diff --git a/poetry.lock b/poetry.lock index 7bdabc2..5a6c5b9 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,6 +1,6 @@ [[package]] name = "absl-py" -version = "1.1.0" +version = "1.2.0" description = "Abseil Python Common Libraries, see https://github.com/abseil/abseil-py." category = "main" optional = true @@ -34,8 +34,8 @@ python-versions = ">=3.6" argon2-cffi-bindings = "*" [package.extras] -dev = ["pre-commit", "cogapp", "tomli", "coverage[toml] (>=5.0.2)", "hypothesis", "pytest", "sphinx", "sphinx-notfound-page", "furo"] -docs = ["sphinx", "sphinx-notfound-page", "furo"] +dev = ["cogapp", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "pre-commit", "pytest", "sphinx", "sphinx-notfound-page", "tomli"] +docs = ["furo", "sphinx", "sphinx-notfound-page"] tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pytest"] [[package]] @@ -50,26 +50,25 @@ python-versions = ">=3.6" cffi = ">=1.0.1" [package.extras] -dev = ["pytest", "cogapp", "pre-commit", "wheel"] +dev = ["cogapp", "pre-commit", "pytest", "wheel"] tests = ["pytest"] [[package]] name = "astroid" -version = "2.11.7" +version = "2.12.5" description = "An abstract syntax tree for Python with inference support." category = "dev" optional = false -python-versions = ">=3.6.2" +python-versions = ">=3.7.2" [package.dependencies] lazy-object-proxy = ">=1.4.0" -setuptools = ">=20.0" typing-extensions = {version = ">=3.10", markers = "python_version < \"3.10\""} -wrapt = ">=1.11,<2" +wrapt = {version = ">=1.11,<2", markers = "python_version < \"3.11\""} [[package]] name = "asttokens" -version = "2.0.5" +version = "2.0.8" description = "Annotate AST trees with source code positions" category = "dev" optional = false @@ -79,7 +78,7 @@ python-versions = "*" six = "*" [package.extras] -test = ["astroid", "pytest"] +test = ["astroid (<=2.5.3)", "pytest"] [[package]] name = "atomicwrites" @@ -91,28 +90,28 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "attrs" -version = "21.4.0" +version = "22.1.0" description = "Classes Without Boilerplate" category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = ">=3.5" [package.extras] -dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "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)", "six", "mypy", "pytest-mypy-plugins", "zope-interface", "cloudpickle"] -tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"] +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"] [[package]] name = "autodocsumm" -version = "0.2.8" +version = "0.2.9" description = "Extended sphinx autodoc including automatic autosummaries" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] -Sphinx = ">=2.2,<5.0" +Sphinx = ">=2.2,<6.0" [[package]] name = "babel" @@ -150,7 +149,7 @@ lxml = ["lxml"] [[package]] name = "black" -version = "22.6.0" +version = "22.8.0" description = "The uncompromising code formatter." category = "dev" optional = false @@ -184,7 +183,7 @@ webencodings = "*" [package.extras] css = ["tinycss2 (>=1.1.0,<1.2)"] -dev = ["build (==0.8.0)", "flake8 (==4.0.1)", "hashin (==0.17.0)", "pip-tools (==6.6.2)", "pytest (==7.1.2)", "Sphinx (==4.3.2)", "tox (==3.25.0)", "twine (==4.0.1)", "wheel (==0.37.1)", "black (==22.3.0)", "mypy (==0.961)"] +dev = ["Sphinx (==4.3.2)", "black (==22.3.0)", "build (==0.8.0)", "flake8 (==4.0.1)", "hashin (==0.17.0)", "mypy (==0.961)", "pip-tools (==6.6.2)", "pytest (==7.1.2)", "tox (==3.25.0)", "twine (==4.0.1)", "wheel (==0.37.1)"] [[package]] name = "brotli" @@ -223,7 +222,7 @@ python-versions = ">=3.6.1" [[package]] name = "charset-normalizer" -version = "2.1.0" +version = "2.1.1" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." category = "dev" optional = false @@ -275,7 +274,7 @@ test = ["flake8 (==3.7.8)", "hypothesis (==3.55.3)"] [[package]] name = "coverage" -version = "6.4.2" +version = "6.4.4" description = "Code coverage measurement for Python" category = "dev" optional = false @@ -299,12 +298,12 @@ python-versions = ">=3.6" cffi = ">=1.12" [package.extras] -docs = ["sphinx (>=1.6.5,!=1.8.0,!=3.1.0,!=3.1.1)", "sphinx-rtd-theme"] -docstest = ["pyenchant (>=1.6.11)", "twine (>=1.12.0)", "sphinxcontrib-spelling (>=4.0.1)"] +docs = ["sphinx (>=1.6.5,!=1.8.0,!=3.1.0,!=3.1.1)", "sphinx_rtd_theme"] +docstest = ["pyenchant (>=1.6.11)", "sphinxcontrib-spelling (>=4.0.1)", "twine (>=1.12.0)"] pep8test = ["black", "flake8", "flake8-import-order", "pep8-naming"] sdist = ["setuptools_rust (>=0.11.4)"] ssh = ["bcrypt (>=3.1.5)"] -test = ["pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-subtests", "pytest-xdist", "pretend", "iso8601", "pytz", "hypothesis (>=1.11.4,!=3.79.2)"] +test = ["hypothesis (>=1.11.4,!=3.79.2)", "iso8601", "pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-subtests", "pytest-xdist", "pytz"] [[package]] name = "customtkinter" @@ -327,7 +326,7 @@ python-versions = ">=3.6" [[package]] name = "darkdetect" -version = "0.7.0" +version = "0.7.1" description = "Detect OS Dark Mode from Python" category = "main" optional = true @@ -353,11 +352,11 @@ plotly = ">=5.0.0" psutil = {version = ">=5.8.0", optional = true, markers = "extra == \"diskcache\""} [package.extras] -celery = ["redis (>=3.5.3)", "celery[redis] (>=5.1.2)"] -ci = ["dash-flow-example (==0.0.5)", "dash-dangerously-set-inner-html", "flake8 (==3.9.2)", "flaky (==3.7.0)", "flask-talisman (==1.0.0)", "mimesis", "mock (==4.0.3)", "numpy", "preconditions", "pylint (==2.13.5)", "pytest-mock", "pytest-sugar (==0.9.4)", "pytest-rerunfailures", "black (==21.6b0)", "isort (==4.3.21)", "orjson (==3.5.4)", "pyarrow (<3)", "pandas (==1.1.5)", "xlrd (<2)", "black (==22.3.0)", "orjson (==3.6.7)", "pyarrow", "openpyxl", "pandas (>=1.4.0)", "xlrd (>=2.0.1)"] -dev = ["coloredlogs (>=15.0.1)", "fire (>=0.4.0)", "PyYAML (>=5.4.1)"] +celery = ["celery[redis] (>=5.1.2)", "redis (>=3.5.3)"] +ci = ["black (==21.6b0)", "black (==22.3.0)", "dash-dangerously-set-inner-html", "dash-flow-example (==0.0.5)", "flake8 (==3.9.2)", "flaky (==3.7.0)", "flask-talisman (==1.0.0)", "isort (==4.3.21)", "mimesis", "mock (==4.0.3)", "numpy", "openpyxl", "orjson (==3.5.4)", "orjson (==3.6.7)", "pandas (==1.1.5)", "pandas (>=1.4.0)", "preconditions", "pyarrow", "pyarrow (<3)", "pylint (==2.13.5)", "pytest-mock", "pytest-rerunfailures", "pytest-sugar (==0.9.4)", "xlrd (<2)", "xlrd (>=2.0.1)"] +dev = ["PyYAML (>=5.4.1)", "coloredlogs (>=15.0.1)", "fire (>=0.4.0)"] diskcache = ["diskcache (>=5.2.1)", "multiprocess (>=0.70.12)", "psutil (>=5.8.0)"] -testing = ["beautifulsoup4 (>=4.8.2)", "lxml (>=4.6.2)", "percy (>=2.0.2)", "pytest (>=6.0.2)", "requests[security] (>=2.21.0)", "selenium (>=3.141.0,<=4.2.0)", "waitress (>=1.4.4)", "cryptography (<3.4)"] +testing = ["beautifulsoup4 (>=4.8.2)", "cryptography (<3.4)", "lxml (>=4.6.2)", "percy (>=2.0.2)", "pytest (>=6.0.2)", "requests[security] (>=2.21.0)", "selenium (>=3.141.0,<=4.2.0)", "waitress (>=1.4.4)"] [[package]] name = "dash-bootstrap-components" @@ -371,7 +370,7 @@ python-versions = ">=3.6, <4" dash = ">=2.0.0" [package.extras] -pandas = ["pandas", "numpy"] +pandas = ["numpy", "pandas"] [[package]] name = "dash-core-components" @@ -399,7 +398,7 @@ python-versions = "*" [[package]] name = "debugpy" -version = "1.6.2" +version = "1.6.3" description = "An implementation of the Debug Adapter Protocol for Python" category = "dev" optional = false @@ -442,7 +441,7 @@ python-versions = ">=3" [[package]] name = "distlib" -version = "0.3.4" +version = "0.3.6" description = "Distribution utilities" category = "dev" optional = false @@ -474,7 +473,7 @@ python-versions = ">=3.6" [[package]] name = "etils" -version = "0.6.0" +version = "0.7.1" description = "Collection of common python utils" category = "main" optional = true @@ -482,28 +481,27 @@ python-versions = ">=3.7" [package.dependencies] importlib_resources = {version = "*", optional = true, markers = "extra == \"epath\""} -typing_extensions = {version = "*", optional = true, markers = "extra == \"epy\""} +typing_extensions = {version = "*", optional = true, markers = "extra == \"epath\""} zipp = {version = "*", optional = true, markers = "extra == \"epath\""} [package.extras] -all = ["etils", "etils", "etils", "etils", "etils", "etils", "etils", "etils", "etils", "etils", "etils"] -array-types = ["numpy"] -dev = ["pytest", "pytest-subtests", "pytest-xdist", "pylint (>=2.6.0)", "yapf", "chex"] -ecolab = ["jupyter", "numpy", "mediapy", "etils"] -edc = ["etils"] -enp = ["numpy", "etils"] -epath = ["importlib-resources", "zipp", "etils"] -epath-no-tf = ["etils"] -epy = ["typing-extensions"] -etqdm = ["absl-py", "tqdm", "etils"] -etree = ["etils", "etils", "etils", "etils"] -etree-dm = ["dm-tree", "etils"] -etree-jax = ["jax", "etils"] -etree-tf = ["tf-nightly", "etils"] +all = ["etils[array-types]", "etils[ecolab]", "etils[edc]", "etils[enp]", "etils[epath]", "etils[epy]", "etils[etqdm]", "etils[etree-dm]", "etils[etree-jax]", "etils[etree-tf]", "etils[etree]"] +array-types = ["etils[enp]"] +dev = ["chex", "pylint (>=2.6.0)", "pytest", "pytest-subtests", "pytest-xdist", "yapf"] +ecolab = ["etils[enp]", "etils[epy]", "jupyter", "mediapy", "numpy"] +edc = ["etils[epy]"] +enp = ["etils[epy]", "numpy"] +epath = ["etils[epy]", "importlib_resources", "typing_extensions", "zipp"] +epy = ["typing_extensions"] +etqdm = ["absl-py", "etils[epy]", "tqdm"] +etree = ["etils[array_types]", "etils[enp]", "etils[epy]", "etils[etqdm]"] +etree-dm = ["dm-tree", "etils[etree]"] +etree-jax = ["etils[etree]", "jax[cpu]"] +etree-tf = ["etils[etree]", "tf-nightly"] [[package]] name = "executing" -version = "0.8.3" +version = "1.0.0" description = "Get the currently executing AST node of a frame, and other information" category = "dev" optional = false @@ -511,26 +509,26 @@ python-versions = "*" [[package]] name = "fastjsonschema" -version = "2.15.3" +version = "2.16.1" description = "Fastest Python implementation of JSON schema" category = "dev" optional = false python-versions = "*" [package.extras] -devel = ["colorama", "jsonschema", "json-spec", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"] +devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"] [[package]] name = "filelock" -version = "3.7.1" +version = "3.8.0" description = "A platform independent file lock." category = "dev" optional = false python-versions = ">=3.7" [package.extras] -docs = ["furo (>=2021.8.17b43)", "sphinx (>=4.1)", "sphinx-autodoc-typehints (>=1.12)"] -testing = ["covdefaults (>=1.2.0)", "coverage (>=4)", "pytest (>=4)", "pytest-cov", "pytest-timeout (>=1.4.2)"] +docs = ["furo (>=2022.6.21)", "sphinx (>=5.1.1)", "sphinx-autodoc-typehints (>=1.19.1)"] +testing = ["covdefaults (>=2.2)", "coverage (>=6.4.2)", "pytest (>=7.1.2)", "pytest-cov (>=3)", "pytest-timeout (>=2.1)"] [[package]] name = "flake8" @@ -547,7 +545,7 @@ pyflakes = ">=2.4.0,<2.5.0" [[package]] name = "flask" -version = "2.1.3" +version = "2.2.2" description = "A simple framework for building complex web applications." category = "main" optional = true @@ -558,7 +556,7 @@ click = ">=8.0" importlib-metadata = {version = ">=3.6.0", markers = "python_version < \"3.10\""} itsdangerous = ">=2.0" Jinja2 = ">=3.0" -Werkzeug = ">=2.0" +Werkzeug = ">=2.2.2" [package.extras] async = ["asgiref (>=3.2)"] @@ -578,7 +576,7 @@ flask = "*" [[package]] name = "flatbuffers" -version = "2.0" +version = "2.0.7" description = "The FlatBuffers serialization format for Python" category = "main" optional = true @@ -586,16 +584,16 @@ python-versions = "*" [[package]] name = "fonttools" -version = "4.34.4" +version = "4.37.1" description = "Tools to manipulate font files" category = "main" optional = true python-versions = ">=3.7" [package.extras] -all = ["fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "zopfli (>=0.1.4)", "lz4 (>=1.7.4.2)", "matplotlib", "sympy", "skia-pathops (>=0.5.0)", "uharfbuzz (>=0.23.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=14.0.0)", "xattr"] +all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "scipy", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=14.0.0)", "xattr", "zopfli (>=0.1.4)"] graphite = ["lz4 (>=1.7.4.2)"] -interpolatable = ["scipy", "munkres"] +interpolatable = ["munkres", "scipy"] lxml = ["lxml (>=4.0,<5)"] pathops = ["skia-pathops (>=0.5.0)"] plot = ["matplotlib"] @@ -604,7 +602,7 @@ symfont = ["sympy"] type1 = ["xattr"] ufo = ["fs (>=2.2.0,<3)"] unicode = ["unicodedata2 (>=14.0.0)"] -woff = ["zopfli (>=0.1.4)", "brotlicffi (>=0.8.0)", "brotli (>=1.0.1)"] +woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"] [[package]] name = "gitdb" @@ -630,7 +628,7 @@ gitdb = ">=4.0.1,<5" [[package]] name = "identify" -version = "2.5.1" +version = "2.5.3" description = "File identification library for Python" category = "dev" optional = false @@ -657,7 +655,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "iminuit" -version = "2.15.2" +version = "2.16.0" description = "Jupyter-friendly Python frontend for MINUIT2 in C++" category = "main" optional = true @@ -667,8 +665,8 @@ python-versions = ">=3.6" numpy = "*" [package.extras] -doc = ["sphinx (>=4.1)", "sphinx-rtd-theme", "Jinja2 (==3.0)", "nbsphinx"] -test = ["cython", "flake8", "ipykernel", "ipywidgets", "jax", "jaxlib", "joblib", "jacobi", "jupyter-client", "matplotlib", "nbconvert", "nbformat", "numba", "numba-stats", "numpy", "pre-commit", "pydocstyle", "pylint", "pytest", "pytest-cov", "pytest-xdist", "scipy", "sphinx", "sphinx-rtd-theme", "tabulate", "nbsphinx", "boost-histogram", "resample"] +doc = ["Jinja2 (==3.0)", "nbsphinx", "sphinx (>=4.1)", "sphinx-rtd-theme"] +test = ["boost-histogram", "cython", "flake8", "ipykernel", "ipywidgets", "jacobi", "jax", "jaxlib", "joblib", "jupyter-client", "matplotlib", "mypy", "nbconvert", "nbformat", "nbsphinx", "numba", "numba-stats", "numpy", "pre-commit", "pydocstyle", "pylint", "pytest", "pytest-cov", "pytest-xdist", "resample", "scipy", "sphinx", "sphinx-rtd-theme", "tabulate"] [[package]] name = "importlib-metadata" @@ -682,13 +680,13 @@ python-versions = ">=3.7" zipp = ">=0.5" [package.extras] -docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"] +docs = ["jaraco.packaging (>=9)", "rst.linker (>=1.9)", "sphinx"] perf = ["ipython"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "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 = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"] [[package]] name = "importlib-resources" -version = "5.8.0" +version = "5.9.0" description = "Read resources from Python packages" category = "main" optional = true @@ -698,8 +696,8 @@ python-versions = ">=3.7" zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} [package.extras] -docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"] +docs = ["jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx"] +testing = ["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" @@ -719,7 +717,7 @@ python-versions = "*" [[package]] name = "ipykernel" -version = "6.15.1" +version = "6.15.2" description = "IPython Kernel for Jupyter" category = "dev" optional = false @@ -739,7 +737,7 @@ tornado = ">=6.1" traitlets = ">=5.1.0" [package.extras] -test = ["flaky", "ipyparallel", "pre-commit", "pytest-cov", "pytest-timeout", "pytest (>=6.0)"] +test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=6.0)", "pytest-cov", "pytest-timeout"] [[package]] name = "ipython" @@ -765,7 +763,7 @@ stack-data = "*" traitlets = ">=5" [package.extras] -all = ["black", "Sphinx (>=1.3)", "ipykernel", "nbconvert", "nbformat", "ipywidgets", "notebook", "ipyparallel", "qtconsole", "pytest (<7.1)", "pytest-asyncio", "testpath", "curio", "matplotlib (!=3.2.0)", "numpy (>=1.19)", "pandas", "trio"] +all = ["Sphinx (>=1.3)", "black", "curio", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.19)", "pandas", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "testpath", "trio"] black = ["black"] doc = ["Sphinx (>=1.3)"] kernel = ["ipykernel"] @@ -775,7 +773,7 @@ notebook = ["ipywidgets", "notebook"] parallel = ["ipyparallel"] qtconsole = ["qtconsole"] test = ["pytest (<7.1)", "pytest-asyncio", "testpath"] -test_extra = ["pytest (<7.1)", "pytest-asyncio", "testpath", "curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.19)", "pandas", "trio"] +test_extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.19)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"] [[package]] name = "ipython-genutils" @@ -787,7 +785,7 @@ python-versions = "*" [[package]] name = "ipywidgets" -version = "7.7.1" +version = "7.7.2" description = "IPython HTML widgets for Jupyter" category = "dev" optional = false @@ -797,12 +795,12 @@ python-versions = "*" ipykernel = ">=4.5.1" ipython = {version = ">=4.0.0", markers = "python_version >= \"3.3\""} ipython-genutils = ">=0.2.0,<0.3.0" -jupyterlab-widgets = {version = ">=1.0.0", markers = "python_version >= \"3.6\""} +jupyterlab-widgets = {version = ">=1.0.0,<3", markers = "python_version >= \"3.6\""} traitlets = ">=4.3.1" widgetsnbextension = ">=3.6.0,<3.7.0" [package.extras] -test = ["pytest (>=3.6.0)", "pytest-cov", "mock"] +test = ["mock", "pytest (>=3.6.0)", "pytest-cov"] [[package]] name = "isort" @@ -813,10 +811,10 @@ optional = false python-versions = ">=3.6.1,<4.0" [package.extras] -pipfile_deprecated_finder = ["pipreqs", "requirementslib"] -requirements_deprecated_finder = ["pipreqs", "pip-api"] colors = ["colorama (>=0.4.3,<0.5.0)"] +pipfile_deprecated_finder = ["pipreqs", "requirementslib"] plugins = ["setuptools"] +requirements_deprecated_finder = ["pip-api", "pipreqs"] [[package]] name = "itsdangerous" @@ -826,9 +824,24 @@ category = "main" optional = true python-versions = ">=3.7" +[[package]] +name = "jaraco-classes" +version = "3.2.2" +description = "Utility functions for Python class constructs" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +more-itertools = "*" + +[package.extras] +docs = ["jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx"] +testing = ["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 = "jax" -version = "0.3.14" +version = "0.3.17" description = "Differentiate, compile, and transform Numpy code." category = "main" optional = true @@ -837,23 +850,24 @@ python-versions = ">=3.7" [package.dependencies] absl-py = "*" etils = {version = "*", extras = ["epath"]} -numpy = ">=1.19" +numpy = ">=1.20" opt_einsum = "*" scipy = ">=1.5" typing_extensions = "*" [package.extras] -ci = ["jaxlib (==0.3.10)"] -cpu = ["jaxlib (==0.3.14)"] -cuda = ["jaxlib (==0.3.14+cuda11.cudnn82)"] -cuda11_cudnn805 = ["jaxlib (==0.3.14+cuda11.cudnn805)"] -cuda11_cudnn82 = ["jaxlib (==0.3.14+cuda11.cudnn82)"] -minimum-jaxlib = ["jaxlib (==0.3.7)"] -tpu = ["jaxlib (==0.3.14)", "libtpu-nightly (==0.1.dev20220627)", "requests"] +australis = ["protobuf (>=3.13,<4)"] +ci = ["jaxlib (==0.3.15)"] +cpu = ["jaxlib (==0.3.15)"] +cuda = ["jaxlib (==0.3.15+cuda11.cudnn82)"] +cuda11_cudnn805 = ["jaxlib (==0.3.15+cuda11.cudnn805)"] +cuda11_cudnn82 = ["jaxlib (==0.3.15+cuda11.cudnn82)"] +minimum-jaxlib = ["jaxlib (==0.3.14)"] +tpu = ["jaxlib (==0.3.15)", "libtpu-nightly (==0.1.dev20220723)", "requests"] [[package]] name = "jaxlib" -version = "0.3.14" +version = "0.3.15" description = "XLA library for JAX" category = "main" optional = true @@ -861,7 +875,6 @@ python-versions = ">=3.7" [package.dependencies] absl-py = "*" -flatbuffers = ">=1.12,<3.0" numpy = ">=1.19" scipy = ">=1.5" @@ -889,8 +902,8 @@ optional = false python-versions = ">=3.7" [package.extras] -test = ["pytest", "pytest-trio", "pytest-asyncio (>=0.17)", "testpath", "trio", "async-timeout"] -trio = ["trio", "async-generator"] +test = ["async-timeout", "pytest", "pytest-asyncio (>=0.17)", "pytest-trio", "testpath", "trio"] +trio = ["async_generator", "trio"] [[package]] name = "jinja2" @@ -916,7 +929,7 @@ python-versions = ">=3.6" [[package]] name = "jsonschema" -version = "4.7.2" +version = "4.15.0" description = "An implementation of JSON Schema validation for Python" category = "dev" optional = false @@ -932,7 +945,7 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- [[package]] name = "jupyter-client" -version = "7.3.4" +version = "7.3.5" description = "Jupyter protocol implementation and client libraries" category = "dev" optional = false @@ -944,11 +957,11 @@ jupyter-core = ">=4.9.2" nest-asyncio = ">=1.5.4" python-dateutil = ">=2.8.2" pyzmq = ">=23.0" -tornado = ">=6.0" +tornado = ">=6.2" traitlets = "*" [package.extras] -doc = ["ipykernel", "myst-parser", "sphinx-rtd-theme", "sphinx (>=1.3.6)", "sphinxcontrib-github-alt"] +doc = ["ipykernel", "myst-parser", "sphinx (>=1.3.6)", "sphinx-rtd-theme", "sphinxcontrib-github-alt"] test = ["codecov", "coverage", "ipykernel (>=6.5)", "ipython", "mypy", "pre-commit", "pytest", "pytest-asyncio (>=0.18)", "pytest-cov", "pytest-timeout"] [[package]] @@ -984,7 +997,7 @@ python-versions = ">=3.6" [[package]] name = "keyring" -version = "23.7.0" +version = "23.9.1" description = "Store and access your passwords safely." category = "dev" optional = false @@ -992,17 +1005,18 @@ python-versions = ">=3.7" [package.dependencies] importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""} +"jaraco.classes" = "*" jeepney = {version = ">=0.4.2", markers = "sys_platform == \"linux\""} pywin32-ctypes = {version = "<0.1.0 || >0.1.0,<0.1.1 || >0.1.1", markers = "sys_platform == \"win32\""} SecretStorage = {version = ">=3.2", markers = "sys_platform == \"linux\""} [package.extras] -docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "jaraco.tidelift (>=1.4)"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"] +docs = ["jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx"] +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 = "kiwisolver" -version = "1.4.3" +version = "1.4.4" description = "A fast implementation of the Cassowary constraint solver" category = "main" optional = true @@ -1018,7 +1032,7 @@ python-versions = ">=3.6" [[package]] name = "llvmlite" -version = "0.39.0" +version = "0.39.1" description = "lightweight wrapper around basic LLVM functionality" category = "main" optional = true @@ -1032,6 +1046,20 @@ category = "main" optional = false python-versions = ">=3.6" +[[package]] +name = "lxml" +version = "4.9.1" +description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API." +category = "dev" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*" + +[package.extras] +cssselect = ["cssselect (>=0.7)"] +html5 = ["html5lib"] +htmlsoup = ["BeautifulSoup4"] +source = ["Cython (>=0.29.7)"] + [[package]] name = "markdown-it-py" version = "2.1.0" @@ -1050,7 +1078,7 @@ compare = ["commonmark (>=0.9.1,<0.10.0)", "markdown (>=3.3.6,<3.4.0)", "mistlet linkify = ["linkify-it-py (>=1.0,<2.0)"] plugins = ["mdit-py-plugins"] profiling = ["gprof2dot"] -rtd = ["attrs", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx-book-theme"] +rtd = ["attrs", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"] testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"] [[package]] @@ -1082,7 +1110,7 @@ setuptools_scm = ">=4,<7" [[package]] name = "matplotlib-inline" -version = "0.1.3" +version = "0.1.6" description = "Inline Matplotlib backend for Jupyter" category = "dev" optional = false @@ -1117,7 +1145,7 @@ testing = ["coverage", "pytest (>=3.6,<4)", "pytest-cov", "pytest-regressions"] [[package]] name = "mdurl" -version = "0.1.1" +version = "0.1.2" description = "Markdown URL utilities" category = "dev" optional = false @@ -1125,12 +1153,20 @@ python-versions = ">=3.7" [[package]] name = "mistune" -version = "0.8.4" -description = "The fastest markdown parser in pure Python" +version = "2.0.4" +description = "A sane Markdown parser with useful plugins and renderers" category = "dev" optional = false python-versions = "*" +[[package]] +name = "more-itertools" +version = "8.14.0" +description = "More routines for operating on iterables, beyond itertools" +category = "dev" +optional = false +python-versions = ">=3.5" + [[package]] name = "multipledispatch" version = "0.6.0" @@ -1181,12 +1217,12 @@ typing-extensions = "*" [package.extras] code_style = ["pre-commit (>=2.12,<3.0)"] linkify = ["linkify-it-py (>=1.0,<2.0)"] -rtd = ["ipython", "sphinx-book-theme", "sphinx-panels", "sphinxcontrib-bibtex (>=2.4,<3.0)", "sphinxext-rediraffe (>=0.2.7,<0.3.0)", "sphinxcontrib.mermaid (>=0.7.1,<0.8.0)", "sphinxext-opengraph (>=0.6.3,<0.7.0)"] -testing = ["beautifulsoup4", "coverage", "docutils (>=0.17.0,<0.18.0)", "pytest (>=6,<7)", "pytest-cov", "pytest-regressions", "pytest-param-files (>=0.3.4,<0.4.0)"] +rtd = ["ipython", "sphinx-book-theme", "sphinx-panels", "sphinxcontrib-bibtex (>=2.4,<3.0)", "sphinxcontrib.mermaid (>=0.7.1,<0.8.0)", "sphinxext-opengraph (>=0.6.3,<0.7.0)", "sphinxext-rediraffe (>=0.2.7,<0.3.0)"] +testing = ["beautifulsoup4", "coverage", "docutils (>=0.17.0,<0.18.0)", "pytest (>=6,<7)", "pytest-cov", "pytest-param-files (>=0.3.4,<0.4.0)", "pytest-regressions"] [[package]] name = "nbclient" -version = "0.6.6" +version = "0.6.7" description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor." category = "dev" optional = false @@ -1199,12 +1235,12 @@ nest-asyncio = "*" traitlets = ">=5.2.2" [package.extras] -sphinx = ["autodoc-traits", "mock", "moto", "myst-parser", "Sphinx (>=1.7)", "sphinx-book-theme"] -test = ["black", "check-manifest", "flake8", "ipykernel", "ipython (<8.0.0)", "ipywidgets (<8.0.0)", "mypy", "pip (>=18.1)", "pre-commit", "pytest (>=4.1)", "pytest-asyncio", "pytest-cov (>=2.6.1)", "setuptools (>=60.0)", "testpath", "twine (>=1.11.0)", "xmltodict"] +sphinx = ["Sphinx (>=1.7)", "autodoc-traits", "mock", "moto", "myst-parser", "sphinx-book-theme"] +test = ["black", "check-manifest", "flake8", "ipykernel", "ipython", "ipywidgets", "mypy", "nbconvert", "pip (>=18.1)", "pre-commit", "pytest (>=4.1)", "pytest-asyncio", "pytest-cov (>=2.6.1)", "setuptools (>=60.0)", "testpath", "twine (>=1.11.0)", "xmltodict"] [[package]] name = "nbconvert" -version = "6.5.0" +version = "7.0.0" description = "Converting Jupyter Notebooks" category = "dev" optional = false @@ -1214,12 +1250,13 @@ python-versions = ">=3.7" beautifulsoup4 = "*" bleach = "*" defusedxml = "*" -entrypoints = ">=0.2.2" +importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""} jinja2 = ">=3.0" jupyter-core = ">=4.7" jupyterlab-pygments = "*" -MarkupSafe = ">=2.0" -mistune = ">=0.8.1,<2" +lxml = "*" +markupsafe = ">=2.0" +mistune = ">=2.0.3,<3" nbclient = ">=0.5.0" nbformat = ">=5.1" packaging = "*" @@ -1229,10 +1266,12 @@ tinycss2 = "*" traitlets = ">=5.0" [package.extras] -all = ["pytest", "pytest-cov", "pytest-dependency", "ipykernel", "ipywidgets (>=7)", "pre-commit", "pyppeteer (>=1,<1.1)", "tornado (>=6.1)", "sphinx (>=1.5.1)", "sphinx-rtd-theme", "nbsphinx (>=0.2.12)", "ipython"] -docs = ["sphinx (>=1.5.1)", "sphinx-rtd-theme", "nbsphinx (>=0.2.12)", "ipython"] +all = ["ipykernel", "ipython", "ipywidgets (>=7)", "nbsphinx (>=0.2.12)", "pre-commit", "pyppeteer (>=1,<1.1)", "pyqtwebengine (>=5.15)", "pytest", "pytest-cov", "pytest-dependency", "sphinx (==5.0.2)", "sphinx-rtd-theme", "tornado (>=6.1)"] +docs = ["ipython", "nbsphinx (>=0.2.12)", "sphinx (==5.0.2)", "sphinx-rtd-theme"] +qtpdf = ["pyqtwebengine (>=5.15)"] +qtpng = ["pyqtwebengine (>=5.15)"] serve = ["tornado (>=6.1)"] -test = ["pytest", "pytest-cov", "pytest-dependency", "ipykernel", "ipywidgets (>=7)", "pre-commit", "pyppeteer (>=1,<1.1)"] +test = ["ipykernel", "ipywidgets (>=7)", "pre-commit", "pyppeteer (>=1,<1.1)", "pytest", "pytest-cov", "pytest-dependency"] webpdf = ["pyppeteer (>=1,<1.1)"] [[package]] @@ -1250,7 +1289,7 @@ jupyter-core = "*" traitlets = ">=5.1" [package.extras] -test = ["check-manifest", "testpath", "pytest", "pre-commit"] +test = ["check-manifest", "pre-commit", "pytest", "testpath"] [[package]] name = "nest-asyncio" @@ -1297,13 +1336,13 @@ tornado = ">=6.1" traitlets = ">=4.2.1" [package.extras] -docs = ["sphinx", "nbsphinx", "sphinxcontrib-github-alt", "sphinx-rtd-theme", "myst-parser"] +docs = ["myst-parser", "nbsphinx", "sphinx", "sphinx-rtd-theme", "sphinxcontrib-github-alt"] json-logging = ["json-logging"] -test = ["pytest", "coverage", "requests", "testpath", "nbval", "selenium", "pytest-cov", "requests-unixsocket"] +test = ["coverage", "nbval", "pytest", "pytest-cov", "requests", "requests-unixsocket", "selenium", "testpath"] [[package]] name = "numba" -version = "0.56.0" +version = "0.56.2" description = "compiling Python code using LLVM" category = "main" optional = true @@ -1311,12 +1350,12 @@ python-versions = ">=3.7" [package.dependencies] llvmlite = ">=0.39.0dev0,<0.40" -numpy = ">=1.18,<1.23" -setuptools = "*" +numpy = ">=1.18,<1.24" +setuptools = "<60" [[package]] name = "numpy" -version = "1.22.4" +version = "1.23.2" description = "NumPy is the fundamental package for array computing with Python." category = "main" optional = false @@ -1324,7 +1363,7 @@ python-versions = ">=3.8" [[package]] name = "numpyro" -version = "0.10.0" +version = "0.10.1" description = "Pyro PPL on NumPy" category = "main" optional = true @@ -1338,13 +1377,13 @@ numpy = "*" tqdm = "*" [package.extras] -tpu = ["jax[tpu] (>=0.2.13)"] -test = ["scipy (>=1.6,<1.7)", "pyro-api (>=0.1.1)", "pytest (>=4.1)", "isort (>=5.0)", "flake8", "black[jupyter] (>=21.8b0)"] -examples = ["wordcloud", "scikit-learn", "seaborn", "pandas", "matplotlib", "jupyter", "arviz"] -doc = ["sphinx-gallery", "sphinx-rtd-theme", "sphinx", "readthedocs-sphinx-search (==0.1.0)", "nbsphinx (>=0.8.5)", "ipython"] -dev = ["tensorflow-probability (>=0.15.0)", "pyyaml", "optax (>=0.0.6)", "jaxns (==1.0.0)", "graphviz", "funsor (>=0.4.1)", "flax", "dm-haiku"] -cuda = ["jax[cuda] (>=0.2.13)"] cpu = ["jax[cpu] (>=0.2.13)"] +cuda = ["jax[cuda] (>=0.2.13)"] +dev = ["dm-haiku", "flax", "funsor (>=0.4.1)", "graphviz", "jaxns (==1.0.0)", "optax (>=0.0.6)", "pyyaml", "tensorflow-probability (>=0.15.0)"] +doc = ["ipython", "nbsphinx (>=0.8.5)", "readthedocs-sphinx-search (==0.1.0)", "sphinx", "sphinx-gallery", "sphinx-rtd-theme"] +examples = ["arviz", "jupyter", "matplotlib", "pandas", "scikit-learn", "seaborn", "wordcloud"] +test = ["black[jupyter] (>=21.8b0)", "flake8", "isort (>=5.0)", "pyro-api (>=0.1.1)", "pytest (>=4.1)", "scipy (>=1.6,<1.7)"] +tpu = ["jax[tpu] (>=0.2.13)"] [[package]] name = "opt-einsum" @@ -1358,12 +1397,12 @@ python-versions = ">=3.5" numpy = ">=1.7" [package.extras] -docs = ["sphinx (==1.2.3)", "sphinxcontrib-napoleon", "sphinx-rtd-theme", "numpydoc"] +docs = ["numpydoc", "sphinx (==1.2.3)", "sphinx-rtd-theme", "sphinxcontrib-napoleon"] tests = ["pytest", "pytest-cov", "pytest-pep8"] [[package]] name = "orjson" -version = "3.7.11" +version = "3.8.0" description = "Fast, correct Python JSON library supporting dataclasses, datetimes, and numpy" category = "main" optional = true @@ -1382,7 +1421,7 @@ pyparsing = ">=2.0.2,<3.0.5 || >3.0.5" [[package]] name = "pandas" -version = "1.4.3" +version = "1.4.4" description = "Powerful data structures for data analysis, time series, and statistics" category = "main" optional = false @@ -1423,11 +1462,11 @@ testing = ["docopt", "pytest (<6.0.0)"] [[package]] name = "pathspec" -version = "0.9.0" +version = "0.10.1" description = "Utility library for gitignore style pattern matching of file paths." category = "dev" optional = false -python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" +python-versions = ">=3.7" [[package]] name = "pexpect" @@ -1469,7 +1508,7 @@ optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" [package.extras] -testing = ["nose", "coverage"] +testing = ["coverage", "nose"] [[package]] name = "platformdirs" @@ -1480,12 +1519,12 @@ optional = false python-versions = ">=3.7" [package.extras] -docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)", "sphinx (>=4)"] -test = ["appdirs (==1.4.4)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)", "pytest (>=6)"] +docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx (>=4)", "sphinx-autodoc-typehints (>=1.12)"] +test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"] [[package]] name = "plotly" -version = "5.9.0" +version = "5.10.0" description = "An open-source, interactive data visualization library for Python" category = "main" optional = true @@ -1546,7 +1585,7 @@ twisted = ["twisted"] [[package]] name = "prompt-toolkit" -version = "3.0.30" +version = "3.0.31" description = "Library for building powerful interactive command lines in Python" category = "dev" optional = false @@ -1557,14 +1596,14 @@ wcwidth = "*" [[package]] name = "psutil" -version = "5.9.1" +version = "5.9.2" description = "Cross-platform lib for process and system monitoring in Python." category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [package.extras] -test = ["ipaddress", "mock", "enum34", "pywin32", "wmi"] +test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"] [[package]] name = "ptyprocess" @@ -1634,8 +1673,8 @@ docutils = "!=0.17.0" sphinx = "*" [package.extras] -coverage = ["pytest-cov", "codecov", "sphinx", "numpydoc", "recommonmark", "pandas", "pytest", "pytest-regressions", "beautifulsoup4", "sphinx-sitemap", "jupyter-sphinx", "plotly", "numpy", "xarray", "docutils (==0.16)"] -test = ["sphinx", "numpydoc", "recommonmark", "pandas", "pytest", "pytest-regressions", "beautifulsoup4", "sphinx-sitemap", "jupyter-sphinx", "plotly", "numpy", "xarray", "docutils (==0.16)"] +coverage = ["beautifulsoup4", "codecov", "docutils (==0.16)", "jupyter-sphinx", "numpy", "numpydoc", "pandas", "plotly", "pytest", "pytest-cov", "pytest-regressions", "recommonmark", "sphinx", "sphinx-sitemap", "xarray"] +test = ["beautifulsoup4", "docutils (==0.16)", "jupyter-sphinx", "numpy", "numpydoc", "pandas", "plotly", "pytest", "pytest-regressions", "recommonmark", "sphinx", "sphinx-sitemap", "xarray"] [[package]] name = "pyflakes" @@ -1647,22 +1686,25 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pygments" -version = "2.12.0" +version = "2.13.0" description = "Pygments is a syntax highlighting package written in Python." category = "main" optional = false python-versions = ">=3.6" +[package.extras] +plugins = ["importlib-metadata"] + [[package]] name = "pylint" -version = "2.14.4" +version = "2.15.0" description = "python code static checker" category = "dev" optional = false python-versions = ">=3.7.2" [package.dependencies] -astroid = ">=2.11.6,<=2.12.0-dev0" +astroid = ">=2.12.4,<=2.14.0-dev0" colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""} dill = ">=0.2" isort = ">=4.2.5,<6" @@ -1685,7 +1727,7 @@ optional = false python-versions = ">=3.6.8" [package.extras] -diagrams = ["railroad-diagrams", "jinja2"] +diagrams = ["jinja2", "railroad-diagrams"] [[package]] name = "pyrsistent" @@ -1729,7 +1771,7 @@ coverage = {version = ">=5.2.1", extras = ["toml"]} pytest = ">=4.6" [package.extras] -testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtualenv"] +testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"] [[package]] name = "python-dateutil" @@ -1744,7 +1786,7 @@ six = ">=1.5" [[package]] name = "python-gitlab" -version = "3.6.0" +version = "3.9.0" description = "Interact with GitLab API" category = "dev" optional = false @@ -1760,7 +1802,7 @@ yaml = ["PyYaml (>=5.2)"] [[package]] name = "python-semantic-release" -version = "7.29.4" +version = "7.31.4" description = "Automatic Semantic Versioning for Python projects" category = "dev" optional = false @@ -1772,22 +1814,23 @@ click-log = ">=0.3,<1" dotty-dict = ">=1.3.0,<2" gitpython = ">=3.0.8,<4" invoke = ">=1.4.1,<2" +packaging = "*" python-gitlab = ">=2,<4" requests = ">=2.25,<3" semver = ">=2.10,<3" -tomlkit = ">=0.10.0,<0.11.0" +tomlkit = ">=0.10,<1.0" twine = ">=3,<4" wheel = "*" [package.extras] -dev = ["tox", "isort", "black"] -docs = ["Sphinx (==1.3.6)", "Jinja2 (==3.0.3)"] +dev = ["black", "isort", "tox"] +docs = ["Jinja2 (==3.0.3)", "Sphinx (==1.3.6)"] mypy = ["mypy", "types-requests"] -test = ["coverage (>=5,<6)", "pytest (>=5,<6)", "pytest-xdist (>=1,<2)", "pytest-mock (>=2,<3)", "responses (==0.13.3)", "mock (==1.3.0)"] +test = ["coverage (>=5,<6)", "mock (==1.3.0)", "pytest (>=5,<6)", "pytest-mock (>=2,<3)", "pytest-xdist (>=1,<2)", "responses (==0.13.3)"] [[package]] name = "pytz" -version = "2022.1" +version = "2022.2.1" description = "World timezone definitions, modern and historical" category = "main" optional = false @@ -1811,7 +1854,7 @@ python-versions = "*" [[package]] name = "pywinpty" -version = "2.0.6" +version = "2.0.7" description = "Pseudo terminal support for Windows from Python." category = "dev" optional = false @@ -1827,7 +1870,7 @@ python-versions = ">=3.6" [[package]] name = "pyzmq" -version = "23.2.0" +version = "23.2.1" description = "Python bindings for 0MQ" category = "dev" optional = false @@ -1839,7 +1882,7 @@ py = {version = "*", markers = "implementation_name == \"pypy\""} [[package]] name = "readme-renderer" -version = "35.0" +version = "37.1" description = "readme_renderer is a library for rendering \"readme\" descriptions for Warehouse" category = "dev" optional = false @@ -1910,7 +1953,7 @@ jupyter = ["ipywidgets (>=7.5.1,<8.0.0)"] [[package]] name = "scipy" -version = "1.9.0" +version = "1.9.1" description = "SciPy: Scientific Library for Python" category = "main" optional = false @@ -1921,7 +1964,7 @@ numpy = ">=1.18.5,<1.25.0" [[package]] name = "secretstorage" -version = "3.3.2" +version = "3.3.3" description = "Python bindings to FreeDesktop.org Secret Service API" category = "dev" optional = false @@ -1948,22 +1991,21 @@ optional = false python-versions = "*" [package.extras] -nativelib = ["pyobjc-framework-cocoa", "pywin32"] -objc = ["pyobjc-framework-cocoa"] +nativelib = ["pyobjc-framework-Cocoa", "pywin32"] +objc = ["pyobjc-framework-Cocoa"] win32 = ["pywin32"] [[package]] name = "setuptools" -version = "63.2.0" +version = "59.8.0" description = "Easily download, build, install, upgrade, and uninstall Python packages" category = "main" optional = false python-versions = ">=3.7" [package.extras] -docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-reredirects", "sphinxcontrib-towncrier", "furo"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-enabler (>=1.3)", "pytest-perf", "mock", "flake8-2020", "virtualenv (>=13.0.0)", "wheel", "pip (>=19.1)", "jaraco.envs (>=2.2)", "pytest-xdist", "jaraco.path (>=3.2.0)", "build", "filelock (>=3.4.0)", "pip-run (>=8.8)", "ini2toml[lite] (>=0.9)", "tomli-w (>=1.0.0)", "pytest-black (>=0.3.7)", "pytest-cov", "pytest-mypy (>=0.9.1)"] -testing-integration = ["pytest", "pytest-xdist", "pytest-enabler", "virtualenv (>=13.0.0)", "tomli", "wheel", "jaraco.path (>=3.2.0)", "jaraco.envs (>=2.2)", "build", "filelock (>=3.4.0)"] +docs = ["furo", "jaraco.packaging (>=8.2)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx", "sphinx-inline-tabs", "sphinxcontrib-towncrier"] +testing = ["flake8-2020", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mock", "paver", "pip (>=19.1)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-flake8", "pytest-mypy", "pytest-virtualenv (>=1.2.7)", "pytest-xdist", "sphinx", "virtualenv (>=13.0.0)", "wheel"] [[package]] name = "setuptools-scm" @@ -1984,11 +2026,11 @@ toml = ["setuptools (>=42)"] [[package]] name = "shellingham" -version = "1.4.0" +version = "1.5.0" description = "Tool to Detect Surrounding Shell" category = "main" optional = false -python-versions = "!=3.0,!=3.1,!=3.2,!=3.3,>=2.6" +python-versions = ">=3.4" [[package]] name = "six" @@ -2051,12 +2093,12 @@ sphinxcontrib-serializinghtml = ">=1.1.5" [package.extras] docs = ["sphinxcontrib-websupport"] -lint = ["flake8 (>=3.5.0)", "isort", "mypy (>=0.931)", "docutils-stubs", "types-typed-ast", "types-requests"] -test = ["pytest", "pytest-cov", "html5lib", "cython", "typed-ast"] +lint = ["docutils-stubs", "flake8 (>=3.5.0)", "isort", "mypy (>=0.931)", "types-requests", "types-typed-ast"] +test = ["cython", "html5lib", "pytest", "pytest-cov", "typed-ast"] [[package]] name = "sphinx-autodoc-typehints" -version = "1.18.3" +version = "1.19.1" description = "Type hints (PEP 484) support for the Sphinx autodoc extension" category = "dev" optional = false @@ -2087,7 +2129,7 @@ sphinx = ">=3,<5" [package.extras] code_style = ["pre-commit (>=2.7.0,<2.8.0)"] live-dev = ["sphinx-autobuild", "web-compile (>=0.2.1,<0.3.0)"] -sphinx = ["ablog (>=0.10.13,<0.11.0)", "ipywidgets", "folium", "numpy", "matplotlib", "myst-nb (>=0.13,<1.0)", "nbclient", "pandas", "plotly", "sphinx (>=4.0,<5.0)", "sphinx-design", "sphinx-copybutton", "sphinx-togglebutton (>=0.2.1)", "sphinx-thebe", "sphinxcontrib-bibtex (>=2.2,<3.0)", "sphinxext-opengraph"] +sphinx = ["ablog (>=0.10.13,<0.11.0)", "folium", "ipywidgets", "matplotlib", "myst-nb (>=0.13,<1.0)", "nbclient", "numpy", "pandas", "plotly", "sphinx (>=4.0,<5.0)", "sphinx-copybutton", "sphinx-design", "sphinx-thebe", "sphinx-togglebutton (>=0.2.1)", "sphinxcontrib-bibtex (>=2.2,<3.0)", "sphinxext-opengraph"] testing = ["coverage", "myst-nb (>=0.13,<1.0)", "pytest (>=6.0.1,<6.1.0)", "pytest-cov", "pytest-regressions (>=2.0.1,<2.1.0)", "sphinx-thebe"] [[package]] @@ -2116,7 +2158,7 @@ sphinx = ">=1.8" [package.extras] code_style = ["pre-commit (==2.12.1)"] -rtd = ["sphinx", "ipython", "myst-nb", "sphinx-book-theme"] +rtd = ["ipython", "myst-nb", "sphinx", "sphinx-book-theme"] [[package]] name = "sphinxcontrib-applehelp" @@ -2127,7 +2169,7 @@ optional = false python-versions = ">=3.5" [package.extras] -lint = ["flake8", "mypy", "docutils-stubs"] +lint = ["docutils-stubs", "flake8", "mypy"] test = ["pytest"] [[package]] @@ -2139,7 +2181,7 @@ optional = false python-versions = ">=3.5" [package.extras] -lint = ["flake8", "mypy", "docutils-stubs"] +lint = ["docutils-stubs", "flake8", "mypy"] test = ["pytest"] [[package]] @@ -2151,8 +2193,8 @@ optional = false python-versions = ">=3.6" [package.extras] -lint = ["flake8", "mypy", "docutils-stubs"] -test = ["pytest", "html5lib"] +lint = ["docutils-stubs", "flake8", "mypy"] +test = ["html5lib", "pytest"] [[package]] name = "sphinxcontrib-jsmath" @@ -2163,7 +2205,7 @@ optional = false python-versions = ">=3.5" [package.extras] -test = ["pytest", "flake8", "mypy"] +test = ["flake8", "mypy", "pytest"] [[package]] name = "sphinxcontrib-mermaid" @@ -2194,7 +2236,7 @@ optional = false python-versions = ">=3.5" [package.extras] -lint = ["flake8", "mypy", "docutils-stubs"] +lint = ["docutils-stubs", "flake8", "mypy"] test = ["pytest"] [[package]] @@ -2206,12 +2248,12 @@ optional = false python-versions = ">=3.5" [package.extras] -lint = ["flake8", "mypy", "docutils-stubs"] +lint = ["docutils-stubs", "flake8", "mypy"] test = ["pytest"] [[package]] name = "stack-data" -version = "0.3.0" +version = "0.5.0" description = "Extract data from python stack frames and tracebacks for informative displays" category = "dev" optional = false @@ -2223,7 +2265,7 @@ executing = "*" pure-eval = "*" [package.extras] -tests = ["pytest", "typeguard", "pygments", "littleutils", "cython"] +tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"] [[package]] name = "tenacity" @@ -2250,7 +2292,7 @@ pywinpty = {version = ">=1.1.0", markers = "os_name == \"nt\""} tornado = ">=6.1.0" [package.extras] -test = ["pre-commit", "pytest-timeout", "pytest (>=6.0)"] +test = ["pre-commit", "pytest (>=6.0)", "pytest-timeout"] [[package]] name = "tinycss2" @@ -2264,8 +2306,8 @@ python-versions = ">=3.6" webencodings = ">=0.4" [package.extras] -doc = ["sphinx", "sphinx-rtd-theme"] -test = ["pytest", "pytest-cov", "pytest-flake8", "pytest-isort", "coverage"] +doc = ["sphinx", "sphinx_rtd_theme"] +test = ["coverage[toml]", "pytest", "pytest-cov", "pytest-flake8", "pytest-isort"] [[package]] name = "toml" @@ -2285,7 +2327,7 @@ python-versions = ">=3.7" [[package]] name = "tomlkit" -version = "0.10.2" +version = "0.11.4" description = "Style preserving TOML library" category = "dev" optional = false @@ -2301,7 +2343,7 @@ python-versions = ">= 3.7" [[package]] name = "tqdm" -version = "4.64.0" +version = "4.64.1" description = "Fast, Extensible Progress Meter" category = "main" optional = false @@ -2362,10 +2404,10 @@ rich = {version = ">=10.11.0,<13.0.0", optional = true, markers = "extra == \"al shellingham = {version = ">=1.3.0,<2.0.0", optional = true, markers = "extra == \"all\""} [package.extras] -all = ["colorama (>=0.4.3,<0.5.0)", "shellingham (>=1.3.0,<2.0.0)", "rich (>=10.11.0,<13.0.0)"] +all = ["colorama (>=0.4.3,<0.5.0)", "rich (>=10.11.0,<13.0.0)", "shellingham (>=1.3.0,<2.0.0)"] dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "pre-commit (>=2.17.0,<3.0.0)"] -doc = ["mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "mdx-include (>=1.4.1,<2.0.0)"] -test = ["shellingham (>=1.3.0,<2.0.0)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (>=2.10.0,<3.0.0)", "coverage (>=5.2,<6.0)", "pytest-xdist (>=1.32.0,<2.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "mypy (==0.910)", "black (>=22.3.0,<23.0.0)", "isort (>=5.0.6,<6.0.0)", "rich (>=10.11.0,<13.0.0)"] +doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)"] +test = ["black (>=22.3.0,<23.0.0)", "coverage (>=5.2,<6.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (>=2.10.0,<3.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "pytest-xdist (>=1.32.0,<2.0.0)", "rich (>=10.11.0,<13.0.0)", "shellingham (>=1.3.0,<2.0.0)"] [[package]] name = "typing-extensions" @@ -2377,34 +2419,33 @@ python-versions = ">=3.7" [[package]] name = "urllib3" -version = "1.26.10" +version = "1.26.12" description = "HTTP library with thread-safe connection pooling, file post, and more." category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, <4" [package.extras] -brotli = ["brotlicffi (>=0.8.0)", "brotli (>=1.0.9)", "brotlipy (>=0.6.0)"] -secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "ipaddress"] +brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"] +secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"] socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] name = "virtualenv" -version = "20.15.1" +version = "20.16.4" description = "Virtual Python Environment builder" category = "dev" optional = false -python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" +python-versions = ">=3.6" [package.dependencies] -distlib = ">=0.3.1,<1" -filelock = ">=3.2,<4" -platformdirs = ">=2,<3" -six = ">=1.9.0,<2" +distlib = ">=0.3.5,<1" +filelock = ">=3.4.1,<4" +platformdirs = ">=2.4,<3" [package.extras] -docs = ["proselint (>=0.10.2)", "sphinx (>=3)", "sphinx-argparse (>=0.2.5)", "sphinx-rtd-theme (>=0.4.3)", "towncrier (>=21.3)"] -testing = ["coverage (>=4)", "coverage-enable-subprocess (>=1)", "flaky (>=3)", "pytest (>=4)", "pytest-env (>=0.6.2)", "pytest-freezegun (>=0.4.1)", "pytest-mock (>=2)", "pytest-randomly (>=1)", "pytest-timeout (>=1)", "packaging (>=20.0)"] +docs = ["proselint (>=0.13)", "sphinx (>=5.1.1)", "sphinx-argparse (>=0.3.1)", "sphinx-rtd-theme (>=1)", "towncrier (>=21.9)"] +testing = ["coverage (>=6.2)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=21.3)", "pytest (>=7.0.1)", "pytest-env (>=0.6.2)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.6.1)", "pytest-randomly (>=3.10.3)", "pytest-timeout (>=2.1)"] [[package]] name = "wcwidth" @@ -2424,12 +2465,15 @@ python-versions = "*" [[package]] name = "werkzeug" -version = "2.1.2" +version = "2.2.2" description = "The comprehensive WSGI web application library." category = "main" optional = true python-versions = ">=3.7" +[package.dependencies] +MarkupSafe = ">=2.1.1" + [package.extras] watchdog = ["watchdog"] @@ -2472,8 +2516,8 @@ optional = false python-versions = ">=3.7" [package.extras] -docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "jaraco.tidelift (>=1.4)"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.3)", "jaraco-itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"] +docs = ["jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx"] +testing = ["func-timeout", "jaraco.itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] [extras] all = ["logger-tt", "iminuit", "numpyro", "joblib", "psutil", "numba", "matplotlib", "plotly", "dash", "dash-bootstrap-components", "orjson", "tqdm", "customtkinter"] @@ -2484,12 +2528,12 @@ viz = ["matplotlib", "plotly", "dash", "dash-bootstrap-components", "orjson", "t [metadata] lock-version = "1.1" python-versions = ">=3.9,<3.11" # 3.11 due to numba -content-hash = "55036e006059ae84da00b4b0bd5876f2a4950f1a535dc9db7baee09dcdd4b312" +content-hash = "fff6c01e3616cc8f6915c0ef0f1b96377c73719601edd4d18e42c6d43f078aba" [metadata.files] absl-py = [ - {file = "absl-py-1.1.0.tar.gz", hash = "sha256:3aa39f898329c2156ff525dfa69ce709e42d77aab18bf4917719d6f260aa6a08"}, - {file = "absl_py-1.1.0-py3-none-any.whl", hash = "sha256:db97287655e30336938f8058d2c81ed2be6af1d9b6ebbcd8df1080a6c7fcd24e"}, + {file = "absl-py-1.2.0.tar.gz", hash = "sha256:f568809938c49abbda89826223c992b630afd23c638160ad7840cfe347710d97"}, + {file = "absl_py-1.2.0-py3-none-any.whl", hash = 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--extras fit @@ -122,6 +124,7 @@ all = [ # poetry install --extras all "joblib", "psutil", "numba", + "flatbuffers", "matplotlib", "plotly", "dash", diff --git a/src/metaDMG/fit/bayesian.py b/src/metaDMG/fit/bayesian.py index 43afad7..628ac80 100644 --- a/src/metaDMG/fit/bayesian.py +++ b/src/metaDMG/fit/bayesian.py @@ -145,6 +145,7 @@ def compute_D_max(mcmc, data): beta = (1 - Dx) * phi pdf = sp_betabinom(N, alpha, beta) + # pdf = sp_betabinom(N, alpha.mean(), beta.mean()) # 1000x faster approximation return { "mu": mu.item(), "std": std.item(),