Modernize Python dependencies

.github/workflows/test.yaml

@@ -13,9 +13,10 @@ jobs:
     strategy:
       matrix:
         py:
-          - "3.9"
           - "3.10"
           - "3.11"
+          - "3.12"
+          - "3.13"
         os:
           - ubuntu-latest
           - windows-latest
@@ -25,7 +26,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.py }}
 

.pre-commit-config.yaml

@@ -1,28 +1,28 @@
 # See https://pre-commit.com for more information
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v5.0.0
     hooks:
       - id: check-toml
       - id: check-yaml
       - id: end-of-file-fixer
       - id: mixed-line-ending
       - id: trailing-whitespace
   - repo: https://github.com/python-poetry/poetry
-    rev: 1.6.1
+    rev: 2.4.1
     hooks:
       - id: poetry-check
       - id: poetry-lock
   - repo: https://github.com/psf/black
-    rev: 24.3.0
+    rev: 25.1.0
     hooks:
       - id: black
   - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 6.0.1
     hooks:
       - id: isort
         args: ["--profile", "black"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.9.0
+    rev: v1.15.0
     hooks:
       - id: mypy

README.md

@@ -4,7 +4,7 @@
 [![License][license-image]][license-url]
 [![Code style][style-image]][style-url]
 
-[python-image]: https://img.shields.io/badge/python-3.9%20|%203.10%20|%203.11-blue.svg
+[python-image]: https://img.shields.io/badge/python-3.10%20|%203.11%20|%203.12%20|%203.13-blue.svg
 [python-url]: https://github.com/parklab/Sonata
 [license-image]: https://img.shields.io/badge/License-MIT-yellow.svg
 [license-url]: https://github.com/parklab/Sonata/blob/main/LICENSE

pyproject.toml

@@ -8,31 +8,37 @@ maintainers = [
     "Benedikt Geiger <benedikt_geiger@g.harvard.edu>",
 ]
 packages = [{ include = "sonata", from = "src" }]
+classifiers = [
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+]
 
 
 readme = "README.md"
 
 [tool.poetry.dependencies]
-python = ">=3.9,<3.12"
-adjustText = "^0.8"
-anndata = ">=0.10.5, <0.10.9"
-fastcluster = "^1.2.6"
-matplotlib = "^3.7.1"
-numba = "^0.59"
-numpy = "^1.24.3"
-pandas = "^1.5.3"
-scikit-learn = "^1.3.0"
-scipy = "^1.10.1"
-seaborn = "^0.13.0"
-umap-learn = "^0.5.4"
+python = ">=3.10,<3.14"
+adjustText = ">=1.3,<2"
+anndata = ">=0.11,<0.13"
+fastcluster = ">=1.2.6,<2"
+matplotlib = ">=3.8,<4"
+numba = ">=0.61,<0.63"
+numpy = ">=1.26,<3"
+pandas = ">=2.2,<3"
+scikit-learn = ">=1.6,<2"
+scipy = ">=1.13,<2"
+seaborn = ">=0.13,<0.14"
+umap-learn = ">=0.5.7,<0.6"
 
 [tool.poetry.group.dev.dependencies]
-mypy = "^1.9"
-pandas-stubs = "^2.2.1"
-pytest = "^7.4.2"
-pre-commit = "^3.4.0"
-tox = "^4.11.3"
-types-seaborn = "^0.13.2"
+mypy = ">=1.15,<2"
+pandas-stubs = ">=2.2,<3"
+pytest = ">=8.3,<9"
+pre-commit = ">=4.2,<5"
+tox = ">=4.25,<5"
+types-seaborn = ">=0.13,<0.14"
 
 [tool.pytest.ini_options]
 # /site-packages/umap/__init__.py:36: DeprecationWarning: pkg_resources is deprecated as an API.

src/sonata/__init__.py

@@ -1,13 +1,13 @@
 """
-Sonata: a non-negative matrix factorization framework for signature analysis
-================================================================================
+Sonata: a non-negative matrix factorization toolkit for signature analysis
+==========================================================================
 """
 
 from . import models
 from . import plot as pl
 from . import tools as tl
 
-__version__ = "0.4.2"
+__version__ = "0.1.0"
 
 pl.set_sonata_style()
 

src/sonata/initialization/__init__.py

@@ -1 +1 @@
-""
+""""""

tox.ini

@@ -1,16 +1,16 @@
 [tox]
-envlist = py{39,310,311}, flake8, pylint
+envlist = py{310,311,312,313}, flake8, pylint
 
 [testenv]
 deps =
-    pytest>=7.4
+    pytest>=8.3,<9
 commands =
     pytest {posargs}
 
 [testenv:flake8]
 skip_install = true
 deps =
-    flake8
+    flake8>=7.1,<8
 commands =
     flake8 src/ --max-line-length 88
     flake8 tests/ --max-line-length 88
@@ -22,14 +22,15 @@ extend-ignore =
 
 [testenv:pylint]
 deps =
-    pylint
+    pylint>=3.3,<4
 commands =
-    # extension-pkg-witelist: see https://github.com/pylint-dev/pylint/issues/3703
     # W0107: unnecessary pass statement. This is (mostly) a style issue: see https://github.com/pylint-dev/pylint/issues/2208
-    pylint src/ --disable=C,R --extension-pkg-whitelist=scipy.special --disable=W0107
+    # ignored-modules: avoid astroid recursion while inspecting scipy internals.
+    pylint src/ --disable=C,R --disable=W0107 --ignored-modules=scipy,scipy.special --persistent=n
 
 [gh-actions]
 python =
-    3.9: py39
     3.10: py310
-    3.11: py311, flake8
+    3.11: py311
+    3.12: py312
+    3.13: py313, flake8, pylint