From 123214a69de1ffd790dfa691b463653a04ef27f3 Mon Sep 17 00:00:00 2001 From: "Huska, Matthew" Date: Fri, 15 Nov 2024 15:32:10 +0100 Subject: [PATCH] Bump all deps, including python (>=3.11,<3.13) --- .github/workflows/release.yml | 2 +- .github/workflows/test-pypi.yml | 2 +- .github/workflows/tests.yml | 2 +- envs/breakfast-dev.yml | 2 +- noxfile.py | 7 +- poetry.lock | 707 +++++++++++++++++--------------- pyproject.toml | 24 +- 7 files changed, 395 insertions(+), 351 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 816723e..9a1d79c 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -9,7 +9,7 @@ jobs: - uses: actions/checkout@v4 - uses: actions/setup-python@v5 with: - python-version: '3.10' + python-version: '3.12' architecture: x64 - run: pip install nox==2024.10.9 - run: pip install poetry==1.8.4 diff --git a/.github/workflows/test-pypi.yml b/.github/workflows/test-pypi.yml index 874dd42..4fc13ef 100644 --- a/.github/workflows/test-pypi.yml +++ b/.github/workflows/test-pypi.yml @@ -10,7 +10,7 @@ jobs: - uses: actions/checkout@v4 - uses: actions/setup-python@v5 with: - python-version: '3.10' + python-version: '3.12' architecture: x64 - run: pip install nox==2024.10.9 - run: pip install poetry==1.8.4 diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index b517770..475ce0f 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -5,7 +5,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.10'] + python-version: ['3.12'] name: Python ${{ matrix.python-version }} steps: - uses: actions/checkout@v4 diff --git a/envs/breakfast-dev.yml b/envs/breakfast-dev.yml index 28fa515..21054d5 100644 --- a/envs/breakfast-dev.yml +++ b/envs/breakfast-dev.yml @@ -4,7 +4,7 @@ channels: - bioconda - nodefaults dependencies: - - python>=3.9,<3.10 + - python>=3.11,<3.13 - poetry - poetry-plugin-export - fortran-compiler diff --git a/noxfile.py b/noxfile.py index 295dffb..a045409 100644 --- a/noxfile.py +++ b/noxfile.py @@ -1,4 +1,5 @@ """Nox sessions.""" + import tempfile from typing import Any @@ -47,7 +48,7 @@ def install_with_constraints(session: Session, *args: str, **kwargs: Any) -> Non session.install("-r", requirements.name, *args, **kwargs) -@nox.session(python="3.9") +@nox.session(python="3.12") def black(session: Session) -> None: """Run black code formatter.""" args = session.posargs or locations @@ -55,7 +56,7 @@ def black(session: Session) -> None: session.run("black", *args) -@nox.session(python="3.9") +@nox.session(python="3.12") def lint(session: Session) -> None: """Lint using flake8.""" args = session.posargs or locations @@ -73,7 +74,7 @@ def lint(session: Session) -> None: session.run("flake8", *args) -@nox.session(python=["3.10", "3.9"]) +@nox.session(python=["3.11", "3.12"]) def tests(session): args = session.posargs or ["--cov"] session.run("poetry", "install", "--without", "dev", external=True) diff 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"sha256:56c1e26c150397e58c4926da8eeee87533b1e32bef131bd4bf6a2f45f3185467"}, + {file = "threadpoolctl-3.5.0.tar.gz", hash = "sha256:082433502dd922bf738de0d8bcc4fdcbf0979ff44c42bd40f5af8a282f6fa107"}, ] [[package]] -name = "typing-extensions" -version = "4.3.0" -description = "Backported and Experimental Type Hints for Python 3.7+" +name = "tzdata" +version = "2024.2" +description = "Provider of IANA time zone data" optional = false -python-versions = ">=3.7" +python-versions = ">=2" files = [ - {file = "typing_extensions-4.3.0-py3-none-any.whl", hash = "sha256:25642c956049920a5aa49edcdd6ab1e06d7e5d467fc00e0506c44ac86fbfca02"}, - {file = "typing_extensions-4.3.0.tar.gz", hash = "sha256:e6d2677a32f47fc7eb2795db1dd15c1f34eff616bcaf2cfb5e997f854fa1c4a6"}, + {file = "tzdata-2024.2-py2.py3-none-any.whl", hash = "sha256:a48093786cdcde33cad18c2555e8532f34422074448fbc874186f0abd79565cd"}, + {file = "tzdata-2024.2.tar.gz", hash = "sha256:7d85cc416e9382e69095b7bdf4afd9e3880418a2413feec7069d533d6b4e31cc"}, ] [metadata] lock-version = "2.0" -python-versions = ">=3.9,<3.11" -content-hash = "d234d66dcb1af947c47543acdb5735b5b3f2bef8a83db986ae2fc61a7d9ecb33" +python-versions = ">=3.11,<3.13" +content-hash = "6f0dd6006d4f888036c5258032771198b312dfb5f525725dae88cadfb6c140c8" diff --git a/pyproject.toml b/pyproject.toml index facbb56..f71435d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,20 +9,20 @@ homepage = "https://github.com/rki-mf1/breakfast" repository = "https://github.com/rki-mf1/breakfast" [tool.poetry.dependencies] -python = ">=3.9,<3.11" -networkx = "^2.8" -pandas = "^1.4.2" -scikit-learn = "^1.0.2" -numpy = "^1.22.3" -scipy = "^1.8.0" -click = "^8.1.3" +python = ">=3.11,<3.13" +networkx = "^3.4.2" +pandas = "^2.2.3" +scikit-learn = "^1.5.2" +numpy = "^2.1.3" +scipy = "^1.14.1" +click = "^8.1.7" [tool.poetry.group.dev.dependencies] -pytest = "^7.1.2" -coverage = {extras = ["toml"], version = 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