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Verified Commit 8f6a6ab2 authored by James Graham's avatar James Graham
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build: update dependencies in lockfile 

Remove cython as a runtime dependency
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poetry.lock
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......@@ -6,27 +6,19 @@ category = "main"
optional = false
python-versions = "*"
[[package]]
name = "appdirs"
version = "1.4.4"
description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
category = "dev"
optional = false
python-versions = "*"
[[package]]
name = "astroid"
version = "2.4.1"
version = "2.8.5"
description = "An abstract syntax tree for Python with inference support."
category = "main"
optional = false
python-versions = ">=3.5"
python-versions = "~=3.6"
[package.dependencies]
lazy-object-proxy = ">=1.4.0,<1.5.0"
six = ">=1.12,<2.0"
typed-ast = {version = ">=1.4.0,<1.5", markers = "implementation_name == \"cpython\" and python_version < \"3.8\""}
wrapt = ">=1.11,<2.0"
lazy-object-proxy = ">=1.4.0"
typed-ast = {version = ">=1.4.0,<2.0", markers = "implementation_name == \"cpython\" and python_version < \"3.8\""}
typing-extensions = {version = ">=3.10", markers = "python_version < \"3.10\""}
wrapt = ">=1.11,<1.14"
[[package]]
name = "astunparse"
......@@ -63,7 +55,7 @@ tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>
[[package]]
name = "babel"
version = "2.9.0"
version = "2.9.1"
description = "Internationalization utilities"
category = "main"
optional = false
......@@ -72,21 +64,39 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[package.dependencies]
pytz = ">=2015.7"
[[package]]
name = "backports.entry-points-selectable"
version = "1.1.1"
description = "Compatibility shim providing selectable entry points for older implementations"
category = "dev"
optional = false
python-versions = ">=2.7"
[package.dependencies]
importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
[package.extras]
docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
testing = ["pytest", "pytest-flake8", "pytest-cov", "pytest-black (>=0.3.7)", "pytest-mypy", "pytest-checkdocs (>=2.4)", "pytest-enabler (>=1.0.1)"]
[[package]]
name = "certifi"
version = "2020.12.5"
version = "2021.10.8"
description = "Python package for providing Mozilla's CA Bundle."
category = "main"
optional = false
python-versions = "*"
[[package]]
name = "chardet"
version = "4.0.0"
description = "Universal encoding detector for Python 2 and 3"
name = "charset-normalizer"
version = "2.0.7"
description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
python-versions = ">=3.5.0"
[package.extras]
unicode_backport = ["unicodedata2"]
[[package]]
name = "colorama"
......@@ -109,22 +119,14 @@ test = ["flake8 (==3.7.8)", "hypothesis (==3.55.3)"]
[[package]]
name = "coverage"
version = "5.5"
version = "6.1.2"
description = "Code coverage measurement for Python"
category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4"
python-versions = ">=3.6"
[package.extras]
toml = ["toml"]
[[package]]
name = "cython"
version = "0.29.23"
description = "The Cython compiler for writing C extensions for the Python language."
category = "main"
optional = false
python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
toml = ["tomli"]
[[package]]
name = "dataclasses"
......@@ -136,7 +138,7 @@ python-versions = ">=3.6, <3.7"
[[package]]
name = "distlib"
version = "0.3.1"
version = "0.3.3"
description = "Distribution utilities"
category = "dev"
optional = false
......@@ -160,11 +162,15 @@ python-versions = "*"
[[package]]
name = "filelock"
version = "3.0.12"
version = "3.3.2"
description = "A platform independent file lock."
category = "dev"
optional = false
python-versions = "*"
python-versions = ">=3.6"
[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)"]
[[package]]
name = "flake8"
......@@ -193,15 +199,15 @@ flake8 = "*"
[[package]]
name = "idna"
version = "2.10"
version = "3.3"
description = "Internationalized Domain Names in Applications (IDNA)"
category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
python-versions = ">=3.5"
[[package]]
name = "imagesize"
version = "1.2.0"
version = "1.3.0"
description = "Getting image size from png/jpeg/jpeg2000/gif file"
category = "main"
optional = false
......@@ -209,7 +215,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[[package]]
name = "importlib-metadata"
version = "4.0.1"
version = "4.8.2"
description = "Read metadata from Python packages"
category = "dev"
optional = false
......@@ -221,22 +227,23 @@ zipp = ">=0.5"
[package.extras]
docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
perf = ["ipython"]
testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
[[package]]
name = "importlib-resources"
version = "5.1.2"
version = "5.4.0"
description = "Read resources from Python packages"
category = "dev"
optional = false
python-versions = ">=3.6"
[package.dependencies]
zipp = {version = ">=0.4", markers = "python_version < \"3.8\""}
zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
[package.extras]
docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
testing = ["pytest (>=4.6)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pytest-cov", "pytest-enabler", "pytest-black (>=0.3.7)", "pytest-mypy"]
testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy"]
[[package]]
name = "iniconfig"
......@@ -248,35 +255,34 @@ python-versions = "*"
[[package]]
name = "isort"
version = "4.3.21"
version = "5.8.0"
description = "A Python utility / library to sort Python imports."
category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
python-versions = ">=3.6,<4.0"
[package.extras]
pipfile = ["pipreqs", "requirementslib"]
pyproject = ["toml"]
requirements = ["pipreqs", "pip-api"]
xdg_home = ["appdirs (>=1.4.0)"]
pipfile_deprecated_finder = ["pipreqs", "requirementslib"]
requirements_deprecated_finder = ["pipreqs", "pip-api"]
colors = ["colorama (>=0.4.3,<0.5.0)"]
[[package]]
name = "jinja2"
version = "2.11.3"
version = "3.0.3"
description = "A very fast and expressive template engine."
category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
python-versions = ">=3.6"
[package.dependencies]
MarkupSafe = ">=0.23"
MarkupSafe = ">=2.0"
[package.extras]
i18n = ["Babel (>=0.8)"]
i18n = ["Babel (>=2.7)"]
[[package]]
name = "joblib"
version = "1.0.1"
version = "1.1.0"
description = "Lightweight pipelining with Python functions"
category = "main"
optional = true
......@@ -284,11 +290,11 @@ python-versions = ">=3.6"
[[package]]
name = "lazy-object-proxy"
version = "1.4.3"
version = "1.6.0"
description = "A fast and thorough lazy object proxy."
category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
[[package]]
name = "markdown-it-py"
......@@ -311,11 +317,11 @@ testing = ["coverage", "pytest (>=3.6,<4)", "pytest-cov", "pytest-regressions",
[[package]]
name = "markupsafe"
version = "1.1.1"
version = "2.0.1"
description = "Safely add untrusted strings to HTML/XML markup."
category = "main"
optional = false
python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*"
python-versions = ">=3.6"
[[package]]
name = "mccabe"
......@@ -354,7 +360,7 @@ scipy = "*"
[[package]]
name = "mdtraj"
version = "1.9.5"
version = "1.9.7"
description = "MDTraj: A modern, open library for the analysis of molecular dynamics trajectories"
category = "main"
optional = false
......@@ -390,7 +396,15 @@ testing = ["beautifulsoup4", "coverage", "docutils (>=0.17.0,<0.18.0)", "pytest
[[package]]
name = "numpy"
version = "1.20.2"
version = "1.19.5"
description = "NumPy is the fundamental package for array computing with Python."
category = "main"
optional = false
python-versions = ">=3.6"
[[package]]
name = "numpy"
version = "1.21.1"
description = "NumPy is the fundamental package for array computing with Python."
category = "main"
optional = false
......@@ -398,11 +412,11 @@ python-versions = ">=3.7"
[[package]]
name = "packaging"
version = "20.9"
version = "21.0"
description = "Core utilities for Python packages"
category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
python-versions = ">=3.6"
[package.dependencies]
pyparsing = ">=2.0.2"
......@@ -418,37 +432,49 @@ python-versions = "*"
[package.dependencies]
flake8-polyfill = ">=1.0.2,<2"
[[package]]
name = "platformdirs"
version = "2.4.0"
description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
category = "dev"
optional = false
python-versions = ">=3.6"
[package.extras]
docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"]
test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"]
[[package]]
name = "pluggy"
version = "0.13.1"
version = "1.0.0"
description = "plugin and hook calling mechanisms for python"
category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
python-versions = ">=3.6"
[package.dependencies]
importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
[package.extras]
dev = ["pre-commit", "tox"]
testing = ["pytest", "pytest-benchmark"]
[[package]]
name = "prospector"
version = "1.3.1"
version = "1.4.1.1"
description = "Prospector: python static analysis tool"
category = "dev"
optional = false
python-versions = "*"
python-versions = ">=3.6"
[package.dependencies]
astroid = "2.4.1"
dodgy = ">=0.1.9"
mccabe = ">=0.5.0"
pep8-naming = ">=0.3.3,<=0.10.0"
pycodestyle = ">=2.6.0,<2.7.0"
pycodestyle = ">=2.6.0,<2.9.0"
pydocstyle = ">=2.0.0"
pyflakes = ">=2.2.0,<2.3.0"
pylint = "2.5.3"
pylint = ">=2.8.3,<3"
pylint-celery = "0.3"
pylint-django = "<2.2.0"
pylint-flask = "0.6"
......@@ -467,11 +493,11 @@ with_vulture = ["vulture (>=1.5)"]
[[package]]
name = "py"
version = "1.10.0"
version = "1.11.0"
description = "library with cross-python path, ini-parsing, io, code, log facilities"
category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
[[package]]
name = "pycodestyle"
......@@ -483,7 +509,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[[package]]
name = "pydocstyle"
version = "6.0.0"
version = "6.1.1"
description = "Python docstring style checker"
category = "dev"
optional = false
......@@ -492,6 +518,9 @@ python-versions = ">=3.6"
[package.dependencies]
snowballstemmer = "*"
[package.extras]
toml = ["toml"]
[[package]]
name = "pyflakes"
version = "2.2.0"
......@@ -502,7 +531,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[[package]]
name = "pygments"
version = "2.8.1"
version = "2.10.0"
description = "Pygments is a syntax highlighting package written in Python."
category = "main"
optional = false
......@@ -510,18 +539,20 @@ python-versions = ">=3.5"
[[package]]
name = "pylint"
version = "2.5.3"
version = "2.11.1"
description = "python code static checker"
category = "dev"
optional = false
python-versions = ">=3.5.*"
python-versions = "~=3.6"
[package.dependencies]
astroid = ">=2.4.0,<=2.5"
astroid = ">=2.8.0,<2.9"
colorama = {version = "*", markers = "sys_platform == \"win32\""}
isort = ">=4.2.5,<5"
isort = ">=4.2.5,<6"
mccabe = ">=0.6,<0.7"
platformdirs = ">=2.2.0"
toml = ">=0.7.1"
typing-extensions = {version = ">=3.10.0", markers = "python_version < \"3.10\""}
[[package]]
name = "pylint-celery"
......@@ -576,15 +607,18 @@ pylint = ">=1.7"
[[package]]
name = "pyparsing"
version = "2.4.7"
version = "3.0.6"
description = "Python parsing module"
category = "main"
optional = false
python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
python-versions = ">=3.6"
[package.extras]
diagrams = ["jinja2", "railroad-diagrams"]
[[package]]
name = "pytest"
version = "6.2.3"
version = "6.2.5"
description = "pytest: simple powerful testing with Python"
category = "dev"
optional = false
......@@ -597,7 +631,7 @@ colorama = {version = "*", markers = "sys_platform == \"win32\""}
importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
iniconfig = "*"
packaging = "*"
pluggy = ">=0.12,<1.0.0a1"
pluggy = ">=0.12,<2.0"
py = ">=1.8.2"
toml = "*"
......@@ -606,7 +640,7 @@ testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xm
[[package]]
name = "pytest-cov"
version = "2.11.1"
version = "2.12.1"
description = "Pytest plugin for measuring coverage."
category = "dev"
optional = false
......@@ -615,13 +649,14 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
[package.dependencies]
coverage = ">=5.2.1"
pytest = ">=4.6"
toml = "*"
[package.extras]
testing = ["fields", "hunter", "process-tests (==2.0.2)", "six", "pytest-xdist", "virtualenv"]
testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtualenv"]
[[package]]
name = "pytz"
version = "2021.1"
version = "2021.3"
description = "World timezone definitions, modern and historical"
category = "main"
optional = false
......@@ -629,29 +664,29 @@ python-versions = "*"
[[package]]
name = "pyyaml"
version = "5.4.1"
version = "6.0"
description = "YAML parser and emitter for Python"
category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
python-versions = ">=3.6"
[[package]]
name = "requests"
version = "2.25.1"
version = "2.26.0"
description = "Python HTTP for Humans."
category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
[package.dependencies]
certifi = ">=2017.4.17"
chardet = ">=3.0.2,<5"
idna = ">=2.5,<3"
charset-normalizer = {version = ">=2.0.0,<2.1.0", markers = "python_version >= \"3\""}
idna = {version = ">=2.5,<4", markers = "python_version >= \"3\""}
urllib3 = ">=1.21.1,<1.27"
[package.extras]
security = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)"]
socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"]
use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"]
[[package]]
name = "requirements-detector"
......@@ -695,7 +730,7 @@ docutils = ">=0.7"
[[package]]
name = "scikit-learn"
version = "0.24.1"
version = "0.24.2"
description = "A set of python modules for machine learning and data mining"
category = "main"
optional = true
......@@ -726,18 +761,18 @@ numpy = ">=1.14.5"
[[package]]
name = "setoptconf"
version = "0.2.0"
version = "0.3.0"
description = "A module for retrieving program settings from various sources in a consistant method."
category = "dev"
optional = false
python-versions = "*"
python-versions = ">=3.0"
[package.extras]
YAML = ["pyyaml"]
yaml = ["pyyaml"]
[[package]]
name = "six"
version = "1.15.0"
version = "1.16.0"
description = "Python 2 and 3 compatibility utilities"
category = "main"
optional = false
......@@ -784,14 +819,14 @@ test = ["pytest", "pytest-cov", "html5lib", "cython", "typed-ast"]
[[package]]
name = "sphinx-autoapi"
version = "1.8.1"
version = "1.8.4"
description = "Sphinx API documentation generator"
category = "main"
optional = false
python-versions = ">=3.6"
[package.dependencies]
astroid = ">=2.4"
astroid = ">=2.7"
Jinja2 = "*"
PyYAML = "*"
sphinx = ">=3.0"
......@@ -843,11 +878,11 @@ test = ["pytest"]
[[package]]
name = "sphinxcontrib-htmlhelp"
version = "1.0.3"
version = "2.0.0"
description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
category = "main"
optional = false
python-versions = ">=3.5"
python-versions = ">=3.6"
[package.extras]
lint = ["flake8", "mypy", "docutils-stubs"]
......@@ -878,7 +913,7 @@ test = ["pytest"]
[[package]]
name = "sphinxcontrib-serializinghtml"
version = "1.1.4"
version = "1.1.5"
description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
category = "main"
optional = false
......@@ -890,11 +925,11 @@ test = ["pytest"]
[[package]]
name = "threadpoolctl"
version = "2.1.0"
version = "3.0.0"
description = "threadpoolctl"
category = "main"
optional = true
python-versions = ">=3.5"
python-versions = ">=3.6"
[[package]]
name = "toml"
......@@ -906,7 +941,7 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
[[package]]
name = "tox"
version = "3.23.0"
version = "3.24.4"
description = "tox is a generic virtualenv management and test command line tool"
category = "dev"
optional = false
......@@ -929,15 +964,15 @@ testing = ["flaky (>=3.4.0)", "freezegun (>=0.3.11)", "psutil (>=5.6.1)", "pytes
[[package]]
name = "typed-ast"
version = "1.4.3"
version = "1.5.0"
description = "a fork of Python 2 and 3 ast modules with type comment support"
category = "main"
optional = false
python-versions = "*"
python-versions = ">=3.6"
[[package]]
name = "typing-extensions"
version = "3.7.4.3"
version = "3.10.0.2"
description = "Backported and Experimental Type Hints for Python 3.5+"
category = "main"
optional = false
......@@ -945,44 +980,45 @@ python-versions = "*"
[[package]]
name = "unidecode"
version = "1.2.0"
version = "1.3.2"
description = "ASCII transliterations of Unicode text"
category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
python-versions = ">=3.5"
[[package]]
name = "urllib3"
version = "1.26.4"
version = "1.26.7"
description = "HTTP library with thread-safe connection pooling, file post, and more."
category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4"
[package.extras]
brotli = ["brotlipy (>=0.6.0)"]
secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "ipaddress"]
socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
brotli = ["brotlipy (>=0.6.0)"]
[[package]]
name = "virtualenv"
version = "20.4.4"
version = "20.10.0"
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pyproject.toml
+ 0
− 1
View file @ 8f6a6ab2
......@@ -32,7 +32,6 @@ numpy = [
{ version = "^1.19.1", python = "<3.7" }, # Support for Python 3.6 was dropped in 1.20
{ version = "^1.20.0", python = ">=3.7" } # But 1.20 should resolve issue with MDTraj on macOS
]
cython = "^0.29.21"
astunparse = "1.6.2" # See https://github.com/mdtraj/mdtraj/issues/1613
mdtraj = "^1.9.5, !=1.9.6"
rich = "^9.2.0"
......
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