diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c560565..b9be69f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -2,25 +2,31 @@ name: CI on: pull_request: + types: + - opened + - synchronize + - reopened + - ready_for_review branches: - main jobs: - lint: + if: github.event.pull_request.draft == false runs-on: ubuntu-latest steps: - uses: actions/checkout@v3 - - uses: jpetrucciani/black-check@master + - uses: jpetrucciani/ruff-check@main - pytest: + pytest-linux: + if: github.event.pull_request.draft == false strategy: matrix: - os: [ubuntu-latest] - python-version: ["3.8", "3.9", "3.10", "3.11"] - runs-on: ${{ matrix.os }} + python-version: ["3.9", "3.10", "3.11"] + + runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Install Poetry run: pipx install poetry @@ -31,13 +37,10 @@ jobs: python-version: ${{ matrix.python-version }} cache: "poetry" - - name: Install HDF5 - run: sudo apt install --fix-missing libhdf5-serial-dev - - name: Install Dependencies run: | poetry env use "${{ matrix.python-version }}" - poetry install + poetry install --extras all - name: Test with pytest - run: poetry run pytest --dist no -n 0 + run: poetry run pytest diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 489af67..352968b 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -15,7 +15,7 @@ jobs: build: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Install Poetry run: pipx install poetry @@ -23,15 +23,17 @@ jobs: - name: Set up Python uses: actions/setup-python@v4 with: - python-version: "3.10" + python-version: "3.11" cache: "poetry" - name: Install Dependencies - run: poetry install + run: | + poetry env use "${{ matrix.python-version }}" + poetry install --extras all - name: Build documentation run: | - poetry env use "3.10" + poetry env use "3.11" poetry run pdoc --docformat google src/doubt -o docs - name: Compress documentation diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 2ef2764..13ef8b6 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,23 +1,28 @@ repos: -- repo: https://github.com/ambv/black - rev: 23.3.0 +- repo: https://github.com/pre-commit/pygrep-hooks + rev: v1.10.0 hooks: - - id: black -- repo: https://github.com/timothycrosley/isort - rev: 5.12.0 + - id: python-use-type-annotations +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.5.0 hooks: - - id: isort -- repo: https://github.com/pycqa/flake8 - rev: 6.0.0 + - id: end-of-file-fixer + - id: trailing-whitespace + - id: debug-statements +- repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.3.2 hooks: - - id: flake8 + - id: ruff + args: [--fix, --exit-non-zero-on-fix] + types_or: [python, pyi, jupyter] + - id: ruff-format + types_or: [python, pyi, jupyter] - repo: https://github.com/kynan/nbstripout - rev: 0.6.0 + rev: 0.7.1 hooks: - id: nbstripout - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.4.1 + rev: v1.9.0 hooks: - id: mypy args: [--install-types, --non-interactive, --ignore-missing-imports, --show-error-codes] - diff --git a/CHANGELOG.md b/CHANGELOG.md index 36f9d09..202cd04 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,12 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). +## [Unreleased] +### Changed +- Updated `tables` dependency to v3.9.x, which fixes issues with installation of the + package. This requires Python 3.9 or above, however, so we require that here as well. + + ## [v5.1.0] - 2023-10-31 ### Added - The `Boot` class now has `save` and `load` methods, which uses `joblib` under the diff --git a/README.md b/README.md index 6a082ef..b73ce71 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ ______________________________________________________________________ [![Documentation](https://img.shields.io/badge/docs-passing-green)](https://saattrupdan.github.io/doubt/doubt.html) [![License](https://img.shields.io/github/license/saattrupdan/doubt)](https://github.com/saattrupdan/doubt/blob/main/LICENSE) [![LastCommit](https://img.shields.io/github/last-commit/saattrupdan/doubt)](https://github.com/saattrupdan/doubt/commits/main) -[![Code Coverage](https://img.shields.io/badge/Coverage-67%25-yellow.svg)](https://github.com/saattrupdan/doubt/tree/dev/tests) +[![Code Coverage](https://img.shields.io/badge/Coverage-66%25-yellow.svg)](https://github.com/saattrupdan/doubt/tree/dev/tests) [![Conference](https://img.shields.io/badge/Conference-AAAI23-blue)](https://doi.org/10.1609/aaai.v37i12.26755) A Python package to include prediction intervals in the predictions of machine diff --git a/makefile b/makefile index a11cc3a..d9f47e3 100644 --- a/makefile +++ b/makefile @@ -44,7 +44,7 @@ install: ## Install dependencies @$(MAKE) setup-git setup-poetry: - @poetry env use python3.10 && poetry install + @poetry env use python3.10 && poetry install --extras all setup-environment-variables: @poetry run python3.10 -m src.scripts.fix_dot_env_file @@ -109,7 +109,7 @@ publish-minor: bump-minor publish ## Publish a minor version publish-patch: bump-patch publish ## Publish a patch version test: ## Run tests - @poetry run pytest && readme-cov + @poetry run pytest && readme-cov && rm .coverage* tree: ## Print directory tree @tree -a \ diff --git a/poetry.lock b/poetry.lock index 3fe7cab..0ccb139 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,104 +1,77 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. 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= ["pytest (>=6.0.0)", "setuptools (>=65)"] - [[package]] name = "xlrd" version = "2.0.1" @@ -1520,9 +1672,10 @@ docs = ["sphinx"] test = ["pytest", "pytest-cov"] [extras] +all = ["openpyxl", "tables", "xlrd"] datasets = ["openpyxl", "tables", "xlrd"] [metadata] lock-version = "2.0" -python-versions = ">=3.8,<3.12" -content-hash = "e465bbb3a4159e6a039f3acbfdba4f052009b45a0797b010c7fff2e98630ecb0" +python-versions = ">=3.9,<3.12" +content-hash = "54d353f94889187ab612e50764a437454a48821b32e0adff8fc08cc575eeb128" diff --git a/pyproject.toml b/pyproject.toml index 7b40e6c..0b28131 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,3 @@ -[build-system] -requires = ["poetry-core>=1.0.0"] -build-backend = "poetry.core.masonry.api" - [tool.poetry] name = "doubt" version = "5.1.0" @@ -12,7 +8,7 @@ license = "MIT" repository = "https://github.com/saattrupdan/doubt" [tool.poetry.dependencies] -python = ">=3.8,<3.12" +python = ">=3.9,<3.12" tqdm = "^4.62.0" numpy = "^1.23.0" pandas = ">=1.4.0,<3.0.0" @@ -20,58 +16,80 @@ joblib = "^1.2.0" scikit-learn = ">=1.1.0,<1.3.0" scipy = "^1.10.0" urllib3 = "^2.0.7" -tables = { version = "^3.8.0", optional = true } +tables = { version = "^3.9.2", optional = true } xlrd = { version = "^2.0.1", optional = true } openpyxl = { version = "^3.0.10", optional = true } [tool.poetry.group.dev.dependencies] -pdoc = "^7.1.1" -pre-commit = "^2.17.0" -black = "^23.1.0" -requests = "^2.28.0" -lxml = "^4.9.0" -isort = "^5.10.1" -pytest-xdist = "^2.5.0" -readme-coverage-badger = ">=0.1.2,<1.0.0" -Pygments = "2.15.0" -pytest = "^7.2.2" -pytest-cov = "^4.0.0" +pdoc = ">=7.1.1" +pytest = ">=8.1.1" +pre-commit = ">=3.6.2" +requests = ">=2.28.0" +lxml = ">=5.1.0" +pytest-cov = ">=4.1.0" +readme-coverage-badger = ">=0.1.2" +ruff = ">=0.3.2" +mypy = ">=1.9.0" +nbstripout = ">=0.7.1" [tool.poetry.extras] datasets = ["tables", "xlrd", "openpyxl"] +all = ["tables", "xlrd", "openpyxl"] [tool.pytest.ini_options] minversion = "6.0" addopts = [ '--verbose', '--durations=10', - '--color=yes', + '--color=no', '-s', '-vv', '--doctest-modules', '--cov=src/doubt', - '-n 8', ] xfail_strict = true -filterwarnings = ["error"] +filterwarnings = [ + "error", + "ignore::UserWarning", + "ignore::DeprecationWarning", + "ignore::PendingDeprecationWarning", + "ignore::ImportWarning", +] log_cli_level = "info" testpaths = ["tests", "src/doubt"] -[tool.black] +[tool.ruff] line-length = 88 -include = '\.pyi?$' -exclude = ''' -/( - \.git -| \.hg -| \.mypy_cache -| \.tox -| \.venv -| _build -| buck-out -| build -)/ -''' +target-version = "py310" +exclude = [ + ".git", + ".mypy_cache", + ".pytest_cache", + ".ruff_cache", + ".venv", +] -[tool.isort] -profile = "black" +[tool.ruff.format] +quote-style = "double" +indent-style = "space" +docstring-code-format = true +skip-magic-trailing-comma = true + +[tool.lint] +extend-select = [ + "I", + "D", +] + +[tool.ruff.lint.extend-per-file-ignores] +"__init__.py" = ["F401"] + +[tool.ruff.lint.isort] +split-on-trailing-comma = false + +[tool.ruff.lint.pydocstyle] +convention = "google" + +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" diff --git a/src/doubt/models/boot/boot.py b/src/doubt/models/boot/boot.py index 9895635..c84b07c 100644 --- a/src/doubt/models/boot/boot.py +++ b/src/doubt/models/boot/boot.py @@ -12,7 +12,7 @@ from numpy.typing import NDArray -def save_model(self, path: Path | str): +def save_model(self, path: Union[Path, str]): """Save a model to disk. Args: @@ -28,7 +28,7 @@ def save_model(self, path: Path | str): joblib.dump(obj, filename=path) -def load_model(cls, path: Path | str) -> "Boot": +def load_model(cls, path: Union[Path, str]) -> "Boot": """Load a model from disk. Args: @@ -383,10 +383,7 @@ def predict( # Run the worker function in parallel with Parallel(n_jobs=jobs) as parallel: bootstrap_preds_list = parallel( - delayed(_model_predict)( - model=self._models[boot_idx], - X=X, - ) + delayed(_model_predict)(model=self._models[boot_idx], X=X) for boot_idx in range(n_boots) )