From 7a401495f47b788054da8c72edfbc04decdf2d31 Mon Sep 17 00:00:00 2001
From: moshi <sy.41211@gmail.com>
Date: Sat, 26 Aug 2023 16:31:19 +0900
Subject: [PATCH 01/11] Replace linter `flake8` to `ruff`

---
 pyproject.toml | 31 +++++++++++++++++++++++++------
 1 file changed, 25 insertions(+), 6 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 9fd1c3f..36f44bd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -26,6 +26,26 @@ minversion = "6.0"
 addopts = "--cov=src --tb=line --cov-report=xml --cov-report=term"
 testpaths = ["tests"]
 
+# Lint Rules: https://beta.ruff.rs/docs/rules
+[tool.ruff]
+select = ["E", "F", "W", "I", "D", "B"]
+ignore = [
+    "D100",
+    "D101",
+    "D104",
+    "D105",
+    "D205",
+    "D400",
+    "D403",
+    "D415",
+    "B905",
+]
+src = ["src", "tests"]
+line-length = 88
+
+[tool.ruff.pydocstyle]
+convention = "numpy"
+
 [tool.poetry.scripts]
 pymsaviz = "pymsaviz.scripts.cli:main"
 
@@ -34,15 +54,14 @@ python = "^3.8"
 biopython = ">=1.79"
 matplotlib = ">=3.5.2"
 
-[tool.poetry.dev-dependencies]
-flake8 = ">=4.0.1"
+[tool.poetry.group.dev.dependencies]
+pytest = ">=7.1.2"
 black = ">=22.10.0"
-pydocstyle = ">=6.1.1"
-pytest = ">=7.2.0"
+ruff = ">=0.0.264"
 pytest-cov = ">=4.0.0"
-ipykernel = ">=6.16.0"
+ipykernel = ">=6.13.0"
 mkdocs = ">=1.2"
-mkdocstrings = {version = ">=0.19.0", extras = ["python"]}
+mkdocstrings = { extras = ["python"], version = ">=0.19.0" }
 mkdocs-jupyter = ">=0.21.0"
 mkdocs-material = ">=8.2"
 

From 3b344f4b3a91934e700a3582053d3ccf20addc91 Mon Sep 17 00:00:00 2001
From: moshi <sy.41211@gmail.com>
Date: Sat, 26 Aug 2023 16:31:44 +0900
Subject: [PATCH 02/11] Update lock dependencies

---
 poetry.lock | 2582 ++++++++++++++++++++++++++++-----------------------
 1 file changed, 1441 insertions(+), 1141 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 76ed174..6752a5f 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -32,22 +32,37 @@ test = ["astroid", "pytest"]
 
 [[package]]
 name = "attrs"
-version = "22.2.0"
+version = "23.1.0"
 description = "Classes Without Boilerplate"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "attrs-22.2.0-py3-none-any.whl", hash = "sha256:29e95c7f6778868dbd49170f98f8818f78f3dc5e0e37c0b1f474e3561b240836"},
-    {file = "attrs-22.2.0.tar.gz", hash = "sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99"},
+    {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"},
+    {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"},
 ]
 
 [package.extras]
-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", "cloudpickle", "hypothesis", "hypothesis", "mypy (>=0.971,<0.990)", "mypy (>=0.971,<0.990)", "pympler", "pympler", "pytest (>=4.3.0)", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-mypy-plugins", "pytest-xdist[psutil]", "pytest-xdist[psutil]"]
+cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
+dev = ["attrs[docs,tests]", "pre-commit"]
+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 (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+
+[[package]]
+name = "babel"
+version = "2.12.1"
+description = "Internationalization utilities"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"},
+    {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"},
+]
+
+[package.dependencies]
+pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
 
 [[package]]
 name = "backcall"
@@ -63,14 +78,14 @@ files = [
 
 [[package]]
 name = "beautifulsoup4"
-version = "4.11.2"
+version = "4.12.2"
 description = "Screen-scraping library"
 category = "dev"
 optional = false
 python-versions = ">=3.6.0"
 files = [
-    {file = "beautifulsoup4-4.11.2-py3-none-any.whl", hash = "sha256:0e79446b10b3ecb499c1556f7e228a53e64a2bfcebd455f370d8927cb5b59e39"},
-    {file = "beautifulsoup4-4.11.2.tar.gz", hash = "sha256:bc4bdda6717de5a2987436fb8d72f45dc90dd856bdfd512a1314ce90349a0106"},
+    {file = "beautifulsoup4-4.12.2-py3-none-any.whl", hash = "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"},
+    {file = "beautifulsoup4-4.12.2.tar.gz", hash = "sha256:492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da"},
 ]
 
 [package.dependencies]
@@ -119,37 +134,34 @@ numpy = "*"
 
 [[package]]
 name = "black"
-version = "23.1.0"
+version = "23.7.0"
 description = "The uncompromising code formatter."
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "black-23.7.0.tar.gz", hash = "sha256:022a582720b0d9480ed82576c920a8c1dde97cc38ff11d8d8859b3bd6ca9eedb"},
 ]
 
 [package.dependencies]
@@ -188,14 +200,14 @@ css = ["tinycss2 (>=1.1.0,<1.2)"]
 
 [[package]]
 name = "certifi"
-version = "2022.12.7"
+version = "2023.7.22"
 description = "Python package for providing Mozilla's CA Bundle."
 category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2022.12.7-py3-none-any.whl", hash = "sha256:4ad3232f5e926d6718ec31cfc1fcadfde020920e278684144551c91769c7bc18"},
-    {file = "certifi-2022.12.7.tar.gz", hash = "sha256:35824b4c3a97115964b408844d64aa14db1cc518f6562e8d7261699d1350a9e3"},
+    {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"},
+    {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"},
 ]
 
 [[package]]
@@ -277,112 +289,99 @@ pycparser = "*"
 
 [[package]]
 name = "charset-normalizer"
-version = "3.0.1"
+version = "3.2.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7.0"
 files = [
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 name = "click"
-version = "8.1.3"
+version = "8.1.7"
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 category = "dev"
 optional = false
 python-versions = ">=3.7"
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 [package.dependencies]
@@ -402,156 +401,143 @@ files = [
 
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+version = "0.1.4"
 description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc."
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 ]
 
 [package.dependencies]
-traitlets = ">=5.3"
+traitlets = ">=4"
 
 [package.extras]
+lint = ["black (>=22.6.0)", "mdformat (>0.7)", "mdformat-gfm (>=0.3.5)", "ruff (>=0.0.156)"]
 test = ["pytest"]
+typing = ["mypy (>=0.990)"]
 
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@@ -667,50 +654,65 @@ tests = ["asttokens", "littleutils", "pytest", "rich"]
 
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 python-versions = "*"
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 [package.extras]
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 graphite = ["lz4 (>=1.7.4.2)"]
 interpolatable = ["munkres", "scipy"]
 lxml = ["lxml (>=4.0,<5)"]
@@ -720,7 +722,7 @@ repacker = ["uharfbuzz (>=0.23.0)"]
 symfont = ["sympy"]
 type1 = ["xattr"]
 ufo = ["fs (>=2.2.0,<3)"]
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+unicode = ["unicodedata2 (>=15.0.0)"]
 woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
 
 [[package]]
@@ -743,22 +745,19 @@ dev = ["flake8", "markdown", "twine", "wheel"]
 
 [[package]]
 name = "griffe"
-version = "0.25.5"
+version = "0.35.0"
 description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "griffe-0.25.5-py3-none-any.whl", hash = "sha256:1fb9edff48e66d4873014a2ebf21aca5f271d0006a4c937826e3cf592ffb3706"},
-    {file = "griffe-0.25.5.tar.gz", hash = "sha256:11ea3403ef0560a1cbcf7f302eb5d21cf4c1d8ed3f8a16a75aa9f6f458caf3f1"},
+    {file = "griffe-0.35.0-py3-none-any.whl", hash = "sha256:52b1dc86dfca6db5877d65a07997f8363f61f14266064cf1cae41b70aac9f395"},
+    {file = "griffe-0.35.0.tar.gz", hash = "sha256:d313f102da3d155fe0a3d284acb0fc93059ee6788903a2e983eb4f64a713fac1"},
 ]
 
 [package.dependencies]
 colorama = ">=0.4"
 
-[package.extras]
-async = ["aiofiles (>=0.7,<1.0)"]
-
 [[package]]
 name = "idna"
 version = "3.4"
@@ -773,14 +772,14 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "6.0.0"
+version = "6.8.0"
 description = "Read metadata from Python packages"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "importlib_metadata-6.0.0-py3-none-any.whl", hash = "sha256:7efb448ec9a5e313a57655d35aa54cd3e01b7e1fbcf72dce1bf06119420f5bad"},
-    {file = "importlib_metadata-6.0.0.tar.gz", hash = "sha256:e354bedeb60efa6affdcc8ae121b73544a7aa74156d047311948f6d711cd378d"},
+    {file = "importlib_metadata-6.8.0-py3-none-any.whl", hash = "sha256:3ebb78df84a805d7698245025b975d9d67053cd94c79245ba4b3eb694abe68bb"},
+    {file = "importlib_metadata-6.8.0.tar.gz", hash = "sha256:dbace7892d8c0c4ac1ad096662232f831d4e64f4c4545bd53016a3e9d4654743"},
 ]
 
 [package.dependencies]
@@ -789,26 +788,26 @@ zipp = ">=0.5"
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
-testing = ["flake8 (<5)", "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)"]
+testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)", "pytest-ruff"]
 
 [[package]]
 name = "importlib-resources"
-version = "5.12.0"
+version = "6.0.1"
 description = "Read resources from Python packages"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "importlib_resources-5.12.0-py3-none-any.whl", hash = "sha256:7b1deeebbf351c7578e09bf2f63fa2ce8b5ffec296e0d349139d43cca061a81a"},
-    {file = "importlib_resources-5.12.0.tar.gz", hash = "sha256:4be82589bf5c1d7999aedf2a45159d10cb3ca4f19b2271f8792bc8e6da7b22f6"},
+    {file = "importlib_resources-6.0.1-py3-none-any.whl", hash = "sha256:134832a506243891221b88b4ae1213327eea96ceb4e407a00d790bb0626f45cf"},
+    {file = "importlib_resources-6.0.1.tar.gz", hash = "sha256:4359457e42708462b9626a04657c6208ad799ceb41e5c58c57ffa0e6a098a5d4"},
 ]
 
 [package.dependencies]
 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)", "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)"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
 
 [[package]]
 name = "iniconfig"
@@ -824,14 +823,14 @@ files = [
 
 [[package]]
 name = "ipykernel"
-version = "6.21.2"
+version = "6.25.1"
 description = "IPython Kernel for Jupyter"
 category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "ipykernel-6.21.2-py3-none-any.whl", hash = "sha256:430d00549b6aaf49bd0f5393150691edb1815afa62d457ee6b1a66b25cb17874"},
-    {file = "ipykernel-6.21.2.tar.gz", hash = "sha256:6e9213484e4ce1fb14267ee435e18f23cc3a0634e635b9fb4ed4677b84e0fdf8"},
+    {file = "ipykernel-6.25.1-py3-none-any.whl", hash = "sha256:c8a2430b357073b37c76c21c52184db42f6b4b0e438e1eb7df3c4440d120497c"},
+    {file = "ipykernel-6.25.1.tar.gz", hash = "sha256:050391364c0977e768e354bdb60cbbfbee7cbb943b1af1618382021136ffd42f"},
 ]
 
 [package.dependencies]
@@ -858,14 +857,14 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio"
 
 [[package]]
 name = "ipython"
-version = "8.10.0"
+version = "8.12.2"
 description = "IPython: Productive Interactive Computing"
 category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "ipython-8.10.0-py3-none-any.whl", hash = "sha256:b38c31e8fc7eff642fc7c597061fff462537cf2314e3225a19c906b7b0d8a345"},
-    {file = "ipython-8.10.0.tar.gz", hash = "sha256:b13a1d6c1f5818bd388db53b7107d17454129a70de2b87481d555daede5eb49e"},
+    {file = "ipython-8.12.2-py3-none-any.whl", hash = "sha256:ea8801f15dfe4ffb76dea1b09b847430ffd70d827b41735c64a0638a04103bfc"},
+    {file = "ipython-8.12.2.tar.gz", hash = "sha256:c7b80eb7f5a855a88efc971fda506ff7a91c280b42cdae26643e0f601ea281ea"},
 ]
 
 [package.dependencies]
@@ -877,10 +876,11 @@ jedi = ">=0.16"
 matplotlib-inline = "*"
 pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""}
 pickleshare = "*"
-prompt-toolkit = ">=3.0.30,<3.1.0"
+prompt-toolkit = ">=3.0.30,<3.0.37 || >3.0.37,<3.1.0"
 pygments = ">=2.4.0"
 stack-data = "*"
 traitlets = ">=5"
+typing-extensions = {version = "*", markers = "python_version < \"3.10\""}
 
 [package.extras]
 all = ["black", "curio", "docrepr", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.21)", "pandas", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"]
@@ -897,22 +897,22 @@ test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pa
 
 [[package]]
 name = "jedi"
-version = "0.18.2"
+version = "0.19.0"
 description = "An autocompletion tool for Python that can be used for text editors."
 category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "jedi-0.18.2-py2.py3-none-any.whl", hash = "sha256:203c1fd9d969ab8f2119ec0a3342e0b49910045abe6af0a3ae83a5764d54639e"},
-    {file = "jedi-0.18.2.tar.gz", hash = "sha256:bae794c30d07f6d910d32a7048af09b5a39ed740918da923c6b780790ebac612"},
+    {file = "jedi-0.19.0-py2.py3-none-any.whl", hash = "sha256:cb8ce23fbccff0025e9386b5cf85e892f94c9b822378f8da49970471335ac64e"},
+    {file = "jedi-0.19.0.tar.gz", hash = "sha256:bcf9894f1753969cbac8022a8c2eaee06bfa3724e4192470aaffe7eb6272b0c4"},
 ]
 
 [package.dependencies]
-parso = ">=0.8.0,<0.9.0"
+parso = ">=0.8.3,<0.9.0"
 
 [package.extras]
 docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alabaster (==0.7.12)", "babel (==2.9.1)", "chardet (==4.0.0)", "commonmark (==0.8.1)", "docutils (==0.17.1)", "future (==0.18.2)", "idna (==2.10)", "imagesize (==1.2.0)", "mock (==1.0.1)", "packaging (==20.9)", "pyparsing (==2.4.7)", "pytz (==2021.1)", "readthedocs-sphinx-ext (==2.1.4)", "recommonmark (==0.5.0)", "requests (==2.25.1)", "six (==1.15.0)", "snowballstemmer (==2.1.0)", "sphinx (==1.8.5)", "sphinx-rtd-theme (==0.4.3)", "sphinxcontrib-serializinghtml (==1.1.4)", "sphinxcontrib-websupport (==1.2.4)", "urllib3 (==1.26.4)"]
-qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
+qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
 testing = ["Django (<3.1)", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
 
 [[package]]
@@ -935,36 +935,54 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "jsonschema"
-version = "4.17.3"
+version = "4.19.0"
 description = "An implementation of JSON Schema validation for Python"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "jsonschema-4.17.3-py3-none-any.whl", hash = "sha256:a870ad254da1a8ca84b6a2905cac29d265f805acc57af304784962a2aa6508f6"},
-    {file = "jsonschema-4.17.3.tar.gz", hash = "sha256:0f864437ab8b6076ba6707453ef8f98a6a0d512a80e93f8abdb676f737ecb60d"},
+    {file = "jsonschema-4.19.0-py3-none-any.whl", hash = "sha256:043dc26a3845ff09d20e4420d6012a9c91c9aa8999fa184e7efcfeccb41e32cb"},
+    {file = "jsonschema-4.19.0.tar.gz", hash = "sha256:6e1e7569ac13be8139b2dd2c21a55d350066ee3f80df06c608b398cdc6f30e8f"},
 ]
 
 [package.dependencies]
-attrs = ">=17.4.0"
+attrs = ">=22.2.0"
 importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
+jsonschema-specifications = ">=2023.03.6"
 pkgutil-resolve-name = {version = ">=1.3.10", markers = "python_version < \"3.9\""}
-pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2"
+referencing = ">=0.28.4"
+rpds-py = ">=0.7.1"
 
 [package.extras]
 format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
 format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
 
+[[package]]
+name = "jsonschema-specifications"
+version = "2023.7.1"
+description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
+category = "dev"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "jsonschema_specifications-2023.7.1-py3-none-any.whl", hash = "sha256:05adf340b659828a004220a9613be00fa3f223f2b82002e273dee62fd50524b1"},
+    {file = "jsonschema_specifications-2023.7.1.tar.gz", hash = "sha256:c91a50404e88a1f6ba40636778e2ee08f6e24c5613fe4c53ac24578a5a7f72bb"},
+]
+
+[package.dependencies]
+importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
+referencing = ">=0.28.0"
+
 [[package]]
 name = "jupyter-client"
-version = "8.0.3"
+version = "8.3.0"
 description = "Jupyter protocol implementation and client libraries"
 category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_client-8.0.3-py3-none-any.whl", hash = "sha256:be48ac6bd659cbbddb7a674cf06b3b8afbf53f228253cf58bde604c03bd487b0"},
-    {file = "jupyter_client-8.0.3.tar.gz", hash = "sha256:ed65498bea6d876ef9d8da3e0db3dd33c5d129f5b2645f56ae03993782966bd0"},
+    {file = "jupyter_client-8.3.0-py3-none-any.whl", hash = "sha256:7441af0c0672edc5d28035e92ba5e32fadcfa8a4e608a434c228836a89df6158"},
+    {file = "jupyter_client-8.3.0.tar.gz", hash = "sha256:3af69921fe99617be1670399a0b857ad67275eefcfa291e2c81a160b7b650f5f"},
 ]
 
 [package.dependencies]
@@ -977,23 +995,23 @@ traitlets = ">=5.3"
 
 [package.extras]
 docs = ["ipykernel", "myst-parser", "pydata-sphinx-theme", "sphinx (>=4)", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"]
-test = ["codecov", "coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pytest", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"]
+test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pytest", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"]
 
 [[package]]
 name = "jupyter-core"
-version = "5.2.0"
+version = "5.3.1"
 description = "Jupyter core package. A base package on which Jupyter projects rely."
 category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_core-5.2.0-py3-none-any.whl", hash = "sha256:4bdc2928c37f6917130c667d8b8708f20aee539d8283c6be72aabd2a4b4c83b0"},
-    {file = "jupyter_core-5.2.0.tar.gz", hash = "sha256:1407cdb4c79ee467696c04b76633fc1884015fa109323365a6372c8e890cc83f"},
+    {file = "jupyter_core-5.3.1-py3-none-any.whl", hash = "sha256:ae9036db959a71ec1cac33081eeb040a79e681f08ab68b0883e9a676c7a90dce"},
+    {file = "jupyter_core-5.3.1.tar.gz", hash = "sha256:5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba"},
 ]
 
 [package.dependencies]
 platformdirs = ">=2.5"
-pywin32 = {version = ">=1.0", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""}
+pywin32 = {version = ">=300", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""}
 traitlets = ">=5.3"
 
 [package.extras]
@@ -1014,18 +1032,18 @@ files = [
 
 [[package]]
 name = "jupytext"
-version = "1.14.4"
+version = "1.15.0"
 description = "Jupyter notebooks as Markdown documents, Julia, Python or R scripts"
 category = "dev"
 optional = false
 python-versions = "~=3.6"
 files = [
-    {file = "jupytext-1.14.4-py3-none-any.whl", hash = "sha256:c5f5647112aa4ea4c61c31e48a216a4c49d315a0fc43d4f483529ed3b0b1a0d9"},
-    {file = "jupytext-1.14.4.tar.gz", hash = "sha256:4c09f1b8f837888dec11c1253e813b5cacdc20eecefcf2f9a0b870ae6bd44a65"},
+    {file = "jupytext-1.15.0-py3-none-any.whl", hash = "sha256:7bb7cf4c0a91f5b1591f7558fa3a6494ac6ccf9810d1aa58565d4d9a2675a4a1"},
+    {file = "jupytext-1.15.0.tar.gz", hash = "sha256:290c0a04b0a0a341d7ca87a2992cf407eb83898873baddf0bc48039a5e301ff8"},
 ]
 
 [package.dependencies]
-markdown-it-py = ">=1.0.0,<3.0.0"
+markdown-it-py = ">=1.0.0"
 mdit-py-plugins = "*"
 nbformat = "*"
 pyyaml = "*"
@@ -1037,203 +1055,255 @@ toml = ["toml"]
 
 [[package]]
 name = "kiwisolver"
-version = "1.4.4"
+version = "1.4.5"
 description = "A fast implementation of the Cassowary constraint solver"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "kiwisolver-1.4.4-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:2f5e60fabb7343a836360c4f0919b8cd0d6dbf08ad2ca6b9cf90bf0c76a3c4f6"},
-    {file = "kiwisolver-1.4.4-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:10ee06759482c78bdb864f4109886dff7b8a56529bc1609d4f1112b93fe6423c"},
-    {file = "kiwisolver-1.4.4-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:c79ebe8f3676a4c6630fd3f777f3cfecf9289666c84e775a67d1d358578dc2e3"},
-    {file = "kiwisolver-1.4.4-cp310-cp310-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:abbe9fa13da955feb8202e215c4018f4bb57469b1b78c7a4c5c7b93001699938"},
-    {file = "kiwisolver-1.4.4-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:7577c1987baa3adc4b3c62c33bd1118c3ef5c8ddef36f0f2c950ae0b199e100d"},
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-    {file = "kiwisolver-1.4.4-cp310-cp310-win_amd64.whl", hash = "sha256:3fe20f63c9ecee44560d0e7f116b3a747a5d7203376abeea292ab3152334d004"},
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 [package.extras]
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 html5 = ["html5lib"]
 htmlsoup = ["BeautifulSoup4"]
-source = ["Cython (>=0.29.7)"]
+source = ["Cython (>=0.29.35)"]
 
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 ]
 
 [package.dependencies]
 importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
 
 [package.extras]
+docs = ["mdx-gh-links (>=0.2)", "mkdocs (>=1.0)", "mkdocs-nature (>=0.4)"]
 testing = ["coverage", "pyyaml"]
 
 [[package]]
 name = "markdown-it-py"
-version = "2.2.0"
+version = "3.0.0"
 description = "Python port of markdown-it. Markdown parsing, done right!"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 [package.dependencies]
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 linkify = ["linkify-it-py (>=1,<3)"]
 plugins = ["mdit-py-plugins"]
 profiling = ["gprof2dot"]
-rtd = ["attrs", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
+rtd = ["jupyter_sphinx", "mdit-py-plugins", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
 testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
+[[package]]
+name = "markdown2"
+version = "2.4.10"
+description = "A fast and complete Python implementation of Markdown"
+category = "dev"
+optional = false
+python-versions = ">=3.5, <4"
+files = [
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+
+[package.extras]
+all = ["pygments (>=2.7.3)", "wavedrom"]
+code-syntax-highlighting = ["pygments (>=2.7.3)"]
+wavedrom = ["wavedrom"]
+
 [[package]]
 name = "markupsafe"
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+version = "2.1.3"
 description = "Safely add untrusted strings to HTML/XML markup."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
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 ]
 
 [package.dependencies]
@@ -1369,7 +1456,7 @@ kiwisolver = ">=1.0.1"
 numpy = ">=1.20"
 packaging = ">=20.0"
 pillow = ">=6.2.0"
-pyparsing = ">=2.3.1"
+pyparsing = ">=2.3.1,<3.1"
 python-dateutil = ">=2.7"
 
 [[package]]
@@ -1387,36 +1474,24 @@ files = [
 [package.dependencies]
 traitlets = "*"
 
-[[package]]
-name = "mccabe"
-version = "0.7.0"
-description = "McCabe checker, plugin for flake8"
-category = "dev"
-optional = false
-python-versions = ">=3.6"
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-]
-
 [[package]]
 name = "mdit-py-plugins"
-version = "0.3.4"
+version = "0.4.0"
 description = "Collection of plugins for markdown-it-py"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
-markdown-it-py = ">=1.0.0,<3.0.0"
+markdown-it-py = ">=1.0.0,<4.0.0"
 
 [package.extras]
 code-style = ["pre-commit"]
-rtd = ["attrs", "myst-parser (>=0.16.1,<0.17.0)", "sphinx-book-theme (>=0.1.0,<0.2.0)"]
+rtd = ["myst-parser", "sphinx-book-theme"]
 testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
 [[package]]
@@ -1445,26 +1520,26 @@ files = [
 
 [[package]]
 name = "mistune"
-version = "0.8.4"
-description = "The fastest markdown parser in pure Python"
+version = "3.0.1"
+description = "A sane and fast Markdown parser with useful plugins and renderers"
 category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7"
 files = [
-    {file = "mistune-0.8.4-py2.py3-none-any.whl", hash = "sha256:88a1051873018da288eee8538d476dffe1262495144b33ecb586c4ab266bb8d4"},
-    {file = "mistune-0.8.4.tar.gz", hash = "sha256:59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e"},
+    {file = "mistune-3.0.1-py3-none-any.whl", hash = "sha256:b9b3e438efbb57c62b5beb5e134dab664800bdf1284a7ee09e8b12b13eb1aac6"},
+    {file = "mistune-3.0.1.tar.gz", hash = "sha256:e912116c13aa0944f9dc530db38eb88f6a77087ab128f49f84a48f4c05ea163c"},
 ]
 
 [[package]]
 name = "mkdocs"
-version = "1.4.2"
+version = "1.5.2"
 description = "Project documentation with Markdown."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "mkdocs-1.4.2-py3-none-any.whl", hash = "sha256:c8856a832c1e56702577023cd64cc5f84948280c1c0fcc6af4cd39006ea6aa8c"},
-    {file = "mkdocs-1.4.2.tar.gz", hash = "sha256:8947af423a6d0facf41ea1195b8e1e8c85ad94ac95ae307fe11232e0424b11c5"},
+    {file = "mkdocs-1.5.2-py3-none-any.whl", hash = "sha256:60a62538519c2e96fe8426654a67ee177350451616118a41596ae7c876bb7eac"},
+    {file = "mkdocs-1.5.2.tar.gz", hash = "sha256:70d0da09c26cff288852471be03c23f0f521fc15cf16ac89c7a3bfb9ae8d24f9"},
 ]
 
 [package.dependencies]
@@ -1473,27 +1548,30 @@ colorama = {version = ">=0.4", markers = "platform_system == \"Windows\""}
 ghp-import = ">=1.0"
 importlib-metadata = {version = ">=4.3", markers = "python_version < \"3.10\""}
 jinja2 = ">=2.11.1"
-markdown = ">=3.2.1,<3.4"
+markdown = ">=3.2.1"
+markupsafe = ">=2.0.1"
 mergedeep = ">=1.3.4"
 packaging = ">=20.5"
+pathspec = ">=0.11.1"
+platformdirs = ">=2.2.0"
 pyyaml = ">=5.1"
 pyyaml-env-tag = ">=0.1"
 watchdog = ">=2.0"
 
 [package.extras]
 i18n = ["babel (>=2.9.0)"]
-min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-import (==1.0)", "importlib-metadata (==4.3)", "jinja2 (==2.11.1)", "markdown (==3.2.1)", "markupsafe (==2.0.1)", "mergedeep (==1.3.4)", "packaging (==20.5)", "pyyaml (==5.1)", "pyyaml-env-tag (==0.1)", "typing-extensions (==3.10)", "watchdog (==2.0)"]
+min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-import (==1.0)", "importlib-metadata (==4.3)", "jinja2 (==2.11.1)", "markdown (==3.2.1)", "markupsafe (==2.0.1)", "mergedeep (==1.3.4)", "packaging (==20.5)", "pathspec (==0.11.1)", "platformdirs (==2.2.0)", "pyyaml (==5.1)", "pyyaml-env-tag (==0.1)", "typing-extensions (==3.10)", "watchdog (==2.0)"]
 
 [[package]]
 name = "mkdocs-autorefs"
-version = "0.4.1"
+version = "0.5.0"
 description = "Automatically link across pages in MkDocs."
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "mkdocs-autorefs-0.4.1.tar.gz", hash = "sha256:70748a7bd025f9ecd6d6feeba8ba63f8e891a1af55f48e366d6d6e78493aba84"},
-    {file = "mkdocs_autorefs-0.4.1-py3-none-any.whl", hash = "sha256:a2248a9501b29dc0cc8ba4c09f4f47ff121945f6ce33d760f145d6f89d313f5b"},
+    {file = "mkdocs_autorefs-0.5.0-py3-none-any.whl", hash = "sha256:7930fcb8ac1249f10e683967aeaddc0af49d90702af111a5e390e8b20b3d97ff"},
+    {file = "mkdocs_autorefs-0.5.0.tar.gz", hash = "sha256:9a5054a94c08d28855cfab967ada10ed5be76e2bfad642302a610b252c3274c0"},
 ]
 
 [package.dependencies]
@@ -1502,41 +1580,52 @@ mkdocs = ">=1.1"
 
 [[package]]
 name = "mkdocs-jupyter"
-version = "0.22.0"
+version = "0.24.2"
 description = "Use Jupyter in mkdocs websites"
 category = "dev"
 optional = false
-python-versions = ">=3.7.1,<4"
+python-versions = ">=3.7"
 files = [
-    {file = "mkdocs-jupyter-0.22.0.tar.gz", hash = "sha256:585cc69bea4cb9faf6898131978dc9a9b225091ed4b6084f5ab65652a5e12185"},
+    {file = "mkdocs_jupyter-0.24.2-py3-none-any.whl", hash = "sha256:5295a34b1d0bd0a7688a857323eaf0319d83c8a14179b2651709b8ced6eae7db"},
+    {file = "mkdocs_jupyter-0.24.2.tar.gz", hash = "sha256:5e0c109d535d48797230719b6941f4d08de95a7a3c95bf158662c412fc15cb2e"},
 ]
 
 [package.dependencies]
-jupytext = ">=1.13.8,<2.0.0"
-mkdocs = ">=1.2.3,<2.0.0"
-mkdocs-material = ">=8.0.0,<9.0.0"
-nbconvert = ">=6.2.0,<7.0.0"
-Pygments = ">=2.12.0,<3.0.0"
+ipykernel = ">6.0.0,<7.0.0"
+jupytext = ">1.13.8,<2"
+mkdocs = ">=1.4.0,<2"
+mkdocs-material = ">9.0.0"
+nbconvert = ">=7.2.9,<8"
+pygments = ">2.12.0"
+
+[package.extras]
+test = ["coverage[toml]", "pymdown-extensions", "pytest", "pytest-cov"]
 
 [[package]]
 name = "mkdocs-material"
-version = "8.5.11"
+version = "9.2.3"
 description = "Documentation that simply works"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "mkdocs_material-8.5.11-py3-none-any.whl", hash = "sha256:c907b4b052240a5778074a30a78f31a1f8ff82d7012356dc26898b97559f082e"},
-    {file = "mkdocs_material-8.5.11.tar.gz", hash = "sha256:b0ea0513fd8cab323e8a825d6692ea07fa83e917bb5db042e523afecc7064ab7"},
+    {file = "mkdocs_material-9.2.3-py3-none-any.whl", hash = "sha256:1cbac871826bbe0b5a42d7a86cfe729e03cef60cbd4d7425c640115bf1936360"},
+    {file = "mkdocs_material-9.2.3.tar.gz", hash = "sha256:7a8c5638e28cb1c0a0c7596dd85835c461a73637ce8640ea9302dbc674c2aa29"},
 ]
 
 [package.dependencies]
-jinja2 = ">=3.0.2"
+babel = ">=2.10.3"
+colorama = ">=0.4"
+jinja2 = ">=3.0"
+lxml = ">=4.6"
 markdown = ">=3.2"
-mkdocs = ">=1.4.0"
+mkdocs = ">=1.5.2"
 mkdocs-material-extensions = ">=1.1"
-pygments = ">=2.12"
-pymdown-extensions = ">=9.4"
+paginate = ">=0.5.6"
+pygments = ">=2.14"
+pymdown-extensions = ">=9.9.1"
+readtime = ">=2.0"
+regex = ">=2022.4.24"
 requests = ">=2.26"
 
 [[package]]
@@ -1553,17 +1642,18 @@ files = [
 
 [[package]]
 name = "mkdocstrings"
-version = "0.20.0"
+version = "0.22.0"
 description = "Automatic documentation from sources, for MkDocs."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "mkdocstrings-0.20.0-py3-none-any.whl", hash = "sha256:f17fc2c4f760ec302b069075ef9e31045aa6372ca91d2f35ded3adba8e25a472"},
-    {file = "mkdocstrings-0.20.0.tar.gz", hash = "sha256:c757f4f646d4f939491d6bc9256bfe33e36c5f8026392f49eaa351d241c838e5"},
+    {file = "mkdocstrings-0.22.0-py3-none-any.whl", hash = "sha256:2d4095d461554ff6a778fdabdca3c00c468c2f1459d469f7a7f622a2b23212ba"},
+    {file = "mkdocstrings-0.22.0.tar.gz", hash = "sha256:82a33b94150ebb3d4b5c73bab4598c3e21468c79ec072eff6931c8f3bfc38256"},
 ]
 
 [package.dependencies]
+importlib-metadata = {version = ">=4.6", markers = "python_version < \"3.10\""}
 Jinja2 = ">=2.11.1"
 Markdown = ">=3.3"
 MarkupSafe = ">=1.1"
@@ -1571,6 +1661,7 @@ mkdocs = ">=1.2"
 mkdocs-autorefs = ">=0.3.1"
 mkdocstrings-python = {version = ">=0.5.2", optional = true, markers = "extra == \"python\""}
 pymdown-extensions = ">=6.3"
+typing-extensions = {version = ">=4.1", markers = "python_version < \"3.10\""}
 
 [package.extras]
 crystal = ["mkdocstrings-crystal (>=0.3.4)"]
@@ -1579,19 +1670,19 @@ python-legacy = ["mkdocstrings-python-legacy (>=0.2.1)"]
 
 [[package]]
 name = "mkdocstrings-python"
-version = "0.8.3"
+version = "1.5.2"
 description = "A Python handler for mkdocstrings."
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "mkdocstrings-python-0.8.3.tar.gz", hash = "sha256:9ae473f6dc599339b09eee17e4d2b05d6ac0ec29860f3fc9b7512d940fc61adf"},
-    {file = "mkdocstrings_python-0.8.3-py3-none-any.whl", hash = "sha256:4e6e1cd6f37a785de0946ced6eb846eb2f5d891ac1cc2c7b832943d3529087a7"},
+    {file = "mkdocstrings_python-1.5.2-py3-none-any.whl", hash = "sha256:ed37ca6d216986e2ac3530c19c3e7be381d1e3d09ea414e4ff467d6fd2cbd9c1"},
+    {file = "mkdocstrings_python-1.5.2.tar.gz", hash = "sha256:81eb4a93bc454a253daf247d1a11397c435d641c64fa165324c17c06170b1dfb"},
 ]
 
 [package.dependencies]
-griffe = ">=0.24"
-mkdocstrings = ">=0.19"
+griffe = ">=0.35"
+mkdocstrings = ">=0.20"
 
 [[package]]
 name = "mypy-extensions"
@@ -1607,75 +1698,76 @@ files = [
 
 [[package]]
 name = "nbclient"
-version = "0.7.2"
+version = "0.8.0"
 description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
 category = "dev"
 optional = false
-python-versions = ">=3.7.0"
+python-versions = ">=3.8.0"
 files = [
-    {file = "nbclient-0.7.2-py3-none-any.whl", hash = "sha256:d97ac6257de2794f5397609df754fcbca1a603e94e924eb9b99787c031ae2e7c"},
-    {file = "nbclient-0.7.2.tar.gz", hash = "sha256:884a3f4a8c4fc24bb9302f263e0af47d97f0d01fe11ba714171b320c8ac09547"},
+    {file = "nbclient-0.8.0-py3-none-any.whl", hash = "sha256:25e861299e5303a0477568557c4045eccc7a34c17fc08e7959558707b9ebe548"},
+    {file = "nbclient-0.8.0.tar.gz", hash = "sha256:f9b179cd4b2d7bca965f900a2ebf0db4a12ebff2f36a711cb66861e4ae158e55"},
 ]
 
 [package.dependencies]
 jupyter-client = ">=6.1.12"
 jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
 nbformat = ">=5.1"
-traitlets = ">=5.3"
+traitlets = ">=5.4"
 
 [package.extras]
 dev = ["pre-commit"]
-docs = ["autodoc-traits", "mock", "moto", "myst-parser", "nbclient[test]", "sphinx (>=1.7)", "sphinx-book-theme"]
-test = ["ipykernel", "ipython", "ipywidgets", "nbconvert (>=7.0.0)", "pytest (>=7.0)", "pytest-asyncio", "pytest-cov (>=4.0)", "testpath", "xmltodict"]
+docs = ["autodoc-traits", "mock", "moto", "myst-parser", "nbclient[test]", "sphinx (>=1.7)", "sphinx-book-theme", "sphinxcontrib-spelling"]
+test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=7.0.0)", "pytest (>=7.0)", "pytest-asyncio", "pytest-cov (>=4.0)", "testpath", "xmltodict"]
 
 [[package]]
 name = "nbconvert"
-version = "6.5.4"
+version = "7.7.4"
 description = "Converting Jupyter Notebooks"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "nbconvert-6.5.4-py3-none-any.whl", hash = "sha256:d679a947f849a966cbbd0bf6e7fedcfdb64be3b20ce7cef11ad55c13f5820e19"},
-    {file = "nbconvert-6.5.4.tar.gz", hash = "sha256:9e3c7c6d491374cbdd5f35d268c05809357716d346f4573186bbeab32ee50bc1"},
+    {file = "nbconvert-7.7.4-py3-none-any.whl", hash = "sha256:ace26f4386d08eb5c55833596a942048c5502a95e05590cb523826a749a40a37"},
+    {file = "nbconvert-7.7.4.tar.gz", hash = "sha256:1113d039fa3fc3a846ffa5a3b0a019e85aaa94c566a09fa0c400fb7638e46087"},
 ]
 
 [package.dependencies]
 beautifulsoup4 = "*"
-bleach = "*"
+bleach = "!=5.0.0"
 defusedxml = "*"
-entrypoints = ">=0.2.2"
+importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""}
 jinja2 = ">=3.0"
 jupyter-core = ">=4.7"
 jupyterlab-pygments = "*"
-lxml = "*"
-MarkupSafe = ">=2.0"
-mistune = ">=0.8.1,<2"
+markupsafe = ">=2.0"
+mistune = ">=2.0.3,<4"
 nbclient = ">=0.5.0"
-nbformat = ">=5.1"
+nbformat = ">=5.7"
 packaging = "*"
 pandocfilters = ">=1.4.1"
 pygments = ">=2.4.1"
 tinycss2 = "*"
-traitlets = ">=5.0"
+traitlets = ">=5.1"
 
 [package.extras]
-all = ["ipykernel", "ipython", "ipywidgets (>=7)", "nbsphinx (>=0.2.12)", "pre-commit", "pyppeteer (>=1,<1.1)", "pytest", "pytest-cov", "pytest-dependency", "sphinx (>=1.5.1)", "sphinx-rtd-theme", "tornado (>=6.1)"]
-docs = ["ipython", "nbsphinx (>=0.2.12)", "sphinx (>=1.5.1)", "sphinx-rtd-theme"]
+all = ["nbconvert[docs,qtpdf,serve,test,webpdf]"]
+docs = ["ipykernel", "ipython", "myst-parser", "nbsphinx (>=0.2.12)", "pydata-sphinx-theme", "sphinx (==5.0.2)", "sphinxcontrib-spelling"]
+qtpdf = ["nbconvert[qtpng]"]
+qtpng = ["pyqtwebengine (>=5.15)"]
 serve = ["tornado (>=6.1)"]
-test = ["ipykernel", "ipywidgets (>=7)", "pre-commit", "pyppeteer (>=1,<1.1)", "pytest", "pytest-cov", "pytest-dependency"]
-webpdf = ["pyppeteer (>=1,<1.1)"]
+test = ["flaky", "ipykernel", "ipywidgets (>=7)", "pre-commit", "pytest", "pytest-dependency"]
+webpdf = ["playwright"]
 
 [[package]]
 name = "nbformat"
-version = "5.7.3"
+version = "5.9.2"
 description = "The Jupyter Notebook format"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "nbformat-5.7.3-py3-none-any.whl", hash = "sha256:22a98a6516ca216002b0a34591af5bcb8072ca6c63910baffc901cfa07fefbf0"},
-    {file = "nbformat-5.7.3.tar.gz", hash = "sha256:4b021fca24d3a747bf4e626694033d792d594705829e5e35b14ee3369f9f6477"},
+    {file = "nbformat-5.9.2-py3-none-any.whl", hash = "sha256:1c5172d786a41b82bcfd0c23f9e6b6f072e8fb49c39250219e4acfff1efe89e9"},
+    {file = "nbformat-5.9.2.tar.gz", hash = "sha256:5f98b5ba1997dff175e77e0c17d5c10a96eaed2cbd1de3533d1fc35d5e111192"},
 ]
 
 [package.dependencies]
@@ -1690,64 +1782,75 @@ test = ["pep440", "pre-commit", "pytest", "testpath"]
 
 [[package]]
 name = "nest-asyncio"
-version = "1.5.6"
+version = "1.5.7"
 description = "Patch asyncio to allow nested event loops"
 category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
-    {file = "nest_asyncio-1.5.6-py3-none-any.whl", hash = "sha256:b9a953fb40dceaa587d109609098db21900182b16440652454a146cffb06e8b8"},
-    {file = "nest_asyncio-1.5.6.tar.gz", hash = "sha256:d267cc1ff794403f7df692964d1d2a3fa9418ffea2a3f6859a439ff482fef290"},
+    {file = "nest_asyncio-1.5.7-py3-none-any.whl", hash = "sha256:5301c82941b550b3123a1ea772ba9a1c80bad3a182be8c1a5ae6ad3be57a9657"},
+    {file = "nest_asyncio-1.5.7.tar.gz", hash = "sha256:6a80f7b98f24d9083ed24608977c09dd608d83f91cccc24c9d2cba6d10e01c10"},
 ]
 
 [[package]]
 name = "numpy"
-version = "1.24.2"
+version = "1.24.4"
 description = "Fundamental package for array computing in Python"
 category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.extras]
-docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinxext-opengraph"]
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 tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
 
 [[package]]
@@ -1922,30 +2002,30 @@ files = [
 
 [[package]]
 name = "platformdirs"
-version = "3.0.0"
+version = "3.10.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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-test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest (>=7.2.1)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.1)", "sphinx-autodoc-typehints (>=1.24)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)"]
 
 [[package]]
 name = "pluggy"
-version = "1.0.0"
+version = "1.2.0"
 description = "plugin and hook calling mechanisms for python"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
@@ -1954,14 +2034,14 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.37"
+version = "3.0.39"
 description = "Library for building powerful interactive command lines in Python"
 category = "dev"
 optional = false
 python-versions = ">=3.7.0"
 files = [
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 ]
 
 [package.dependencies]
@@ -1969,26 +2049,26 @@ wcwidth = "*"
 
 [[package]]
 name = "psutil"
-version = "5.9.4"
+version = "5.9.5"
 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.*"
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 ]
 
 [package.extras]
@@ -2021,18 +2101,6 @@ files = [
 [package.extras]
 tests = ["pytest"]
 
-[[package]]
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-version = "2.9.1"
-description = "Python style guide checker"
-category = "dev"
-optional = false
-python-versions = ">=3.6"
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-]
-
 [[package]]
 name = "pycparser"
 version = "2.21"
@@ -2045,46 +2113,16 @@ files = [
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 ]
 
-[[package]]
-name = "pydocstyle"
-version = "6.3.0"
-description = "Python docstring style checker"
-category = "dev"
-optional = false
-python-versions = ">=3.6"
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-
-[package.dependencies]
-snowballstemmer = ">=2.2.0"
-
-[package.extras]
-toml = ["tomli (>=1.2.3)"]
-
-[[package]]
-name = "pyflakes"
-version = "2.5.0"
-description = "passive checker of Python programs"
-category = "dev"
-optional = false
-python-versions = ">=3.6"
-files = [
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-]
-
 [[package]]
 name = "pygments"
-version = "2.14.0"
+version = "2.16.1"
 description = "Pygments is a syntax highlighting package written in Python."
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
@@ -2092,18 +2130,19 @@ plugins = ["importlib-metadata"]
 
 [[package]]
 name = "pymdown-extensions"
-version = "9.9.2"
+version = "10.1"
 description = "Extension pack for Python Markdown."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
 markdown = ">=3.2"
+pyyaml = "*"
 
 [[package]]
 name = "pyparsing"
@@ -2121,56 +2160,37 @@ files = [
 diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
-name = "pyrsistent"
-version = "0.19.3"
-description = "Persistent/Functional/Immutable data structures"
+name = "pyquery"
+version = "2.0.0"
+description = "A jquery-like library for python"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = "*"
 files = [
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+lxml = ">=2.1"
+
+[package.extras]
+test = ["pytest", "pytest-cov", "requests", "webob", "webtest"]
+
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+version = "7.4.0"
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 tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 
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+version = "4.1.0"
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 [package.dependencies]
 six = ">=1.5"
 
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 [[package]]
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 description = "Python bindings for 0MQ"
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 optional = false
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 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+python-versions = ">=3.7"
 files = [
-    {file = "urllib3-1.26.14-py2.py3-none-any.whl", hash = "sha256:75edcdc2f7d85b137124a6c3c9fc3933cdeaa12ecb9a6a959f22797a0feca7e1"},
-    {file = "urllib3-1.26.14.tar.gz", hash = "sha256:076907bf8fd355cde77728471316625a4d2f7e713c125f51953bb5b3eecf4f72"},
+    {file = "urllib3-2.0.4-py3-none-any.whl", hash = "sha256:de7df1803967d2c2a98e4b11bb7d6bd9210474c46e8a0401514e3a42a75ebde4"},
+    {file = "urllib3-2.0.4.tar.gz", hash = "sha256:8d22f86aae8ef5e410d4f539fde9ce6b2113a001bb4d189e0aed70642d602b11"},
 ]
 
 [package.extras]
-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)"]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "watchdog"
-version = "2.3.0"
+version = "3.0.0"
 description = "Filesystem events monitoring"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "watchdog-2.3.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:c1b3962e5463a848ba2a342cb66c80251dca27a102933b8f38d231d2a9e5a543"},
-    {file = "watchdog-2.3.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:9e651b4874477c1bf239417d43818bbfd047aaf641b029fa60d6f5109ede0db0"},
-    {file = "watchdog-2.3.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:d04662017efd00a014cff9068708e085d67f2fac43f48bbbb95a7f97490487f3"},
-    {file = "watchdog-2.3.0-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:0f7d759299ce21a3d2a77e18d430c24811369c3432453701790acc6ff45a7101"},
-    {file = "watchdog-2.3.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:a4b9bece40d46bf6fb8621817ea7d903eae2b9b3ebac55a51ed50354a79061a8"},
-    {file = "watchdog-2.3.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:242e57253e84a736e6777ba756c48cf6a68d3d90cb9e01bd6bfd371a949ace3a"},
-    {file = "watchdog-2.3.0-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:3fa74b0ef4825f9112932675a002296cb2d3d3e400d7a44c32fafd1ecc83ada0"},
-    {file = "watchdog-2.3.0-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:15bf5b165d7a6b48265411dad74fb0d33053f8270eb6575faad0e016035cf9f7"},
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-    {file = "watchdog-2.3.0-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:4e648df44a4c6ea6da4d9eb6722745c986b9d70268f25ae60f140082d7c8908e"},
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-    {file = "watchdog-2.3.0-pp38-pypy38_pp73-macosx_10_9_x86_64.whl", hash = "sha256:5ddbbe87f9ed726940d174076da030cd01ec45433ef2b1b2e6094c84f2af17f1"},
-    {file = "watchdog-2.3.0-pp39-pypy39_pp73-macosx_10_9_x86_64.whl", hash = "sha256:3fa1572f5a2f6d17d4d860edbc04488fef31b007c25c2f3b11203fb8179b7c67"},
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-    {file = "watchdog-2.3.0-py3-none-manylinux2014_i686.whl", hash = "sha256:f1a655f4a49f9232311b9967f42cc2eaf43fd4903f3bed850dd4570fda5d5eff"},
-    {file = "watchdog-2.3.0-py3-none-manylinux2014_ppc64.whl", hash = "sha256:aa4773160b9cb21ba369cb42d59a947087330b3a02480173033a6a6cc137a510"},
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-    {file = "watchdog-2.3.0-py3-none-manylinux2014_x86_64.whl", hash = "sha256:7767a3da3307d9cf597832f692702441a97c259e5d0d560f2e57c43ad0d191d2"},
-    {file = "watchdog-2.3.0-py3-none-win32.whl", hash = "sha256:8863913ea2c3f256d18c33d84546518636e391cd8f50d209b9a31221e0f7d3fd"},
-    {file = "watchdog-2.3.0-py3-none-win_amd64.whl", hash = "sha256:6d79b5954db8f41d6a7f5763042b988f7a4afd40b7d141456061fa7c5b7f2159"},
-    {file = "watchdog-2.3.0-py3-none-win_ia64.whl", hash = "sha256:a3559ee82a10976de1ec544b6ebe3b4aa398d491860a283d80ec0f550076d068"},
-    {file = "watchdog-2.3.0.tar.gz", hash = "sha256:9d39effe6909be898ba3e7286a9e9b17a6a9f734fb1ef9dde3e9bb68715fca39"},
+    {file = "watchdog-3.0.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:336adfc6f5cc4e037d52db31194f7581ff744b67382eb6021c868322e32eef41"},
+    {file = "watchdog-3.0.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:a70a8dcde91be523c35b2bf96196edc5730edb347e374c7de7cd20c43ed95397"},
+    {file = "watchdog-3.0.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:adfdeab2da79ea2f76f87eb42a3ab1966a5313e5a69a0213a3cc06ef692b0e96"},
+    {file = "watchdog-3.0.0-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:2b57a1e730af3156d13b7fdddfc23dea6487fceca29fc75c5a868beed29177ae"},
+    {file = "watchdog-3.0.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:7ade88d0d778b1b222adebcc0927428f883db07017618a5e684fd03b83342bd9"},
+    {file = "watchdog-3.0.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:7e447d172af52ad204d19982739aa2346245cc5ba6f579d16dac4bfec226d2e7"},
+    {file = "watchdog-3.0.0-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:9fac43a7466eb73e64a9940ac9ed6369baa39b3bf221ae23493a9ec4d0022674"},
+    {file = "watchdog-3.0.0-cp38-cp38-macosx_10_9_universal2.whl", hash = "sha256:8ae9cda41fa114e28faf86cb137d751a17ffd0316d1c34ccf2235e8a84365c7f"},
+    {file = "watchdog-3.0.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:25f70b4aa53bd743729c7475d7ec41093a580528b100e9a8c5b5efe8899592fc"},
+    {file = "watchdog-3.0.0-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:4f94069eb16657d2c6faada4624c39464f65c05606af50bb7902e036e3219be3"},
+    {file = "watchdog-3.0.0-cp39-cp39-macosx_10_9_universal2.whl", hash = "sha256:7c5f84b5194c24dd573fa6472685b2a27cc5a17fe5f7b6fd40345378ca6812e3"},
+    {file = "watchdog-3.0.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:3aa7f6a12e831ddfe78cdd4f8996af9cf334fd6346531b16cec61c3b3c0d8da0"},
+    {file = "watchdog-3.0.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:233b5817932685d39a7896b1090353fc8efc1ef99c9c054e46c8002561252fb8"},
+    {file = "watchdog-3.0.0-pp37-pypy37_pp73-macosx_10_9_x86_64.whl", hash = "sha256:13bbbb462ee42ec3c5723e1205be8ced776f05b100e4737518c67c8325cf6100"},
+    {file = "watchdog-3.0.0-pp38-pypy38_pp73-macosx_10_9_x86_64.whl", hash = "sha256:8f3ceecd20d71067c7fd4c9e832d4e22584318983cabc013dbf3f70ea95de346"},
+    {file = "watchdog-3.0.0-pp39-pypy39_pp73-macosx_10_9_x86_64.whl", hash = "sha256:c9d8c8ec7efb887333cf71e328e39cffbf771d8f8f95d308ea4125bf5f90ba64"},
+    {file = "watchdog-3.0.0-py3-none-manylinux2014_aarch64.whl", hash = "sha256:0e06ab8858a76e1219e68c7573dfeba9dd1c0219476c5a44d5333b01d7e1743a"},
+    {file = "watchdog-3.0.0-py3-none-manylinux2014_armv7l.whl", hash = "sha256:d00e6be486affb5781468457b21a6cbe848c33ef43f9ea4a73b4882e5f188a44"},
+    {file = "watchdog-3.0.0-py3-none-manylinux2014_i686.whl", hash = "sha256:c07253088265c363d1ddf4b3cdb808d59a0468ecd017770ed716991620b8f77a"},
+    {file = "watchdog-3.0.0-py3-none-manylinux2014_ppc64.whl", hash = "sha256:5113334cf8cf0ac8cd45e1f8309a603291b614191c9add34d33075727a967709"},
+    {file = "watchdog-3.0.0-py3-none-manylinux2014_ppc64le.whl", hash = "sha256:51f90f73b4697bac9c9a78394c3acbbd331ccd3655c11be1a15ae6fe289a8c83"},
+    {file = "watchdog-3.0.0-py3-none-manylinux2014_s390x.whl", hash = "sha256:ba07e92756c97e3aca0912b5cbc4e5ad802f4557212788e72a72a47ff376950d"},
+    {file = "watchdog-3.0.0-py3-none-manylinux2014_x86_64.whl", hash = "sha256:d429c2430c93b7903914e4db9a966c7f2b068dd2ebdd2fa9b9ce094c7d459f33"},
+    {file = "watchdog-3.0.0-py3-none-win32.whl", hash = "sha256:3ed7c71a9dccfe838c2f0b6314ed0d9b22e77d268c67e015450a29036a81f60f"},
+    {file = "watchdog-3.0.0-py3-none-win_amd64.whl", hash = "sha256:4c9956d27be0bb08fc5f30d9d0179a855436e655f046d288e2bcc11adfae893c"},
+    {file = "watchdog-3.0.0-py3-none-win_ia64.whl", hash = "sha256:5d9f3a10e02d7371cd929b5d8f11e87d4bad890212ed3901f9b4d68767bee759"},
+    {file = "watchdog-3.0.0.tar.gz", hash = "sha256:4d98a320595da7a7c5a18fc48cb633c2e73cda78f93cac2ef42d42bf609a33f9"},
 ]
 
 [package.extras]
@@ -2648,21 +2948,21 @@ files = [
 
 [[package]]
 name = "zipp"
-version = "3.14.0"
+version = "3.16.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.14.0-py3-none-any.whl", hash = "sha256:188834565033387710d046e3fe96acfc9b5e86cbca7f39ff69cf21a4128198b7"},
-    {file = "zipp-3.14.0.tar.gz", hash = "sha256:9e5421e176ef5ab4c0ad896624e87a7b2f07aca746c9b2aa305952800cb8eecb"},
+    {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"},
+    {file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools", "more-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)"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.8"
-content-hash = "5374e9fbe57ddff0535c86cebfc7ceea83efaca10c9ff2ddc47cf6c951868731"
+content-hash = "44bd2d3d72716db3be8a461e16921c52035881e26f318cfc34896661b26dcef3"

From b8eb38109c66be029bba2c8d3aabf0325b8b193a Mon Sep 17 00:00:00 2001
From: moshi <sy.41211@gmail.com>
Date: Sat, 26 Aug 2023 16:33:25 +0900
Subject: [PATCH 03/11] Apply ruff linter rule

---
 src/pymsaviz/msaviz.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/pymsaviz/msaviz.py b/src/pymsaviz/msaviz.py
index 734ccc8..d370fc2 100644
--- a/src/pymsaviz/msaviz.py
+++ b/src/pymsaviz/msaviz.py
@@ -630,7 +630,7 @@ def _get_consensus_identity_list(
         start = 0 if start is None else start
         end = self.alignment_length if end is None else end
         consensus_identity_list = []
-        for idx, seq_char in enumerate(self.consensus_seq[start:end], start):
+        for idx, _ in enumerate(self.consensus_seq[start:end], start):
             column_chars = str(self.msa[:, idx])
             counter = Counter(filter(lambda c: c not in ("-", "*"), column_chars))
             count = counter.most_common()[0][1] if len(counter) != 0 else 0
@@ -741,7 +741,7 @@ def _parse_positions(self, positions: list[tuple[int, int] | int]) -> list[int]:
         for pos in positions:
             if isinstance(pos, (tuple, list)):
                 result_positions.extend(list(range(pos[0] - 1, pos[1])))
-            elif type(pos) == int:
+            elif isinstance(pos, int):
                 result_positions.append(pos - 1)
             else:
                 raise ValueError(f"{positions=} is invalid.")

From 1a94372feea4b96604c9f47101893d58aababf72 Mon Sep 17 00:00:00 2001
From: moshi <sy.41211@gmail.com>
Date: Sat, 26 Aug 2023 16:37:11 +0900
Subject: [PATCH 04/11] Replace `set_layout_engine` to `tight_layout`

To suppress error in older version of matplotlib (#7)
---
 src/pymsaviz/msaviz.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pymsaviz/msaviz.py b/src/pymsaviz/msaviz.py
index d370fc2..d752710 100644
--- a/src/pymsaviz/msaviz.py
+++ b/src/pymsaviz/msaviz.py
@@ -417,7 +417,7 @@ def plotfig(self, dpi: int = 100) -> Figure:
         y_size_list = [ax_type2y_size[t] for t in plot_ax_types]
         figsize = (self._wrap_length * self._x_unit_size, sum(y_size_list))
         fig: Figure = plt.figure(figsize=figsize, dpi=dpi)  # type: ignore
-        fig.set_layout_engine("tight")
+        fig.tight_layout()
         gs = GridSpec(nrows=len(plot_ax_types), ncols=1, height_ratios=y_size_list)
         gs.update(left=0, right=1, bottom=0, top=1, hspace=0, wspace=0)
 

From d8493ee41b880672cf19d9765081cb17df2e2f47 Mon Sep 17 00:00:00 2001
From: moshi <sy.41211@gmail.com>
Date: Sat, 26 Aug 2023 16:40:07 +0900
Subject: [PATCH 05/11] Update CI workflow

---
 .github/workflows/ci.yml | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8ceabcb..d11207a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -14,7 +14,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [3.8, 3.9, "3.10"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
     steps:
       - name: Checkout
         uses: actions/checkout@v3
@@ -24,11 +24,9 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      # Install poetry v1.4.0 to avoid _WheelFileValidationError in debugpy
-      # Latest poetry v1.4.1 cannot install debugpy
       - name: Install Poetry
         run: |
-          curl -sSL https://install.python-poetry.org | python3 - --version 1.4.0
+          curl -sSL https://install.python-poetry.org | python3 -
           echo "$HOME/.local/bin" >> $GITHUB_PATH
 
       - name: Install Dependencies
@@ -37,8 +35,8 @@ jobs:
       - name: Run black format check
         run: poetry run black src tests --check --diff --verbose
 
-      - name: Run flake8 lint check
-        run: poetry run flake8 src tests --max-line-length=88 --ignore=E203,W503,W504
+      - name: Run ruff lint check
+        run: poetry run ruff .
 
       - name: Run pytest
         run: poetry run pytest tests --tb=line --cov=src --cov-report=xml --cov-report=term

From 6842eb0f12ebd2723ac0264e7812a0147085a830 Mon Sep 17 00:00:00 2001
From: moshi <sy.41211@gmail.com>
Date: Sat, 26 Aug 2023 16:55:05 +0900
Subject: [PATCH 06/11] Ignore ruff linter rule D401

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 36f44bd..fb7e34a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -36,6 +36,7 @@ ignore = [
     "D105",
     "D205",
     "D400",
+    "D401",
     "D403",
     "D415",
     "B905",

From 29921ef558e6601f52e6ff7d4a229e9304dab304 Mon Sep 17 00:00:00 2001
From: moshi <sy.41211@gmail.com>
Date: Thu, 7 Sep 2023 21:43:19 +0900
Subject: [PATCH 07/11] Update deps lock

---
 poetry.lock | 631 +++++++++++++++++++---------------------------------
 1 file changed, 230 insertions(+), 401 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 6752a5f..bf11a29 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -14,18 +14,18 @@ files = [
 
 [[package]]
 name = "asttokens"
-version = "2.2.1"
+version = "2.4.0"
 description = "Annotate AST trees with source code positions"
 category = "dev"
 optional = false
 python-versions = "*"
 files = [
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@@ -480,64 +480,64 @@ test-no-images = ["pytest", "pytest-cov", "wurlitzer"]
 
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@@ -546,18 +546,6 @@ tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.1
 [package.extras]
 toml = ["tomli"]
 
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 python-versions = ">=3.8"
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 description = "Jupyter notebooks as Markdown documents, Julia, Python or R scripts"
 category = "dev"
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 python-versions = "~=3.6"
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-
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-cssselect = ["cssselect (>=0.7)"]
-html5 = ["html5lib"]
-htmlsoup = ["BeautifulSoup4"]
-source = ["Cython (>=0.29.35)"]
-
 [[package]]
 name = "markdown"
 version = "3.4.4"
@@ -1319,23 +1199,6 @@ profiling = ["gprof2dot"]
 rtd = ["jupyter_sphinx", "mdit-py-plugins", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
 testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
-[[package]]
-name = "markdown2"
-version = "2.4.10"
-description = "A fast and complete Python implementation of Markdown"
-category = "dev"
-optional = false
-python-versions = ">=3.5, <4"
-files = [
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-]
-
-[package.extras]
-all = ["pygments (>=2.7.3)", "wavedrom"]
-code-syntax-highlighting = ["pygments (>=2.7.3)"]
-wavedrom = ["wavedrom"]
-
 [[package]]
 name = "markupsafe"
 version = "2.1.3"
@@ -1603,30 +1466,28 @@ test = ["coverage[toml]", "pymdown-extensions", "pytest", "pytest-cov"]
 
 [[package]]
 name = "mkdocs-material"
-version = "9.2.3"
+version = "9.2.8"
 description = "Documentation that simply works"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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 [package.dependencies]
-babel = ">=2.10.3"
-colorama = ">=0.4"
-jinja2 = ">=3.0"
-lxml = ">=4.6"
-markdown = ">=3.2"
-mkdocs = ">=1.5.2"
-mkdocs-material-extensions = ">=1.1"
-paginate = ">=0.5.6"
-pygments = ">=2.14"
-pymdown-extensions = ">=9.9.1"
-readtime = ">=2.0"
-regex = ">=2022.4.24"
-requests = ">=2.26"
+babel = ">=2.12,<3.0"
+colorama = ">=0.4,<1.0"
+jinja2 = ">=3.1,<4.0"
+markdown = ">=3.4,<4.0"
+mkdocs = ">=1.5,<2.0"
+mkdocs-material-extensions = ">=1.1,<2.0"
+paginate = ">=0.5,<1.0"
+pygments = ">=2.16,<3.0"
+pymdown-extensions = ">=10.3,<11.0"
+regex = ">=2023.8,<2024.0"
+requests = ">=2.31,<3.0"
 
 [[package]]
 name = "mkdocs-material-extensions"
@@ -1642,14 +1503,14 @@ files = [
 
 [[package]]
 name = "mkdocstrings"
-version = "0.22.0"
+version = "0.23.0"
 description = "Automatic documentation from sources, for MkDocs."
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "mkdocstrings-0.23.0.tar.gz", hash = "sha256:d9c6a37ffbe7c14a7a54ef1258c70b8d394e6a33a1c80832bce40b9567138d1c"},
 ]
 
 [package.dependencies]
@@ -1670,14 +1531,14 @@ python-legacy = ["mkdocstrings-python-legacy (>=0.2.1)"]
 
 [[package]]
 name = "mkdocstrings-python"
-version = "1.5.2"
+version = "1.6.2"
 description = "A Python handler for mkdocstrings."
 category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "mkdocstrings_python-1.6.2-py3-none-any.whl", hash = "sha256:cf560df975faf712808e44c1c2e52b8267f17bc89c8b23e7b9bfe679561adf4d"},
+    {file = "mkdocstrings_python-1.6.2.tar.gz", hash = "sha256:edf0f81899bee8024971bf2c18b6fc17f66085992f01c72840a3ee0ee42113fb"},
 ]
 
 [package.dependencies]
@@ -1721,14 +1582,14 @@ test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=
 
 [[package]]
 name = "nbconvert"
-version = "7.7.4"
+version = "7.8.0"
 description = "Converting Jupyter Notebooks"
 category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "nbconvert-7.8.0.tar.gz", hash = "sha256:f5bc15a1247e14dd41ceef0c0a3bc70020e016576eb0578da62f1c5b4f950479"},
 ]
 
 [package.dependencies]
@@ -2018,14 +1879,14 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-co
 
 [[package]]
 name = "pluggy"
-version = "1.2.0"
+version = "1.3.0"
 description = "plugin and hook calling mechanisms for python"
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "pluggy-1.3.0-py3-none-any.whl", hash = "sha256:d89c696a773f8bd377d18e5ecda92b7a3793cbe66c87060a6fb58c7b6e1061f7"},
+    {file = "pluggy-1.3.0.tar.gz", hash = "sha256:cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12"},
 ]
 
 [package.extras]
@@ -2130,20 +1991,23 @@ plugins = ["importlib-metadata"]
 
 [[package]]
 name = "pymdown-extensions"
-version = "10.1"
+version = "10.3"
 description = "Extension pack for Python Markdown."
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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-    {file = "pymdown_extensions-10.1.tar.gz", hash = "sha256:508009b211373058debb8247e168de4cbcb91b1bff7b5e961b2c3e864e00b195"},
+    {file = "pymdown_extensions-10.3-py3-none-any.whl", hash = "sha256:77a82c621c58a83efc49a389159181d570e370fff9f810d3a4766a75fc678b66"},
+    {file = "pymdown_extensions-10.3.tar.gz", hash = "sha256:94a0d8a03246712b64698af223848fd80aaf1ae4c4be29c8c61939b0467b5722"},
 ]
 
 [package.dependencies]
 markdown = ">=3.2"
 pyyaml = "*"
 
+[package.extras]
+extra = ["pygments (>=2.12)"]
+
 [[package]]
 name = "pyparsing"
 version = "3.0.9"
@@ -2159,35 +2023,16 @@ files = [
 [package.extras]
 diagrams = ["jinja2", "railroad-diagrams"]
 
-[[package]]
-name = "pyquery"
-version = "2.0.0"
-description = "A jquery-like library for python"
-category = "dev"
-optional = false
-python-versions = "*"
-files = [
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-    {file = "pyquery-2.0.0.tar.gz", hash = "sha256:963e8d4e90262ff6d8dec072ea97285dc374a2f69cad7776f4082abcf6a1d8ae"},
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-
-[package.dependencies]
-cssselect = ">=1.2.0"
-lxml = ">=2.1"
-
-[package.extras]
-test = ["pytest", "pytest-cov", "requests", "webob", "webtest"]
-
 [[package]]
 name = "pytest"
-version = "7.4.0"
+version = "7.4.1"
 description = "pytest: simple powerful testing with Python"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pytest-7.4.0-py3-none-any.whl", hash = "sha256:78bf16451a2eb8c7a2ea98e32dc119fd2aa758f1d5d66dbf0a59d69a3969df32"},
-    {file = "pytest-7.4.0.tar.gz", hash = "sha256:b4bf8c45bd59934ed84001ad51e11b4ee40d40a1229d2c79f9c592b0a3f6bd8a"},
+    {file = "pytest-7.4.1-py3-none-any.whl", hash = "sha256:460c9a59b14e27c602eb5ece2e47bec99dc5fc5f6513cf924a7d03a578991b1f"},
+    {file = "pytest-7.4.1.tar.gz", hash = "sha256:2f2301e797521b23e4d2585a0a3d7b5e50fdddaaf7e7d6773ea26ddb17c213ab"},
 ]
 
 [package.dependencies]
@@ -2237,14 +2082,14 @@ six = ">=1.5"
 
 [[package]]
 name = "pytz"
-version = "2023.3"
+version = "2023.3.post1"
 description = "World timezone definitions, modern and historical"
 category = "dev"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [[package]]
@@ -2442,22 +2287,6 @@ files = [
 [package.dependencies]
 cffi = {version = "*", markers = "implementation_name == \"pypy\""}
 
-[[package]]
-name = "readtime"
-version = "3.0.0"
-description = "Calculates the time some text takes the average human to read, based on Medium's read time forumula"
-category = "dev"
-optional = false
-python-versions = "*"
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-
-[package.dependencies]
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-markdown2 = ">=2.4.3"
-pyquery = ">=1.2"
-
 [[package]]
 name = "referencing"
 version = "0.30.2"
@@ -2596,136 +2425,136 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
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-version = "0.9.2"
+version = "0.10.2"
 description = "Python bindings to Rust's persistent data structures (rpds)"
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 python-versions = ">=3.8"
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 ]
 
 [[package]]
 name = "ruff"
-version = "0.0.286"
+version = "0.0.287"
 description = "An extremely fast Python linter, written in Rust."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "ruff-0.0.287-py3-none-win_arm64.whl", hash = "sha256:44bceb3310ac04f0e59d4851e6227f7b1404f753997c7859192e41dbee9f5c8d"},
+    {file = "ruff-0.0.287.tar.gz", hash = "sha256:02dc4f5bf53ef136e459d467f3ce3e04844d509bc46c025a05b018feb37bbc39"},
 ]
 
 [[package]]
@@ -2742,14 +2571,14 @@ files = [
 
 [[package]]
 name = "soupsieve"
-version = "2.4.1"
+version = "2.5"
 description = "A modern CSS selector implementation for Beautiful Soup."
 category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "soupsieve-2.4.1-py3-none-any.whl", hash = "sha256:1c1bfee6819544a3447586c889157365a27e10d88cde3ad3da0cf0ddf646feb8"},
-    {file = "soupsieve-2.4.1.tar.gz", hash = "sha256:89d12b2d5dfcd2c9e8c22326da9d9aa9cb3dfab0a83a024f05704076ee8d35ea"},
+    {file = "soupsieve-2.5-py3-none-any.whl", hash = "sha256:eaa337ff55a1579b6549dc679565eac1e3d000563bcb1c8ab0d0fefbc0c2cdc7"},
+    {file = "soupsieve-2.5.tar.gz", hash = "sha256:5663d5a7b3bfaeee0bc4372e7fc48f9cff4940b3eec54a6451cc5299f1097690"},
 ]
 
 [[package]]

From 0e194ffc6d77a55b7b1da7e4c146c24e966e7542 Mon Sep 17 00:00:00 2001
From: moshi <sy.41211@gmail.com>
Date: Thu, 7 Sep 2023 21:44:16 +0900
Subject: [PATCH 08/11] Fix to suppress `mv.savefig()` memory leak

---
 src/pymsaviz/msaviz.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/pymsaviz/msaviz.py b/src/pymsaviz/msaviz.py
index d752710..72446f1 100644
--- a/src/pymsaviz/msaviz.py
+++ b/src/pymsaviz/msaviz.py
@@ -469,6 +469,9 @@ def savefig(
             dpi=dpi,
             pad_inches=pad_inches,
         )
+        # Clear & close figure to suppress memory leak
+        fig.clear()
+        plt.close(fig)
 
     ############################################################
     # Private Method

From 36c61a4c37085e6272dd95d4f63031b2fa5fe62e Mon Sep 17 00:00:00 2001
From: moshi <sy.41211@gmail.com>
Date: Thu, 7 Sep 2023 21:44:56 +0900
Subject: [PATCH 09/11] Add `label_type` option to CLI

---
 src/pymsaviz/scripts/cli.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/src/pymsaviz/scripts/cli.py b/src/pymsaviz/scripts/cli.py
index 7bc29ab..504a6a0 100644
--- a/src/pymsaviz/scripts/cli.py
+++ b/src/pymsaviz/scripts/cli.py
@@ -21,6 +21,7 @@ def run(
     end: int | None = None,
     wrap_length: int | None = None,
     wrap_space_size: float = 3.0,
+    label_type: str = "id",
     show_grid: bool = False,
     show_count: bool = False,
     show_consensus: bool = False,
@@ -37,6 +38,7 @@ def run(
         end=end,
         wrap_length=wrap_length,
         wrap_space_size=wrap_space_size,
+        label_type=label_type,
         color_scheme=color_scheme,
         show_grid=show_grid,
         show_count=show_count,
@@ -129,6 +131,15 @@ def get_args() -> argparse.Namespace:
         default=default_wrap_space_size,
         metavar="",
     )
+    default_label_type = "id"
+    parser.add_argument(
+        "--label_type",
+        type=str,
+        help="Label type ('id'[default]|'description')",
+        default=default_label_type,
+        choices=("id", "description"),
+        metavar="",
+    )
     parser.add_argument(
         "--show_grid",
         help="Show grid (Default: OFF)",

From 4391fbb9bae2cf07858603143d7862602aff4c15 Mon Sep 17 00:00:00 2001
From: moshi <sy.41211@gmail.com>
Date: Thu, 7 Sep 2023 21:46:05 +0900
Subject: [PATCH 10/11] Update CLI option docs

---
 README.md                 | 1 +
 docs/cli-docs/pymsaviz.md | 1 +
 2 files changed, 2 insertions(+)

diff --git a/README.md b/README.md
index 5991798..e88c3f9 100644
--- a/README.md
+++ b/README.md
@@ -118,6 +118,7 @@ pyMSAviz provides simple MSA visualization CLI.
     --end               End position of MSA visualization (Default: 'MSA Length')
     --wrap_length       Wrap length (Default: None)
     --wrap_space_size   Space size between wrap MSA plot area (Default: 3.0)
+    --label_type        Label type ('id'[default]|'description')
     --show_grid         Show grid (Default: OFF)
     --show_count        Show seq char count without gap on right side (Default: OFF)
     --show_consensus    Show consensus sequence (Default: OFF)
diff --git a/docs/cli-docs/pymsaviz.md b/docs/cli-docs/pymsaviz.md
index 0b8907b..48da9db 100644
--- a/docs/cli-docs/pymsaviz.md
+++ b/docs/cli-docs/pymsaviz.md
@@ -16,6 +16,7 @@
     --end               End position of MSA visualization (Default: 'MSA Length')
     --wrap_length       Wrap length (Default: None)
     --wrap_space_size   Space size between wrap MSA plot area (Default: 3.0)
+    --label_type        Label type ('id'[default]|'description')
     --show_grid         Show grid (Default: OFF)
     --show_count        Show seq char count without gap on right side (Default: OFF)
     --show_consensus    Show consensus sequence (Default: OFF)

From d3a8af1bbd2c579f37a7b9cef3324857d94f5306 Mon Sep 17 00:00:00 2001
From: moshi <sy.41211@gmail.com>
Date: Thu, 7 Sep 2023 21:46:45 +0900
Subject: [PATCH 11/11] Change v0.4.0 to v0.4.1

---
 pyproject.toml           | 2 +-
 src/pymsaviz/__init__.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index fb7e34a..e970b0a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyMSAviz"
-version = "0.4.0"
+version = "0.4.1"
 description = "MSA visualization python package for sequence analysis"
 authors = ["moshi4"]
 license = "MIT"
diff --git a/src/pymsaviz/__init__.py b/src/pymsaviz/__init__.py
index fa3c146..8656edd 100644
--- a/src/pymsaviz/__init__.py
+++ b/src/pymsaviz/__init__.py
@@ -12,7 +12,7 @@
     "get_msa_testdata",
 ]
 
-__version__ = "0.4.0"
+__version__ = "0.4.1"
 
 # Setting matplotlib rc(runtime configuration) parameters
 # https://matplotlib.org/stable/tutorials/introductory/customizing.html