 Nov 2024 11:42:43 -0400 Subject: [PATCH 12/22] fix style of uv badge and remove github pages badge --- README_STAC_MODEL.md | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/README_STAC_MODEL.md b/README_STAC_MODEL.md index b60a37f..32a9f4a 100644 --- a/README_STAC_MODEL.md +++ b/README_STAC_MODEL.md @@ -8,7 +8,6 @@ [![PyPI Release][bp3]][bp2] [![Repository][bscm1]][bp4] [![Releases][bscm2]][bp5] -[![Docs][bdoc1]][bdoc2] [![Contributions Welcome][bp8]][bp9] @@ -73,7 +72,7 @@ See [LICENSE][blic2] for more details. [bp7]: https://kutt.it/7fYqQl [bp8]: https://img.shields.io/static/v1.svg?label=Contributions&message=Welcome&color=0059b3&style=for-the-badge [bp9]: https://github.com/stac-extensions/mlm/blob/main/CONTRIBUTING.md -[bp11]: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json +[bp11]: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json&style=for-the-badge [bp12]: https://docs.astral.sh/uv/ [bp15]: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white&style=for-the-badge @@ -95,6 +94,3 @@ See [LICENSE][blic2] for more details. [hub6]: https://docs.github.com/en/code-security/dependabot [hub8]: https://github.com/stac-extensions/mlm/blob/main/.github/release-drafter.yml [hub9]: https://github.com/stac-extensions/mlm/blob/main/.github/.stale.yml - -[bdoc1]: https://img.shields.io/badge/docs-github%20pages-0a507a?style=for-the-badge -[bdoc2]: https://github.com/stac-extensions/mlm/blob/main/README_STAC_MODEL.md From 8471a496325eb115bb1ae066008fabf56c4a04e2 Mon Sep 17 00:00:00 2001 From: Ryan Avery Date: Tue, 5 Nov 2024 09:58:53 -0800 Subject: [PATCH 13/22] ignore line length for certain lists, remove remove command --- .github/workflows/test.yaml | 2 +- README_STAC_MODEL.md | 2 +- pyproject.toml | 2 +- stac_model/input.py | 26 ++++++++++++++++++++++++-- 4 files changed, 27 insertions(+), 5 deletions(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 03169a5..9d8e0ac 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -11,5 +11,5 @@ jobs: - uses: actions/checkout@v4 - run: | npm install - npm test npm list + npm test diff --git a/README_STAC_MODEL.md b/README_STAC_MODEL.md index 32a9f4a..0217e7e 100644 --- a/README_STAC_MODEL.md +++ b/README_STAC_MODEL.md @@ -29,7 +29,7 @@ _A PydanticV2 and PySTAC validation and serialization library for the STAC ML Mo pip install -U stac-model ``` -or install with `uv`: +or install with uv: ```shell uv add stac-model diff --git a/pyproject.toml b/pyproject.toml index 0bd5f97..39e68c9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -86,7 +86,7 @@ stac-model = "stac_model.__main__:app" # NOTE: # Although these definitions are provided in this 'stac-model' project file, # they are actually intented for versioning the MLM specification itself. -# To version 'stac-model', use the 'bumpversion bump' operation. +# To version 'stac-model', use the 'bump-my-version bump' operation. # See also https://github.com/stac-extensions/mlm/blob/main/CONTRIBUTING.md#building-and-releasing current_version = "1.3.0" parse = "(?P\\d+)\\.(?P\\d+)\\.(?P\\d+)" diff --git a/stac_model/input.py b/stac_model/input.py index 3001941..b40a458 100644 --- a/stac_model/input.py +++ b/stac_model/input.py @@ -28,9 +28,31 @@ class MLMStatistic(MLMBaseModel): # FIXME: add 'Statistics' dep from raster ext valid_percent: Annotated[Number | None, OmitIfNone] = None -NormalizeType: TypeAlias = Literal["min-max", "z-score", "l1", "l2", "l2sqr", "hamming", "hamming2", "type-mask", "relative", "inf"] | None +NormalizeType: TypeAlias = Literal[ + "min-max", + "z-score", + "l1", + "l2", + "l2sqr", + "hamming", + "hamming2", + "type-mask", + "relative", + "inf", + ] | None # noqa: E501 -ResizeType: TypeAlias = Literal["crop", "pad", "interpolation-nearest", "interpolation-linear", "interpolation-cubic", "interpolation-area", "interpolation-lanczos4", "interpolation-max", "wrap-fill-outliers", "wrap-inverse-map"] | None +ResizeType: TypeAlias = Literal[ + "crop", + "pad", + "interpolation-nearest", + "interpolation-linear", + "interpolation-cubic", + "interpolation-area", + "interpolation-lanczos4", + "interpolation-max", + "wrap-fill-outliers", + "wrap-inverse-map", + ] | None # noqa: E501 class ModelBand(MLMBaseModel): From d7278bf79472ea105e15390f768985372e53ae24 Mon Sep 17 00:00:00 2001 From: Ryan Avery Date: Tue, 5 Nov 2024 10:01:05 -0800 Subject: [PATCH 14/22] make format --- CONTRIBUTING.md | 6 +++--- Makefile | 12 ------------ stac_model/input.py | 14 ++++++++++---- stac_model/schema.py | 9 +++------ 4 files changed, 16 insertions(+), 25 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index d1a29ab..47b5169 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -2,7 +2,7 @@ ## Project setup -1. If you don't have `uv` installed run: +1. If you don't have uv installed run: ```bash make setup @@ -18,8 +18,8 @@ make install-dev make pre-commit-install ``` -This will install project dependencies into the currently active environment. If you would like to -use uv's default behavior of managing a project-scoped environment, use uv commands directly to +This will install project dependencies into the currently active environment. If you would like to +use uv's default behavior of managing a project-scoped environment, use uv commands directly to install dependencies. `uv sync` will install dependencies and dev dependencies in `.venv` and update the `uv.lock`. ## PR submission diff --git a/Makefile b/Makefile index 29f54cc..4e51def 100644 --- a/Makefile +++ b/Makefile @@ -11,18 +11,6 @@ setup: echo "uv is already installed"; \ fi -.PHONY: remove -remove: - @read -p "Are you sure you want to remove uv and all its data? [y/N] " confirm && \ - if [ "$$confirm" = "y" ]; then \ - uv cache clean; \ - rm -r "$$(uv python dir)"; \ - rm -r "$$(uv tool dir)"; \ - rm ~/.cargo/bin/uv ~/.cargo/bin/uvx; \ - else \ - echo "Operation cancelled."; \ - fi - .PHONY: publish publish: uv publish --build diff --git a/stac_model/input.py b/stac_model/input.py index b40a458..8e831db 100644 --- a/stac_model/input.py +++ b/stac_model/input.py @@ -28,7 +28,8 @@ class MLMStatistic(MLMBaseModel): # FIXME: add 'Statistics' dep from raster ext valid_percent: Annotated[Number | None, OmitIfNone] = None -NormalizeType: TypeAlias = Literal[ +NormalizeType: TypeAlias = ( + Literal[ "min-max", "z-score", "l1", @@ -39,9 +40,12 @@ class MLMStatistic(MLMBaseModel): # FIXME: add 'Statistics' dep from raster ext "type-mask", "relative", "inf", - ] | None # noqa: E501 + ] + | None +) # noqa: E501 -ResizeType: TypeAlias = Literal[ +ResizeType: TypeAlias = ( + Literal[ "crop", "pad", "interpolation-nearest", @@ -52,7 +56,9 @@ class MLMStatistic(MLMBaseModel): # FIXME: add 'Statistics' dep from raster ext "interpolation-max", "wrap-fill-outliers", "wrap-inverse-map", - ] | None # noqa: E501 + ] + | None +) # noqa: E501 class ModelBand(MLMBaseModel): diff --git a/stac_model/schema.py b/stac_model/schema.py index aea1e41..e2d2b5a 100644 --- a/stac_model/schema.py +++ b/stac_model/schema.py @@ -94,18 +94,15 @@ def get_schema_uri(cls) -> str: @overload @classmethod - def ext(cls, obj: pystac.Asset, add_if_missing: bool = False) -> "AssetMLModelExtension": - ... + def ext(cls, obj: pystac.Asset, add_if_missing: bool = False) -> "AssetMLModelExtension": ... @overload @classmethod - def ext(cls, obj: pystac.Item, add_if_missing: bool = False) -> "ItemMLModelExtension": - ... + def ext(cls, obj: pystac.Item, add_if_missing: bool = False) -> "ItemMLModelExtension": ... @overload @classmethod - def ext(cls, obj: pystac.Collection, add_if_missing: bool = False) -> "CollectionMLModelExtension": - ... + def ext(cls, obj: pystac.Collection, add_if_missing: bool = False) -> "CollectionMLModelExtension": ... # @overload # @classmethod From 277b1d7bbb458cacb6e324cb85e0cd818ecda3b8 Mon Sep 17 00:00:00 2001 From: Ryan Avery Date: Tue, 5 Nov 2024 10:30:12 -0800 Subject: [PATCH 15/22] fix if condition on linux, linitng --- Makefile | 7 ++++--- tests/test_schema.py | 2 +- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/Makefile b/Makefile index 4e51def..2240e8f 100644 --- a/Makefile +++ b/Makefile @@ -5,10 +5,11 @@ ACTIVEPYTHON = $(shell which python) #* UV .PHONY: setup setup: - @if ! command -v uv &> /dev/null; then \ - curl -LsSf https://astral.sh/uv/install.sh | sh; \ - else \ + @if command -v uv &> /dev/null; then \ echo "uv is already installed"; \ + else \ + echo "uv not found, installing..."; \ + curl -LsSf https://astral.sh/uv/install.sh | sh; \ fi .PHONY: publish diff --git a/tests/test_schema.py b/tests/test_schema.py index 7864f14..0f949b2 100644 --- a/tests/test_schema.py +++ b/tests/test_schema.py @@ -34,7 +34,7 @@ def test_mlm_schema( ) def test_mlm_no_undefined_prefixed_field( mlm_validator: STACValidator, - mlm_example: Dict[str, JSON], + mlm_example: dict[str, JSON], ) -> None: mlm_data = copy.deepcopy(mlm_example) mlm_item = pystac.Item.from_dict(mlm_data) From a8cf7ca13adf0f0e29470596013e7fbc6fc52e38 Mon Sep 17 00:00:00 2001 From: Ryan Avery Date: Tue, 5 Nov 2024 10:40:47 -0800 Subject: [PATCH 16/22] don't run setup on every command in makefile --- Makefile | 27 +++++++++++---------------- tests/test_schema.py | 5 +---- 2 files changed, 12 insertions(+), 20 deletions(-) diff --git a/Makefile b/Makefile index 2240e8f..f7733f9 100644 --- a/Makefile +++ b/Makefile @@ -5,12 +5,7 @@ ACTIVEPYTHON = $(shell which python) #* UV .PHONY: setup setup: - @if command -v uv &> /dev/null; then \ - echo "uv is already installed"; \ - else \ - echo "uv not found, installing..."; \ - curl -LsSf https://astral.sh/uv/install.sh | sh; \ - fi + curl -LsSf https://astral.sh/uv/install.sh | sh .PHONY: publish publish: @@ -18,22 +13,22 @@ publish: #* Installation .PHONY: install -install: setup +install: uv export --format requirements-txt -o requirements.txt --no-dev uv pip install --python $(ACTIVEPYTHON) -r requirements.txt .PHONY: install-dev -install-dev: setup +install-dev: uv export --format requirements-txt -o requirements-dev.txt uv pip install --python $(ACTIVEPYTHON) -r requirements-dev.txt .PHONY: pre-commit-install -pre-commit-install: setup +pre-commit-install: uv run --python $(ACTIVEPYTHON) pre-commit install #* Formatters .PHONY: codestyle -codestyle: setup +codestyle: uv run --python $(ACTIVEPYTHON) ruff format --config=pyproject.toml stac_model tests .PHONY: format @@ -41,7 +36,7 @@ format: codestyle #* Linting .PHONY: test -test: setup +test: uv run --python $(ACTIVEPYTHON) pytest -c pyproject.toml --cov-report=html --cov=stac_model tests/ .PHONY: check @@ -51,19 +46,19 @@ check: check-examples check-markdown check-lint check-mypy check-safety check-ci check-all: check .PHONY: mypy -mypy: setup +mypy: uv run --python $(ACTIVEPYTHON) mypy --config-file pyproject.toml ./ .PHONY: check-mypy check-mypy: mypy .PHONY: check-safety -check-safety: setup +check-safety: uv run --python $(ACTIVEPYTHON) safety check --full-report uv run --python $(ACTIVEPYTHON) bandit -ll --recursive stac_model tests .PHONY: lint -lint: setup +lint: uv run --python $(ACTIVEPYTHON) ruff check --fix --config=pyproject.toml ./ .PHONY: check-lint @@ -71,7 +66,7 @@ check-lint: lint uv run --python $(ACTIVEPYTHON) ruff check --config=pyproject.toml ./ .PHONY: format-lint -format-lint: setup lint +format-lint: lint ruff format --config=pyproject.toml ./ .PHONY: install-npm @@ -101,7 +96,7 @@ $(addprefix fix-, $(FORMATTERS)): fix-%: format-% lint-all: lint mypy check-safety check-markdown .PHONY: update-dev-deps -update-dev-deps: setup +update-dev-deps: uv export --only-dev --format requirements-txt -o requirements-only-dev.txt uv pip install --python $(ACTIVEPYTHON) -r requirements-only-dev.txt diff --git a/tests/test_schema.py b/tests/test_schema.py index 0f949b2..6825a51 100644 --- a/tests/test_schema.py +++ b/tests/test_schema.py @@ -44,10 +44,7 @@ def test_mlm_no_undefined_prefixed_field( with pytest.raises(pystac.errors.STACValidationError) as exc: mlm_item = pystac.Item.from_dict(mlm_data) pystac.validation.validate(mlm_item, validator=mlm_validator) - assert all( - field in str(exc.value.source) - for field in ["mlm:unknown", "^(?!mlm:)"] - ) + assert all(field in str(exc.value.source) for field in ["mlm:unknown", "^(?!mlm:)"]) @pytest.mark.parametrize( From 2a5963d4f01d3f8e614e7c4d7098f81d0c018553 Mon Sep 17 00:00:00 2001 From: Ryan Avery Date: Tue, 5 Nov 2024 10:44:37 -0800 Subject: [PATCH 17/22] disable dependabot --- .github/dependabot.yml | 44 +++++++++++++++++++++--------------------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index ff92d7a..6cce39a 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -1,25 +1,25 @@ -# Configuration: https://dependabot.com/docs/config-file/ -# Docs: https://docs.github.com/en/github/administering-a-repository/keeping-your-dependencies-updated-automatically +# # Configuration: https://dependabot.com/docs/config-file/ +# # Docs: https://docs.github.com/en/github/administering-a-repository/keeping-your-dependencies-updated-automatically -version: 2 +# version: 2 -updates: - - package-ecosystem: "pip" - directory: "/" - schedule: - interval: "monthly" - allow: - - dependency-type: "all" - commit-message: - prefix: ":arrow_up:" - open-pull-requests-limit: 5 +# updates: +# - package-ecosystem: "pip" +# directory: "/" +# schedule: +# interval: "monthly" +# allow: +# - dependency-type: "all" +# commit-message: +# prefix: ":arrow_up:" +# open-pull-requests-limit: 5 - - package-ecosystem: "github-actions" - directory: "/" - schedule: - interval: "monthly" - allow: - - dependency-type: "all" - commit-message: - prefix: ":arrow_up:" - open-pull-requests-limit: 5 +# - package-ecosystem: "github-actions" +# directory: "/" +# schedule: +# interval: "monthly" +# allow: +# - dependency-type: "all" +# commit-message: +# prefix: ":arrow_up:" +# open-pull-requests-limit: 5 From e15f0adbb0defa3a1aa056015c9cefde28caf2ae Mon Sep 17 00:00:00 2001 From: Ryan Avery Date: Tue, 5 Nov 2024 10:45:23 -0800 Subject: [PATCH 18/22] temporarily remove dependabot --- .github/dependabot.yml | 25 ------------------------- 1 file changed, 25 deletions(-) delete mode 100644 .github/dependabot.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml deleted file mode 100644 index 6cce39a..0000000 --- a/.github/dependabot.yml +++ /dev/null @@ -1,25 +0,0 @@ -# # Configuration: https://dependabot.com/docs/config-file/ -# # Docs: https://docs.github.com/en/github/administering-a-repository/keeping-your-dependencies-updated-automatically - -# version: 2 - -# updates: -# - package-ecosystem: "pip" -# directory: "/" -# schedule: -# interval: "monthly" -# allow: -# - dependency-type: "all" -# commit-message: -# prefix: ":arrow_up:" -# open-pull-requests-limit: 5 - -# - package-ecosystem: "github-actions" -# directory: "/" -# schedule: -# interval: "monthly" -# allow: -# - dependency-type: "all" -# commit-message: -# prefix: ":arrow_up:" -# open-pull-requests-limit: 5 From 9c18aba6f891a386a4e887c52e187ab237dc3db3 Mon Sep 17 00:00:00 2001 From: Ryan Avery Date: Mon, 11 Nov 2024 11:27:21 -0800 Subject: [PATCH 19/22] update setup command, add back dependabot --- .github/dependabot.yml | 35 +++++++++++++++++++++++++++++++++++ Makefile | 20 ++++++++++---------- 2 files changed, 45 insertions(+), 10 deletions(-) create mode 100644 .github/dependabot.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..8f872f1 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,35 @@ +# Configuration: https://dependabot.com/docs/config-file/ +# Docs: https://docs.github.com/en/github/administering-a-repository/keeping-your-dependencies-updated-automatically + +version: 2 + +updates: + - package-ecosystem: "pip" + directory: "/" + schedule: + interval: "monthly" + allow: + - dependency-type: "all" + commit-message: + prefix: ":arrow_up:" + open-pull-requests-limit: 5 + + - package-ecosystem: "github-actions" + directory: "/" + schedule: + interval: "monthly" + allow: + - dependency-type: "all" + commit-message: + prefix: ":arrow_up:" + open-pull-requests-limit: 5 + + - package-ecosystem: "docker" + directory: "/docker" + schedule: + interval: "monthly" + allow: + - dependency-type: "all" + commit-message: + prefix: ":arrow_up:" + open-pull-requests-limit: 5 diff --git a/Makefile b/Makefile index f7733f9..301aea7 100644 --- a/Makefile +++ b/Makefile @@ -5,7 +5,7 @@ ACTIVEPYTHON = $(shell which python) #* UV .PHONY: setup setup: - curl -LsSf https://astral.sh/uv/install.sh | sh + which uv >/dev/null || (curl -LsSf https://astral.sh/uv/install.sh | sh) .PHONY: publish publish: @@ -13,22 +13,22 @@ publish: #* Installation .PHONY: install -install: +install: setup uv export --format requirements-txt -o requirements.txt --no-dev uv pip install --python $(ACTIVEPYTHON) -r requirements.txt .PHONY: install-dev -install-dev: +install-dev: setup uv export --format requirements-txt -o requirements-dev.txt uv pip install --python $(ACTIVEPYTHON) -r requirements-dev.txt .PHONY: pre-commit-install -pre-commit-install: +pre-commit-install: setup uv run --python $(ACTIVEPYTHON) pre-commit install #* Formatters .PHONY: codestyle -codestyle: +codestyle: setup uv run --python $(ACTIVEPYTHON) ruff format --config=pyproject.toml stac_model tests .PHONY: format @@ -36,7 +36,7 @@ format: codestyle #* Linting .PHONY: test -test: +test: setup uv run --python $(ACTIVEPYTHON) pytest -c pyproject.toml --cov-report=html --cov=stac_model tests/ .PHONY: check @@ -46,19 +46,19 @@ check: check-examples check-markdown check-lint check-mypy check-safety check-ci check-all: check .PHONY: mypy -mypy: +mypy: setup uv run --python $(ACTIVEPYTHON) mypy --config-file pyproject.toml ./ .PHONY: check-mypy check-mypy: mypy .PHONY: check-safety -check-safety: +check-safety: setup uv run --python $(ACTIVEPYTHON) safety check --full-report uv run --python $(ACTIVEPYTHON) bandit -ll --recursive stac_model tests .PHONY: lint -lint: +lint: setup uv run --python $(ACTIVEPYTHON) ruff check --fix --config=pyproject.toml ./ .PHONY: check-lint @@ -96,7 +96,7 @@ $(addprefix fix-, $(FORMATTERS)): fix-%: format-% lint-all: lint mypy check-safety check-markdown .PHONY: update-dev-deps -update-dev-deps: +update-dev-deps: setup uv export --only-dev --format requirements-txt -o requirements-only-dev.txt uv pip install --python $(ACTIVEPYTHON) -r requirements-only-dev.txt From 021d0a2a126ecc4d7633da46b241af28198ffa8b Mon Sep 17 00:00:00 2001 From: Ryan Avery Date: Mon, 11 Nov 2024 14:52:22 -0800 Subject: [PATCH 20/22] add backticks, remove extra | None --- CONTRIBUTING.md | 4 ++-- stac_model/input.py | 1 - 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 47b5169..07a47c9 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -11,7 +11,7 @@ make setup > This installs uv as a [standalone application][uv-install].
> For more details, see also the [uv documentation][uv-docs].
-2. Initialize project dependencies with uv and install `pre-commit` hooks: +2. Initialize project dependencies with `uv` and install `pre-commit` hooks: ```bash make install-dev @@ -19,7 +19,7 @@ make pre-commit-install ``` This will install project dependencies into the currently active environment. If you would like to -use uv's default behavior of managing a project-scoped environment, use uv commands directly to +use uv's default behavior of managing a project-scoped environment, use `uv` commands directly to install dependencies. `uv sync` will install dependencies and dev dependencies in `.venv` and update the `uv.lock`. ## PR submission diff --git a/stac_model/input.py b/stac_model/input.py index 2989f2f..c0a2972 100644 --- a/stac_model/input.py +++ b/stac_model/input.py @@ -71,7 +71,6 @@ class ValueScalingProcessingExpression(ProcessingExpression): ValueScalingScale, ValueScalingProcessingExpression, ] - | None ] # noqa: E501 ResizeType: TypeAlias = ( From eb2e5c62ba7d33bbbf0f39fab737d56f453c6ab8 Mon Sep 17 00:00:00 2001 From: Ryan Avery Date: Tue, 12 Nov 2024 10:20:35 -0800 Subject: [PATCH 21/22] remove noqa, make format --- stac_model/examples.py | 2 +- stac_model/input.py | 5 +++-- tests/test_schema.py | 11 +++++++---- 3 files changed, 11 insertions(+), 7 deletions(-) diff --git a/stac_model/examples.py b/stac_model/examples.py index 731830b..e5047cc 100644 --- a/stac_model/examples.py +++ b/stac_model/examples.py @@ -70,7 +70,7 @@ def eurosat_resnet() -> ItemMLModelExtension: type="z-score", mean=mean, stddev=stddev, - ) + ), ) for mean, stddev in zip(stats_mean, stats_stddev, strict=False) ] diff --git a/stac_model/input.py b/stac_model/input.py index c0a2972..e69d8c0 100644 --- a/stac_model/input.py +++ b/stac_model/input.py @@ -18,6 +18,7 @@ def validate_dimensions(self) -> Self: raise ValueError("Dimension order and shape must be of equal length for corresponding indices.") return self + class ValueScalingClipMin(MLMBaseModel): type: Literal["clip-min"] = "clip-min" minimum: Number @@ -71,7 +72,7 @@ class ValueScalingProcessingExpression(ProcessingExpression): ValueScalingScale, ValueScalingProcessingExpression, ] - ] # noqa: E501 +] ResizeType: TypeAlias = ( Literal[ @@ -87,7 +88,7 @@ class ValueScalingProcessingExpression(ProcessingExpression): "wrap-inverse-map", ] | None -) # noqa: E501 +) class ModelBand(MLMBaseModel): diff --git a/tests/test_schema.py b/tests/test_schema.py index 5e41393..53addef 100644 --- a/tests/test_schema.py +++ b/tests/test_schema.py @@ -122,10 +122,13 @@ def test_mlm_no_input_allowed_but_explicit_empty_array_required( ([{"type": "z-score", "mean": 1, "stddev": 2, "minimum": 1, "maximum": 2}], True), # extra must be ignored ([{"type": "processing"}], False), ([{"type": "processing", "format": "test", "expression": "test"}], True), - ([ - {"type": "processing", "format": "test", "expression": "test"}, - {"type": "min-max", "minimum": 1, "maximum": 2} - ], True), + ( + [ + {"type": "processing", "format": "test", "expression": "test"}, + {"type": "min-max", "minimum": 1, "maximum": 2}, + ], + True, + ), ], ) def test_mlm_input_scaling_combination( From 9752f5ef02fc9a86279b0cee4ded409098e0a5f4 Mon Sep 17 00:00:00 2001 From: Ryan Avery Date: Tue, 12 Nov 2024 13:46:02 -0800 Subject: [PATCH 22/22] backticks, use Optional instead of | None --- CONTRIBUTING.md | 6 +++--- stac_model/input.py | 9 ++++----- 2 files changed, 7 insertions(+), 8 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 07a47c9..ddb3127 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -2,14 +2,14 @@ ## Project setup -1. If you don't have uv installed run: +1. If you don't have `uv` installed run: ```bash make setup ``` -> This installs uv as a [standalone application][uv-install].
-> For more details, see also the [uv documentation][uv-docs].
+> This installs `uv` as a [standalone application][uv-install].
+> For more details, see also the [`uv` documentation][uv-docs].
2. Initialize project dependencies with `uv` and install `pre-commit` hooks: diff --git a/stac_model/input.py b/stac_model/input.py index e69d8c0..7a189d2 100644 --- a/stac_model/input.py +++ b/stac_model/input.py @@ -74,7 +74,7 @@ class ValueScalingProcessingExpression(ProcessingExpression): ] ] -ResizeType: TypeAlias = ( +ResizeType: TypeAlias = Optional[ Literal[ "crop", "pad", @@ -87,8 +87,7 @@ class ValueScalingProcessingExpression(ProcessingExpression): "wrap-fill-outliers", "wrap-inverse-map", ] - | None -) +] class ModelBand(MLMBaseModel): @@ -99,11 +98,11 @@ class ModelBand(MLMBaseModel): ) ) # similar to 'ProcessingExpression', but they can be omitted here - format: Annotated[str | None, OmitIfNone] = Field( + format: Annotated[Optional[str], OmitIfNone] = Field( default=None, description="", ) - expression: Annotated[Any | None, OmitIfNone] = Field( + expression: Annotated[Optional[Any], OmitIfNone] = Field( default=None, description="", )