From de4e26b577111f1111a096da63c6e6bd8f9da466 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 21 Jan 2025 10:47:51 +0100
Subject: [PATCH] Bump lxml from 5.2.2 to 5.3.0 (#452)

* Bump lxml from 5.2.2 to 5.3.0

Bumps [lxml](https://github.com/lxml/lxml) from 5.2.2 to 5.3.0.
- [Release notes](https://github.com/lxml/lxml/releases)
- [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt)
- [Commits](https://github.com/lxml/lxml/compare/lxml-5.2.2...lxml-5.3.0)

---
updated-dependencies:
- dependency-name: lxml
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

* update lock

* update lock

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Rodrigo V. Honorato <r.vargashonorato@uu.nl>
---
 poetry.lock    | 1650 ++++++++++++++++++++++++++++--------------------
 pyproject.toml |    2 +-
 2 files changed, 956 insertions(+), 696 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 0c8f771..8627539 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,28 +1,53 @@
-# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand.
+# This file is automatically @generated by Poetry and should not be changed by hand.
+
+[[package]]
+name = "anyio"
+version = "4.8.0"
+description = "High level compatibility layer for multiple asynchronous event loop implementations"
+category = "main"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "anyio-4.8.0-py3-none-any.whl", hash = "sha256:b5011f270ab5eb0abf13385f851315585cc37ef330dd88e27ec3d34d651fd47a"},
+    {file = "anyio-4.8.0.tar.gz", hash = "sha256:1d9fe889df5212298c0c0723fa20479d1b94883a2df44bd3897aa91083316f7a"},
+]
+
+[package.dependencies]
+exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""}
+idna = ">=2.8"
+sniffio = ">=1.1"
+typing_extensions = {version = ">=4.5", markers = "python_version < \"3.13\""}
+
+[package.extras]
+doc = ["Sphinx (>=7.4,<8.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx_rtd_theme"]
+test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "trustme", "truststore (>=0.9.1)", "uvloop (>=0.21)"]
+trio = ["trio (>=0.26.1)"]
 
 [[package]]
 name = "attrs"
-version = "23.2.0"
+version = "24.3.0"
 description = "Classes Without Boilerplate"
+category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"},
-    {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"},
+    {file = "attrs-24.3.0-py3-none-any.whl", hash = "sha256:ac96cd038792094f438ad1f6ff80837353805ac950cd2aa0e0625ef19850c308"},
+    {file = "attrs-24.3.0.tar.gz", hash = "sha256:8f5c07333d543103541ba7be0e2ce16eeee8130cb0b3f9238ab904ce1e85baff"},
 ]
 
 [package.extras]
-cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
-dev = ["attrs[tests]", "pre-commit"]
-docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
-tests = ["attrs[tests-no-zope]", "zope-interface"]
-tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
-tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
+benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit-uv", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
+tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
 
 [[package]]
 name = "bio"
 version = "1.6.2"
 description = "bio"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -42,6 +67,7 @@ tqdm = "*"
 name = "biopython"
 version = "1.84"
 description = "Freely available tools for computational molecular biology."
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -77,137 +103,144 @@ numpy = "*"
 
 [[package]]
 name = "biothings-client"
-version = "0.3.1"
+version = "0.4.1"
 description = "Python Client for BioThings API services."
+category = "main"
 optional = false
-python-versions = ">=2.7"
+python-versions = ">=3.6"
 files = [
-    {file = "biothings_client-0.3.1-py2.py3-none-any.whl", hash = "sha256:c08437f652d9282da785e098288ef7cf3aa2a79f5d90c480eadfce96b846013e"},
-    {file = "biothings_client-0.3.1.tar.gz", hash = "sha256:c972bf2e02b6f9cc78f7f2fbc5ef02cc56fe4f8a2adcb8801ec902f4ab7011e6"},
+    {file = "biothings_client-0.4.1-py3-none-any.whl", hash = "sha256:9cbc17461b2bf6af6ed200929b886d6670d450af2034b428cd833f725695265a"},
+    {file = "biothings_client-0.4.1.tar.gz", hash = "sha256:5b34e09c905280b5bd2538f1f34b6fc780c53c8da9b4074e3ff304836046f613"},
 ]
 
 [package.dependencies]
-requests = ">=2.3.0"
+httpx = ">=0.22.0"
 
 [package.extras]
-caching = ["requests-cache (>=0.4.13)"]
-dataframe = ["pandas (>=0.18.0)"]
+caching = ["anysqlite", "hishel[sqlite]"]
+dataframe = ["pandas (>=1.1.5)"]
 jsonld = ["PyLD (>=0.7.2)"]
+tests = ["pytest (>=7.0.1)", "pytest-asyncio (>=0.16.0)"]
 
 [[package]]
 name = "certifi"
-version = "2024.7.4"
+version = "2024.12.14"
 description = "Python package for providing Mozilla's CA Bundle."
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"},
-    {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"},
+    {file = "certifi-2024.12.14-py3-none-any.whl", hash = "sha256:1275f7a45be9464efc1173084eaa30f866fe2e47d389406136d332ed4967ec56"},
+    {file = "certifi-2024.12.14.tar.gz", hash = "sha256:b650d30f370c2b724812bee08008be0c4163b163ddaec3f2546c1caf65f191db"},
 ]
 
 [[package]]
 name = "charset-normalizer"
-version = "3.3.2"
+version = "3.4.1"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
+category = "main"
 optional = false
-python-versions = ">=3.7.0"
-files = [
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 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
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 ]
 
 [package.dependencies]
-numpy = ">=1.20"
+numpy = ">=1.23"
 
 [package.extras]
 bokeh = ["bokeh", "selenium"]
 docs = ["furo", "sphinx (>=7.2)", "sphinx-copybutton"]
-mypy = ["contourpy[bokeh,docs]", "docutils-stubs", "mypy (==1.8.0)", "types-Pillow"]
+mypy = ["contourpy[bokeh,docs]", "docutils-stubs", "mypy (==1.11.1)", "types-Pillow"]
 test = ["Pillow", "contourpy[test-no-images]", "matplotlib"]
-test-no-images = ["pytest", "pytest-cov", "pytest-xdist", "wurlitzer"]
+test-no-images = ["pytest", "pytest-cov", "pytest-rerunfailures", "pytest-xdist", "wurlitzer"]
 
 [[package]]
 name = "coverage"
 version = "7.6.10"
 description = "Code coverage measurement for Python"
+category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -359,6 +415,7 @@ toml = ["tomli"]
 name = "cycler"
 version = "0.12.1"
 description = "Composable style cycles"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -372,24 +429,26 @@ tests = ["pytest", "pytest-cov", "pytest-xdist"]
 
 [[package]]
 name = "et-xmlfile"
-version = "1.1.0"
+version = "2.0.0"
 description = "An implementation of lxml.xmlfile for the standard library"
+category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
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 ]
 
 [[package]]
 name = "exceptiongroup"
-version = "1.2.1"
+version = "1.2.2"
 description = "Backport of PEP 654 (exception groups)"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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-    {file = "exceptiongroup-1.2.1.tar.gz", hash = "sha256:a4785e48b045528f5bfe627b6ad554ff32def154f42372786903b7abcfe1aa16"},
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 ]
 
 [package.extras]
@@ -399,6 +458,7 @@ test = ["pytest (>=6)"]
 name = "fasteners"
 version = "0.19"
 description = "A python package that provides useful locks"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -408,53 +468,62 @@ files = [
 
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@@ -475,6 +544,7 @@ woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
 name = "gprofiler-official"
 version = "1.0.0"
 description = "Functional enrichment analysis and more via the g:Profiler toolkit"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -489,6 +559,7 @@ requests = "*"
 name = "griddataformats"
 version = "1.0.2"
 description = "Reading and writing of data on regular grids in Python"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -501,15 +572,75 @@ mrcfile = "*"
 numpy = ">=1.21"
 scipy = "*"
 
+[[package]]
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+description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1"
+category = "main"
+optional = false
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+trio = ["trio (>=0.22.0,<1.0)"]
+
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+description = "The next generation HTTP client."
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+
+[package.extras]
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+http2 = ["h2 (>=3,<5)"]
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+zstd = ["zstandard (>=0.18.0)"]
+
 [[package]]
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+category = "dev"
 optional = false
 python-versions = ">=3.9"
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 [package.dependencies]
@@ -518,10 +649,10 @@ exceptiongroup = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 sortedcontainers = ">=2.1.0,<3.0.0"
 
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+all = ["black (>=19.10b0)", "click (>=7.0)", "crosshair-tool (>=0.0.81)", "django (>=4.2)", "dpcontracts (>=0.4)", "hypothesis-crosshair (>=0.0.18)", "lark (>=0.10.1)", "libcst (>=0.3.16)", "numpy (>=1.19.3)", "pandas (>=1.1)", "pytest (>=4.6)", "python-dateutil (>=1.4)", "pytz (>=2014.1)", "redis (>=3.0.0)", "rich (>=9.0.0)", "tzdata (>=2024.2)"]
 cli = ["black (>=19.10b0)", "click (>=7.0)", "rich (>=9.0.0)"]
 codemods = ["libcst (>=0.3.16)"]
-crosshair = ["crosshair-tool (>=0.0.78)", "hypothesis-crosshair (>=0.0.18)"]
+crosshair = ["crosshair-tool (>=0.0.81)", "hypothesis-crosshair (>=0.0.18)"]
 dateutil = ["python-dateutil (>=1.4)"]
 django = ["django (>=4.2)"]
 dpcontracts = ["dpcontracts (>=0.4)"]
@@ -536,37 +667,47 @@ zoneinfo = ["tzdata (>=2024.2)"]
 
 [[package]]
 name = "idna"
-version = "3.7"
+version = "3.10"
 description = "Internationalized Domain Names in Applications (IDNA)"
+category = "main"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
 files = [
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+    {file = "idna-3.10-py3-none-any.whl", hash = "sha256:946d195a0d259cbba61165e88e65941f16e9b36ea6ddb97f00452bae8b1287d3"},
+    {file = "idna-3.10.tar.gz", hash = "sha256:12f65c9b470abda6dc35cf8e63cc574b1c52b11df2c86030af0ac09b01b13ea9"},
 ]
 
+[package.extras]
+all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2)"]
+
 [[package]]
 name = "importlib-resources"
-version = "6.4.0"
+version = "6.5.2"
 description = "Read resources from Python packages"
+category = "main"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 [package.dependencies]
 zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
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-testing = ["jaraco.test (>=5.4)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)", "zipp (>=3.17)"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["jaraco.test (>=5.4)", "pytest (>=6,!=8.1.*)", "zipp (>=3.17)"]
+type = ["pytest-mypy"]
 
 [[package]]
 name = "iniconfig"
 version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -578,6 +719,7 @@ files = [
 name = "joblib"
 version = "1.4.2"
 description = "Lightweight pipelining with Python functions"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -589,6 +731,7 @@ files = [
 name = "jsonpickle"
 version = "4.0.0"
 description = "jsonpickle encodes/decodes any Python object to/from JSON"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -607,6 +750,7 @@ testing = ["PyYAML", "atheris (>=2.3.0,<2.4.0)", "bson", "ecdsa", "feedparser",
 name = "kaleido"
 version = "0.2.1"
 description = "Static image export for web-based visualization libraries with zero dependencies"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -620,266 +764,274 @@ files = [
 
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+version = "1.4.7"
 description = "A fast implementation of the Cassowary constraint solver"
+category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
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 [package.extras]
@@ -887,12 +1039,13 @@ cssselect = ["cssselect (>=0.7)"]
 html-clean = ["lxml-html-clean"]
 html5 = ["html5lib"]
 htmlsoup = ["BeautifulSoup4"]
-source = ["Cython (>=3.0.10)"]
+source = ["Cython (>=3.0.11)"]
 
 [[package]]
 name = "matplotlib"
 version = "3.9.4"
 description = "Python plotting package"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
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 version = "0.2.0"
 description = "Stand-alone XDRLIB module (from cpython 3.10.8)"
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 optional = false
 python-versions = ">=3.7"
 files = [
@@ -972,6 +1126,7 @@ testing = ["pytest"]
 name = "mdanalysis"
 version = "2.7.0"
 description = "An object-oriented toolkit to analyze molecular dynamics trajectories."
+category = "main"
 optional = false
 python-versions = ">=3.9"
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 name = "mmtf-python"
 version = "1.1.3"
 description = "A decoding libary for the PDB mmtf format"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1036,13 +1192,14 @@ test = ["coverage"]
 
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 version = "3.2.2"
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 python-versions = "*"
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 ]
 
 [package.dependencies]
-mypy-extensions = ">=1.0.0"
+mypy_extensions = ">=1.0.0"
 tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
-typing-extensions = ">=4.1.0"
+typing_extensions = ">=4.6.0"
 
 [package.extras]
 dmypy = ["psutil (>=4.0)"]
+faster-cache = ["orjson"]
 install-types = ["pip"]
 mypyc = ["setuptools (>=50)"]
 reports = ["lxml"]
@@ -1178,6 +1358,7 @@ reports = ["lxml"]
 name = "mypy-extensions"
 version = "1.0.0"
 description = "Type system extensions for programs checked with the mypy type checker."
+category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1189,6 +1370,7 @@ files = [
 name = "numpy"
 version = "1.26.4"
 description = "Fundamental package for array computing in Python"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1234,6 +1416,7 @@ files = [
 name = "openpyxl"
 version = "3.1.5"
 description = "A Python library to read/write Excel 2010 xlsx/xlsm files"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1246,19 +1429,21 @@ et-xmlfile = "*"
 
 [[package]]
 name = "packaging"
-version = "24.0"
+version = "24.2"
 description = "Core utilities for Python packages"
+category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
 name = "pandas"
 version = "2.2.3"
 description = "Powerful data structures for data analysis, time series, and statistics"
+category = "main"
 optional = false
 python-versions = ">=3.9"
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 name = "pdb-tools"
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 description = "A swiss army knife for PDB files."
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 version = "1.5"
 description = "A lightweight pure python package for reading, writing and manipulating mmCIF files distributed by the wwPDB."
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 optional = false
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 ]
 
 [package.extras]
-docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-removed-in", "sphinxext-opengraph"]
+docs = ["furo", "olefile", "sphinx (>=8.1)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinxext-opengraph"]
 fpx = ["olefile"]
 mic = ["olefile"]
-tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
+tests = ["check-manifest", "coverage (>=7.4.2)", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout", "trove-classifiers (>=2024.10.12)"]
 typing = ["typing-extensions"]
 xmp = ["defusedxml"]
 
 [[package]]
 name = "platformdirs"
-version = "4.2.2"
+version = "4.3.6"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.extras]
-docs = ["furo (>=2023.9.10)", "proselint (>=0.13)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"]
-test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)"]
-type = ["mypy (>=1.8)"]
+docs = ["furo (>=2024.8.6)", "proselint (>=0.14)", "sphinx (>=8.0.2)", "sphinx-autodoc-typehints (>=2.4)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=8.3.2)", "pytest-cov (>=5)", "pytest-mock (>=3.14)"]
+type = ["mypy (>=1.11.2)"]
 
 [[package]]
 name = "plotly"
 version = "5.24.1"
 description = "An open-source, interactive data visualization library for Python"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1484,6 +1676,7 @@ tenacity = ">=6.2.0"
 name = "pluggy"
 version = "1.5.0"
 description = "plugin and hook calling mechanisms for python"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1497,13 +1690,14 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "pooch"
-version = "1.8.1"
-description = "\"Pooch manages your Python library's sample data files: it automatically downloads and stores them in a local directory, with support for versioning and corruption checks.\""
+version = "1.8.2"
+description = "A friend to fetch your data files"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "pooch-1.8.2.tar.gz", hash = "sha256:76561f0de68a01da4df6af38e9955c4c9d1a5c90da73f7e40276a5728ec83d10"},
 ]
 
 [package.dependencies]
@@ -1518,13 +1712,14 @@ xxhash = ["xxhash (>=1.4.3)"]
 
 [[package]]
 name = "pyparsing"
-version = "3.1.2"
+version = "3.2.1"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
+category = "main"
 optional = false
-python-versions = ">=3.6.8"
+python-versions = ">=3.9"
 files = [
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+    {file = "pyparsing-3.2.1-py3-none-any.whl", hash = "sha256:506ff4f4386c4cec0590ec19e6302d3aedb992fdc02c761e90416f158dacf8e1"},
+    {file = "pyparsing-3.2.1.tar.gz", hash = "sha256:61980854fd66de3a90028d679a954d5f2623e83144b5afe5ee86f43d762e5f0a"},
 ]
 
 [package.extras]
@@ -1534,6 +1729,7 @@ diagrams = ["jinja2", "railroad-diagrams"]
 name = "pytest"
 version = "8.3.4"
 description = "pytest: simple powerful testing with Python"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1556,6 +1752,7 @@ dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments
 name = "pytest-cov"
 version = "6.0.0"
 description = "Pytest plugin for measuring coverage."
+category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1574,6 +1771,7 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "virtualenv"]
 name = "pytest-mock"
 version = "3.14.0"
 description = "Thin-wrapper around the mock package for easier use with pytest"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1591,6 +1789,7 @@ dev = ["pre-commit", "pytest-asyncio", "tox"]
 name = "python-dateutil"
 version = "2.9.0.post0"
 description = "Extensions to the standard Python datetime module"
+category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
@@ -1603,19 +1802,21 @@ six = ">=1.5"
 
 [[package]]
 name = "pytz"
-version = "2024.1"
+version = "2024.2"
 description = "World timezone definitions, modern and historical"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
-    {file = "pytz-2024.1-py2.py3-none-any.whl", hash = "sha256:328171f4e3623139da4983451950b28e95ac706e13f3f2630a879749e7a8b319"},
-    {file = "pytz-2024.1.tar.gz", hash = "sha256:2a29735ea9c18baf14b448846bde5a48030ed267578472d8955cd0e7443a9812"},
+    {file = "pytz-2024.2-py2.py3-none-any.whl", hash = "sha256:31c7c1817eb7fae7ca4b8c7ee50c72f93aa2dd863de768e1ef4245d426aa0725"},
+    {file = "pytz-2024.2.tar.gz", hash = "sha256:2aa355083c50a0f93fa581709deac0c9ad65cca8a9e9beac660adcbd493c798a"},
 ]
 
 [[package]]
 name = "requests"
 version = "2.32.3"
 description = "Python HTTP for Humans."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1637,6 +1838,7 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 name = "scipy"
 version = "1.13.1"
 description = "Fundamental algorithms for scientific computing in Python"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1677,19 +1879,33 @@ test = ["array-api-strict", "asv", "gmpy2", "hypothesis (>=6.30)", "mpmath", "po
 
 [[package]]
 name = "six"
-version = "1.16.0"
+version = "1.17.0"
 description = "Python 2 and 3 compatibility utilities"
+category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
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+    {file = "six-1.17.0-py2.py3-none-any.whl", hash = "sha256:4721f391ed90541fddacab5acf947aa0d3dc7d27b2e1e8eda2be8970586c3274"},
+    {file = "six-1.17.0.tar.gz", hash = "sha256:ff70335d468e7eb6ec65b95b99d3a2836546063f63acc5171de367e834932a81"},
+]
+
+[[package]]
+name = "sniffio"
+version = "1.3.1"
+description = "Sniff out which async library your code is running under"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "sniffio-1.3.1-py3-none-any.whl", hash = "sha256:2f6da418d1f1e0fddd844478f41680e794e6051915791a034ff65e5f100525a2"},
+    {file = "sniffio-1.3.1.tar.gz", hash = "sha256:f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc"},
 ]
 
 [[package]]
 name = "sortedcontainers"
 version = "2.4.0"
 description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set"
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -1699,13 +1915,14 @@ files = [
 
 [[package]]
 name = "tenacity"
-version = "8.3.0"
+version = "9.0.0"
 description = "Retry code until it succeeds"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "tenacity-8.3.0.tar.gz", hash = "sha256:953d4e6ad24357bceffbc9707bc74349aca9d245f68eb65419cf0c249a1949a2"},
+    {file = "tenacity-9.0.0-py3-none-any.whl", hash = "sha256:93de0c98785b27fcf659856aa9f54bfbd399e29969b0621bc7f762bd441b4539"},
+    {file = "tenacity-9.0.0.tar.gz", hash = "sha256:807f37ca97d62aa361264d497b0e31e92b8027044942bfa756160d908320d73b"},
 ]
 
 [package.extras]
@@ -1716,6 +1933,7 @@ test = ["pytest", "tornado (>=4.5)", "typeguard"]
 name = "threadpoolctl"
 version = "3.5.0"
 description = "threadpoolctl"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1725,44 +1943,78 @@ files = [
 
 [[package]]
 name = "tomli"
-version = "2.0.1"
+version = "2.2.1"
 description = "A lil' TOML parser"
+category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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-    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
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+    {file = "tomli-2.2.1-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a92ef1a44547e894e2a17d24e7557a5e85a9e1d0048b0b5e7541f76c5032cb13"},
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+    {file = "tomli-2.2.1-cp313-cp313-musllinux_1_2_i686.whl", hash = "sha256:d920f33822747519673ee656a4b6ac33e382eca9d331c87770faa3eef562aeb2"},
+    {file = "tomli-2.2.1-cp313-cp313-musllinux_1_2_x86_64.whl", hash = "sha256:a198f10c4d1b1375d7687bc25294306e551bf1abfa4eace6650070a5c1ae2744"},
+    {file = "tomli-2.2.1-cp313-cp313-win32.whl", hash = "sha256:d3f5614314d758649ab2ab3a62d4f2004c825922f9e370b29416484086b264ec"},
+    {file = "tomli-2.2.1-cp313-cp313-win_amd64.whl", hash = "sha256:a38aa0308e754b0e3c67e344754dff64999ff9b513e691d0e786265c93583c69"},
+    {file = "tomli-2.2.1-py3-none-any.whl", hash = "sha256:cb55c73c5f4408779d0cf3eef9f762b9c9f147a77de7b258bef0a5628adc85cc"},
+    {file = "tomli-2.2.1.tar.gz", hash = "sha256:cd45e1dc79c835ce60f7404ec8119f2eb06d38b1deba146f07ced3bbc44505ff"},
 ]
 
 [[package]]
 name = "tqdm"
-version = "4.66.4"
+version = "4.67.1"
 description = "Fast, Extensible Progress Meter"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "tqdm-4.66.4-py3-none-any.whl", hash = "sha256:b75ca56b413b030bc3f00af51fd2c1a1a5eac6a0c1cca83cbb37a5c52abce644"},
-    {file = "tqdm-4.66.4.tar.gz", hash = "sha256:e4d936c9de8727928f3be6079590e97d9abfe8d39a590be678eb5919ffc186bb"},
+    {file = "tqdm-4.67.1-py3-none-any.whl", hash = "sha256:26445eca388f82e72884e0d580d5464cd801a3ea01e63e5601bdff9ba6a48de2"},
+    {file = "tqdm-4.67.1.tar.gz", hash = "sha256:f8aef9c52c08c13a65f30ea34f4e5aac3fd1a34959879d7e59e63027286627f2"},
 ]
 
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
 [package.extras]
-dev = ["pytest (>=6)", "pytest-cov", "pytest-timeout", "pytest-xdist"]
+dev = ["nbval", "pytest (>=6)", "pytest-asyncio (>=0.24)", "pytest-cov", "pytest-timeout"]
+discord = ["requests"]
 notebook = ["ipywidgets (>=6)"]
 slack = ["slack-sdk"]
 telegram = ["requests"]
 
 [[package]]
 name = "types-requests"
-version = "2.32.0.20240521"
+version = "2.32.0.20241016"
 description = "Typing stubs for requests"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "types-requests-2.32.0.20240521.tar.gz", hash = "sha256:c5c4a0ae95aad51f1bf6dae9eed04a78f7f2575d4b171da37b622e08b93eb5d3"},
-    {file = "types_requests-2.32.0.20240521-py3-none-any.whl", hash = "sha256:ab728ba43ffb073db31f21202ecb97db8753ded4a9dc49cb480d8a5350c5c421"},
+    {file = "types-requests-2.32.0.20241016.tar.gz", hash = "sha256:0d9cad2f27515d0e3e3da7134a1b6f28fb97129d86b867f24d9c726452634d95"},
+    {file = "types_requests-2.32.0.20241016-py3-none-any.whl", hash = "sha256:4195d62d6d3e043a4eaaf08ff8a62184584d2e8684e9d2aa178c7915a7da3747"},
 ]
 
 [package.dependencies]
@@ -1770,35 +2022,38 @@ urllib3 = ">=2"
 
 [[package]]
 name = "typing-extensions"
-version = "4.11.0"
+version = "4.12.2"
 description = "Backported and Experimental Type Hints for Python 3.8+"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "typing_extensions-4.11.0-py3-none-any.whl", hash = "sha256:c1f94d72897edaf4ce775bb7558d5b79d8126906a14ea5ed1635921406c0387a"},
-    {file = "typing_extensions-4.11.0.tar.gz", hash = "sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0"},
+    {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"},
+    {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"},
 ]
 
 [[package]]
 name = "tzdata"
-version = "2024.1"
+version = "2024.2"
 description = "Provider of IANA time zone data"
+category = "main"
 optional = false
 python-versions = ">=2"
 files = [
-    {file = "tzdata-2024.1-py2.py3-none-any.whl", hash = "sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252"},
-    {file = "tzdata-2024.1.tar.gz", hash = "sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd"},
+    {file = "tzdata-2024.2-py2.py3-none-any.whl", hash = "sha256:a48093786cdcde33cad18c2555e8532f34422074448fbc874186f0abd79565cd"},
+    {file = "tzdata-2024.2.tar.gz", hash = "sha256:7d85cc416e9382e69095b7bdf4afd9e3880418a2413feec7069d533d6b4e31cc"},
 ]
 
 [[package]]
 name = "urllib3"
-version = "2.2.2"
+version = "2.3.0"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
+category = "main"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "urllib3-2.2.2-py3-none-any.whl", hash = "sha256:a448b2f64d686155468037e1ace9f2d2199776e17f0a46610480d311f73e3472"},
-    {file = "urllib3-2.2.2.tar.gz", hash = "sha256:dd505485549a7a552833da5e6063639d0d177c04f23bc3864e41e5dc5f612168"},
+    {file = "urllib3-2.3.0-py3-none-any.whl", hash = "sha256:1cee9ad369867bfdbbb48b7dd50374c0967a0bb7710050facf0dd6911440e3df"},
+    {file = "urllib3-2.3.0.tar.gz", hash = "sha256:f8c5449b3cf0861679ce7e0503c7b44b5ec981bec0d1d3795a07f1ba96f0204d"},
 ]
 
 [package.extras]
@@ -1809,20 +2064,25 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "zipp"
-version = "3.19.1"
+version = "3.21.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
+category = "main"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "zipp-3.19.1-py3-none-any.whl", hash = "sha256:2828e64edb5386ea6a52e7ba7cdb17bb30a73a858f5eb6eb93d8d36f5ea26091"},
-    {file = "zipp-3.19.1.tar.gz", hash = "sha256:35427f6d5594f4acf82d25541438348c26736fa9b3afa2754bcd63cdb99d8e8f"},
+    {file = "zipp-3.21.0-py3-none-any.whl", hash = "sha256:ac1bbe05fd2991f160ebce24ffbac5f6d11d83dc90891255885223d42b3cd931"},
+    {file = "zipp-3.21.0.tar.gz", hash = "sha256:2c9958f6430a2040341a52eb608ed6dd93ef4392e02ffe219417c1b28b5dd1f4"},
 ]
 
 [package.extras]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
+type = ["pytest-mypy"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "bfd893d534792e9b76f175db1b7521e4e317b48a66513c03b07819d2eb7fa368"
+content-hash = "28ad6f6649c0e348b8f38a04e800329495860074df05ec66c16a4d93432a75c8"
diff --git a/pyproject.toml b/pyproject.toml
index 531106c..2c01cff 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ classifiers = [
 [tool.poetry.dependencies]
 python = ">=3.9,<3.12"
 bio = "1.6.2"
-lxml = "5.2.2"
+lxml = "5.3.0"
 mdanalysis = "2.7.0"
 requests = "2.32.3"
 biopython = "1.84"