Fix poetry and nox versions to latest, bump dependency versions, update pyproject.toml format

Author: matthuska

.github/workflows/release.yml

@@ -11,8 +11,8 @@ jobs:
       with:
         python-version: '3.12'
         architecture: x64
-    - run: pip install nox==2024.10.9
-    - run: pip install poetry==1.8.4
+    - run: pip install nox==2025.5.1
+    - run: pip install poetry==2.1.3
     - run: nox
     - run: poetry build
     - run: poetry publish --username=__token__ --password=${{ secrets.PYPI_TOKEN }}

.github/workflows/test-pypi.yml

@@ -12,8 +12,8 @@ jobs:
       with:
         python-version: '3.12'
         architecture: x64
-    - run: pip install nox==2024.10.9
-    - run: pip install poetry==1.8.4
+    - run: pip install nox==2025.5.1
+    - run: pip install poetry==2.1.3
     - run: nox
     - run: version=$(poetry version --short) && poetry version $version.dev.$(date +%s)
     - run: poetry build

.github/workflows/tests.yml

@@ -13,6 +13,6 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
         architecture: x64
-    - run: pip install nox==2024.10.9
-    - run: pip install poetry==1.8.4
+    - run: pip install nox==2025.5.1
+    - run: pip install poetry==2.1.3
     - run: nox

envs/breakfast-dev.yml

@@ -5,8 +5,8 @@ channels:
   - nodefaults
 dependencies:
   - python>=3.11,<3.13
-  - poetry
+  - poetry==2.1.3
   - poetry-plugin-export
   - fortran-compiler
-  - nox
+  - nox==2025.5.1
   - pre-commit

noxfile.py

@@ -27,14 +27,6 @@ def install_with_constraints(session: Session, *args: str, **kwargs: Any) -> Non
         kwargs: Additional keyword arguments for Session.install.
     """
     with tempfile.NamedTemporaryFile() as requirements:
-        # Hide a warning that I have already handled
-        session.run(
-            "poetry",
-            "config",
-            "warnings.export",
-            "false",
-            external=True,
-        )
         session.run(
             "poetry",
             "export",

poetry.lock

@@ -1,13 +1,20 @@
-[tool.poetry]
+[project]
 name = "breakfast"
 version = "0.4.5"
-description = "breakfast: fast putative outbreak cluster and infection chain detection using SNPs"
-authors = ["Matthew Huska <HuskaM@rki.de>", "Denis Beslic <BeslicD@rki.de>"]
-license = "MIT"
+description = "Fast putative outbreak cluster and infection chain detection using SNPs."
 readme = "README.md"
-homepage = "https://github.com/rki-mf1/breakfast"
+license = "MIT"
+authors = [
+  {name = "Matthew Huska", email = "HuskaM@rki.de"},
+  {name = "Denis Beslic", email = "BeslicD@rki.de"},
+]
+
+[project.urls]
 repository = "https://github.com/rki-mf1/breakfast"
 
+[project.scripts]
+breakfast = "breakfast.console:main"
+
 [tool.poetry.dependencies]
 python = ">=3.11,<3.13"
 networkx = "^3.4.2"
@@ -26,9 +33,6 @@ flake8 = "^7.1.1"
 flake8-black = "^0.3.2"
 flake8-import-order = "^0.18.1"
 
-[tool.poetry.scripts]
-breakfast = "breakfast.console:main"
-
 [tool.coverage.paths]
 source = ["src", "*/site-packages"]