Repository: UCL-Chimera/medical-waveforms (language: python)

Issue:
Some dependencies outdated
GitHub is issuing dependabot alerts


Discussion / hints:

Fix patch:
diff --git a/poetry.lock b/poetry.lock
index 9d8866b..7a5a572 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,28 +1,14 @@
 [[package]]
 name = "appnope"
-version = "0.1.2"
+version = "0.1.3"
 description = "Disable App Nap on macOS >= 10.9"
 category = "dev"
 optional = false
 python-versions = "*"
 
-[[package]]
-name = "argcomplete"
-version = "1.12.3"
-description = "Bash tab completion for argparse"
-category = "dev"
-optional = false
-python-versions = "*"
-
-[package.dependencies]
-importlib-metadata = {version = ">=0.23,<5", markers = "python_version == \"3.7\""}
-
-[package.extras]
-test = ["coverage", "flake8", "pexpect", "wheel"]
-
 [[package]]
 name = "atomicwrites"
-version = "1.4.0"
+version = "1.4.1"
 description = "Atomic file writes."
 category = "dev"
 optional = false
@@ -30,17 +16,17 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "attrs"
-version = "21.2.0"
+version = "21.4.0"
 description = "Classes Without Boilerplate"
 category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [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"]
+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"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"]
+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"]
 
 [[package]]
 name = "backcall"
@@ -75,7 +61,7 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "cffi"
-version = "1.15.0"
+version = "1.15.1"
 description = "Foreign Function Interface for Python calling C code."
 category = "dev"
 optional = false
@@ -98,7 +84,7 @@ importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
 
 [[package]]
 name = "colorama"
-version = "0.4.4"
+version = "0.4.5"
 description = "Cross-platform colored terminal text."
 category = "dev"
 optional = false
@@ -128,15 +114,15 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "debugpy"
-version = "1.5.1"
+version = "1.6.2"
 description = "An implementation of the Debug Adapter Protocol for Python"
 category = "dev"
 optional = false
-python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
+python-versions = ">=3.7"
 
 [[package]]
 name = "decorator"
-version = "5.1.0"
+version = "5.1.1"
 description = "Decorators for Humans"
 category = "dev"
 optional = false
@@ -144,49 +130,50 @@ python-versions = ">=3.5"
 
 [[package]]
 name = "entrypoints"
-version = "0.3"
+version = "0.4"
 description = "Discover and load entry points from installed packages."
 category = "dev"
 optional = false
-python-versions = ">=2.7"
+python-versions = ">=3.6"
 
 [[package]]
 name = "fonttools"
-version = "4.28.5"
+version = "4.34.4"
 description = "Tools to manipulate font files"
 category = "main"
 optional = false
 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)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=13.0.0)", "xattr"]
+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"]
 graphite = ["lz4 (>=1.7.4.2)"]
 interpolatable = ["scipy", "munkres"]
 lxml = ["lxml (>=4.0,<5)"]
 pathops = ["skia-pathops (>=0.5.0)"]
 plot = ["matplotlib"]
+repacker = ["uharfbuzz (>=0.23.0)"]
 symfont = ["sympy"]
 type1 = ["xattr"]
 ufo = ["fs (>=2.2.0,<3)"]
-unicode = ["unicodedata2 (>=13.0.0)"]
+unicode = ["unicodedata2 (>=14.0.0)"]
 woff = ["zopfli (>=0.1.4)", "brotlicffi (>=0.8.0)", "brotli (>=1.0.1)"]
 
 [[package]]
 name = "importlib-metadata"
-version = "4.8.2"
+version = "4.12.0"
 description = "Read metadata from Python packages"
-category = "dev"
+category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
 typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
 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)"]
+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)"]
 
 [[package]]
 name = "iniconfig"
@@ -198,7 +185,7 @@ python-versions = "*"
 
 [[package]]
 name = "ipykernel"
-version = "6.6.0"
+version = "6.15.1"
 description = "IPython Kernel for Jupyter"
 category = "dev"
 optional = false
@@ -206,21 +193,23 @@ python-versions = ">=3.7"
 
 [package.dependencies]
 appnope = {version = "*", markers = "platform_system == \"Darwin\""}
-argcomplete = {version = ">=1.12.3", markers = "python_version < \"3.8.0\""}
-debugpy = ">=1.0.0,<2.0"
-importlib-metadata = {version = "<5", markers = "python_version < \"3.8.0\""}
+debugpy = ">=1.0"
 ipython = ">=7.23.1"
-jupyter-client = "<8.0"
-matplotlib-inline = ">=0.1.0,<0.2.0"
-tornado = ">=4.2,<7.0"
-traitlets = ">=5.1.0,<6.0"
+jupyter-client = ">=6.1.12"
+matplotlib-inline = ">=0.1"
+nest-asyncio = "*"
+packaging = "*"
+psutil = "*"
+pyzmq = ">=17"
+tornado = ">=6.1"
+traitlets = ">=5.1.0"
 
 [package.extras]
-test = ["pytest (!=5.3.4)", "pytest-cov", "flaky", "ipyparallel"]
+test = ["flaky", "ipyparallel", "pre-commit", "pytest-cov", "pytest-timeout", "pytest (>=6.0)"]
 
 [[package]]
 name = "ipython"
-version = "7.30.1"
+version = "7.34.0"
 description = "IPython: Productive Interactive Computing"
 category = "dev"
 optional = false
@@ -267,48 +256,54 @@ testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<7.0.0)"]
 
 [[package]]
 name = "jupyter-client"
-version = "7.1.0"
+version = "7.3.4"
 description = "Jupyter protocol implementation and client libraries"
 category = "dev"
 optional = false
-python-versions = ">=3.6.1"
+python-versions = ">=3.7"
 
 [package.dependencies]
 entrypoints = "*"
-jupyter-core = ">=4.6.0"
-nest-asyncio = ">=1.5"
-python-dateutil = ">=2.1"
-pyzmq = ">=13"
-tornado = ">=4.1"
+jupyter-core = ">=4.9.2"
+nest-asyncio = ">=1.5.4"
+python-dateutil = ">=2.8.2"
+pyzmq = ">=23.0"
+tornado = ">=6.0"
 traitlets = "*"
 
 [package.extras]
-doc = ["myst-parser", "sphinx (>=1.3.6)", "sphinx-rtd-theme", "sphinxcontrib-github-alt"]
-test = ["codecov", "coverage", "ipykernel", "ipython", "mock", "mypy", "pre-commit", "pytest", "pytest-asyncio", "pytest-cov", "pytest-timeout", "jedi (<0.18)"]
+doc = ["ipykernel", "myst-parser", "sphinx-rtd-theme", "sphinx (>=1.3.6)", "sphinxcontrib-github-alt"]
+test = ["codecov", "coverage", "ipykernel (>=6.5)", "ipython", "mypy", "pre-commit", "pytest", "pytest-asyncio (>=0.18)", "pytest-cov", "pytest-timeout"]
 
 [[package]]
 name = "jupyter-core"
-version = "4.9.1"
+version = "4.11.1"
 description = "Jupyter core package. A base package on which Jupyter projects rely."
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
 pywin32 = {version = ">=1.0", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""}
 traitlets = "*"
 
+[package.extras]
+test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"]
+
 [[package]]
 name = "kiwisolver"
-version = "1.3.2"
+version = "1.4.4"
 description = "A fast implementation of the Cassowary constraint solver"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 
+[package.dependencies]
+typing-extensions = {version = "*", markers = "python_version < \"3.8\""}
+
 [[package]]
 name = "matplotlib"
-version = "3.5.1"
+version = "3.5.2"
 description = "Python plotting package"
 category = "main"
 optional = false
@@ -365,7 +360,7 @@ python-versions = "*"
 
 [[package]]
 name = "nest-asyncio"
-version = "1.5.4"
+version = "1.5.5"
 description = "Patch asyncio to allow nested event loops"
 category = "dev"
 optional = false
@@ -373,7 +368,7 @@ python-versions = ">=3.5"
 
 [[package]]
 name = "numpy"
-version = "1.21.4"
+version = "1.21.6"
 description = "NumPy is the fundamental package for array computing with Python."
 category = "main"
 optional = false
@@ -392,7 +387,7 @@ pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
 
 [[package]]
 name = "pandas"
-version = "1.3.4"
+version = "1.3.5"
 description = "Powerful data structures for data analysis, time series, and statistics"
 category = "main"
 optional = false
@@ -467,12 +462,16 @@ python-versions = "*"
 
 [[package]]
 name = "pillow"
-version = "9.0.0"
+version = "9.2.0"
 description = "Python Imaging Library (Fork)"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 
+[package.extras]
+docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinxext-opengraph"]
+tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
+
 [[package]]
 name = "platformdirs"
 version = "2.5.2"
@@ -502,7 +501,7 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.23"
+version = "3.0.30"
 description = "Library for building powerful interactive command lines in Python"
 category = "dev"
 optional = false
@@ -511,6 +510,17 @@ python-versions = ">=3.6.2"
 [package.dependencies]
 wcwidth = "*"
 
+[[package]]
+name = "psutil"
+version = "5.9.1"
+description = "Cross-platform lib for process and system monitoring in Python."
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+
+[package.extras]
+test = ["ipaddress", "mock", "enum34", "pywin32", "wmi"]
+
 [[package]]
 name = "ptyprocess"
 version = "0.7.0"
@@ -549,22 +559,22 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "pygments"
-version = "2.10.0"
+version = "2.12.0"
 description = "Pygments is a syntax highlighting package written in Python."
 category = "dev"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
 
 [[package]]
 name = "pyparsing"
-version = "3.0.6"
-description = "Python parsing module"
+version = "3.0.9"
+description = "pyparsing module - Classes and methods to define and execute parsing grammars"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.6.8"
 
 [package.extras]
-diagrams = ["jinja2", "railroad-diagrams"]
+diagrams = ["railroad-diagrams", "jinja2"]
 
 [[package]]
 name = "pytest"
@@ -616,7 +626,7 @@ six = ">=1.5"
 
 [[package]]
 name = "pytz"
-version = "2021.3"
+version = "2022.1"
 description = "World timezone definitions, modern and historical"
 category = "main"
 optional = false
@@ -624,7 +634,7 @@ python-versions = "*"
 
 [[package]]
 name = "pywin32"
-version = "302"
+version = "304"
 description = "Python for Window Extensions"
 category = "dev"
 optional = false
@@ -632,7 +642,7 @@ python-versions = "*"
 
 [[package]]
 name = "pyzmq"
-version = "22.3.0"
+version = "23.2.0"
 description = "Python bindings for 0MQ"
 category = "dev"
 optional = false
@@ -655,18 +665,21 @@ numpy = ">=1.16.5,<1.23.0"
 
 [[package]]
 name = "setuptools-scm"
-version = "6.3.2"
+version = "7.0.5"
 description = "the blessed package to manage your versions by scm tags"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
+importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
 packaging = ">=20.0"
 tomli = ">=1.0.0"
+typing-extensions = "*"
 
 [package.extras]
-toml = ["setuptools (>=42)", "tomli (>=1.0.0)"]
+test = ["pytest (>=6.2)", "virtualenv (>20)"]
+toml = ["setuptools (>=42)"]
 
 [[package]]
 name = "six"
@@ -678,7 +691,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 
 [[package]]
 name = "statsmodels"
-version = "0.13.1"
+version = "0.13.2"
 description = "Statistical computations and models for Python"
 category = "dev"
 optional = false
@@ -686,13 +699,14 @@ python-versions = ">=3.7"
 
 [package.dependencies]
 numpy = ">=1.17"
+packaging = ">=21.3"
 pandas = ">=0.25"
 patsy = ">=0.5.2"
 scipy = ">=1.3"
 
 [package.extras]
-build = ["cython (>=0.29.22)"]
-develop = ["cython (>=0.29.22)"]
+build = ["cython (>=0.29.26)"]
+develop = ["cython (>=0.29.26)"]
 docs = ["sphinx", "nbconvert", "jupyter-client", "ipykernel", "matplotlib", "nbformat", "numpydoc", "pandas-datareader"]
 
 [[package]]
@@ -705,7 +719,7 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 
 [[package]]
 name = "tomli"
-version = "2.0.0"
+version = "2.0.1"
 description = "A lil' TOML parser"
 category = "main"
 optional = false
@@ -713,22 +727,22 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "tornado"
-version = "6.1"
+version = "6.2"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
 category = "dev"
 optional = false
-python-versions = ">= 3.5"
+python-versions = ">= 3.7"
 
 [[package]]
 name = "traitlets"
-version = "5.1.1"
-description = "Traitlets Python configuration system"
+version = "5.3.0"
+description = ""
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-test = ["pytest"]
+test = ["pre-commit", "pytest"]
 
 [[package]]
 name = "typed-ast"
@@ -740,11 +754,11 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "typing-extensions"
-version = "4.0.1"
-description = "Backported and Experimental Type Hints for Python 3.6+"
-category = "dev"
+version = "4.3.0"
+description = "Backported and Experimental Type Hints for Python 3.7+"
+category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [[package]]
 name = "wcwidth"
@@ -756,15 +770,15 @@ python-versions = "*"
 
 [[package]]
 name = "zipp"
-version = "3.6.0"
+version = "3.8.1"
 description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "dev"
+category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [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)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
+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)"]
 
 [metadata]
 lock-version = "1.1"
@@ -773,234 +787,55 @@ content-hash = "dd38df5ac3590b7dec6d1024e7593e8e1557d82511b31e77826bff1123db2518
 
 [metadata.files]
 appnope = [
-    {file = "appnope-0.1.2-py2.py3-none-any.whl", hash = "sha256:93aa393e9d6c54c5cd570ccadd8edad61ea0c4b9ea7a01409020c9aa019eb442"},
-    {file = "appnope-0.1.2.tar.gz", hash = "sha256:dd83cd4b5b460958838f6eb3000c660b1f9caf2a5b1de4264e941512f603258a"},
-]
-argcomplete = [
-    {file = "argcomplete-1.12.3-py2.py3-none-any.whl", hash = "sha256:291f0beca7fd49ce285d2f10e4c1c77e9460cf823eef2de54df0c0fec88b0d81"},
-    {file = "argcomplete-1.12.3.tar.gz", hash = "sha256:2c7dbffd8c045ea534921e63b0be6fe65e88599990d8dc408ac8c542b72a5445"},
-]
-atomicwrites = [
-    {file = "atomicwrites-1.4.0-py2.py3-none-any.whl", hash = "sha256:6d1784dea7c0c8d4a5172b6c620f40b6e4cbfdf96d783691f2e1302a7b88e197"},
-    {file = "atomicwrites-1.4.0.tar.gz", hash = "sha256:ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a"},
+    {file = "appnope-0.1.3-py2.py3-none-any.whl", hash = "sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e"},
+    {file = "appnope-0.1.3.tar.gz", hash = "sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24"},
 ]
+atomicwrites = []
 attrs = [
-    {file = "attrs-21.2.0-py2.py3-none-any.whl", hash = "sha256:149e90d6d8ac20db7a955ad60cf0e6881a3f20d37096140088356da6c716b0b1"},
-    {file = "attrs-21.2.0.tar.gz", hash = "sha256:ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb"},
+    {file = "attrs-21.4.0-py2.py3-none-any.whl", hash = "sha256:2d27e3784d7a565d36ab851fe94887c5eccd6a463168875832a1be79c82828b4"},
+    {file = "attrs-21.4.0.tar.gz", hash = "sha256:626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd"},
 ]
 backcall = [
     {file = "backcall-0.2.0-py2.py3-none-any.whl", hash = "sha256:fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255"},
     {file = "backcall-0.2.0.tar.gz", hash = "sha256:5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e"},
 ]
 black = []
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Test patch:
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
index 1f87b94..a49278c 100644
--- a/.github/workflows/run_tests.yml
+++ b/.github/workflows/run_tests.yml
@@ -1,6 +1,6 @@
 name: Run tests
 
-on: [push, pull_request]
+on: pull_request
 
 jobs: