From 7bbe8db57f9a39895d402fc733a95cf5ee3a8301 Mon Sep 17 00:00:00 2001 From: Lukas Kremer Date: Thu, 2 Feb 2023 15:56:55 +0100 Subject: [PATCH] version bump & release --- poetry.lock | 130 ++++++++++++++++++++--------------------------- pyproject.toml | 2 +- scbs/__init__.py | 2 +- 3 files changed, 57 insertions(+), 77 deletions(-) diff --git a/poetry.lock b/poetry.lock index 9adc06c..1095dcc 100644 --- a/poetry.lock +++ b/poetry.lock @@ -8,7 +8,7 @@ python-versions = "*" [[package]] name = "astroid" -version = "2.12.12" +version = "2.14.1" description = "An abstract syntax tree for Python with inference support." category = "dev" optional = false @@ -16,22 +16,24 @@ python-versions = ">=3.7.2" [package.dependencies] lazy-object-proxy = ">=1.4.0" -typing-extensions = {version = ">=3.10", markers = "python_version < \"3.10\""} +typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} wrapt = {version = ">=1.11,<2", markers = "python_version < \"3.11\""} [[package]] name = "attrs" -version = "22.1.0" +version = "22.2.0" description = "Classes Without Boilerplate" category = "dev" optional = false -python-versions = ">=3.5" +python-versions = ">=3.6" [package.extras] -dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"] -docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"] -tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "cloudpickle"] -tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "cloudpickle"] +cov = ["attrs", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"] +dev = ["attrs"] +docs = ["furo", "sphinx", "myst-parser", "zope.interface", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier"] +tests = ["attrs", "zope.interface"] +tests-no-zope = ["hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist", "cloudpickle", "mypy (>=0.971,<0.990)", "pytest-mypy-plugins"] +tests_no_zope = ["hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist", "cloudpickle", "mypy (>=0.971,<0.990)", "pytest-mypy-plugins"] [[package]] name = "black" @@ -117,7 +119,7 @@ python-versions = "*" [[package]] name = "exceptiongroup" -version = "1.0.4" +version = "1.1.0" description = "Backport of PEP 654 (exception groups)" category = "dev" optional = false @@ -128,15 +130,15 @@ test = ["pytest (>=6)"] [[package]] name = "filelock" -version = "3.8.0" +version = "3.9.0" description = "A platform independent file lock." category = "dev" optional = false python-versions = ">=3.7" [package.extras] -testing = ["pytest-timeout (>=2.1)", "pytest-cov (>=3)", "pytest (>=7.1.2)", "coverage (>=6.4.2)", "covdefaults (>=2.2)"] -docs = ["sphinx-autodoc-typehints (>=1.19.1)", "sphinx (>=5.1.1)", "furo (>=2022.6.21)"] +docs = ["furo (>=2022.12.7)", "sphinx-autodoc-typehints (>=1.19.5)", "sphinx (>=5.3)"] +testing = ["covdefaults (>=2.2.2)", "coverage (>=7.0.1)", "pytest-cov (>=4)", "pytest-timeout (>=2.1)", "pytest (>=7.2)"] [[package]] name = "flake8" @@ -153,7 +155,7 @@ pyflakes = ">=2.3.0,<2.4.0" [[package]] name = "flake8-bugbear" -version = "22.10.27" +version = "22.12.6" description = "A plugin for flake8 finding likely bugs and design problems in your program. Contains warnings that don't belong in pyflakes and pycodestyle." category = "dev" optional = false @@ -195,7 +197,7 @@ six = "*" [[package]] name = "identify" -version = "2.5.8" +version = "2.5.17" description = "File identification library for Python" category = "dev" optional = false @@ -206,7 +208,7 @@ license = ["ukkonen"] [[package]] name = "importlib-metadata" -version = "5.0.0" +version = "6.0.0" description = "Read metadata from Python packages" category = "main" optional = false @@ -216,35 +218,35 @@ python-versions = ">=3.7" zipp = ">=0.5" [package.extras] -docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"] +docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"] perf = ["ipython"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "pytest-flake8", "importlib-resources (>=1.3)"] [[package]] name = "iniconfig" -version = "1.1.1" -description = "iniconfig: brain-dead simple config-ini parsing" +version = "2.0.0" +description = "brain-dead simple config-ini parsing" category = "dev" optional = false -python-versions = "*" +python-versions = ">=3.7" [[package]] name = "isort" -version = "5.10.1" +version = "5.12.0" description = "A Python utility / library to sort Python imports." category = "dev" optional = false -python-versions = ">=3.6.1,<4.0" +python-versions = ">=3.8.0" [package.extras] -pipfile_deprecated_finder = ["pipreqs", "requirementslib"] -requirements_deprecated_finder = ["pipreqs", "pip-api"] -colors = ["colorama (>=0.4.3,<0.5.0)"] +colors = ["colorama (>=0.4.3)"] +requirements-deprecated-finder = ["pip-api", "pipreqs"] +pipfile-deprecated-finder = ["pip-shims (>=0.5.2)", "pipreqs", "requirementslib"] plugins = ["setuptools"] [[package]] name = "lazy-object-proxy" -version = "1.8.0" +version = "1.9.0" description = "A fast and thorough lazy object proxy." category = "dev" optional = false @@ -297,7 +299,7 @@ numpy = ">=1.18,<1.24" [[package]] name = "numpy" -version = "1.23.4" +version = "1.23.5" description = "NumPy is the fundamental package for array computing with Python." category = "main" optional = false @@ -305,18 +307,15 @@ python-versions = ">=3.8" [[package]] name = "packaging" -version = "21.3" +version = "23.0" description = "Core utilities for Python packages" category = "main" optional = false -python-versions = ">=3.6" - -[package.dependencies] -pyparsing = ">=2.0.2,<3.0.5 || >3.0.5" +python-versions = ">=3.7" [[package]] name = "pandas" -version = "1.5.1" +version = "1.5.3" description = "Powerful data structures for data analysis, time series, and statistics" category = "main" optional = false @@ -335,7 +334,7 @@ test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"] [[package]] name = "pathspec" -version = "0.10.2" +version = "0.11.0" description = "Utility library for gitignore style pattern matching of file paths." category = "dev" optional = false @@ -358,15 +357,15 @@ test = ["pytest", "pytest-cov", "scipy"] [[package]] name = "platformdirs" -version = "2.5.4" +version = "2.6.2" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." category = "dev" optional = false python-versions = ">=3.7" [package.extras] -docs = ["furo (>=2022.9.29)", "proselint (>=0.13)", "sphinx-autodoc-typehints (>=1.19.4)", "sphinx (>=5.3)"] -test = ["appdirs (==1.4.4)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest (>=7.2)"] +docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx-autodoc-typehints (>=1.19.5)", "sphinx (>=5.3)"] +test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest (>=7.2)"] [[package]] name = "pluggy" @@ -382,7 +381,7 @@ testing = ["pytest", "pytest-benchmark"] [[package]] name = "pre-commit" -version = "2.20.0" +version = "2.21.0" description = "A framework for managing and maintaining multi-language pre-commit hooks." category = "dev" optional = false @@ -393,8 +392,7 @@ cfgv = ">=2.0.0" identify = ">=1.0.0" nodeenv = ">=0.11.1" pyyaml = ">=5.1" -toml = "*" -virtualenv = ">=20.0.8" +virtualenv = ">=20.10.0" [[package]] name = "pycodestyle" @@ -414,16 +412,16 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pylint" -version = "2.15.5" +version = "2.16.0" description = "python code static checker" category = "dev" optional = false python-versions = ">=3.7.2" [package.dependencies] -astroid = ">=2.12.12,<=2.14.0-dev0" +astroid = ">=2.14.1,<=2.16.0-dev0" colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""} -dill = ">=0.2" +dill = {version = ">=0.2", markers = "python_version < \"3.11\""} isort = ">=4.2.5,<6" mccabe = ">=0.6,<0.8" platformdirs = ">=2.2.0" @@ -435,20 +433,9 @@ typing-extensions = {version = ">=3.10.0", markers = "python_version < \"3.10\"" spelling = ["pyenchant (>=3.2,<4.0)"] testutils = ["gitpython (>3)"] -[[package]] -name = "pyparsing" -version = "3.0.9" -description = "pyparsing module - Classes and methods to define and execute parsing grammars" -category = "main" -optional = false -python-versions = ">=3.6.8" - -[package.extras] -diagrams = ["railroad-diagrams", "jinja2"] - [[package]] name = "pytest" -version = "7.2.0" +version = "7.2.1" description = "pytest: simple powerful testing with Python" category = "dev" optional = false @@ -479,7 +466,7 @@ six = ">=1.5" [[package]] name = "pytz" -version = "2022.6" +version = "2022.7.1" description = "World timezone definitions, modern and historical" category = "main" optional = false @@ -514,19 +501,19 @@ numpy = ">=1.17.3,<1.25.0" [[package]] name = "scipy" -version = "1.9.3" +version = "1.10.0" description = "Fundamental algorithms for scientific computing in Python" category = "main" optional = false -python-versions = ">=3.8" +python-versions = "<3.12,>=3.8" [package.dependencies] -numpy = ">=1.18.5,<1.26.0" +numpy = ">=1.19.5,<1.27.0" [package.extras] -test = ["pytest", "pytest-cov", "pytest-xdist", "asv", "mpmath", "gmpy2", "threadpoolctl", "scikit-umfpack"] -doc = ["sphinx (!=4.1.0)", "pydata-sphinx-theme (==0.9.0)", "sphinx-panels (>=0.5.2)", "matplotlib (>2)", "numpydoc", "sphinx-tabs"] -dev = ["mypy", "typing-extensions", "pycodestyle", "flake8"] +test = ["pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "asv", "mpmath", "gmpy2", "threadpoolctl", "scikit-umfpack", "pooch"] +doc = ["sphinx (!=4.1.0)", "pydata-sphinx-theme (==0.9.0)", "sphinx-design (>=0.2.0)", "matplotlib (>2)", "numpydoc"] +dev = ["mypy", "typing-extensions", "pycodestyle", "flake8", "rich-click", "click", "doit (>=0.36.0)", "pydevtool"] [[package]] name = "six" @@ -604,7 +591,7 @@ python-versions = ">=3.7" [[package]] name = "virtualenv" -version = "20.16.7" +version = "20.17.1" description = "Virtual Python Environment builder" category = "dev" optional = false @@ -629,15 +616,15 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" [[package]] name = "zipp" -version = "3.10.0" +version = "3.12.0" description = "Backport of pathlib-compatible object wrapper for zip files" category = "main" optional = false python-versions = ">=3.7" [package.extras] -docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "jaraco.itertools", "func-timeout", "jaraco.functools", "more-itertools", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"] +docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "jaraco.itertools", "func-timeout", "jaraco.functools", "more-itertools", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "pytest-flake8"] [metadata] lock-version = "1.1" @@ -687,10 +674,7 @@ flake8-print = [ identify = [] importlib-metadata = [] iniconfig = [] -isort = [ - {file = "isort-5.10.1-py3-none-any.whl", hash = "sha256:6f62d78e2f89b4500b080fe3a81690850cd254227f27f75c3a0c491a1f351ba7"}, - {file = "isort-5.10.1.tar.gz", hash = "sha256:e8443a5e7a020e9d7f97f1d7d9cd17c88bcb3bc7e218bf9cf5095fe550be2951"}, -] +isort = [] lazy-object-proxy = [] llvmlite = [] mccabe = [ @@ -704,10 +688,7 @@ mypy-extensions = [ nodeenv = [] numba = [] numpy = [] -packaging = [ - {file = "packaging-21.3-py3-none-any.whl", hash = "sha256:ef103e05f519cdc783ae24ea4e2e0f508a9c99b2d4969652eed6a2e1ea5bd522"}, - {file = "packaging-21.3.tar.gz", hash = "sha256:dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb"}, -] +packaging = [] pandas = [] pathspec = [] patsy = [] @@ -723,7 +704,6 @@ pyflakes = [ {file = "pyflakes-2.3.1.tar.gz", hash = "sha256:f5bc8ecabc05bb9d291eb5203d6810b49040f6ff446a756326104746cc00c1db"}, ] pylint = [] -pyparsing = [] pytest = [] python-dateutil = [ {file = "python-dateutil-2.8.2.tar.gz", hash = "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86"}, diff --git a/pyproject.toml b/pyproject.toml index 7e48070..a4d5b5a 100755 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "scbs" -version = "0.5.4" +version = "0.6.0" description = "command line tool for the analysis of single-cell bisulfite-sequencing data" authors = [ "Lukas PM Kremer ", diff --git a/scbs/__init__.py b/scbs/__init__.py index 6b27eee..906d362 100755 --- a/scbs/__init__.py +++ b/scbs/__init__.py @@ -1 +1 @@ -__version__ = "0.5.4" +__version__ = "0.6.0"