From 72ea0f5de2cd9f39b005ed0652e45fdadb219e81 Mon Sep 17 00:00:00 2001 From: clintval Date: Tue, 22 Apr 2025 15:08:42 -1000 Subject: [PATCH 1/2] chore: update the typeline dependency --- bedspec/_reader.py | 4 +- bedspec/_writer.py | 4 +- poetry.lock | 264 ++++++++++++++++++++++++--------------------- pyproject.toml | 90 +++++++++------- 4 files changed, 200 insertions(+), 162 deletions(-) diff --git a/bedspec/_reader.py b/bedspec/_reader.py index c0b5f16..6c00566 100644 --- a/bedspec/_reader.py +++ b/bedspec/_reader.py @@ -6,7 +6,7 @@ from typing import get_args from typing import get_origin -from typeline import TsvRecordReader +from typeline import TsvReader from typing_extensions import Self from typing_extensions import override @@ -17,7 +17,7 @@ from bedspec._bedspec import BedType -class BedReader(TsvRecordReader[BedType]): +class BedReader(TsvReader[BedType]): """A reader of BED records.""" @override diff --git a/bedspec/_writer.py b/bedspec/_writer.py index f5b9b0f..0d55d60 100644 --- a/bedspec/_writer.py +++ b/bedspec/_writer.py @@ -1,6 +1,6 @@ from typing import Any -from typeline import TsvRecordWriter +from typeline import TsvWriter from typing_extensions import override from bedspec._bedspec import COMMENT_PREFIXES @@ -8,7 +8,7 @@ from bedspec._bedspec import BedType -class BedWriter(TsvRecordWriter[BedType]): +class BedWriter(TsvWriter[BedType]): """A writer for writing dataclasses into BED text data.""" @override diff --git a/poetry.lock b/poetry.lock index 63960db..e71b608 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,14 +1,15 @@ -# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.1.2 and should not be changed by hand. [[package]] name = "basedpyright" -version = "1.22.0" +version = "1.29.0" description = "static type checking for Python (but based)" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ - {file = "basedpyright-1.22.0-py3-none-any.whl", hash = "sha256:6376107086ad25525429b8a94a2ffdb67c6dd2b1a6be38bf3c6ea9b5c3d1f688"}, - {file = "basedpyright-1.22.0.tar.gz", hash = "sha256:457e97ac4c3f694b900453d3f8824af36d17b9cef3d76c623e665dd4c7872d9c"}, + {file = "basedpyright-1.29.0-py3-none-any.whl", hash = "sha256:926ae39eaccfe15e7dbd997dd4e48b22f98bcf201e4cbb8620aa6b8cfbee723b"}, + {file = "basedpyright-1.29.0.tar.gz", hash = "sha256:90742d5a59e4f877ad3639bafb7a40280512129572b56dd51d8cb9375070d7c0"}, ] [package.dependencies] @@ -20,6 +21,8 @@ version = "0.4.6" description = "Cross-platform colored terminal text." optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" +groups = ["dev"] +markers = "sys_platform == \"win32\"" files = [ 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description = "The Cython compiler for writing C extensions in the Python language." optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7" +groups = ["main"] files = [ {file = "Cython-3.0.11-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:44292aae17524abb4b70a25111fe7dec1a0ad718711d47e3786a211d5408fdaa"}, {file = "Cython-3.0.11-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a75d45fbc20651c1b72e4111149fed3b33d270b0a4fb78328c54d965f28d55e1"}, @@ -183,6 +188,8 @@ version = "1.2.2" description = "Backport of PEP 654 (exception groups)" optional = false python-versions = ">=3.7" +groups = ["dev"] +markers = "python_version == \"3.10\"" files = [ {file = "exceptiongroup-1.2.2-py3-none-any.whl", hash = "sha256:3111b9d131c238bec2f8f516e123e14ba243563fb135d3fe885990585aa7795b"}, {file = "exceptiongroup-1.2.2.tar.gz", hash = "sha256:47c2edf7c6738fafb49fd34290706d1a1a2f4d1c6df275526b62cbb4aa5393cc"}, @@ -197,6 +204,7 @@ version = "2.0.0" 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"https://github.com/clintval/bedspec" -repository = "https://github.com/clintval/bedspec" keywords = ["bioinformatics", "BED", "NGS", "HTS", "interval"] +include = ["CONTRIBUTING.md", "LICENSE"] +requires-python = ">=3.10" +dependencies = [ + "superintervals >=0.2.10", + "typeline >=0.11", + "typing-extensions >=4.12", +] classifiers = [ "Development Status :: 3 - Alpha", "Environment :: Console", @@ -20,28 +25,32 @@ classifiers = [ "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", "Topic :: File Formats", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Software Development :: Documentation", "Topic :: Software Development :: Libraries :: Python Modules", "Typing :: Typed", ] -include = ["CONTRIBUTING.md", "LICENSE"] -packages = [{ include = "bedspec" }] -[tool.poetry.dependencies] -python = "^3.10.0,<4.0.0" -superintervals = "^0.2.2" -typeline = 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"return_non_zero" check-all.sequence = [ "check-lock", "check-format", @@ -81,7 +90,7 @@ check-all.sequence = [ "check-typing" ] -fix-and-check-all.ignore_fail = true +fix-and-check-all.ignore_fail = "return_non_zero" fix-and-check-all.sequence = [ "fix-all", "check-all" @@ -108,7 +117,7 @@ doctest_optionflags = [ [tool.mypy] files = ["bedspec/", "tests/"] -strict_optional = false +strict_optional = true strict_equality = true check_untyped_defs = true disallow_incomplete_defs = true @@ -122,11 +131,15 @@ warn_return_any = true warn_unreachable = true warn_unused_configs = true warn_unused_ignores = true -enable_error_code = "ignore-without-code" +enable_error_code = [ + "ignore-without-code", + "possibly-undefined", +] [tool.pyright] include = ["bedspec/"] reportAny = false +reportExplicitAny = false pythonVersion = "3.10" [tool.ruff] @@ -138,27 +151,30 @@ preview = true [tool.ruff.lint] select = [ - "ARG", # Unused arguments - "C901", # McCabe complexity - "B", # bugbear - "D", # pydocstyle (docstrings. We have the "google" convention enabled) - "D204", # Blank line between class docstring and first (__init__) method - "D212", # summary line should be located on the same line as opening quotes - "E", # pycodestyle errors - "F", # pyflakes - "I", # isort - "N", # PEP8 naming - "W", # pycodestyle warnings - "Q" # flake8-quotes + "ARG", # Unused arguments + "C901", # McCabe complexity + "B", # bugbear + "D", # pydocstyle (docstrings. We have the "google" convention enabled) + "D204", # Blank line between class docstring and first (__init__) method + "D213", # Summary line should be located on the line after opening quotes + "E", # pycodestyle errors + "LOG", # flake8-logging + "LOG015", # (preview rule) Prohibit calls to the root logger + "F", # pyflakes + "I", # isort + "N", # PEP8 naming + "W", # pycodestyle warnings + "Q", # flake8-quotes ] ignore = [ "E203", "E701", - "D213", # Summary line should be located on the line after opening quote + "D213", # summary line should be located on the line after opening quote "D100", # missing docstring in public module "D104", # missing docstring in public package ] unfixable = ["B"] +preview = true [tool.ruff.lint.mccabe] max-complexity = 13 From 4e62f9da0200c5bb1ef19c97963e7a5bf17cb01d Mon Sep 17 00:00:00 2001 From: clintval Date: Tue, 22 Apr 2025 15:11:34 -1000 Subject: [PATCH 2/2] chore: support Python 3.13 too --- .github/workflows/publish_bedspec.yml | 12 +++++++----- .github/workflows/tests.yml | 16 +++++++--------- .github/workflows/wheels.yml | 2 +- CONTRIBUTING.md | 18 ------------------ README.md | 2 +- 5 files changed, 16 insertions(+), 34 deletions(-) diff --git a/.github/workflows/publish_bedspec.yml b/.github/workflows/publish_bedspec.yml index e8137a9..4b74025 100644 --- a/.github/workflows/publish_bedspec.yml +++ b/.github/workflows/publish_bedspec.yml @@ -5,7 +5,8 @@ on: tags: '[0-9]+.[0-9]+.[0-9]+' env: - POETRY_VERSION: 1.6 + POETRY_VERSION: 2.1.1 + jobs: on-main-branch-check: @@ -48,10 +49,11 @@ jobs: with: python-version: 3.12 - - name: Install poetry - run: | - python -m pip install --upgrade pip - python -m pip install poetry==${{env.POETRY_VERSION}} + - name: Install and configure Poetry + uses: snok/install-poetry@v1 + with: + version: ${{ env.POETRY_VERSION }} + installer-parallel: true - name: Configure poetry shell: bash diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 19f2002..d5e961b 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -9,14 +9,14 @@ on: workflow_call: env: - POETRY_VERSION: 1.8 + POETRY_VERSION: 2.1.1 jobs: Tests: runs-on: ubuntu-latest strategy: matrix: - PYTHON_VERSION: ["3.10", "3.11", "3.12"] + PYTHON_VERSION: ["3.10", "3.11", "3.12", "3.13"] steps: - uses: actions/checkout@v4 @@ -30,10 +30,11 @@ jobs: shell: bash run: echo "version=$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")" >> $GITHUB_OUTPUT - - name: Install poetry - run: | - python -m pip install --upgrade pipx - pipx install poetry==${{env.POETRY_VERSION}} + - name: Install and configure Poetry + uses: snok/install-poetry@v1 + with: + version: ${{ env.POETRY_VERSION }} + installer-parallel: true - name: Set up cache uses: actions/cache@v4 @@ -50,8 +51,5 @@ jobs: - name: Install the library run: poetry install -v - - name: Install the task runner poethepoet - run: poetry self add 'poethepoet[poetry_plugin]' - - name: Test the library run: poetry task check-all diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml index 86813d0..42fa50b 100644 --- a/.github/workflows/wheels.yml +++ b/.github/workflows/wheels.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - PYTHON_VERSION: ["3.10", "3.11", "3.12"] + PYTHON_VERSION: ["3.10", "3.11", "3.12", "3.13"] steps: - uses: actions/checkout@v4 diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 6fb7cad..7902631 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -40,24 +40,6 @@ poetry check --lock ## Shortcut Task Commands -To be able to run shortcut task commands, first install the Poetry plugin [`poethepoet`](https://poethepoet.natn.io/index.html): - -```console -poetry self add 'poethepoet[poetry_plugin]' -``` - -> [!NOTE] -> Upon the release of Poetry [v2.0.0](https://github.com/orgs/python-poetry/discussions/9793#discussioncomment-11043205), Poetry will automatically support bootstrap installation of [project-specific plugins](https://github.com/python-poetry/poetry/pull/9547) and installation of the task runner will become automatic for this project. -> The `pyproject.toml` syntax will be: -> -> ```toml -> [tool.poetry] -> requires-poetry = ">=2.0" -> -> [tool.poetry.requires-plugins] -> poethepoet = ">=0.29" -> ``` - ### For Running Individual Checks ```console diff --git a/README.md b/README.md index 015a86e..c1e47d0 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![PyPi Release](https://badge.fury.io/py/bedspec.svg)](https://badge.fury.io/py/bedspec) [![CI](https://github.com/clintval/bedspec/actions/workflows/tests.yml/badge.svg?branch=main)](https://github.com/clintval/bedspec/actions/workflows/tests.yml?query=branch%3Amain) -[![Python Versions](https://img.shields.io/badge/python-3.10_|_3.11_|_3.12-blue)](https://github.com/clintval/typeline) +[![Python Versions](https://img.shields.io/badge/python-3.10_|_3.11_|_3.12_|_3.13-blue)](https://github.com/clintval/typeline) [![basedpyright](https://img.shields.io/badge/basedpyright-checked-42b983)](https://docs.basedpyright.com/latest/) [![mypy](https://www.mypy-lang.org/static/mypy_badge.svg)](https://mypy-lang.org/) [![Poetry](https://img.shields.io/endpoint?url=https://python-poetry.org/badge/v0.json)](https://python-poetry.org/)