Merge pull request #24 from rki-mf1/bump-all-versions

Bump all deps, including python (>=3.11,<3.13)

.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

.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

.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

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

noxfile.py

@@ -1,4 +1,5 @@
 """Nox sessions."""
+
 import tempfile
 from typing import Any
 
@@ -47,15 +48,15 @@ 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
     install_with_constraints(session)
     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)

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 = "^6.3.2"}
-pytest-cov = "^3.0.0"
-black = "^22.3.0"
-flake8 = "^4.0.1"
+pytest = "^8.3.3"
+coverage = "^7.6.6"
+pytest-cov = "^6.0.0"
+black = "^24.10.0"
+flake8 = "^7.1.1"
 flake8-black = "^0.3.2"
 flake8-import-order = "^0.18.1"