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"python_version == \"3.10\""} + +[[package]] +name = "tzdata" +version = "2026.2" +description = "Provider of IANA time zone data" +optional = false +python-versions = ">=2" +groups = ["main"] +files = [ + {file = "tzdata-2026.2-py2.py3-none-any.whl", hash = "sha256:bbe9af844f658da81a5f95019480da3a89415801f6cc966806612cc7169bffe7"}, + {file = "tzdata-2026.2.tar.gz", hash = "sha256:9173fde7d80d9018e02a662e168e5a2d04f87c41ea174b139fbef642eda62d10"}, +] [[package]] name = "umap-learn" @@ -1722,6 +1874,7 @@ version = "0.5.12" description = "Uniform Manifold Approximation and Projection" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "umap_learn-0.5.12-py3-none-any.whl", hash = "sha256:f2a85d2a2adcb52b541bed9b27a23ca169b56bb1b23283abeebfb8dfb8a42fe5"}, {file = "umap_learn-0.5.12.tar.gz", hash = "sha256:6aff02ecac5f2aad9f3c65ee518d7ae93e1a985ae38721fdcffceee4232c33c7"}, @@ -1741,33 +1894,13 @@ plot = ["bokeh", "colorcet", "dask", "datashader", "holoviews", 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(>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] - [[package]] name = "virtualenv" version = "21.4.2" description = "Virtual Python Environment builder" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "virtualenv-21.4.2-py3-none-any.whl", hash = "sha256:854210ca524a1a4d0d744734f4acbc721c3ffe163b85bbf5d56d14d5ae2f0fae"}, {file = "virtualenv-21.4.2.tar.gz", hash = "sha256:38e6ee0a555615c0ea9da2ac7e9998fe8dc3b911dd33ad8eaad2020957653b0c"}, @@ -1775,31 +1908,12 @@ files = [ [package.dependencies] distlib = ">=0.3.7,<1" -filelock = {version = ">=3.16.1,<=3.19.1", markers = "python_version < \"3.10\""} +filelock = {version = ">=3.24.2,<4", markers = "python_version >= \"3.10\""} platformdirs = ">=3.9.1,<5" python-discovery = ">=1.4" typing-extensions = {version = ">=4.13.2", markers = "python_version < \"3.11\""} -[[package]] -name = "zipp" -version = "3.23.1" -description = "Backport of pathlib-compatible object wrapper for zip files" -optional = false -python-versions = ">=3.9" -files = [ - {file = "zipp-3.23.1-py3-none-any.whl", hash = "sha256:0b3596c50a5c700c9cb40ba8d86d9f2cc4807e9bedb06bcdf7fac85633e444dc"}, - {file = "zipp-3.23.1.tar.gz", hash = "sha256:32120e378d32cd9714ad503c1d024619063ec28aad2248dc6672ad13edfa5110"}, -] - -[package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] -cover = ["pytest-cov"] -doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -enabler = ["pytest-enabler (>=2.2)"] -test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more_itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] -type = ["pytest-mypy"] - [metadata] -lock-version = "2.0" -python-versions = ">=3.9,<3.12" -content-hash = "c268c9857d943d946077c509d0623c79c263ea7d9c3efca505d41b4e994287ce" +lock-version = "2.1" +python-versions = ">=3.10,<3.14" +content-hash = "52eadd376faa7375c8f35badf3f14a89539f217ff818c9b41ad090f45e39c2cd" diff --git a/poetry.toml b/poetry.toml deleted file mode 100644 index 084377a..0000000 --- a/poetry.toml +++ /dev/null @@ -1,2 +0,0 @@ -[virtualenvs] -create = false diff --git a/pyproject.toml b/pyproject.toml index 793660d..43dc1ba 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,31 +8,37 @@ maintainers = [ "Benedikt Geiger ", ] 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. diff --git a/src/sonata/__init__.py b/src/sonata/__init__.py index 4ca8fa6..84adac4 100644 --- a/src/sonata/__init__.py +++ b/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() diff --git a/src/sonata/initialization/__init__.py b/src/sonata/initialization/__init__.py index e16c76d..f3b0d32 100644 --- a/src/sonata/initialization/__init__.py +++ b/src/sonata/initialization/__init__.py @@ -1 +1 @@ -"" +"""""" diff --git a/tox.ini b/tox.ini index 99aaae1..af51d5f 100644 --- a/tox.ini +++ b/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