diff --git a/.github/workflows/checks.yaml b/.github/workflows/checks.yaml index eef7a79..f42525a 100644 --- a/.github/workflows/checks.yaml +++ b/.github/workflows/checks.yaml @@ -6,54 +6,52 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.11", "3.12", "3.13"] + python-version: ["3.11", "3.12", "3.13", "3.14"] steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: Set up Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v6 with: python-version: ${{ matrix.python-version }} + - name: Install uv + uses: astral-sh/setup-uv@v7 + with: + enable-cache: true + - name: Install dependencies - run: | - python3 -m pip install ".[tests]" + run: uv sync --extra tests - name: Run tests - run: python3 -m pytest + run: uv run pytest precommit_hooks: runs-on: ubuntu-latest - strategy: - matrix: - cmd: - - "end-of-file-fixer" - - "trailing-whitespace" - - "mixed-line-ending" steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - - name: Set up Python 3.12 - uses: actions/setup-python@v5 + - uses: j178/prek-action@v1 with: - python-version: 3.12 + extra_args: '--all-files --skip "ruff-format" --skip "ruff-check"' - - uses: pre-commit/action@v3.0.1 - with: - extra_args: ${{ matrix.cmd }} --all-files lint: - name: lint runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - - name: Setup Python - uses: actions/setup-python@v5 - with: - python-version: "3.11" + - name: Install uv + uses: astral-sh/setup-uv@v7 + with: + enable-cache: true - - name: Install dependencies - run: python3 -m pip install ".[dev]" + - name: Set up Python + uses: actions/setup-python@v6 + with: + python-version: 3.13 + + - name: Install dependencies + run: uv sync --extra dev - - name: Check style - run: python3 -m ruff check . && python3 -m ruff format --check . + - name: Check style + run: uv run ruff check . && uv run ruff format --check . diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d3c995e..6fcb5f2 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,21 +1,28 @@ repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v5.0.0 # pre-commit-hooks version + rev: v6.0.0 # pre-commit-hooks version hooks: - - id: check-added-large-files - args: ['--maxkb=1500'] # for clinicaltrials.gov API fixture - - id: detect-private-key - - id: trailing-whitespace - - id: end-of-file-fixer - - id: check-merge-conflict - id: detect-aws-credentials args: [ --allow-missing-credentials ] + - repo: builtin + hooks: + - id: trailing-whitespace + - id: check-added-large-files + args: ['--maxkb=1500'] + - id: check-case-conflict + - id: end-of-file-fixer + - id: fix-byte-order-marker + - id: check-json + - id: check-toml + - id: check-yaml - id: mixed-line-ending args: [ --fix=lf ] + - id: check-merge-conflict + - id: detect-private-key - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.12.1 # ruff version + rev: v0.14.10 # ruff version hooks: - id: ruff-format - - id: ruff + - id: ruff-check args: [ --fix, --exit-non-zero-on-fix ] -minimum_pre_commit_version: 4.2.0 +minimum_prek_version: 0.2.23 diff --git a/pyproject.toml b/pyproject.toml index e328491..dfd6619 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,23 +9,23 @@ classifiers = [ "Intended Audience :: Science/Research", "Intended Audience :: Developers", "Topic :: Scientific/Engineering :: Bio-Informatics", - "License :: OSI Approved :: MIT License", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", "Programming Language :: Python :: 3.13", ] +license = "MIT" +license-files = ["LICENSE"] requires-python = ">=3.11" -description = "Fetch regulatory approval data for drug terms" -license = {file = "LICENSE"} +description = "Easily fetch and operate on data from medical & drug regulatory agencies" dependencies = ["requests"] dynamic = ["version"] [project.optional-dependencies] tests = ["pytest", "pytest-cov", "requests-mock"] dev = [ - "pre-commit>=4.2.0", - "ruff==0.12.1", + "prek>=0.2.23", + "ruff==0.14.10", ] [project.urls] @@ -58,109 +58,74 @@ src = ["src"] [tool.ruff.lint] -select = [ - "F", # https://docs.astral.sh/ruff/rules/#pyflakes-f - "E", "W", # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w - "I", # https://docs.astral.sh/ruff/rules/#isort-i - "N", # https://docs.astral.sh/ruff/rules/#pep8-naming-n - "D", # https://docs.astral.sh/ruff/rules/#pydocstyle-d - "UP", # https://docs.astral.sh/ruff/rules/#pyupgrade-up - "ANN", # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann - "ASYNC", # https://docs.astral.sh/ruff/rules/#flake8-async-async - "S", # https://docs.astral.sh/ruff/rules/#flake8-bandit-s - "B", # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b - "A", # https://docs.astral.sh/ruff/rules/#flake8-builtins-a - "C4", # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4 - "DTZ", # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz - "T10", # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz - "EM", # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em - "LOG", # https://docs.astral.sh/ruff/rules/#flake8-logging-log - "G", # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g - "INP", # https://docs.astral.sh/ruff/rules/#flake8-no-pep420-inp - "PIE", # https://docs.astral.sh/ruff/rules/#flake8-pie-pie - "T20", # https://docs.astral.sh/ruff/rules/#flake8-print-t20 - "PT", # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt - "Q", # https://docs.astral.sh/ruff/rules/#flake8-quotes-q - "RSE", # https://docs.astral.sh/ruff/rules/#flake8-raise-rse - "RET", # https://docs.astral.sh/ruff/rules/#flake8-return-ret - "SLF", # https://docs.astral.sh/ruff/rules/#flake8-self-slf - "SLOT", # https://docs.astral.sh/ruff/rules/#flake8-slots-slot - "SIM", # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim - "ARG", # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg - "PTH", # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth - "PGH", # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh - "PLC", # https://docs.astral.sh/ruff/rules/#convention-c - "PLE", # https://docs.astral.sh/ruff/rules/#error-e_1 - "TRY", # https://docs.astral.sh/ruff/rules/#tryceratops-try - "PERF", # https://docs.astral.sh/ruff/rules/#perflint-perf - "FURB", # https://docs.astral.sh/ruff/rules/#refurb-furb - "RUF", # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf -] -fixable = [ - "I", - "F401", - "D", - "UP", - "ANN", - "B", - "C4", - "LOG", - "G", - "PIE", - "PT", - "RSE", - "SIM", - "PLC", - "PLE", - "TRY", - "PERF", - "FURB", - "RUF" -] -# ANN003 - missing-type-kwargs -# D203 - one-blank-line-before-class -# D205 - blank-line-after-summary -# D206 - indent-with-spaces* -# D213 - multi-line-summary-second-line -# D300 - triple-single-quotes* -# D400 - ends-in-period -# D415 - ends-in-punctuation -# E111 - indentation-with-invalid-multiple* -# E114 - indentation-with-invalid-multiple-comment* -# E117 - over-indented* -# E501 - line-too-long* -# W191 - tab-indentation* -# S321 - suspicious-ftp-lib-usage -# PLC0206 - dict-index-missing-items -# *ignored for compatibility with formatter +select = ["ALL"] ignore = [ - "ANN003", - "D203", "D205", "D206", "D213", "D300", "D400", "D415", - "E111", "E114", "E117", "E501", + # unused + "AIR", + "ERA", + "YTT", + "BLE", + "FBT", + "CPY", + "DJ", + "EXE", + "FIX", + "FA", + "PYI", + "TD", + "C90", + "NPY", + "PD", + # ignore for compatibility with formatter + "D206", + "D300", + "W191", + "E111", + "E114", + "E117", + "E501", "W191", "S321", + "COM812", + "COM819", + "Q000", + "Q001", + "Q002", + "Q003", + # don't require types on *args, **kwargs + "ANN002", + "ANN003", + # subjective pylint thresholds + "PLR0904", + "PLR091", + "PLR1702", "PLC0206", + # misc unnecessary stuff + "S321", + "D203", + "D205", + "D213", + "D400", + "D415", ] [tool.ruff.lint.per-file-ignores] # ANN001 - missing-type-function-argument # ANN2 - missing-return-type -# D100 - undocumented-public-module -# D102 - undocumented-public-class # S101 - assert # B011 - assert-false # INP001 - implicit-namespace-package -# D103 - missing-docstring-public-function +# PLR2004 - magic-value-comparison "tests/*" = [ "ANN001", "ANN2", - "D100", - "D102", - "D103", + "D", "S101", "B011", - "INP001" + "INP001", + "PLR2004", ] + [tool.ruff.lint.flake8-annotations] mypy-init-return = true diff --git a/src/regbot/fetch/drugsfda.py b/src/regbot/fetch/drugsfda.py index 85da1e0..1e60c89 100644 --- a/src/regbot/fetch/drugsfda.py +++ b/src/regbot/fetch/drugsfda.py @@ -636,6 +636,7 @@ def make_drugsatfda_request(url: str, limit: int = 500) -> list[Result] | None: results = [] remaining = True skip = 0 + skip_ceiling = 25000 # arbitrary, unrealistic ceiling to prevent insane skip values while remaining: full_url = f"{url}&limit={limit}&skip={skip}" _logger.debug("Issuing GET request to %s", full_url) @@ -650,7 +651,7 @@ def make_drugsatfda_request(url: str, limit: int = 500) -> list[Result] | None: data = r.json() results += data["results"] skip = data["meta"]["results"]["skip"] + len(data["results"]) - remaining = (data["meta"]["results"]["total"] > skip) or (skip >= 25000) + remaining = (data["meta"]["results"]["total"] > skip) or (skip >= skip_ceiling) return [_get_result(r) for r in results]