From fca81db8ead4d2759d1ba9b3d5baf64360908216 Mon Sep 17 00:00:00 2001
From: Vincent Menger <vmenger@protonmail.com>
Date: Tue, 6 May 2025 10:01:49 +0200
Subject: [PATCH 1/2] update dependencies

---
 CHANGELOG.md   |    6 +
 poetry.lock    | 1104 +++++++++++++++++++++++++-----------------------
 pyproject.toml |    4 +-
 3 files changed, 580 insertions(+), 534 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d0e70f25..c7e50bb5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## 3.0.4 (2025-05-06)
+
+### Changed
+
+- Updated dependencies
+
 ## 3.0.3 (2024-07-16)
 
 ### Added
diff --git a/poetry.lock b/poetry.lock
index 4d0faf9a..595b3364 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,25 +1,25 @@
-# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
-version = "0.7.13"
-description = "A configurable sidebar-enabled Sphinx theme"
+version = "0.7.16"
+description = "A light, configurable Sphinx theme"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.9"
 files = [
-    {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
-    {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
+    {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"},
+    {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
 ]
 
 [[package]]
 name = "astroid"
-version = "3.0.1"
+version = "3.3.9"
 description = "An abstract syntax tree for Python with inference support."
 optional = false
-python-versions = ">=3.8.0"
+python-versions = ">=3.9.0"
 files = [
-    {file = "astroid-3.0.1-py3-none-any.whl", hash = "sha256:7d5895c9825e18079c5aeac0572bc2e4c83205c95d416e0b4fee8bc361d2d9ca"},
-    {file = "astroid-3.0.1.tar.gz", hash = "sha256:86b0bb7d7da0be1a7c4aedb7974e391b32d4ed89e33de6ed6902b4b15c97577e"},
+    {file = "astroid-3.3.9-py3-none-any.whl", hash = "sha256:d05bfd0acba96a7bd43e222828b7d9bc1e138aaeb0649707908d3702a9831248"},
+    {file = "astroid-3.3.9.tar.gz", hash = "sha256:622cc8e3048684aa42c820d9d218978021c3c3d174fb03a9f0d615921744f550"},
 ]
 
 [package.dependencies]
@@ -27,38 +27,36 @@ typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "attrs"
-version = "23.1.0"
+version = "25.3.0"
 description = "Classes Without Boilerplate"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"},
-    {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"},
+    {file = "attrs-25.3.0-py3-none-any.whl", hash = "sha256:427318ce031701fea540783410126f03899a97ffc6f61596ad581ac2e40e3bc3"},
+    {file = "attrs-25.3.0.tar.gz", hash = "sha256:75d7cefc7fb576747b2c81b4442d4d4a1ce0900973527c011d1030fd3bf4af1b"},
 ]
 
 [package.extras]
-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]"]
+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"]
+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 = "babel"
-version = "2.13.1"
+version = "2.17.0"
 description = "Internationalization utilities"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "Babel-2.13.1-py3-none-any.whl", hash = "sha256:7077a4984b02b6727ac10f1f7294484f737443d7e2e66c5e4380e41a3ae0b4ed"},
-    {file = "Babel-2.13.1.tar.gz", hash = "sha256:33e0952d7dd6374af8dbf6768cc4ddf3ccfefc244f9986d4074704f2fbd18900"},
+    {file = "babel-2.17.0-py3-none-any.whl", hash = "sha256:4d0b53093fdfb4b21c92b5213dba5a1b23885afa8383709427046b21c366e5f2"},
+    {file = "babel-2.17.0.tar.gz", hash = "sha256:0c54cffb19f690cdcc52a3b50bcbf71e07a808d1c80d549f2459b9d2cf0afb9d"},
 ]
 
-[package.dependencies]
-setuptools = {version = "*", markers = "python_version >= \"3.12\""}
-
 [package.extras]
-dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
+dev = ["backports.zoneinfo", "freezegun (>=1.0,<2.0)", "jinja2 (>=3.0)", "pytest (>=6.0)", "pytest-cov", "pytz", "setuptools", "tzdata"]
 
 [[package]]
 name = "black"
@@ -97,123 +95,125 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "certifi"
-version = "2023.11.17"
+version = "2025.4.26"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"},
-    {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"},
+    {file = "certifi-2025.4.26-py3-none-any.whl", hash = "sha256:30350364dfe371162649852c63336a15c70c6510c2ad5015b21c2345311805f3"},
+    {file = "certifi-2025.4.26.tar.gz", hash = "sha256:0a816057ea3cdefcef70270d2c515e4506bbc954f417fa5ade2021213bb8f0c6"},
 ]
 
 [[package]]
 name = "charset-normalizer"
-version = "3.3.2"
+version = "3.4.2"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
-python-versions = ">=3.7.0"
-files = [
-    {file = "charset-normalizer-3.3.2.tar.gz", hash = "sha256:f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5"},
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-    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:9063e24fdb1e498ab71cb7419e24622516c4a04476b17a2dab57e8baa30d6e03"},
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 ]
 
 [package.dependencies]
@@ -299,32 +310,33 @@ toml = ["tomli"]
 
 [[package]]
 name = "dill"
-version = "0.3.7"
+version = "0.4.0"
 description = "serialize all of Python"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
 graph = ["objgraph (>=1.7.2)"]
+profile = ["gprof2dot (>=2022.7.29)"]
 
 [[package]]
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+version = "1.0.1"
 description = "Create your own document de-identifier using docdeid, a simple framework independent of language or domain."
 optional = false
-python-versions = ">=3.9,<4.0"
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 files = [
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 [package.dependencies]
 frozendict = ">=2.3.10,<3.0.0"
-numpy = ">=1.23.1,<2.0.0"
+numpy = ">=1.23.1,<3.0"
 
 [[package]]
 name = "docformatter"
@@ -357,27 +369,27 @@ files = [
 
 [[package]]
 name = "emoji"
-version = "2.9.0"
+version = "2.14.1"
 description = "Emoji for Python"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
-dev = ["coverage", "coveralls", "pytest"]
+dev = ["coverage", "pytest (>=7.4.4)"]
 
 [[package]]
 name = "exceptiongroup"
-version = "1.2.0"
+version = "1.2.2"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
@@ -401,13 +413,13 @@ pyflakes = ">=2.5.0,<2.6.0"
 
 [[package]]
 name = "flake8-annotations"
-version = "3.0.1"
+version = "3.1.1"
 description = "Flake8 Type Annotation Checks"
 optional = false
 python-versions = ">=3.8.1"
 files = [
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 ]
 
 [package.dependencies]
@@ -433,61 +445,66 @@ dev = ["pyTest", "pyTest-cov"]
 
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 ]
 
 [[package]]
 name = "idna"
-version = "3.6"
+version = "3.10"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
 files = [
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-    {file = "idna-3.6.tar.gz", hash = "sha256:9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca"},
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 ]
 
+[package.extras]
+all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2)"]
+
 [[package]]
 name = "imagesize"
 version = "1.4.1"
@@ -501,60 +518,61 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "6.9.0"
+version = "8.7.0"
 description = "Read metadata from Python packages"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
-zipp = ">=0.5"
+zipp = ">=3.20"
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
+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)"]
 perf = ["ipython"]
-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"]
+test = ["flufl.flake8", "importlib_resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"]
+type = ["pytest-mypy"]
 
 [[package]]
 name = "iniconfig"
-version = "2.0.0"
+version = "2.1.0"
 description = "brain-dead simple config-ini parsing"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
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 ]
 
 [[package]]
 name = "isort"
-version = "5.12.0"
+version = "5.13.2"
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 optional = false
 python-versions = ">=3.8.0"
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-plugins = ["setuptools"]
-requirements-deprecated-finder = ["pip-api", "pipreqs"]
+colors = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "jinja2"
-version = "3.1.2"
+version = "3.1.6"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -599,71 +617,72 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
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@@ -910,13 +938,13 @@ testutils = ["gitpython (>3)"]
 
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@@ -950,61 +978,64 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtuale
 
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 [[package]]
@@ -1226,13 +1257,13 @@ files = [
 
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 description = "Python HTTP for Humans."
 optional = false
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 [package.dependencies]
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 use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
-[[package]]
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-version = "69.0.2"
-description = "Easily download, build, install, upgrade, and uninstall Python packages"
-optional = false
-python-versions = ">=3.8"
-files = [
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-
-[package.extras]
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-
 [[package]]
 name = "snowballstemmer"
 version = "2.2.0"
@@ -1309,56 +1324,50 @@ test = ["cython", "html5lib", "pytest (>=4.6)", "typed_ast"]
 
 [[package]]
 name = "sphinxcontrib-applehelp"
-version = "1.0.7"
+version = "2.0.0"
 description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
 optional = false
 python-versions = ">=3.9"
 files = [
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-[package.dependencies]
-Sphinx = ">=5"
-
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-devhelp"
-version = "1.0.5"
+version = "2.0.0"
 description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
 optional = false
 python-versions = ">=3.9"
 files = [
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 ]
 
-[package.dependencies]
-Sphinx = ">=5"
-
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-htmlhelp"
-version = "2.0.4"
+version = "2.1.0"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
 optional = false
 python-versions = ">=3.9"
 files = [
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 ]
 
-[package.dependencies]
-Sphinx = ">=5"
-
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
+standalone = ["Sphinx (>=5)"]
 test = ["html5lib", "pytest"]
 
 [[package]]
@@ -1377,38 +1386,34 @@ test = ["flake8", "mypy", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-qthelp"
-version = "1.0.6"
+version = "2.0.0"
 description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
 optional = false
 python-versions = ">=3.9"
 files = [
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-[package.dependencies]
-Sphinx = ">=5"
-
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
-test = ["pytest"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
+standalone = ["Sphinx (>=5)"]
+test = ["defusedxml (>=0.7.1)", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-serializinghtml"
-version = "1.1.9"
+version = "2.0.0"
 description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
 optional = false
 python-versions = ">=3.9"
 files = [
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-[package.dependencies]
-Sphinx = ">=5"
-
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
@@ -1424,35 +1429,65 @@ files = [
 
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-version = "2.0.1"
+version = "2.2.1"
 description = "A lil' TOML parser"
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-python-versions = ">=3.7"
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 ]
 
 [[package]]
 name = "tomlkit"
-version = "0.12.3"
+version = "0.13.2"
 description = "Style preserving TOML library"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
 name = "typing-extensions"
-version = "4.8.0"
+version = "4.13.2"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
@@ -1467,36 +1502,41 @@ files = [
 
 [[package]]
 name = "urllib3"
-version = "2.1.0"
+version = "2.4.0"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.extras]
 brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+h2 = ["h2 (>=4,<5)"]
 socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
 zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "zipp"
-version = "3.17.0"
+version = "3.21.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 [package.extras]
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+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 = ["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"
-content-hash = "0aa47f24ef708b11b56e5a478275eabb54bc44670ce7aa5fa2f30f0b39d1ce66"
+content-hash = "f41f31311c3ba4f52137737c0a1229da1fb6ebd7bb89f1b93b115e11e3d7f20e"
diff --git a/pyproject.toml b/pyproject.toml
index ba06e034..feb0ce35 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "deduce"
-version = "3.0.3"
+version = "3.0.4"
 description = "Deduce: de-identification method for Dutch medical text"
 authors = ["Vincent Menger <vmenger@protonmail.com>"]
 maintainers = ["Vincent Menger <vmenger@protonmail.com>"]
@@ -27,7 +27,7 @@ author = "Vincent Menger"
 [tool.poetry.dependencies]
 python = "^3.9"
 rapidfuzz = "^2.11.1"
-docdeid = "1.0.0"
+docdeid = "1.0.1"
 regex = "^2022.9.13"
 frozendict = "^2.3.10"
 

From 265cc2d516ecd577e26a0abf6d5513145ed683c3 Mon Sep 17 00:00:00 2001
From: Vincent Menger <vmenger@protonmail.com>
Date: Tue, 6 May 2025 10:06:07 +0200
Subject: [PATCH 2/2] Disable updated pylints

---
 deduce/annotator.py      | 2 +-
 deduce/deduce.py         | 2 +-
 deduce/lookup_structs.py | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/deduce/annotator.py b/deduce/annotator.py
index 788bb546..45e45e0d 100644
--- a/deduce/annotator.py
+++ b/deduce/annotator.py
@@ -143,7 +143,7 @@ def _get_chained_token(
 
         return token
 
-    def _match_sequence(  # pylint: disable=R0913
+    def _match_sequence(  # pylint: disable=R0913, R0917
         self,
         text: str,
         pattern: list[dict],
diff --git a/deduce/deduce.py b/deduce/deduce.py
index 3bd1356f..84c62299 100644
--- a/deduce/deduce.py
+++ b/deduce/deduce.py
@@ -62,7 +62,7 @@ class Deduce(dd.DocDeid):  # pylint: disable=R0903
             using the cache when this is set to `True`.
     """
 
-    def __init__(  # pylint: disable=R0913
+    def __init__(  # pylint: disable=R0913, R0917
         self,
         load_base_config: bool = True,
         config: Optional[Union[str, dict]] = None,
diff --git a/deduce/lookup_structs.py b/deduce/lookup_structs.py
index fa89ecac..10cd4af6 100644
--- a/deduce/lookup_structs.py
+++ b/deduce/lookup_structs.py
@@ -201,7 +201,7 @@ def cache_lookup_structs(
         pickle.dump(cache, file)
 
 
-def get_lookup_structs(  # pylint: disable=R0913
+def get_lookup_structs(  # pylint: disable=R0913, R0917
     lookup_path: Path,
     cache_path: Path,
     tokenizer: Tokenizer,