diff --git a/poetry.lock b/poetry.lock index e41a53b..d95a222 100644 --- a/poetry.lock +++ b/poetry.lock @@ -27,7 +27,7 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7" [[package]] name = "astroid" -version = "2.12.13" +version = "2.13.2" description = "An abstract syntax tree for Python with inference support." category = "dev" optional = false @@ -35,22 +35,24 @@ 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 = ">=4.0.0" 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 = "main" optional = false -python-versions = ">=3.5" +python-versions = ">=3.6" [package.extras] -dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"] -docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"] -tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "zope.interface"] -tests-no-zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins"] +cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"] +dev = ["attrs[docs,tests]"] +docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope.interface"] +tests = ["attrs[tests-no-zope]", "zope.interface"] +tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=0.971,<0.990)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] +tests_no_zope = ["cloudpickle", "hypothesis", "mypy (>=0.971,<0.990)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] [[package]] name = "bids-validator" @@ -154,7 +156,7 @@ optional = false python-versions = ">=3.6.0" [package.extras] -unicode-backport = ["unicodedata2"] +unicode_backport = ["unicodedata2"] [[package]] name = "click" @@ -176,7 +178,7 @@ optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" [[package]] -name = "configargparse" +name = "ConfigArgParse" version = "1.5.3" description = "A drop-in replacement for argparse that allows options to also be set via config files and/or environment variables." category = "main" @@ -188,7 +190,7 @@ test = ["PyYAML", "mock", "pytest"] yaml = ["PyYAML"] [[package]] -name = "connection-pool" +name = "connection_pool" version = "0.0.3" description = "thread safe connection pool" category = "main" @@ -265,7 +267,7 @@ python-versions = ">=3.7" [[package]] name = "dpath" -version = "2.1.3" +version = "2.1.4" description = "Filesystem-like pathing and searching for dictionaries" category = "main" optional = false @@ -273,7 +275,7 @@ python-versions = ">=3.7" [[package]] name = "exceptiongroup" -version = "1.0.4" +version = "1.1.0" description = "Backport of PEP 654 (exception groups)" category = "main" optional = false @@ -295,15 +297,15 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc [[package]] name = "filelock" -version = "3.8.2" +version = "3.9.0" description = "A platform independent file lock." category = "dev" optional = false python-versions = ">=3.7" [package.extras] -docs = ["furo (>=2022.9.29)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.5)"] -testing = ["covdefaults (>=2.2.2)", "coverage (>=6.5)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-timeout (>=2.1)"] +docs = ["furo (>=2022.12.7)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.5)"] +testing = ["covdefaults (>=2.2.2)", "coverage (>=7.0.1)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-timeout (>=2.1)"] [[package]] name = "flake8" @@ -350,8 +352,8 @@ python-versions = ">=3.7" smmap = ">=3.0.1,<6" [[package]] -name = "gitpython" -version = "3.1.29" +name = "GitPython" +version = "3.1.30" description = "GitPython is a python library used to interact with Git repositories" category = "main" optional = false @@ -362,7 +364,7 @@ gitdb = ">=4.0.1,<5" [[package]] name = "identify" -version = "2.5.9" +version = "2.5.12" description = "File identification library for Python" category = "dev" optional = false @@ -396,7 +398,7 @@ testing = ["importlib-resources (>=1.3)", "packaging", "pep517"] [[package]] name = "importlib-resources" -version = "5.10.1" +version = "5.10.2" description = "Read resources from Python packages" category = "main" optional = false @@ -406,16 +408,16 @@ python-versions = ">=3.7" zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} [package.extras] -docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"] +docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] [[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 = "main" optional = false -python-versions = "*" +python-versions = ">=3.7" [[package]] name = "interface-meta" @@ -427,7 +429,7 @@ python-versions = ">=3.7,<4.0" [[package]] name = "isort" -version = "5.11.1" +version = "5.11.4" description = "A Python utility / library to sort Python imports." category = "dev" optional = false @@ -440,7 +442,7 @@ plugins = ["setuptools"] requirements-deprecated-finder = ["pip-api", "pipreqs"] [[package]] -name = "jinja2" +name = "Jinja2" version = "3.1.2" description = "A very fast and expressive template engine." category = "main" @@ -485,7 +487,7 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- [[package]] name = "jupyter-core" -version = "5.1.0" +version = "5.1.3" description = "Jupyter core package. A base package on which Jupyter projects rely." category = "main" optional = false @@ -497,19 +499,32 @@ pywin32 = {version = ">=1.0", markers = "sys_platform == \"win32\" and platform_ traitlets = ">=5.3" [package.extras] -docs = ["myst-parser", "sphinxcontrib-github-alt", "traitlets"] +docs = ["myst-parser", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"] test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"] [[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 python-versions = ">=3.7" [[package]] -name = "markupsafe" +name = "maison" +version = "1.4.0" +description = "Maison" +category = "dev" +optional = false +python-versions = ">=3.6.1,<4.0.0" + +[package.dependencies] +click = ">=8.0.1,<9.0.0" +pydantic = ">=1.8.2,<2.0.0" +toml = ">=0.10.2,<0.11.0" + +[[package]] +name = "MarkupSafe" version = "2.1.1" description = "Safely add untrusted strings to HTML/XML markup." category = "main" @@ -526,7 +541,7 @@ python-versions = "*" [[package]] name = "mock" -version = "4.0.3" +version = "5.0.1" description = "Rolling backport of unittest.mock for all Pythons" category = "main" optional = false @@ -535,7 +550,7 @@ python-versions = ">=3.6" [package.extras] build = ["blurb", "twine", "wheel"] docs = ["sphinx"] -test = ["pytest (<5.4)", "pytest-cov"] +test = ["pytest", "pytest-cov"] [[package]] name = "more-itertools" @@ -574,7 +589,7 @@ python-versions = "*" [[package]] name = "nbformat" -version = "5.7.0" +version = "5.7.1" description = "The Jupyter Notebook format" category = "main" optional = false @@ -587,7 +602,8 @@ jupyter-core = "*" traitlets = ">=5.1" [package.extras] -test = ["check-manifest", "pep440", "pre-commit", "pytest", "testpath"] +docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinxcontrib-github-alt"] +test = ["pep440", "pre-commit", "pytest", "testpath"] [[package]] name = "nexus-sdk" @@ -654,15 +670,15 @@ docopt = ">=0.6.2" [[package]] name = "numpy" -version = "1.23.5" -description = "NumPy is the fundamental package for array computing with Python." +version = "1.24.1" +description = "Fundamental package for array computing in Python" category = "main" optional = false python-versions = ">=3.8" [[package]] name = "packaging" -version = "22.0" +version = "23.0" description = "Core utilities for Python packages" category = "main" optional = false @@ -704,7 +720,7 @@ optional = false python-versions = ">=3.7" [[package]] -name = "pkgutil-resolve-name" +name = "pkgutil_resolve_name" version = "1.3.10" description = "Resolve a name to an object." category = "main" @@ -721,15 +737,15 @@ python-versions = "*" [[package]] name = "platformdirs" -version = "2.6.0" +version = "2.6.2" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." category = "main" optional = false python-versions = ">=3.7" [package.extras] -docs = ["furo (>=2022.9.29)", "proselint (>=0.13)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.4)"] -test = ["appdirs (==1.4.4)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"] +docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.5)"] +test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"] [[package]] name = "pluggy" @@ -756,11 +772,11 @@ pastel = ">=0.2.1,<0.3.0" tomli = ">=1.2.2" [package.extras] -poetry-plugin = ["poetry (>=1.0,<2.0)"] +poetry_plugin = ["poetry (>=1.0,<2.0)"] [[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 @@ -771,8 +787,7 @@ 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 = "psutil" @@ -786,7 +801,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"] [[package]] -name = "pulp" +name = "PuLP" version = "2.7.0" description = "PuLP is an LP modeler written in python. PuLP can generate MPS or LP files and call GLPK, COIN CLP/CBC, CPLEX, and GUROBI to solve linear problems." category = "main" @@ -821,7 +836,7 @@ scipy = "*" sqlalchemy = "<1.4.0.dev0" [package.extras] -ci-tests = ["bsmschema", "codecov", "graphviz", "pytest (>=3.3)", "pytest-cov", "pytest-xdist"] +ci_tests = ["bsmschema", "codecov", "graphviz", "pytest (>=3.3)", "pytest-cov", "pytest-xdist"] dev = ["bsmschema", "graphviz", "jupytext", "myst-nb", "numpydoc", "pytest (>=3.3)", "sphinx (>=2.2,!=5.1.0)", "sphinx-rtd-theme"] doc = ["jupytext", "myst-nb", "numpydoc", "sphinx (>=2.2,!=5.1.0)", "sphinx-rtd-theme"] docs = ["jupytext", "myst-nb", "numpydoc", "sphinx (>=2.2,!=5.1.0)", "sphinx-rtd-theme"] @@ -838,6 +853,21 @@ category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +[[package]] +name = "pydantic" +version = "1.10.4" +description = "Data validation and settings management using python type hints" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +typing-extensions = ">=4.2.0" + +[package.extras] +dotenv = ["python-dotenv (>=0.10.4)"] +email = ["email-validator (>=1.0.3)"] + [[package]] name = "pyflakes" version = "2.4.0" @@ -848,7 +878,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pylint" -version = "2.15.8" +version = "2.15.10" description = "python code static checker" category = "dev" optional = false @@ -857,7 +887,7 @@ python-versions = ">=3.7.2" [package.dependencies] astroid = ">=2.12.13,<=2.14.0-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" @@ -871,7 +901,7 @@ testutils = ["gitpython (>3)"] [[package]] name = "pyrsistent" -version = "0.19.2" +version = "0.19.3" description = "Persistent/Functional/Immutable data structures" category = "main" optional = false @@ -936,7 +966,7 @@ unidecode = ["Unidecode (>=1.1.1)"] [[package]] name = "pytz" -version = "2022.6" +version = "2022.7" description = "World timezone definitions, modern and historical" category = "main" optional = false @@ -951,7 +981,7 @@ optional = false python-versions = "*" [[package]] -name = "pyyaml" +name = "PyYAML" version = "6.0" description = "YAML parser and emitter for Python" category = "main" @@ -974,15 +1004,15 @@ urllib3 = ">=1.21.1,<1.27" [package.extras] socks = ["PySocks (>=1.5.6,!=1.5.7)"] -use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] +use_chardet_on_py3 = ["chardet (>=3.0.2,<6)"] [[package]] name = "reretry" -version = "0.11.1" +version = "0.11.8" description = "An easy to use, but functional decorator for retrying on exceptions." category = "main" optional = false -python-versions = ">=3.5" +python-versions = ">=3.7" [[package]] name = "ruyaml" @@ -1001,19 +1031,19 @@ docs = ["Sphinx"] [[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] -dev = ["flake8", "mypy", "pycodestyle", "typing_extensions"] -doc = ["matplotlib (>2)", "numpydoc", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-panels (>=0.5.2)", "sphinx-tabs"] -test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "scikit-umfpack", "threadpoolctl"] +dev = ["click", "doit (>=0.36.0)", "flake8", "mypy", "pycodestyle", "pydevtool", "rich-click", "typing_extensions"] +doc = ["matplotlib (>2)", "numpydoc", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-design (>=0.2.0)"] +test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"] [[package]] name = "setuptools" @@ -1030,7 +1060,7 @@ testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs ( [[package]] name = "simplejson" -version = "3.18.0" +version = "3.18.1" description = "Simple, fast, extensible JSON encoder/decoder for Python" category = "main" optional = false @@ -1107,7 +1137,7 @@ toml = ">=0.10.2,<0.11.0" [[package]] name = "snakemake" -version = "7.19.0" +version = "7.19.1" description = "Snakemake is a workflow management system that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern specification language in python style. Snakemake workflows are essentially Python scripts extended by declarative code to define rules. Rules describe how to create output files from input files." category = "main" optional = false @@ -1143,7 +1173,7 @@ pep = ["eido", "peppy"] reports = ["jinja2", "pygments"] [[package]] -name = "sqlalchemy" +name = "SQLAlchemy" version = "1.3.24" description = "Database Abstraction Library" category = "main" @@ -1152,14 +1182,14 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [package.extras] mssql = ["pyodbc"] -mssql-pymssql = ["pymssql"] -mssql-pyodbc = ["pyodbc"] +mssql_pymssql = ["pymssql"] +mssql_pyodbc = ["pyodbc"] mysql = ["mysqlclient"] oracle = ["cx_oracle"] postgresql = ["psycopg2"] -postgresql-pg8000 = ["pg8000 (<1.16.6)"] -postgresql-psycopg2binary = ["psycopg2-binary"] -postgresql-psycopg2cffi = ["psycopg2cffi"] +postgresql_pg8000 = ["pg8000 (<1.16.6)"] +postgresql_psycopg2binary = ["psycopg2-binary"] +postgresql_psycopg2cffi = ["psycopg2cffi"] pymysql = ["pymysql", "pymysql (<1)"] [[package]] @@ -1195,7 +1225,7 @@ widechars = ["wcwidth"] [[package]] name = "termcolor" -version = "2.1.1" +version = "2.2.0" description = "ANSI color formatting for output in terminal" category = "main" optional = false @@ -1249,15 +1279,15 @@ python-versions = ">=3.6" [[package]] name = "toposort" -version = "1.7" -description = "\"Implements a topological sort algorithm.\"" +version = "1.8" +description = "Implements a topological sort algorithm." category = "main" optional = false python-versions = "*" [[package]] name = "traitlets" -version = "5.7.1" +version = "5.8.1" description = "Traitlets Python configuration system" category = "main" optional = false @@ -1265,9 +1295,7 @@ python-versions = ">=3.7" [package.extras] docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"] -lint = ["black (>=22.6.0)", "mdformat (>0.7)", "ruff (>=0.0.156)"] -test = ["pre-commit", "pytest"] -typing = ["mypy (>=0.990)"] +test = ["argcomplete (>=2.0)", "pre-commit", "pytest", "pytest-mock"] [[package]] name = "typing-extensions" @@ -1338,14 +1366,15 @@ viz = ["matplotlib", "nc-time-axis", "seaborn"] [[package]] name = "yamlfix" -version = "1.1.1" +version = "1.3.1" description = "A simple opionated yaml formatter that keeps your comments!" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.7.2" [package.dependencies] -click = ">=8.0.3" +click = ">=8.1.3" +maison = ">=1.4.0" ruyaml = ">=0.91.0" [[package]] @@ -1392,12 +1421,12 @@ astor = [ {file = "astor-0.8.1.tar.gz", hash = "sha256:6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e"}, ] astroid = [ - {file = "astroid-2.12.13-py3-none-any.whl", hash = "sha256:10e0ad5f7b79c435179d0d0f0df69998c4eef4597534aae44910db060baeb907"}, - {file = "astroid-2.12.13.tar.gz", hash = "sha256:1493fe8bd3dfd73dc35bd53c9d5b6e49ead98497c47b2307662556a5692d29d7"}, + {file = "astroid-2.13.2-py3-none-any.whl", hash = "sha256:8f6a8d40c4ad161d6fc419545ae4b2f275ed86d1c989c97825772120842ee0d2"}, + {file = "astroid-2.13.2.tar.gz", hash = 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