From 5d651630a7e9d29802652a60dd50b22aafff3515 Mon Sep 17 00:00:00 2001
From: "Mark A. Miller" <MAM@lbl.gov>
Date: Fri, 17 Apr 2026 13:19:42 -0400
Subject: [PATCH] Run poetry update to close Dependabot alerts (draft for
 discussion)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Bumps ~40 packages via poetry update. See PR description for full
strengths/weaknesses analysis.

Does NOT close the critical h11 alert — 0.16.0 is the latest and no
patch has been released yet.
---
 poetry.lock | 7389 ++++++++++++++++++++++++++++-----------------------
 1 file changed, 4135 insertions(+), 3254 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 8a5bd43f..4356c7be 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,16 +1,4 @@
-# This file is automatically @generated by Poetry 2.3.2 and should not be changed by hand.
-
-[[package]]
-name = "aiofiles"
-version = "24.1.0"
-description = "File support for asyncio."
-optional = false
-python-versions = ">=3.8"
-groups = ["main"]
-files = [
-    {file = "aiofiles-24.1.0-py3-none-any.whl", hash = "sha256:b4ec55f4195e3eb5d7abd1bf7e061763e864dd4954231fb8539a0ef8bb8260e5"},
-    {file = "aiofiles-24.1.0.tar.gz", hash = "sha256:22a075c9e5a3810f0c2e48f3008c94d68c65d763b9b03857924c99e57355166c"},
-]
+# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand.
 
 [[package]]
 name = "aiohappyeyeballs"
@@ -26,103 +14,137 @@ files = [
 
 [[package]]
 name = "aiohttp"
-version = "3.12.13"
+version = "3.13.5"
 description = "Async http client/server framework (asyncio)"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
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 ]
 
 [package.dependencies]
 aiohappyeyeballs = ">=2.5.0"
-aiosignal = ">=1.1.2"
+aiosignal = ">=1.4.0"
 async-timeout = {version = ">=4.0,<6.0", markers = "python_version < \"3.11\""}
 attrs = ">=17.3.0"
 frozenlist = ">=1.1.1"
@@ -131,22 +153,23 @@ propcache = ">=0.2.0"
 yarl = ">=1.17.0,<2.0"
 
 [package.extras]
-speedups = ["Brotli ; platform_python_implementation == \"CPython\"", "aiodns (>=3.3.0)", "brotlicffi ; platform_python_implementation != \"CPython\""]
+speedups = ["Brotli (>=1.2) ; platform_python_implementation == \"CPython\"", "aiodns (>=3.3.0)", "backports.zstd ; platform_python_implementation == \"CPython\" and python_version < \"3.14\"", "brotlicffi (>=1.2) ; platform_python_implementation != \"CPython\""]
 
 [[package]]
 name = "aiosignal"
-version = "1.3.2"
+version = "1.4.0"
 description = "aiosignal: a list of registered asynchronous callbacks"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
 files = [
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 ]
 
 [package.dependencies]
 frozenlist = ">=1.1.0"
+typing-extensions = {version = ">=4.2", markers = "python_version < \"3.13\""}
 
 [[package]]
 name = "airium"
@@ -201,26 +224,23 @@ files = [
 
 [[package]]
 name = "anyio"
-version = "4.9.0"
-description = "High level compatibility layer for multiple asynchronous event loop implementations"
+version = "4.13.0"
+description = "High-level concurrency and networking framework on top of asyncio or Trio"
 optional = false
-python-versions = ">=3.9"
-groups = ["main", "dev"]
+python-versions = ">=3.10"
+groups = ["dev"]
 files = [
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 [package.dependencies]
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-sniffio = ">=1.1"
 typing_extensions = {version = ">=4.5", markers = "python_version < \"3.13\""}
 
 [package.extras]
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-trio = ["trio (>=0.26.1)"]
+trio = ["trio (>=0.32.0)"]
 
 [[package]]
 name = "appdirs"
@@ -264,105 +284,97 @@ argon2-cffi-bindings = "*"
 
 [[package]]
 name = "argon2-cffi-bindings"
-version = "21.2.0"
+version = "25.1.0"
 description = "Low-level CFFI bindings for Argon2"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.9"
 groups = ["dev"]
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-
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-tests = ["pytest"]
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+]
+
+[package.dependencies]
+cffi = [
+    {version = ">=1.0.1", markers = "python_version < \"3.14\""},
+    {version = ">=2.0.0b1", markers = "python_version >= \"3.14\""},
+]
 
 [[package]]
 name = "arrow"
-version = "1.3.0"
+version = "1.4.0"
 description = "Better dates & times for Python"
 optional = false
 python-versions = ">=3.8"
 groups = ["main", "dev"]
 files = [
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 ]
 
 [package.dependencies]
 python-dateutil = ">=2.7.0"
-types-python-dateutil = ">=2.8.10"
+tzdata = {version = "*", markers = "python_version >= \"3.9\""}
 
 [package.extras]
 doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"]
-test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"]
+test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2025.2)", "simplejson (==3.*)"]
 
 [[package]]
 name = "asttokens"
-version = "3.0.0"
+version = "3.0.1"
 description = "Annotate AST trees with source code positions"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
 files = [
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 ]
 
 [package.extras]
-astroid = ["astroid (>=2,<4)"]
-test = ["astroid (>=2,<4)", "pytest", "pytest-cov", "pytest-xdist"]
+astroid = ["astroid (>=2,<5)"]
+test = ["astroid (>=2,<5)", "pytest (<9.0)", "pytest-cov", "pytest-xdist"]
 
 [[package]]
 name = "async-lru"
-version = "2.0.5"
+version = "2.3.0"
 description = "Simple LRU cache for asyncio"
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 groups = ["dev"]
 files = [
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+    {file = "async_lru-2.3.0.tar.gz", hash = "sha256:89bdb258a0140d7313cf8f4031d816a042202faa61d0ab310a0a538baa1c24b6"},
 ]
 
 [package.dependencies]
 typing_extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
 
-[[package]]
-name = "async-property"
-version = "0.2.2"
-description = "Python decorator for async properties."
-optional = false
-python-versions = "*"
-groups = ["main"]
-files = [
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-]
-
 [[package]]
 name = "async-timeout"
 version = "5.0.1"
@@ -378,24 +390,16 @@ files = [
 
 [[package]]
 name = "attrs"
-version = "25.3.0"
+version = "26.1.0"
 description = "Classes Without Boilerplate"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 groups = ["main", "dev"]
 files = [
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+    {file = "attrs-26.1.0-py3-none-any.whl", hash = "sha256:c647aa4a12dfbad9333ca4e71fe62ddc36f4e63b2d260a37a8b83d2f043ac309"},
+    {file = "attrs-26.1.0.tar.gz", hash = "sha256:d03ceb89cb322a8fd706d4fb91940737b6642aa36998fe130a9bc96c985eff32"},
 ]
 
-[package.extras]
-benchmark = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
-cov = ["cloudpickle ; platform_python_implementation == \"CPython\"", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
-dev = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pre-commit-uv", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
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-tests = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
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-
 [[package]]
 name = "aws"
 version = "0.2.5"
@@ -414,14 +418,14 @@ prettytable = ">=0.7"
 
 [[package]]
 name = "babel"
-version = "2.17.0"
+version = "2.18.0"
 description = "Internationalization utilities"
 optional = false
 python-versions = ">=3.8"
 groups = ["main", "dev", "docs"]
 files = [
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+    {file = "babel-2.18.0-py3-none-any.whl", hash = "sha256:e2b422b277c2b9a9630c1d7903c2a00d0830c409c59ac8cae9081c92f1aeba35"},
+    {file = "babel-2.18.0.tar.gz", hash = "sha256:b80b99a14bd085fcacfa15c9165f651fbb3406e66cc603abf11c5750937c992d"},
 ]
 
 [package.extras]
@@ -429,18 +433,17 @@ dev = ["backports.zoneinfo ; python_version < \"3.9\"", "freezegun (>=1.0,<2.0)"
 
 [[package]]
 name = "bacdive"
-version = "1.0.0"
+version = "2.0.0"
 description = "BacDive-API - Programmatic Access to the BacDive Database"
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
 files = [
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+    {file = "bacdive-2.0.0-py3-none-any.whl", hash = "sha256:d9998ff50bcd2c439e12882bca41f6a8c7f8d998a3cb0b0acab71d42cbc9afdd"},
+    {file = "bacdive-2.0.0.tar.gz", hash = "sha256:4056328f36505e9ba27c36f80fe93687917b4fe4856524d8e8061b95e3868e66"},
 ]
 
 [package.dependencies]
-python-keycloak = "*"
 requests = ">=2.25.1"
 urllib3 = ">=1.26.5"
 
@@ -458,63 +461,75 @@ files = [
 
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-version = "4.3.0"
+version = "5.0.0"
 description = "Modern password hashing for your software and your servers"
 optional = false
 python-versions = ">=3.8"
 groups = ["s3"]
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 [package.extras]
@@ -523,18 +538,18 @@ typecheck = ["mypy"]
 
 [[package]]
 name = "beautifulsoup4"
-version = "4.13.4"
+version = "4.14.3"
 description = "Screen-scraping library"
 optional = false
 python-versions = ">=3.7.0"
 groups = ["main", "dev"]
 files = [
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 ]
 
 [package.dependencies]
-soupsieve = ">1.2"
+soupsieve = ">=1.6.1"
 typing-extensions = ">=4.0.0"
 
 [package.extras]
@@ -546,148 +561,176 @@ lxml = ["lxml"]
 
 [[package]]
 name = "biolink-model"
-version = "3.6.0"
-description = "'A high level datamodel of biological entities and associations'"
+version = "4.3.9"
+description = "The Biolink Model is a high-level data model designed to standardize types and relationships in biological knowledgebases."
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 groups = ["main"]
 files = [
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 ]
 
 [package.dependencies]
-curies = "*"
-linkml = "*"
-prefixmaps = "*"
+beautifulsoup4 = ">=4.0.0"
+click = ">8.0.0,<8.2.0"
+curies = ">=0.9.0,<1"
+linkml = "1.9.4"
+linkml-runtime = "1.9.5"
+path = ">=17.0.0,<18"
+prefixmaps = ">=0.2.3,<1"
+pyyaml = ">=6.0.1,<7"
+requests = ">=2.32.3"
+stringcase = ">=1.2.0,<2"
+
+[package.extras]
+docs = ["mkdocs-material"]
 
 [[package]]
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+gha = ["more-itertools"]
+health = ["click-default-group", "jinja2", "pandas (<3.0)", "pyyaml", "tabulate"]
+mapping-checking = ["pandas (<3.0)", "sentence-transformers"]
+paper-ranking = ["pandas (<3.0)", "pubmed-downloader (>=0.0.12)", "scikit-learn", "tabulate"]
+web = ["a2wsgi", "api-analytics[fastapi]", "bootstrap-flask", "curies[fastapi]", "fastapi", "flask (>=3.0.0)", "markdown", "pyyaml", "rdflib", "rdflib-endpoint (>=0.5.3)", "rdflib-jsonld", "uvicorn", "werkzeug (>=3.0.0)"]
 
 [[package]]
 name = "bioversions"
-version = "0.8.58"
+version = "0.8.325"
 description = "Get the current version for biological databases"
 optional = false
 python-versions = ">=3.10"
 groups = ["main"]
 files = [
-    {file = "bioversions-0.8.58-py3-none-any.whl", hash = "sha256:96d8c07965093c40267c87f2400641726831a93aaa4802707b81010333e0e6d2"},
-    {file = "bioversions-0.8.58.tar.gz", hash = "sha256:72d49d10a67f96e612ddf5a8f6efc134b0ac38d3517bd3a8efbc6a721354983d"},
+    {file = "bioversions-0.8.325-py3-none-any.whl", hash = "sha256:7d29ea7306adac3187e937ee6d1893a86ca02bcb5c2ba3412b7858b6d8a8c855"},
+    {file = "bioversions-0.8.325.tar.gz", hash = "sha256:d75cbdc89b5ecf60a122d0bdefcc9b308ff23ed37ceee0eb592d1d7301de9035"},
 ]
 
 [package.dependencies]
 beautifulsoup4 = "*"
 bioregistry = {version = ">=0.11.35", extras = ["align"]}
 cachier = ">=2.2.1"
+class-resolver = ">=0.7.1"
 click = "*"
 click-default-group = "*"
 dataclasses-json = "*"
@@ -695,9 +738,11 @@ lxml = "*"
 more-click = "*"
 psycopg2-binary = "*"
 pydantic = ">=2.0"
-pystow = ">=0.1.0"
+pystow = {version = ">=0.7.8", extras = ["bs4"]}
+python-dateutil = "*"
 pyyaml = "*"
 requests = "*"
+ror-downloader = ">=0.0.4"
 tabulate = "*"
 tqdm = "*"
 
@@ -709,14 +754,14 @@ web = ["bootstrap-flask", "flask"]
 
 [[package]]
 name = "bleach"
-version = "6.2.0"
+version = "6.3.0"
 description = "An easy safelist-based HTML-sanitizing tool."
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 groups = ["dev"]
 files = [
-    {file = "bleach-6.2.0-py3-none-any.whl", hash = "sha256:117d9c6097a7c3d22fd578fcd8d35ff1e125df6736f554da4e432fdd63f31e5e"},
-    {file = "bleach-6.2.0.tar.gz", hash = "sha256:123e894118b8a599fd80d3ec1a6d4cc7ce4e5882b1317a7e1ba69b56e95f991f"},
+    {file = "bleach-6.3.0-py3-none-any.whl", hash = "sha256:fe10ec77c93ddf3d13a73b035abaac7a9f5e436513864ccdad516693213c65d6"},
+    {file = "bleach-6.3.0.tar.gz", hash = "sha256:6f3b91b1c0a02bb9a78b5a454c92506aa0fdf197e1d5e114d2e00c6f64306d22"},
 ]
 
 [package.dependencies]
@@ -728,19 +773,19 @@ css = ["tinycss2 (>=1.1.0,<1.5)"]
 
 [[package]]
 name = "bmt"
-version = "1.4.5"
+version = "1.4.8"
 description = "Biolink Model Toolkit: A Python API for working with the Biolink Model"
 optional = false
-python-versions = "<4.0,>=3.9"
+python-versions = "<4,>=3.10"
 groups = ["main"]
 files = [
-    {file = "bmt-1.4.5-py3-none-any.whl", hash = "sha256:987efdbd76e15aa3a9f1d6170bfe10de959a97df01d34f37020fe12cdd56f019"},
-    {file = "bmt-1.4.5.tar.gz", hash = "sha256:847386e83b2c5d4e62050ad4a336dc5c043330593b8d07216c5b18feba763e23"},
+    {file = "bmt-1.4.8-py3-none-any.whl", hash = "sha256:cba57f58a2ae85a5f29ab30cac84b7c5032d095741b07e8f252395bbee4ce276"},
+    {file = "bmt-1.4.8.tar.gz", hash = "sha256:9286dbc83caf61117fbe45eee23308dcdbfaa0413c0514ae9d3505aa9f6a5781"},
 ]
 
 [package.dependencies]
+biolink-model = ">=4.3.3,<5.0.0"
 deprecation = ">=2.1.0,<3.0.0"
-linkml-runtime = ">=1.6.3,<2.0.0"
 stringcase = ">=1.2.0,<2.0.0"
 
 [[package]]
@@ -757,34 +802,34 @@ files = [
 
 [[package]]
 name = "boto3"
-version = "1.39.2"
+version = "1.42.90"
 description = "The AWS SDK for Python"
 optional = false
 python-versions = ">=3.9"
 groups = ["main", "s3"]
 files = [
-    {file = "boto3-1.39.2-py3-none-any.whl", hash = "sha256:a37f202978f11f384e3fd1f0ff8938367b527845493f9509357e1732debc390f"},
-    {file = "boto3-1.39.2.tar.gz", hash = "sha256:edad811edacb8c99f2fe59b117d9b9d8ee3972beb6c090c8aa164ddbc506d67d"},
+    {file = "boto3-1.42.90-py3-none-any.whl", hash = "sha256:fde7f7bcad6ec8342d6bf18f56d118d0cb6df189310cfaf73e2eb6443b1cb418"},
+    {file = "boto3-1.42.90.tar.gz", hash = "sha256:bafb5bb1dea262ac95f9afb1e415f06a9490f05cb203bdd897d0afdcd17733c6"},
 ]
 
 [package.dependencies]
-botocore = ">=1.39.2,<1.40.0"
+botocore = ">=1.42.90,<1.43.0"
 jmespath = ">=0.7.1,<2.0.0"
-s3transfer = ">=0.13.0,<0.14.0"
+s3transfer = ">=0.16.0,<0.17.0"
 
 [package.extras]
 crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "botocore"
-version = "1.39.2"
+version = "1.42.90"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">=3.9"
 groups = ["main", "s3"]
 files = [
-    {file = "botocore-1.39.2-py3-none-any.whl", hash = "sha256:921cab9aa6e1e4ceddcece5b55b57daae7722168e74409f1aafcc2c5589df676"},
-    {file = "botocore-1.39.2.tar.gz", hash = "sha256:474445fa8b281dd5db8fc62184f0f6e494d4f1efb96fe10312490583e67a9dd0"},
+    {file = "botocore-1.42.90-py3-none-any.whl", hash = "sha256:5c95504720346990adc8e3ae1023eb46f9409084b79688e4773ba7099c5fd3db"},
+    {file = "botocore-1.42.90.tar.gz", hash = "sha256:234c39492cd3088acb021d999e3392a4d50238ae3e70b9d9ae1504c30d9009d1"},
 ]
 
 [package.dependencies]
@@ -793,7 +838,22 @@ python-dateutil = ">=2.1,<3.0.0"
 urllib3 = {version = ">=1.25.4,<2.2.0 || >2.2.0,<3", markers = "python_version >= \"3.10\""}
 
 [package.extras]
-crt = ["awscrt (==0.23.8)"]
+crt = ["awscrt (==0.31.2)"]
+
+[[package]]
+name = "bs4"
+version = "0.0.2"
+description = "Dummy package for Beautiful Soup (beautifulsoup4)"
+optional = false
+python-versions = "*"
+groups = ["main"]
+files = [
+    {file = "bs4-0.0.2-py2.py3-none-any.whl", hash = "sha256:abf8742c0805ef7f662dce4b51cca104cffe52b835238afc169142ab9b3fbccc"},
+    {file = "bs4-0.0.2.tar.gz", hash = "sha256:a48685c58f50fe127722417bae83fe6badf500d54b55f7e39ffe43b798653925"},
+]
+
+[package.dependencies]
+beautifulsoup4 = "*"
 
 [[package]]
 name = "cachetools"
@@ -809,139 +869,165 @@ files = [
 
 [[package]]
 name = "cachier"
-version = "3.1.2"
+version = "4.2.0"
 description = "Persistent, stale-free, local and cross-machine caching for Python functions."
 optional = false
-python-versions = "*"
+python-versions = ">=3.10"
 groups = ["main"]
 files = [
-    {file = "cachier-3.1.2-py3-none-any.whl", hash = "sha256:24c0fefd6aef1d38a4337590aba82f3c4bd844df18393ba93c7fd7dcc98da304"},
-    {file = "cachier-3.1.2.tar.gz", hash = "sha256:8ef53b6ae83ba04d8864d2e1f45eb8b46eecb611d0f6a24c006e8fda074c6557"},
+    {file = "cachier-4.2.0-py3-none-any.whl", hash = "sha256:0c33b79e3cb6f250ce90d5225fbe4e0d9ec7133a7ea8b700428eb2b7d12402a0"},
+    {file = "cachier-4.2.0.tar.gz", hash = "sha256:db9626237176ca837fa77dd5d15581453b2e9926a1a9ead94d4e676f6af8c5e4"},
 ]
 
 [package.dependencies]
 portalocker = ">=2.3.2"
+pympler = ">=1"
 watchdog = ">=2.3.1"
 
+[package.extras]
+all = ["boto3 (>=1.26)", "pymongo (>=4)", "redis (>=4)", "sqlalchemy (>=2)"]
+mongo = ["pymongo (>=4)"]
+redis = ["redis (>=4)"]
+s3 = ["boto3 (>=1.26)"]
+sql = ["sqlalchemy (>=2)"]
+
 [[package]]
 name = "cattrs"
-version = "25.1.1"
+version = "26.1.0"
 description = "Composable complex class support for attrs and dataclasses."
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 groups = ["main"]
 files = [
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+    {file = "cattrs-26.1.0-py3-none-any.whl", hash = "sha256:d1e0804c42639494d469d08d4f26d6b9de9b8ab26b446db7b5f8c2e97f7c3096"},
+    {file = "cattrs-26.1.0.tar.gz", hash = "sha256:fa239e0f0ec0715ba34852ce813986dfed1e12117e209b816ab87401271cdd40"},
 ]
 
 [package.dependencies]
-attrs = ">=24.3.0"
+attrs = ">=25.4.0"
 exceptiongroup = {version = ">=1.1.1", markers = "python_version < \"3.11\""}
-typing-extensions = ">=4.12.2"
+typing-extensions = ">=4.14.0"
 
 [package.extras]
 bson = ["pymongo (>=4.4.0)"]
 cbor2 = ["cbor2 (>=5.4.6)"]
 msgpack = ["msgpack (>=1.0.5)"]
 msgspec = ["msgspec (>=0.19.0) ; implementation_name == \"cpython\""]
-orjson = ["orjson (>=3.10.7) ; implementation_name == \"cpython\""]
+orjson = ["orjson (>=3.11.3) ; implementation_name == \"cpython\""]
 pyyaml = ["pyyaml (>=6.0)"]
 tomlkit = ["tomlkit (>=0.11.8)"]
+tomllib = ["tomli (>=1.1.0) ; python_version < \"3.11\"", "tomli-w (>=1.1.0)"]
 ujson = ["ujson (>=5.10.0)"]
 
 [[package]]
 name = "certifi"
-version = "2025.6.15"
+version = "2026.2.25"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.7"
 groups = ["main", "dev", "docs"]
 files = [
-    {file = "certifi-2025.6.15-py3-none-any.whl", hash = "sha256:2e0c7ce7cb5d8f8634ca55d2ba7e6ec2689a2fd6537d8dec1296a477a4910057"},
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+    {file = "certifi-2026.2.25-py3-none-any.whl", hash = "sha256:027692e4402ad994f1c42e52a4997a9763c646b73e4096e4d5d6db8af1d6f0fa"},
+    {file = "certifi-2026.2.25.tar.gz", hash = "sha256:e887ab5cee78ea814d3472169153c2d12cd43b14bd03329a39a9c6e2e80bfba7"},
 ]
 
 [[package]]
 name = "cffi"
-version = "1.17.1"
+version = "2.0.0"
 description = "Foreign Function Interface for Python calling C code."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 groups = ["main", "dev", "s3"]
 files = [
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 ]
 
 [[package]]
 name = "chembl-downloader"
-version = "0.5.1"
+version = "0.5.2"
 description = "Reproducibly download, open, parse, and query ChEMBL"
 optional = false
 python-versions = ">=3.10"
 groups = ["main"]
 files = [
-    {file = "chembl_downloader-0.5.1-py3-none-any.whl", hash = "sha256:08a2f10ae8b45a91b886fc2420406c0d0bee30ef847492be9b6638b59a46d8c7"},
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+    {file = "chembl_downloader-0.5.2-py3-none-any.whl", hash = "sha256:565a5dfc4f7ebaf91035b8c88f6aba3e4ca7d6e77e1cbebed13fb64aa4f2b66b"},
+    {file = "chembl_downloader-0.5.2.tar.gz", hash = "sha256:b74f7067fb8017e98b19ba1df2629165cffeaabb034551dda623b7b3eb1f3816"},
 ]
 
 [package.dependencies]
 click = "*"
 more-click = "*"
-pystow = "*"
+pystow = ">=0.7.6"
 tqdm = "*"
 typing-extensions = "*"
 
 [package.extras]
 docs = ["sphinx (>=8)", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme (>=3.0)"]
+notebooks = ["biomappings (>=0.4.0)", "matplotlib", "matplotlib-venn", "pyobo[gilda-slim]", "rdkit", "scikit-learn", "scipy", "seaborn"]
 pandas = ["pandas"]
 rdkit = ["rdkit-pypi"]
 tests = ["coverage[toml]", "pytest"]
 
 [[package]]
 name = "class-resolver"
-version = "0.6.0"
+version = "0.7.1"
 description = "Lookup and instantiate classes with style."
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 groups = ["main"]
 files = [
-    {file = "class_resolver-0.6.0-py3-none-any.whl", hash = "sha256:cc629187a10bacff2e360939f8a4e8e7d209583dc8b318485ff91a0d24d5c9d0"},
-    {file = "class_resolver-0.6.0.tar.gz", hash = "sha256:8a3c20ab771925477f65cad8a49bb431e11543c82fbfadbf611c6769228a6cae"},
+    {file = "class_resolver-0.7.1-py3-none-any.whl", hash = "sha256:d177909a48fdf6d6a0c297d117742a83ea799e0f601a922aa9ccb23ca1200e00"},
+    {file = "class_resolver-0.7.1.tar.gz", hash = "sha256:86f73b8cc5ed9111b7d9c5e331b51856a32f205179c66a56a9c520d0f6e82f66"},
 ]
 
 [package.dependencies]
 typing-extensions = "*"
 
 [package.extras]
-click = ["click"]
+click = ["click (>=8.2)"]
 numpy = ["numpy"]
 optuna = ["optuna"]
 sklearn = ["scikit-learn"]
@@ -1134,14 +1258,14 @@ torch-geometric = ["torch", "torch-geometric", "torch-sparse"]
 
 [[package]]
 name = "click"
-version = "8.2.1"
+version = "8.1.8"
 description = "Composable command line interface toolkit"
 optional = false
-python-versions = ">=3.10"
+python-versions = ">=3.7"
 groups = ["main", "dev", "docs"]
 files = [
-    {file = "click-8.2.1-py3-none-any.whl", hash = "sha256:61a3265b914e850b85317d0b3109c7f8cd35a670f963866005d6ef1d5175a12b"},
-    {file = "click-8.2.1.tar.gz", hash = "sha256:27c491cc05d968d271d5a1db13e3b5a184636d9d930f148c50b038f0d0646202"},
+    {file = "click-8.1.8-py3-none-any.whl", hash = "sha256:63c132bbbed01578a06712a2d1f497bb62d9c1c0d329b7903a866228027263b2"},
+    {file = "click-8.1.8.tar.gz", hash = "sha256:ed53c9d8990d83c2a27deae68e4ee337473f6330c040a31d4225c9574d16096a"},
 ]
 
 [package.dependencies]
@@ -1203,19 +1327,16 @@ markers = {docs = "platform_system == \"Windows\" or sys_platform == \"win32\""}
 
 [[package]]
 name = "comm"
-version = "0.2.2"
+version = "0.2.3"
 description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc."
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
 files = [
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-
 [package.extras]
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 test = ["dict_hash", "pytest", "pytest-readme", "random_dict", "validate_version_code"]
 
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+typing-extensions = {version = ">=4.13.2", markers = "python_full_version < \"3.11.0\""}
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 sdist = ["build (>=1.0.0)"]
 ssh = ["bcrypt (>=3.1.5)"]
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 test-randomorder = ["pytest-randomly"]
 
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-version = "0.10.19"
+version = "0.13.4"
 description = "Idiomatic conversion between URIs and compact URIs (CURIEs)"
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 [package.dependencies]
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 typing-extensions = "*"
 
 [package.extras]
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 fastapi = ["defusedxml", "fastapi", "httpx", "python-multipart", "uvicorn"]
 flask = ["defusedxml", "flask"]
 pandas = ["pandas"]
 rdflib = ["rdflib"]
-tests = ["coverage[toml]", "pytest", "requests"]
+sqlalchemy = ["sqlalchemy"]
+sqlmodel = ["sqlmodel"]
 
 [[package]]
 name = "curies-processing"
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+version = "0.1.6"
 description = "Pre- and post-processing configuration for prefixes, CURIEs, and URIs"
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 python-versions = ">=3.10"
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 [package.dependencies]
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 [[package]]
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 [[package]]
 name = "deprecated"
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 description = "Python @deprecated decorator to deprecate old python classes, functions or methods."
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
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 ]
 
 [package.dependencies]
-wrapt = ">=1.10,<2"
+wrapt = ">=1.10,<3"
 
 [package.extras]
 dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "setuptools ; python_version >= \"3.12\"", "tox"]
@@ -1459,28 +1716,28 @@ packaging = "*"
 
 [[package]]
 name = "deptry"
-version = "0.24.0"
+version = "0.25.1"
 description = "A command line utility to check for unused, missing and transitive dependencies in a Python project."
 optional = false
 python-versions = ">=3.10"
 groups = ["dev"]
 files = [
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 ]
 
 [package.dependencies]
@@ -1488,40 +1745,40 @@ click = ">=8.0.0,<9"
 colorama = {version = ">=0.4.6", markers = "sys_platform == \"win32\""}
 packaging = ">=23.2"
 requirements-parser = ">=0.11.0,<1"
-tomli = {version = ">=2.0.1", markers = "python_full_version < \"3.11.0\""}
+tomli = {version = ">=2.0.1", markers = "python_full_version < \"3.15.0\""}
 
 [[package]]
 name = "distlib"
-version = "0.3.9"
+version = "0.4.0"
 description = "Distribution utilities"
 optional = false
 python-versions = "*"
 groups = ["main", "dev"]
 files = [
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 ]
 
 [[package]]
 name = "dnspython"
-version = "2.7.0"
+version = "2.8.0"
 description = "DNS toolkit"
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 groups = ["main"]
 files = [
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 ]
 
 [package.extras]
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-dnssec = ["cryptography (>=43)"]
-doh = ["h2 (>=4.1.0)", "httpcore (>=1.0.0)", "httpx (>=0.26.0)"]
-doq = ["aioquic (>=1.0.0)"]
-idna = ["idna (>=3.7)"]
-trio = ["trio (>=0.23)"]
-wmi = ["wmi (>=1.5.1)"]
+dev = ["black (>=25.1.0)", "coverage (>=7.0)", "flake8 (>=7)", "hypercorn (>=0.17.0)", "mypy (>=1.17)", "pylint (>=3)", "pytest (>=8.4)", "pytest-cov (>=6.2.0)", "quart-trio (>=0.12.0)", "sphinx (>=8.2.0)", "sphinx-rtd-theme (>=3.0.0)", "twine (>=6.1.0)", "wheel (>=0.45.0)"]
+dnssec = ["cryptography (>=45)"]
+doh = ["h2 (>=4.2.0)", "httpcore (>=1.0.0)", "httpx (>=0.28.0)"]
+doq = ["aioquic (>=1.2.0)"]
+idna = ["idna (>=3.10)"]
+trio = ["trio (>=0.30)"]
+wmi = ["wmi (>=1.5.1) ; platform_system == \"Windows\""]
 
 [[package]]
 name = "docker"
@@ -1552,11 +1809,25 @@ description = "Docutils -- Python Documentation Utilities"
 optional = false
 python-versions = ">=3.9"
 groups = ["main", "docs"]
+markers = "python_version == \"3.10\""
 files = [
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 ]
 
+[[package]]
+name = "docutils"
+version = "0.22.4"
+description = "Docutils -- Python Documentation Utilities"
+optional = false
+python-versions = ">=3.9"
+groups = ["main", "docs"]
+markers = "python_version >= \"3.11\""
+files = [
+    {file = "docutils-0.22.4-py3-none-any.whl", hash = "sha256:d0013f540772d1420576855455d050a2180186c91c15779301ac2ccb3eeb68de"},
+    {file = "docutils-0.22.4.tar.gz", hash = "sha256:4db53b1fde9abecbb74d91230d32ab626d94f6badfc575d6db9194a49df29968"},
+]
+
 [[package]]
 name = "drugbank-downloader"
 version = "0.2.0"
@@ -1582,49 +1853,51 @@ tests = ["coverage", "pytest"]
 
 [[package]]
 name = "duckdb"
-version = "1.3.1"
+version = "1.5.2"
 description = "DuckDB in-process database"
 optional = false
-python-versions = ">=3.7.0"
-groups = ["main"]
-files = [
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+]
+
+[package.extras]
+all = ["adbc-driver-manager", "fsspec", "ipython", "numpy", "pandas", "pyarrow"]
 
 [[package]]
 name = "elastic-transport"
@@ -1647,14 +1920,14 @@ develop = ["aiohttp", "furo", "httpx", "opentelemetry-api", "opentelemetry-sdk",
 
 [[package]]
 name = "elasticsearch"
-version = "8.18.1"
+version = "8.19.3"
 description = "Python client for Elasticsearch"
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
 files = [
-    {file = "elasticsearch-8.18.1-py3-none-any.whl", hash = "sha256:1a8c8b5ec3ce5be88f96d2f898375671648e96272978bce0dee3137d9326aabb"},
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+    {file = "elasticsearch-8.19.3.tar.gz", hash = "sha256:e84dd618a220cac25b962790085045dd27ac72e01c0a5d81bd29a2d47a71f03f"},
 ]
 
 [package.dependencies]
@@ -1664,7 +1937,7 @@ typing-extensions = "*"
 
 [package.extras]
 async = ["aiohttp (>=3,<4)"]
-dev = ["aiohttp", "black", "build", "coverage", "isort", "jinja2", "mapbox-vector-tile", "mypy", "nltk", "nox", "numpy", "orjson", "pandas", "pyarrow", "pyright", "pytest", "pytest-asyncio", "pytest-cov", "pytest-mock", "python-dateutil", "pyyaml (>=5.4)", "requests (>=2,<3)", "sentence-transformers", "simsimd", "tqdm", "twine", "types-python-dateutil", "types-tqdm", "unasync"]
+dev = ["aiohttp", "black", "build", "coverage", "isort", "jinja2", "mapbox-vector-tile", "mypy", "nox", "numpy", "orjson", "pandas", "pyarrow ; python_version < \"3.14\"", "pyright", "pytest", "pytest-asyncio", "pytest-cov", "pytest-mock", "python-dateutil", "pyyaml (>=5.4)", "requests (>=2,<3)", "simsimd", "tqdm", "twine", "types-python-dateutil", "types-tqdm", "unasync"]
 docs = ["sphinx", "sphinx-autodoc-typehints", "sphinx-rtd-theme (>=2.0)"]
 orjson = ["orjson (>=3)"]
 pyarrow = ["pyarrow (>=1)"]
@@ -1673,14 +1946,14 @@ vectorstore-mmr = ["numpy (>=1)", "simsimd (>=3)"]
 
 [[package]]
 name = "email-validator"
-version = "2.2.0"
+version = "2.3.0"
 description = "A robust email address syntax and deliverability validation library."
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
 files = [
-    {file = "email_validator-2.2.0-py3-none-any.whl", hash = "sha256:561977c2d73ce3611850a06fa56b414621e0c8faa9d66f2611407d87465da631"},
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 ]
 
 [package.dependencies]
@@ -1706,6 +1979,7 @@ description = "\"Python interface to NCBI's eutilities API\""
 optional = false
 python-versions = ">=3.6"
 groups = ["main"]
+markers = "python_version < \"3.12\""
 files = [
     {file = "eutils-0.6.0-py2.py3-none-any.whl", hash = "sha256:4938c4baff6ca52141204ff3eff3a91ec1e83e52a6c5d92e7163585117b96566"},
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@@ -1719,17 +1993,34 @@ requests = "*"
 [package.extras]
 dev = ["flake8", "ipython", "mock", "pytest", "pytest-cov", "restview", "setuptools", "sphinx", "sphinx-rtd-theme", "tox", "vcrpy", "yapf"]
 
+[[package]]
+name = "eutils"
+version = "0.6.1"
+description = "Python interface to NCBI's eutilities API"
+optional = false
+python-versions = ">=3.12"
+groups = ["main"]
+markers = "python_version >= \"3.12\""
+files = [
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+    {file = "eutils-0.6.1.tar.gz", hash = "sha256:68d4e007996d4b08171a936413f6ec2cd4c045ac83acf7df9e9b7110df06c030"},
+]
+
+[package.dependencies]
+lxml = "*"
+requests = "*"
+
 [[package]]
 name = "exceptiongroup"
-version = "1.3.0"
+version = "1.3.1"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 groups = ["main", "dev"]
 markers = "python_version == \"3.10\""
 files = [
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 ]
 
 [package.dependencies]
@@ -1740,14 +2031,14 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "executing"
-version = "2.2.0"
+version = "2.2.1"
 description = "Get the currently executing AST node of a frame, and other information"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
 files = [
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+    {file = "executing-2.2.1.tar.gz", hash = "sha256:3632cc370565f6648cc328b32435bd120a1e4ebb20c77e3fdde9a13cd1e533c4"},
 ]
 
 [package.extras]
@@ -1755,20 +2046,20 @@ tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipyth
 
 [[package]]
 name = "fabric"
-version = "3.2.2"
+version = "3.2.3"
 description = "High level SSH command execution"
 optional = false
 python-versions = "*"
 groups = ["s3"]
 files = [
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+    {file = "fabric-3.2.3.tar.gz", hash = "sha256:dcbd2c47ad87688facaef5cc11aab6d1ec9ed05645fed97a5de7204d5d17cc44"},
 ]
 
 [package.dependencies]
 decorator = ">=5"
 deprecated = ">=1.2"
-invoke = ">=2.0"
+invoke = ">=2.0,<3.0"
 paramiko = ">=2.4"
 
 [package.extras]
@@ -1776,37 +2067,33 @@ pytest = ["pytest (>=7)"]
 
 [[package]]
 name = "fairsharing-client"
-version = "0.1.0"
+version = "0.3.0"
 description = "A client to the FAIRsharing API"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.10"
 groups = ["main"]
 files = [
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+    {file = "fairsharing_client-0.3.0.tar.gz", hash = "sha256:b88021a9ce86a29a91e2e2f800d147f9d9715df0dc7f30615f74f4443a199d35"},
 ]
 
 [package.dependencies]
+click = "*"
 more-itertools = "*"
 pystow = "*"
 pyyaml = "*"
-requests = "*"
 tqdm = "*"
 
-[package.extras]
-docs = ["sphinx", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-rtd-theme"]
-tests = ["coverage", "pytest"]
-
 [[package]]
 name = "fastjsonschema"
-version = "2.21.1"
+version = "2.21.2"
 description = "Fastest Python implementation of JSON schema"
 optional = false
 python-versions = "*"
 groups = ["dev"]
 files = [
-    {file = "fastjsonschema-2.21.1-py3-none-any.whl", hash = "sha256:c9e5b7e908310918cf494a434eeb31384dd84a98b57a30bcb1f535015b554667"},
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+    {file = "fastjsonschema-2.21.2.tar.gz", hash = "sha256:b1eb43748041c880796cd077f1a07c3d94e93ae84bba5ed36800a33554ae05de"},
 ]
 
 [package.extras]
@@ -1814,66 +2101,67 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc
 
 [[package]]
 name = "fastobo"
-version = "0.13.0"
+version = "0.14.1"
 description = "Faultless AST for Open Biomedical Ontologies in Python."
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
 files = [
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+    {file = "frozenlist-1.8.0.tar.gz", hash = "sha256:3ede829ed8d842f6cd48fc7081d7a41001a56f1f38603f9d49bf3020d59a31ad"},
 ]
 
 [[package]]
@@ -2022,14 +2336,14 @@ rfc3987 = "*"
 
 [[package]]
 name = "gdown"
-version = "5.2.0"
+version = "6.0.0"
 description = "Google Drive Public File/Folder Downloader"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.10"
 groups = ["main"]
 files = [
-    {file = "gdown-5.2.0-py3-none-any.whl", hash = "sha256:33083832d82b1101bdd0e9df3edd0fbc0e1c5f14c9d8c38d2a35bf1683b526d6"},
-    {file = "gdown-5.2.0.tar.gz", hash = "sha256:2145165062d85520a3cd98b356c9ed522c5e7984d408535409fd46f94defc787"},
+    {file = "gdown-6.0.0-py3-none-any.whl", hash = "sha256:c82d39a6b09ed7778012515c2fa4ab4dc36d7789300cd0b16b87d3a3e4a09955"},
+    {file = "gdown-6.0.0.tar.gz", hash = "sha256:1f1f735a174ef3599fca95786aafac1219b9d85d4c729ccb95e674996c47fd44"},
 ]
 
 [package.dependencies]
@@ -2037,83 +2351,80 @@ beautifulsoup4 = "*"
 filelock = "*"
 requests = {version = "*", extras = ["socks"]}
 tqdm = "*"
-
-[package.extras]
-test = ["build", "mypy", "pytest", "pytest-xdist", "ruff", "twine", "types-requests", "types-setuptools"]
+typing-extensions = {version = ">=4.0", markers = "python_version < \"3.12\""}
 
 [[package]]
 name = "google-api-core"
-version = "2.25.1"
+version = "2.30.3"
 description = "Google API client core library"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.9"
 groups = ["main"]
 files = [
-    {file = "google_api_core-2.25.1-py3-none-any.whl", hash = "sha256:8a2a56c1fef82987a524371f99f3bd0143702fecc670c72e600c1cda6bf8dbb7"},
-    {file = "google_api_core-2.25.1.tar.gz", hash = "sha256:d2aaa0b13c78c61cb3f4282c464c046e45fbd75755683c9c525e6e8f7ed0a5e8"},
+    {file = "google_api_core-2.30.3-py3-none-any.whl", hash = "sha256:a85761ba72c444dad5d611c2220633480b2b6be2521eca69cca2dbb3ffd6bfe8"},
+    {file = "google_api_core-2.30.3.tar.gz", hash = "sha256:e601a37f148585319b26db36e219df68c5d07b6382cff2d580e83404e44d641b"},
 ]
 
 [package.dependencies]
 google-auth = ">=2.14.1,<3.0.0"
-googleapis-common-protos = ">=1.56.2,<2.0.0"
+googleapis-common-protos = ">=1.63.2,<2.0.0"
 proto-plus = [
     {version = ">=1.25.0,<2.0.0", markers = "python_version >= \"3.13\""},
     {version = ">=1.22.3,<2.0.0", markers = "python_version < \"3.13\""},
 ]
-protobuf = ">=3.19.5,<3.20.0 || >3.20.0,<3.20.1 || >3.20.1,<4.21.0 || >4.21.0,<4.21.1 || >4.21.1,<4.21.2 || >4.21.2,<4.21.3 || >4.21.3,<4.21.4 || >4.21.4,<4.21.5 || >4.21.5,<7.0.0"
-requests = ">=2.18.0,<3.0.0"
+protobuf = ">=4.25.8,<8.0.0"
+requests = ">=2.20.0,<3.0.0"
 
 [package.extras]
 async-rest = ["google-auth[aiohttp] (>=2.35.0,<3.0.0)"]
-grpc = ["grpcio (>=1.33.2,<2.0.0)", "grpcio (>=1.49.1,<2.0.0) ; python_version >= \"3.11\"", "grpcio-status (>=1.33.2,<2.0.0)", "grpcio-status (>=1.49.1,<2.0.0) ; python_version >= \"3.11\""]
-grpcgcp = ["grpcio-gcp (>=0.2.2,<1.0.0)"]
-grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.0)"]
+grpc = ["grpcio (>=1.33.2,<2.0.0)", "grpcio (>=1.49.1,<2.0.0) ; python_version >= \"3.11\"", "grpcio (>=1.75.1,<2.0.0) ; python_version >= \"3.14\"", "grpcio-status (>=1.33.2,<2.0.0)", "grpcio-status (>=1.49.1,<2.0.0) ; python_version >= \"3.11\"", "grpcio-status (>=1.75.1,<2.0.0) ; python_version >= \"3.14\""]
 
 [[package]]
 name = "google-auth"
-version = "2.40.3"
+version = "2.49.2"
 description = "Google Authentication Library"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 groups = ["main"]
 files = [
-    {file = "google_auth-2.40.3-py2.py3-none-any.whl", hash = "sha256:1370d4593e86213563547f97a92752fc658456fe4514c809544f330fed45a7ca"},
-    {file = "google_auth-2.40.3.tar.gz", hash = "sha256:500c3a29adedeb36ea9cf24b8d10858e152f2412e3ca37829b3fa18e33d63b77"},
+    {file = "google_auth-2.49.2-py3-none-any.whl", hash = "sha256:c2720924dfc82dedb962c9f52cabb2ab16714fd0a6a707e40561d217574ed6d5"},
+    {file = "google_auth-2.49.2.tar.gz", hash = "sha256:c1ae38500e73065dcae57355adb6278cf8b5c8e391994ae9cbadbcb9631ab409"},
 ]
 
 [package.dependencies]
-cachetools = ">=2.0.0,<6.0"
+cryptography = ">=38.0.3"
 pyasn1-modules = ">=0.2.1"
-rsa = ">=3.1.4,<5"
 
 [package.extras]
 aiohttp = ["aiohttp (>=3.6.2,<4.0.0)", "requests (>=2.20.0,<3.0.0)"]
-enterprise-cert = ["cryptography", "pyopenssl"]
-pyjwt = ["cryptography (<39.0.0) ; python_version < \"3.8\"", "cryptography (>=38.0.3)", "pyjwt (>=2.0)"]
-pyopenssl = ["cryptography (<39.0.0) ; python_version < \"3.8\"", "cryptography (>=38.0.3)", "pyopenssl (>=20.0.0)"]
+cryptography = ["cryptography (>=38.0.3)"]
+enterprise-cert = ["pyopenssl"]
+pyjwt = ["pyjwt (>=2.0)"]
+pyopenssl = ["pyopenssl (>=20.0.0)"]
 reauth = ["pyu2f (>=0.1.5)"]
 requests = ["requests (>=2.20.0,<3.0.0)"]
-testing = ["aiohttp (<3.10.0)", "aiohttp (>=3.6.2,<4.0.0)", "aioresponses", "cryptography (<39.0.0) ; python_version < \"3.8\"", "cryptography (>=38.0.3)", "flask", "freezegun", "grpcio", "mock", "oauth2client", "packaging", "pyjwt (>=2.0)", "pyopenssl (<24.3.0)", "pyopenssl (>=20.0.0)", "pytest", "pytest-asyncio", "pytest-cov", "pytest-localserver", "pyu2f (>=0.1.5)", "requests (>=2.20.0,<3.0.0)", "responses", "urllib3"]
+rsa = ["rsa (>=3.1.4,<5)"]
+testing = ["aiohttp (<3.10.0)", "aiohttp (>=3.6.2,<4.0.0)", "aioresponses", "flask", "freezegun", "grpcio", "packaging", "pyjwt (>=2.0)", "pyopenssl (<24.3.0)", "pyopenssl (>=20.0.0)", "pytest", "pytest-asyncio", "pytest-cov", "pytest-localserver", "pyu2f (>=0.1.5)", "requests (>=2.20.0,<3.0.0)", "responses", "urllib3"]
 urllib3 = ["packaging", "urllib3"]
 
 [[package]]
 name = "google-cloud-core"
-version = "2.4.3"
+version = "2.5.1"
 description = "Google Cloud API client core library"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.9"
 groups = ["main"]
 files = [
-    {file = "google_cloud_core-2.4.3-py2.py3-none-any.whl", hash = "sha256:5130f9f4c14b4fafdff75c79448f9495cfade0d8775facf1b09c3bf67e027f6e"},
-    {file = "google_cloud_core-2.4.3.tar.gz", hash = "sha256:1fab62d7102844b278fe6dead3af32408b1df3eb06f5c7e8634cbd40edc4da53"},
+    {file = "google_cloud_core-2.5.1-py3-none-any.whl", hash = "sha256:ea62cdf502c20e3e14be8a32c05ed02113d7bef454e40ff3fab6fe1ec9f1f4e7"},
+    {file = "google_cloud_core-2.5.1.tar.gz", hash = "sha256:3dc94bdec9d05a31d9f355045ed0f369fbc0d8c665076c734f065d729800f811"},
 ]
 
 [package.dependencies]
-google-api-core = ">=1.31.6,<2.0.dev0 || >2.3.0,<3.0.0.dev0"
-google-auth = ">=1.25.0,<3.0.dev0"
+google-api-core = ">=2.11.0,<3.0.0"
+google-auth = ">=2.14.1,<2.24.0 || >2.24.0,<2.25.0 || >2.25.0,<3.0.0"
 
 [package.extras]
-grpc = ["grpcio (>=1.38.0,<2.0.dev0)", "grpcio-status (>=1.38.0,<2.0.dev0)"]
+grpc = ["grpcio (>=1.38.0,<2.0.0) ; python_version < \"3.14\"", "grpcio (>=1.75.1,<2.0.0) ; python_version >= \"3.14\"", "grpcio-status (>=1.38.0,<2.0.0)"]
 
 [[package]]
 name = "google-cloud-storage"
@@ -2128,97 +2439,93 @@ files = [
 ]
 
 [package.dependencies]
-google-api-core = ">=2.15.0,<3.0.0.dev0"
-google-auth = ">=2.26.1,<3.0.dev0"
-google-cloud-core = ">=2.3.0,<3.0.dev0"
-google-crc32c = ">=1.0,<2.0.dev0"
+google-api-core = ">=2.15.0,<3.0.0dev"
+google-auth = ">=2.26.1,<3.0dev"
+google-cloud-core = ">=2.3.0,<3.0dev"
+google-crc32c = ">=1.0,<2.0dev"
 google-resumable-media = ">=2.7.2"
-requests = ">=2.18.0,<3.0.0.dev0"
+requests = ">=2.18.0,<3.0.0dev"
 
 [package.extras]
-protobuf = ["protobuf (<6.0.0.dev0)"]
+protobuf = ["protobuf (<6.0.0dev)"]
 tracing = ["opentelemetry-api (>=1.1.0)"]
 
 [[package]]
 name = "google-crc32c"
-version = "1.7.1"
+version = "1.8.0"
 description = "A python wrapper of the C library 'Google CRC32C'"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
 files = [
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 [package.extras]
 docs = ["Sphinx", "furo"]
-test = ["objgraph", "psutil"]
+test = ["objgraph", "psutil", "setuptools"]
 
 [[package]]
 name = "h11"
@@ -2315,7 +2627,7 @@ version = "0.16.0"
 description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1"
 optional = false
 python-versions = ">=3.8"
-groups = ["main", "dev"]
+groups = ["dev"]
 files = [
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@@ -2339,7 +2651,7 @@ version = "1.0.9"
 description = "A minimal low-level HTTP client."
 optional = false
 python-versions = ">=3.8"
-groups = ["main", "dev"]
+groups = ["dev"]
 files = [
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@@ -2361,7 +2673,7 @@ version = "0.28.1"
 description = "The next generation HTTP client."
 optional = false
 python-versions = ">=3.8"
-groups = ["main", "dev"]
+groups = ["dev"]
 files = [
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@@ -2382,14 +2694,14 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "humanize"
-version = "4.12.3"
+version = "4.15.0"
 description = "Python humanize utilities"
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 groups = ["main"]
 files = [
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 ]
 
 [package.extras]
@@ -2397,14 +2709,14 @@ tests = ["freezegun", "pytest", "pytest-cov"]
 
 [[package]]
 name = "identify"
-version = "2.6.12"
+version = "2.6.18"
 description = "File identification library for Python"
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 groups = ["dev"]
 files = [
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 ]
 
 [package.extras]
@@ -2412,14 +2724,14 @@ license = ["ukkonen"]
 
 [[package]]
 name = "idna"
-version = "3.10"
+version = "3.11"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 groups = ["main", "dev", "docs"]
 files = [
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 ]
 
 [package.extras]
@@ -2427,109 +2739,133 @@ all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2
 
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 name = "ijson"
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 python-versions = ">=3.9"
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 [[package]]
 name = "imagesize"
-version = "1.4.1"
+version = "1.5.0"
 description = "Getting image size from png/jpeg/jpeg2000/gif file"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
 groups = ["main", "docs"]
+markers = "python_version >= \"3.14\""
 files = [
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+]
+
+[[package]]
+name = "imagesize"
+version = "2.0.0"
+description = "Get image size from headers (BMP/PNG/JPEG/JPEG2000/GIF/TIFF/SVG/Netpbm/WebP/AVIF/HEIC/HEIF)"
+optional = false
+python-versions = "<3.15,>=3.10"
+groups = ["main", "docs"]
+markers = "python_version < \"3.14\""
+files = [
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 [[package]]
@@ -2552,26 +2888,6 @@ docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.link
 perf = ["ipython"]
 testing = ["flufl.flake8", "importlib-resources (>=1.3) ; python_version < \"3.9\"", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7) ; platform_python_implementation != \"PyPy\"", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1) ; platform_python_implementation != \"PyPy\"", "pytest-perf (>=0.9.2)", "pytest-ruff"]
 
-[[package]]
-name = "importlib-resources"
-version = "6.5.2"
-description = "Read resources from Python packages"
-optional = false
-python-versions = ">=3.9"
-groups = ["main"]
-files = [
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-]
-
-[package.extras]
-check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
-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 = "inflection"
 version = "0.5.1"
@@ -2586,73 +2902,73 @@ files = [
 
 [[package]]
 name = "iniconfig"
-version = "2.1.0"
+version = "2.3.0"
 description = "brain-dead simple config-ini parsing"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.10"
 groups = ["main", "dev"]
 files = [
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 ]
 
 [[package]]
 name = "invoke"
-version = "2.2.0"
+version = "2.2.1"
 description = "Pythonic task execution"
 optional = false
 python-versions = ">=3.6"
 groups = ["s3"]
 files = [
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+    {file = "invoke-2.2.1.tar.gz", hash = "sha256:515bf49b4a48932b79b024590348da22f39c4942dff991ad1fb8b8baea1be707"},
 ]
 
 [[package]]
 name = "ipykernel"
-version = "6.29.5"
+version = "7.2.0"
 description = "IPython Kernel for Jupyter"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.10"
 groups = ["dev"]
 files = [
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 ]
 
 [package.dependencies]
-appnope = {version = "*", markers = "platform_system == \"Darwin\""}
+appnope = {version = ">=0.1.2", markers = "platform_system == \"Darwin\""}
 comm = ">=0.1.1"
 debugpy = ">=1.6.5"
 ipython = ">=7.23.1"
-jupyter-client = ">=6.1.12"
-jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
+jupyter-client = ">=8.8.0"
+jupyter-core = ">=5.1,<6.0.dev0 || >=6.1.dev0"
 matplotlib-inline = ">=0.1"
-nest-asyncio = "*"
-packaging = "*"
-psutil = "*"
-pyzmq = ">=24"
-tornado = ">=6.1"
+nest-asyncio = ">=1.4"
+packaging = ">=22"
+psutil = ">=5.7"
+pyzmq = ">=25"
+tornado = ">=6.4.1"
 traitlets = ">=5.4.0"
 
 [package.extras]
-cov = ["coverage[toml]", "curio", "matplotlib", "pytest-cov", "trio"]
-docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "trio"]
+cov = ["coverage[toml]", "matplotlib", "pytest-cov", "trio"]
+docs = ["intersphinx-registry", "myst-parser", "pydata-sphinx-theme", "sphinx (<8.2.0)", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "trio"]
 pyqt5 = ["pyqt5"]
 pyside6 = ["pyside6"]
-test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.23.5)", "pytest-cov", "pytest-timeout"]
+test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0,<10)", "pytest-asyncio (>=0.23.5)", "pytest-cov", "pytest-timeout"]
 
 [[package]]
 name = "ipython"
-version = "8.37.0"
+version = "8.39.0"
 description = "IPython: Productive Interactive Computing"
 optional = false
 python-versions = ">=3.10"
 groups = ["dev"]
 markers = "python_version == \"3.10\""
 files = [
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-    {file = "ipython-8.37.0.tar.gz", hash = "sha256:ca815841e1a41a1e6b73a0b08f3038af9b2252564d01fc405356d34033012216"},
+    {file = "ipython-8.39.0-py3-none-any.whl", hash = "sha256:bb3c51c4fa8148ab1dea07a79584d1c854e234ea44aa1283bcb37bc75054651f"},
+    {file = "ipython-8.39.0.tar.gz", hash = "sha256:4110ae96012c379b8b6db898a07e186c40a2a1ef5d57a7fa83166047d9da7624"},
 ]
 
 [package.dependencies]
@@ -2684,37 +3000,70 @@ test-extra = ["curio", "ipython[test]", "jupyter_ai", "matplotlib (!=3.2.0)", "n
 
 [[package]]
 name = "ipython"
-version = "9.4.0"
+version = "9.10.1"
 description = "IPython: Productive Interactive Computing"
 optional = false
 python-versions = ">=3.11"
 groups = ["dev"]
-markers = "python_version >= \"3.11\""
+markers = "python_version == \"3.11\""
 files = [
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-    {file = "ipython-9.4.0.tar.gz", hash = "sha256:c033c6d4e7914c3d9768aabe76bbe87ba1dc66a92a05db6bfa1125d81f2ee270"},
+    {file = "ipython-9.10.1-py3-none-any.whl", hash = "sha256:82d18ae9fb9164ded080c71ef92a182ee35ee7db2395f67616034bebb020a232"},
+    {file = "ipython-9.10.1.tar.gz", hash = "sha256:e170e9b2a44312484415bdb750492699bf329233b03f2557a9692cce6466ada4"},
 ]
 
 [package.dependencies]
-colorama = {version = "*", markers = "sys_platform == \"win32\""}
-decorator = "*"
-ipython-pygments-lexers = "*"
-jedi = ">=0.16"
-matplotlib-inline = "*"
+colorama = {version = ">=0.4.4", markers = "sys_platform == \"win32\""}
+decorator = ">=4.3.2"
+ipython-pygments-lexers = ">=1.0.0"
+jedi = ">=0.18.1"
+matplotlib-inline = ">=0.1.5"
 pexpect = {version = ">4.3", markers = "sys_platform != \"win32\" and sys_platform != \"emscripten\""}
 prompt_toolkit = ">=3.0.41,<3.1.0"
-pygments = ">=2.4.0"
-stack_data = "*"
+pygments = ">=2.11.0"
+stack_data = ">=0.6.0"
 traitlets = ">=5.13.0"
 typing_extensions = {version = ">=4.6", markers = "python_version < \"3.12\""}
 
 [package.extras]
-all = ["ipython[doc,matplotlib,test,test-extra]"]
+all = ["argcomplete (>=3.0)", "ipython[doc,matplotlib,terminal,test,test-extra]"]
 black = ["black"]
-doc = ["docrepr", "exceptiongroup", "intersphinx_registry", "ipykernel", "ipython[test]", "matplotlib", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "sphinx_toml (==0.0.4)", "typing_extensions"]
-matplotlib = ["matplotlib"]
-test = ["packaging", "pytest", "pytest-asyncio (<0.22)", "testpath"]
-test-extra = ["curio", "ipykernel", "ipython[test]", "jupyter_ai", "matplotlib (!=3.2.0)", "nbclient", "nbformat", "numpy (>=1.23)", "pandas", "trio"]
+doc = ["docrepr", "exceptiongroup", "intersphinx_registry", "ipykernel", "ipython[matplotlib,test]", "setuptools (>=70.0)", "sphinx (>=8.0)", "sphinx-rtd-theme (>=0.1.8)", "sphinx_toml (==0.0.4)", "typing_extensions"]
+matplotlib = ["matplotlib (>3.9)"]
+test = ["packaging (>=20.1.0)", "pytest (>=7.0.0)", "pytest-asyncio (>=1.0.0)", "setuptools (>=61.2)", "testpath (>=0.2)"]
+test-extra = ["curio", "ipykernel (>6.30)", "ipython[matplotlib]", "ipython[test]", "jupyter_ai", "nbclient", "nbformat", "numpy (>=1.27)", "pandas (>2.1)", "trio (>=0.1.0)"]
+
+[[package]]
+name = "ipython"
+version = "9.12.0"
+description = "IPython: Productive Interactive Computing"
+optional = false
+python-versions = ">=3.12"
+groups = ["dev"]
+markers = "python_version >= \"3.12\""
+files = [
+    {file = "ipython-9.12.0-py3-none-any.whl", hash = "sha256:0f2701e8ee86e117e37f50563205d36feaa259d2e08d4a6bc6b6d74b18ce128d"},
+    {file = "ipython-9.12.0.tar.gz", hash = "sha256:01daa83f504b693ba523b5a407246cabde4eb4513285a3c6acaff11a66735ee4"},
+]
+
+[package.dependencies]
+colorama = {version = ">=0.4.4", markers = "sys_platform == \"win32\""}
+decorator = ">=5.1.0"
+ipython-pygments-lexers = ">=1.0.0"
+jedi = ">=0.18.2"
+matplotlib-inline = ">=0.1.6"
+pexpect = {version = ">4.6", markers = "sys_platform != \"win32\" and sys_platform != \"emscripten\""}
+prompt_toolkit = ">=3.0.41,<3.1.0"
+pygments = ">=2.14.0"
+stack_data = ">=0.6.0"
+traitlets = ">=5.13.0"
+
+[package.extras]
+all = ["argcomplete (>=3.0)", "ipython[doc,matplotlib,terminal,test,test-extra]", "types-decorator"]
+black = ["black"]
+doc = ["docrepr", "exceptiongroup", "intersphinx_registry", "ipykernel", "ipython[matplotlib,test]", "setuptools (>=80.0)", "sphinx (>=8.0)", "sphinx-rtd-theme (>=0.1.8)", "sphinx_toml (==0.0.4)", "typing_extensions"]
+matplotlib = ["matplotlib (>3.9)"]
+test = ["packaging (>=23.0.0)", "pytest (>=7.0.0)", "pytest-asyncio (>=1.0.0)", "setuptools (>=80.0)", "testpath (>=0.2)"]
+test-extra = ["curio", "ipykernel (>6.30)", "ipython[matplotlib]", "ipython[test]", "jupyter_ai", "nbclient", "nbformat", "numpy (>=2.0)", "pandas (>2.1)", "trio (>=0.22.0)"]
 
 [[package]]
 name = "ipython-genutils"
@@ -2829,16 +3178,53 @@ MarkupSafe = ">=2.0"
 [package.extras]
 i18n = ["Babel (>=2.7)"]
 
+[[package]]
+name = "jinjanator"
+version = "25.3.1"
+description = "Command-line interface to Jinja2 for templating in shell scripts."
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+files = [
+    {file = "jinjanator-25.3.1-py3-none-any.whl", hash = "sha256:d62d64df9b8dce2f973def96f26206f791b532a7da131ca284813f98a4bb88b5"},
+    {file = "jinjanator-25.3.1.tar.gz", hash = "sha256:cdf48a654748b79a6fea8789e520a97343b665bb74ca4179cead88ab4cd1c5a7"},
+]
+
+[package.dependencies]
+attrs = "*"
+jinja2 = ">=2.7.2"
+jinjanator-plugins = "==25.1.*"
+python-dotenv = ">=1"
+pyyaml = "*"
+typing-extensions = "*"
+
+[[package]]
+name = "jinjanator-plugins"
+version = "25.1.0"
+description = "Package which provides the plugin API for the jinjanator tool"
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+files = [
+    {file = "jinjanator_plugins-25.1.0-py3-none-any.whl", hash = "sha256:7c4361fd2450e4b0928a47e252ea384ca6c93ac389f7dde07875d0709e22b849"},
+    {file = "jinjanator_plugins-25.1.0.tar.gz", hash = "sha256:46fdc53dc375bd6f460b2095f3073579a7a7a115487418156e9611ca5c8a96a8"},
+]
+
+[package.dependencies]
+attrs = "*"
+pluggy = "*"
+typing-extensions = "*"
+
 [[package]]
 name = "jmespath"
-version = "1.0.1"
+version = "1.1.0"
 description = "JSON Matching Expressions"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.9"
 groups = ["main", "s3"]
 files = [
-    {file = "jmespath-1.0.1-py3-none-any.whl", hash = "sha256:02e2e4cc71b5bcab88332eebf907519190dd9e6e82107fa7f83b1003a6252980"},
-    {file = "jmespath-1.0.1.tar.gz", hash = "sha256:90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe"},
+    {file = "jmespath-1.1.0-py3-none-any.whl", hash = "sha256:a5663118de4908c91729bea0acadca56526eb2698e83de10cd116ae0f4e97c64"},
+    {file = "jmespath-1.1.0.tar.gz", hash = "sha256:472c87d80f36026ae83c6ddd0f1d05d4e510134ed462851fd5f754c8c3cbb88d"},
 ]
 
 [[package]]
@@ -2859,19 +3245,16 @@ pyyaml = "*"
 
 [[package]]
 name = "json5"
-version = "0.12.0"
+version = "0.14.0"
 description = "A Python implementation of the JSON5 data format."
 optional = false
 python-versions = ">=3.8.0"
 groups = ["dev"]
 files = [
-    {file = "json5-0.12.0-py3-none-any.whl", hash = "sha256:6d37aa6c08b0609f16e1ec5ff94697e2cbbfbad5ac112afa05794da9ab7810db"},
-    {file = "json5-0.12.0.tar.gz", hash = "sha256:0b4b6ff56801a1c7dc817b0241bca4ce474a0e6a163bfef3fc594d3fd263ff3a"},
+    {file = "json5-0.14.0-py3-none-any.whl", hash = "sha256:56cf861bab076b1178eb8c92e1311d273a9b9acea2ccc82c276abf839ebaef3a"},
+    {file = "json5-0.14.0.tar.gz", hash = "sha256:b3f492fad9f6cdbced8b7d40b28b9b1c9701c5f561bef0d33b81c2ff433fefcb"},
 ]
 
-[package.extras]
-dev = ["build (==1.2.2.post1)", "coverage (==7.5.4) ; python_version < \"3.9\"", "coverage (==7.8.0) ; python_version >= \"3.9\"", "mypy (==1.14.1) ; python_version < \"3.9\"", "mypy (==1.15.0) ; python_version >= \"3.9\"", "pip (==25.0.1)", "pylint (==3.2.7) ; python_version < \"3.9\"", "pylint (==3.3.6) ; python_version >= \"3.9\"", "ruff (==0.11.2)", "twine (==6.1.0)", "uv (==0.6.11)"]
-
 [[package]]
 name = "jsonasobj"
 version = "1.3.1"
@@ -2916,26 +3299,26 @@ attrs = ">=19.2.0"
 
 [[package]]
 name = "jsonpointer"
-version = "3.0.0"
-description = "Identify specific nodes in a JSON document (RFC 6901)"
+version = "3.1.1"
+description = "Identify specific nodes in a JSON document (RFC 6901) "
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.10"
 groups = ["main", "dev"]
 files = [
-    {file = "jsonpointer-3.0.0-py2.py3-none-any.whl", hash = "sha256:13e088adc14fca8b6aa8177c044e12701e6ad4b28ff10e65f2267a90109c9942"},
-    {file = "jsonpointer-3.0.0.tar.gz", hash = "sha256:2b2d729f2091522d61c3b31f82e11870f60b68f43fbc705cb76bf4b832af59ef"},
+    {file = "jsonpointer-3.1.1-py3-none-any.whl", hash = "sha256:8ff8b95779d071ba472cf5bc913028df06031797532f08a7d5b602d8b2a488ca"},
+    {file = "jsonpointer-3.1.1.tar.gz", hash = "sha256:0b801c7db33a904024f6004d526dcc53bbb8a4a0f4e32bfd10beadf60adf1900"},
 ]
 
 [[package]]
 name = "jsonschema"
-version = "4.24.0"
+version = "4.26.0"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 groups = ["main", "dev"]
 files = [
-    {file = "jsonschema-4.24.0-py3-none-any.whl", hash = "sha256:a462455f19f5faf404a7902952b6f0e3ce868f3ee09a359b05eca6673bd8412d"},
-    {file = "jsonschema-4.24.0.tar.gz", hash = "sha256:0b4e8069eb12aedfa881333004bccaec24ecef5a8a6a4b6df142b2cc9599d196"},
+    {file = "jsonschema-4.26.0-py3-none-any.whl", hash = "sha256:d489f15263b8d200f8387e64b4c3a75f06629559fb73deb8fdfb525f2dab50ce"},
+    {file = "jsonschema-4.26.0.tar.gz", hash = "sha256:0c26707e2efad8aa1bfc5b7ce170f3fccc2e4918ff85989ba9ffa9facb2be326"},
 ]
 
 [package.dependencies]
@@ -2956,7 +3339,7 @@ jsonpointer = [
     {version = ">1.13", optional = true, markers = "extra == \"format\""},
     {version = ">1.13", optional = true, markers = "extra == \"format-nongpl\""},
 ]
-jsonschema-specifications = ">=2023.3.6"
+jsonschema-specifications = ">=2023.03.6"
 referencing = ">=0.28.4"
 rfc3339-validator = [
     {version = "*", optional = true, markers = "extra == \"format\""},
@@ -2964,7 +3347,8 @@ rfc3339-validator = [
 ]
 rfc3986-validator = {version = ">0.1.0", optional = true, markers = "extra == \"format-nongpl\""}
 rfc3987 = {version = "*", optional = true, markers = "extra == \"format\""}
-rpds-py = ">=0.7.1"
+rfc3987-syntax = {version = ">=1.1.0", optional = true, markers = "extra == \"format-nongpl\""}
+rpds-py = ">=0.25.0"
 uri-template = [
     {version = "*", optional = true, markers = "extra == \"format\""},
     {version = "*", optional = true, markers = "extra == \"format-nongpl\""},
@@ -2976,18 +3360,18 @@ webcolors = [
 
 [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 (>=24.6.0)"]
+format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "rfc3987-syntax (>=1.1.0)", "uri-template", "webcolors (>=24.6.0)"]
 
 [[package]]
 name = "jsonschema-specifications"
-version = "2025.4.1"
+version = "2025.9.1"
 description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
 optional = false
 python-versions = ">=3.9"
 groups = ["main", "dev"]
 files = [
-    {file = "jsonschema_specifications-2025.4.1-py3-none-any.whl", hash = "sha256:4653bffbd6584f7de83a67e0d620ef16900b390ddc7939d56684d6c81e33f1af"},
-    {file = "jsonschema_specifications-2025.4.1.tar.gz", hash = "sha256:630159c9f4dbea161a6a2205c3011cc4f18ff381b189fff48bb39b9bf26ae608"},
+    {file = "jsonschema_specifications-2025.9.1-py3-none-any.whl", hash = "sha256:98802fee3a11ee76ecaca44429fda8a41bff98b00a0f2838151b113f210cc6fe"},
+    {file = "jsonschema_specifications-2025.9.1.tar.gz", hash = "sha256:b540987f239e745613c7a9176f3edb72b832a4ac465cf02712288397832b5e8d"},
 ]
 
 [package.dependencies]
@@ -3014,26 +3398,27 @@ test = ["tox"]
 
 [[package]]
 name = "jupyter-client"
-version = "8.6.3"
+version = "8.8.0"
 description = "Jupyter protocol implementation and client libraries"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.10"
 groups = ["dev"]
 files = [
-    {file = "jupyter_client-8.6.3-py3-none-any.whl", hash = "sha256:e8a19cc986cc45905ac3362915f410f3af85424b4c0905e94fa5f2cb08e8f23f"},
-    {file = "jupyter_client-8.6.3.tar.gz", hash = "sha256:35b3a0947c4a6e9d589eb97d7d4cd5e90f910ee73101611f01283732bd6d9419"},
+    {file = "jupyter_client-8.8.0-py3-none-any.whl", hash = "sha256:f93a5b99c5e23a507b773d3a1136bd6e16c67883ccdbd9a829b0bbdb98cd7d7a"},
+    {file = "jupyter_client-8.8.0.tar.gz", hash = "sha256:d556811419a4f2d96c869af34e854e3f059b7cc2d6d01a9cd9c85c267691be3e"},
 ]
 
 [package.dependencies]
-jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
+jupyter-core = ">=5.1"
 python-dateutil = ">=2.8.2"
-pyzmq = ">=23.0"
-tornado = ">=6.2"
+pyzmq = ">=25.0"
+tornado = ">=6.4.1"
 traitlets = ">=5.3"
 
 [package.extras]
 docs = ["ipykernel", "myst-parser", "pydata-sphinx-theme", "sphinx (>=4)", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"]
-test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko ; sys_platform == \"win32\"", "pre-commit", "pytest (<8.2.0)", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"]
+orjson = ["orjson"]
+test = ["anyio", "coverage", "ipykernel (>=6.14)", "msgpack", "mypy ; platform_python_implementation != \"PyPy\"", "paramiko ; sys_platform == \"win32\"", "pre-commit", "pytest", "pytest-cov", "pytest-jupyter[client] (>=0.6.2)", "pytest-timeout"]
 
 [[package]]
 name = "jupyter-contrib-core"
@@ -3084,19 +3469,18 @@ test = ["mock ; python_version == \"3.8\"", "nbformat", "nose", "pip", "requests
 
 [[package]]
 name = "jupyter-core"
-version = "5.8.1"
+version = "5.9.1"
 description = "Jupyter core package. A base package on which Jupyter projects rely."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.10"
 groups = ["dev"]
 files = [
-    {file = "jupyter_core-5.8.1-py3-none-any.whl", hash = "sha256:c28d268fc90fb53f1338ded2eb410704c5449a358406e8a948b75706e24863d0"},
-    {file = "jupyter_core-5.8.1.tar.gz", hash = "sha256:0a5f9706f70e64786b75acba995988915ebd4601c8a52e534a40b51c95f59941"},
+    {file = "jupyter_core-5.9.1-py3-none-any.whl", hash = "sha256:ebf87fdc6073d142e114c72c9e29a9d7ca03fad818c5d300ce2adc1fb0743407"},
+    {file = "jupyter_core-5.9.1.tar.gz", hash = "sha256:4d09aaff303b9566c3ce657f580bd089ff5c91f5f89cf7d8846c3cdf465b5508"},
 ]
 
 [package.dependencies]
 platformdirs = ">=2.5"
-pywin32 = {version = ">=300", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""}
 traitlets = ">=5.3"
 
 [package.extras]
@@ -3144,18 +3528,18 @@ files = [
 
 [[package]]
 name = "jupyter-lsp"
-version = "2.2.5"
+version = "2.3.1"
 description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab server"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
 files = [
-    {file = "jupyter-lsp-2.2.5.tar.gz", hash = "sha256:793147a05ad446f809fd53ef1cd19a9f5256fd0a2d6b7ce943a982cb4f545001"},
-    {file = "jupyter_lsp-2.2.5-py3-none-any.whl", hash = "sha256:45fbddbd505f3fbfb0b6cb2f1bc5e15e83ab7c79cd6e89416b248cb3c00c11da"},
+    {file = "jupyter_lsp-2.3.1-py3-none-any.whl", hash = "sha256:71b954d834e85ff3096400554f2eefaf7fe37053036f9a782b0f7c5e42dadb81"},
+    {file = "jupyter_lsp-2.3.1.tar.gz", hash = "sha256:fdf8a4aa7d85813976d6e29e95e6a2c8f752701f926f2715305249a3829805a6"},
 ]
 
 [package.dependencies]
-jupyter-server = ">=1.1.2"
+jupyter_server = ">=1.1.2"
 
 [[package]]
 name = "jupyter-nbextensions-configurator"
@@ -3182,14 +3566,14 @@ test = ["jupyter-contrib-core[testing-utils]", "mock ; python_version == \"3.9\"
 
 [[package]]
 name = "jupyter-server"
-version = "2.16.0"
+version = "2.17.0"
 description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications."
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
 files = [
-    {file = "jupyter_server-2.16.0-py3-none-any.whl", hash = "sha256:3d8db5be3bc64403b1c65b400a1d7f4647a5ce743f3b20dbdefe8ddb7b55af9e"},
-    {file = "jupyter_server-2.16.0.tar.gz", hash = "sha256:65d4b44fdf2dcbbdfe0aa1ace4a842d4aaf746a2b7b168134d5aaed35621b7f6"},
+    {file = "jupyter_server-2.17.0-py3-none-any.whl", hash = "sha256:e8cb9c7db4251f51ed307e329b81b72ccf2056ff82d50524debde1ee1870e13f"},
+    {file = "jupyter_server-2.17.0.tar.gz", hash = "sha256:c38ea898566964c888b4772ae1ed58eca84592e88251d2cfc4d171f81f7e99d5"},
 ]
 
 [package.dependencies]
@@ -3202,7 +3586,7 @@ jupyter-events = ">=0.11.0"
 jupyter-server-terminals = ">=0.4.4"
 nbconvert = ">=6.4.4"
 nbformat = ">=5.3.0"
-overrides = ">=5.0"
+overrides = {version = ">=5.0", markers = "python_version < \"3.12\""}
 packaging = ">=22.0"
 prometheus-client = ">=0.9"
 pywinpty = {version = ">=2.0.1", markers = "os_name == \"nt\""}
@@ -3219,14 +3603,14 @@ test = ["flaky", "ipykernel", "pre-commit", "pytest (>=7.0,<9)", "pytest-console
 
 [[package]]
 name = "jupyter-server-terminals"
-version = "0.5.3"
+version = "0.5.4"
 description = "A Jupyter Server Extension Providing Terminals."
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
 files = [
-    {file = "jupyter_server_terminals-0.5.3-py3-none-any.whl", hash = "sha256:41ee0d7dc0ebf2809c668e0fc726dfaf258fcd3e769568996ca731b6194ae9aa"},
-    {file = "jupyter_server_terminals-0.5.3.tar.gz", hash = "sha256:5ae0295167220e9ace0edcfdb212afd2b01ee8d179fe6f23c899590e9b8a5269"},
+    {file = "jupyter_server_terminals-0.5.4-py3-none-any.whl", hash = "sha256:55be353fc74a80bc7f3b20e6be50a55a61cd525626f578dcb66a5708e2007d14"},
+    {file = "jupyter_server_terminals-0.5.4.tar.gz", hash = "sha256:bbda128ed41d0be9020349f9f1f2a4ab9952a73ed5f5ac9f1419794761fb87f5"},
 ]
 
 [package.dependencies]
@@ -3239,25 +3623,25 @@ test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (>
 
 [[package]]
 name = "jupyterlab"
-version = "4.4.4"
+version = "4.5.6"
 description = "JupyterLab computational environment"
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
 files = [
-    {file = "jupyterlab-4.4.4-py3-none-any.whl", hash = "sha256:711611e4f59851152eb93316c3547c3ec6291f16bb455f1f4fa380d25637e0dd"},
-    {file = "jupyterlab-4.4.4.tar.gz", hash = "sha256:163fee1ef702e0a057f75d2eed3ed1da8a986d59eb002cbeb6f0c2779e6cd153"},
+    {file = "jupyterlab-4.5.6-py3-none-any.whl", hash = "sha256:d6b3dac883aa4d9993348e0f8e95b24624f75099aed64eab6a4351a9cdd1e580"},
+    {file = "jupyterlab-4.5.6.tar.gz", hash = "sha256:642fe2cfe7f0f5922a8a558ba7a0d246c7bc133b708dfe43f7b3a826d163cf42"},
 ]
 
 [package.dependencies]
 async-lru = ">=1.0.0"
-httpx = ">=0.25.0"
-ipykernel = ">=6.5.0"
+httpx = ">=0.25.0,<1"
+ipykernel = ">=6.5.0,<6.30.0 || >6.30.0"
 jinja2 = ">=3.0.3"
 jupyter-core = "*"
 jupyter-lsp = ">=2.0.0"
 jupyter-server = ">=2.4.0,<3"
-jupyterlab-server = ">=2.27.1,<3"
+jupyterlab-server = ">=2.28.0,<3"
 notebook-shim = ">=0.2"
 packaging = "*"
 setuptools = ">=41.1.0"
@@ -3266,9 +3650,9 @@ tornado = ">=6.2.0"
 traitlets = "*"
 
 [package.extras]
-dev = ["build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.11.4)"]
+dev = ["build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.11.12)"]
 docs = ["jsx-lexer", "myst-parser", "pydata-sphinx-theme (>=0.13.0)", "pytest", "pytest-check-links", "pytest-jupyter", "sphinx (>=1.8,<8.2.0)", "sphinx-copybutton"]
-docs-screenshots = ["altair (==5.5.0)", "ipython (==8.16.1)", "ipywidgets (==8.1.5)", "jupyterlab-geojson (==3.4.0)", "jupyterlab-language-pack-zh-cn (==4.3.post1)", "matplotlib (==3.10.0)", "nbconvert (>=7.0.0)", "pandas (==2.2.3)", "scipy (==1.15.1)", "vega-datasets (==0.9.0)"]
+docs-screenshots = ["altair (==6.0.0)", "ipython (==8.16.1)", "ipywidgets (==8.1.5)", "jupyterlab-geojson (==3.4.0)", "jupyterlab-language-pack-zh-cn (==4.3.post1)", "matplotlib (==3.10.0)", "nbconvert (>=7.0.0)", "pandas (==2.2.3)", "scipy (==1.15.1)"]
 test = ["coverage", "pytest (>=7.0)", "pytest-check-links (>=0.7)", "pytest-console-scripts", "pytest-cov", "pytest-jupyter (>=0.5.3)", "pytest-timeout", "pytest-tornasync", "requests", "requests-cache", "virtualenv"]
 upgrade-extension = ["copier (>=9,<10)", "jinja2-time (<0.3)", "pydantic (<3.0)", "pyyaml-include (<3.0)", "tomli-w (<2.0)"]
 
@@ -3286,14 +3670,14 @@ files = [
 
 [[package]]
 name = "jupyterlab-server"
-version = "2.27.3"
+version = "2.28.0"
 description = "A set of server components for JupyterLab and JupyterLab like applications."
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
 files = [
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@@ -3310,22 +3694,6 @@ docs = ["autodoc-traits", "jinja2 (<3.2.0)", "mistune (<4)", "myst-parser", "pyd
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 [[package]]
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@@ -3432,37 +3800,39 @@ validators = ">=0.20.0,<0.21.0"
 
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 nearley = ["js2py"]
 regex = ["regex"]
 
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+version = "1.9.4"
 description = "Linked Open Data Modeling Language"
 optional = false
 python-versions = ">=3.9"
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 [package.dependencies]
 antlr4-python3-runtime = ">=4.9.0,<4.10"
-click = ">=7.0"
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 graphviz = ">=0.10.1"
 hbreader = "*"
 isodate = ">=0.6.0"
 jinja2 = ">=3.1.0"
 jsonasobj2 = ">=1.0.3,<2.0.0"
 jsonschema = {version = ">=4.0.0", extras = ["format"]}
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+linkml-runtime = ">=1.9.5,<2.0.0"
 openpyxl = "*"
 parse = "*"
 prefixcommons = ">=0.1.7"
@@ -3510,14 +3981,6 @@ sqlalchemy = ">=1.4.31"
 typing-extensions = {version = ">=4.6.0", markers = "python_version < \"3.12\""}
 watchdog = ">=0.9.0"
 
-[package.extras]
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-
 [[package]]
 name = "linkml-renderer"
 version = "0.3.1"
@@ -3538,14 +4001,14 @@ pydantic = "*"
 
 [[package]]
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+version = "1.9.5"
 description = "Runtime environment for LinkML, the Linked open data modeling language"
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 python-versions = ">=3.9"
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 ]
 
 [package.dependencies]
@@ -3609,110 +4072,150 @@ colorama = {version = ">=0.3.4", markers = "sys_platform == \"win32\""}
 win32-setctime = {version = ">=1.0.0", markers = "sys_platform == \"win32\""}
 
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 [package.extras]
@@ -3728,6 +4231,7 @@ description = "Python port of markdown-it. Markdown parsing, done right!"
 optional = false
 python-versions = ">=3.8"
 groups = ["main", "docs"]
+markers = "python_version == \"3.10\""
 files = [
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 testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
+[[package]]
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+version = "4.0.0"
+description = "Python port of markdown-it. Markdown parsing, done right!"
+optional = false
+python-versions = ">=3.10"
+groups = ["main", "docs"]
+markers = "python_version >= \"3.11\""
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+
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+
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+profiling = ["gprof2dot"]
+rtd = ["ipykernel", "jupyter_sphinx", "mdit-py-plugins (>=0.5.0)", "myst-parser", "pyyaml", "sphinx", "sphinx-book-theme (>=1.0,<2.0)", "sphinx-copybutton", "sphinx-design"]
+testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions", "requests"]
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 ]
 
 [[package]]
 name = "marshmallow"
-version = "3.26.1"
+version = "3.26.2"
 description = "A lightweight library for converting complex datatypes to and from native Python datatypes."
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
 files = [
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 ]
 
 [package.dependencies]
@@ -3839,33 +4338,36 @@ tests = ["pytest", "simplejson"]
 
 [[package]]
 name = "matplotlib-inline"
-version = "0.1.7"
+version = "0.2.1"
 description = "Inline Matplotlib backend for Jupyter"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 groups = ["dev"]
 files = [
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 ]
 
 [package.dependencies]
 traitlets = "*"
 
+[package.extras]
+test = ["flake8", "nbdime", "nbval", "notebook", "pytest"]
+
 [[package]]
 name = "mdit-py-plugins"
-version = "0.4.2"
+version = "0.5.0"
 description = "Collection of plugins for markdown-it-py"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.10"
 groups = ["docs"]
 files = [
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 ]
 
 [package.dependencies]
-markdown-it-py = ">=1.0.0,<4.0.0"
+markdown-it-py = ">=2.0.0,<5.0.0"
 
 [package.extras]
 code-style = ["pre-commit"]
@@ -3884,16 +4386,28 @@ files = [
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 ]
 
+[[package]]
+name = "mergedeep"
+version = "1.3.4"
+description = "A deep merge function for 🐍."
+optional = false
+python-versions = ">=3.6"
+groups = ["main"]
+files = [
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+]
+
 [[package]]
 name = "mistune"
-version = "3.1.3"
+version = "3.2.0"
 description = "A sane and fast Markdown parser with useful plugins and renderers"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
 files = [
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 ]
 
 [package.dependencies]
@@ -3901,152 +4415,185 @@ typing-extensions = {version = "*", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "more-click"
-version = "0.1.2"
-description = "More click."
+version = "0.1.3"
+description = "Implementations of common CLI patterns on top of Click"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.10"
 groups = ["main"]
 files = [
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+    {file = "more_click-0.1.3.tar.gz", hash = "sha256:c170987d37334278169fe3b9b388f1fcd9fc96439579354fd7c537537a182128"},
 ]
 
 [package.dependencies]
 click = "*"
 
-[package.extras]
-tests = ["coverage", "pytest"]
-
 [[package]]
 name = "more-itertools"
-version = "10.7.0"
+version = "11.0.2"
 description = "More routines for operating on iterables, beyond itertools"
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 groups = ["main"]
 files = [
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 ]
 
 [[package]]
 name = "multidict"
-version = "6.6.3"
+version = "6.7.1"
 description = "multidict implementation"
 optional = false
 python-versions = ">=3.9"
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+    {file = "mypy-1.20.1.tar.gz", hash = "sha256:6fc3f4ecd52de81648fed1945498bf42fa2993ddfad67c9056df36ae5757f804"},
+]
+
+[package.dependencies]
+librt = {version = ">=0.8.0", markers = "platform_python_implementation != \"PyPy\""}
 mypy_extensions = ">=1.0.0"
-pathspec = ">=0.9.0"
+pathspec = ">=1.0.0"
 tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
 typing_extensions = ">=4.6.0"
 
@@ -4105,6 +4665,7 @@ dmypy = ["psutil (>=4.0)"]
 faster-cache = ["orjson"]
 install-types = ["pip"]
 mypyc = ["setuptools (>=50)"]
+native-parser = ["ast-serialize (>=0.1.1,<1.0.0)"]
 reports = ["lxml"]
 
 [[package]]
@@ -4126,6 +4687,7 @@ description = "An extended [CommonMark](https://spec.commonmark.org/) compliant
 optional = false
 python-versions = ">=3.10"
 groups = ["docs"]
+markers = "python_version == \"3.10\""
 files = [
     {file = "myst_parser-4.0.1-py3-none-any.whl", hash = "sha256:9134e88959ec3b5780aedf8a99680ea242869d012e8821db3126d427edc9c95d"},
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@@ -4146,39 +4708,67 @@ rtd = ["ipython", "sphinx (>=7)", "sphinx-autodoc2 (>=0.5.0,<0.6.0)", "sphinx-bo
 testing = ["beautifulsoup4", "coverage[toml]", "defusedxml", "pygments (<2.19)", "pytest (>=8,<9)", "pytest-cov", "pytest-param-files (>=0.6.0,<0.7.0)", "pytest-regressions", "sphinx-pytest"]
 testing-docutils = ["pygments", "pytest (>=8,<9)", "pytest-param-files (>=0.6.0,<0.7.0)"]
 
+[[package]]
+name = "myst-parser"
+version = "5.0.0"
+description = "An extended [CommonMark](https://spec.commonmark.org/) compliant parser,"
+optional = false
+python-versions = ">=3.11"
+groups = ["docs"]
+markers = "python_version >= \"3.11\""
+files = [
+    {file = "myst_parser-5.0.0-py3-none-any.whl", hash = "sha256:ab31e516024918296e169139072b81592336f2fef55b8986aa31c9f04b5f7211"},
+    {file = "myst_parser-5.0.0.tar.gz", hash = "sha256:f6f231452c56e8baa662cc352c548158f6a16fcbd6e3800fc594978002b94f3a"},
+]
+
+[package.dependencies]
+docutils = ">=0.20,<0.23"
+jinja2 = "*"
+markdown-it-py = ">=4.0,<5.0"
+mdit-py-plugins = ">=0.5,<1.0"
+pyyaml = "*"
+sphinx = ">=8,<10"
+
+[package.extras]
+code-style = ["pre-commit (>=4.0,<5.0)"]
+linkify = ["linkify-it-py (>=2.0,<3.0)"]
+rtd = ["ipython", "sphinx (>=8)", "sphinx-autodoc2 (>=0.5.0,<0.6.0)", "sphinx-book-theme (>=1.1,<2.0)", "sphinx-copybutton", "sphinx-design", "sphinx-pyscript", "sphinx-tippy (>=0.4.3)", "sphinx-togglebutton", "sphinxext-opengraph (>=0.13.0,<0.14.0)", "sphinxext-rediraffe (>=0.3.0,<0.4.0)"]
+testing = ["beautifulsoup4", "coverage[toml]", "defusedxml", "pygments (<2.20)", "pytest (>=9,<10)", "pytest-cov", "pytest-param-files (>=0.6.0,<0.7.0)", "pytest-regressions", "sphinx-pytest (>=0.3.0,<0.4.0)"]
+testing-docutils = ["pygments", "pytest (>=9,<10)", "pytest-param-files (>=0.6.0,<0.7.0)"]
+
 [[package]]
 name = "nbclient"
-version = "0.10.2"
+version = "0.10.4"
 description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
 optional = false
-python-versions = ">=3.9.0"
+python-versions = ">=3.10.0"
 groups = ["dev"]
 files = [
-    {file = "nbclient-0.10.2-py3-none-any.whl", hash = "sha256:4ffee11e788b4a27fabeb7955547e4318a5298f34342a4bfd01f2e1faaeadc3d"},
-    {file = "nbclient-0.10.2.tar.gz", hash = "sha256:90b7fc6b810630db87a6d0c2250b1f0ab4cf4d3c27a299b0cde78a4ed3fd9193"},
+    {file = "nbclient-0.10.4-py3-none-any.whl", hash = "sha256:9162df5a7373d70d606527300a95a975a47c137776cd942e52d9c7e29ff83440"},
+    {file = "nbclient-0.10.4.tar.gz", hash = "sha256:1e54091b16e6da39e297b0ece3e10f6f29f4ac4e8ee515d29f8a7099bd6553c9"},
 ]
 
 [package.dependencies]
 jupyter-client = ">=6.1.12"
 jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
-nbformat = ">=5.1"
+nbformat = ">=5.1.3"
 traitlets = ">=5.4"
 
 [package.extras]
 dev = ["pre-commit"]
-docs = ["autodoc-traits", "flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "mock", "moto", "myst-parser", "nbconvert (>=7.1.0)", "pytest (>=7.0,<8)", "pytest-asyncio", "pytest-cov (>=4.0)", "sphinx (>=1.7)", "sphinx-book-theme", "sphinxcontrib-spelling", "testpath", "xmltodict"]
-test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=7.1.0)", "pytest (>=7.0,<8)", "pytest-asyncio", "pytest-cov (>=4.0)", "testpath", "xmltodict"]
+docs = ["autodoc-traits", "flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "mock", "moto", "myst-parser", "nbconvert (>=7.1.0)", "pytest (>=9.0.1,<10)", "pytest-asyncio (>=1.3.0)", "pytest-cov (>=4.0)", "sphinx (>=1.7)", "sphinx-book-theme", "sphinxcontrib-spelling", "testpath", "xmltodict"]
+test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=7.1.0)", "pytest (>=9.0.1,<10)", "pytest-asyncio (>=1.3.0)", "pytest-cov (>=4.0)", "testpath", "xmltodict"]
 
 [[package]]
 name = "nbconvert"
-version = "7.16.6"
-description = "Converting Jupyter Notebooks (.ipynb files) to other formats.  Output formats include asciidoc, html, latex, markdown, pdf, py, rst, script.  nbconvert can be used both as a Python library (`import nbconvert`) or as a command line tool (invoked as `jupyter nbconvert ...`)."
+version = "7.17.1"
+description = "Convert Jupyter Notebooks (.ipynb files) to other formats."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 groups = ["dev"]
 files = [
-    {file = "nbconvert-7.16.6-py3-none-any.whl", hash = "sha256:1375a7b67e0c2883678c48e506dc320febb57685e5ee67faa51b18a90f3a712b"},
-    {file = "nbconvert-7.16.6.tar.gz", hash = "sha256:576a7e37c6480da7b8465eefa66c17844243816ce1ccc372633c6b71c3c0f582"},
+    {file = "nbconvert-7.17.1-py3-none-any.whl", hash = "sha256:aa85c087b435e7bf1ffd03319f658e285f2b89eccab33bc1ba7025495ab3e7c8"},
+    {file = "nbconvert-7.17.1.tar.gz", hash = "sha256:34d0d0a7e73ce3cbab6c5aae8f4f468797280b01fd8bd2ca746da8569eddd7d2"},
 ]
 
 [package.dependencies]
@@ -4198,8 +4788,8 @@ pygments = ">=2.4.1"
 traitlets = ">=5.1"
 
 [package.extras]
-all = ["flaky", "ipykernel", "ipython", "ipywidgets (>=7.5)", "myst-parser", "nbsphinx (>=0.2.12)", "playwright", "pydata-sphinx-theme", "pyqtwebengine (>=5.15)", "pytest (>=7)", "sphinx (==5.0.2)", "sphinxcontrib-spelling", "tornado (>=6.1)"]
-docs = ["ipykernel", "ipython", "myst-parser", "nbsphinx (>=0.2.12)", "pydata-sphinx-theme", "sphinx (==5.0.2)", "sphinxcontrib-spelling"]
+all = ["flaky", "intersphinx-registry", "ipykernel", "ipython", "ipywidgets (>=7.5)", "myst-parser", "nbsphinx (>=0.2.12)", "playwright", "pydata-sphinx-theme", "pyqtwebengine (>=5.15)", "pytest (>=7)", "sphinx (>=5.0.2)", "sphinxcontrib-spelling", "tornado (>=6.1)"]
+docs = ["intersphinx-registry", "ipykernel", "ipython", "myst-parser", "nbsphinx (>=0.2.12)", "pydata-sphinx-theme", "sphinx (>=5.0.2)", "sphinxcontrib-spelling"]
 qtpdf = ["pyqtwebengine (>=5.15)"]
 qtpng = ["pyqtwebengine (>=5.15)"]
 serve = ["tornado (>=6.1)"]
@@ -4230,14 +4820,14 @@ test = ["pep440", "pre-commit", "pytest", "testpath"]
 
 [[package]]
 name = "ndex2"
-version = "3.10.0"
+version = "3.11.0"
 description = "Nice CX Python includes a client and a data model."
 optional = false
 python-versions = "*"
 groups = ["main"]
 files = [
-    {file = "ndex2-3.10.0-py2.py3-none-any.whl", hash = "sha256:fdb8307ccdbdf49044c9119373852242ca24a4926df1c5566e94965e59b70b67"},
-    {file = "ndex2-3.10.0.tar.gz", hash = "sha256:7e8cfc3fc940cddfd612810fc8c913ab61e01a43e4f482608e86c6548b81b7e1"},
+    {file = "ndex2-3.11.0-py2.py3-none-any.whl", hash = "sha256:cafb2efa38e9faf3f7e47805429d2498cfd127b5a452df020bf3c8e199c9c072"},
+    {file = "ndex2-3.11.0.tar.gz", hash = "sha256:3fbf4d96254f0e85a2162c9f77d970687fe5a41622671a553111238e81350512"},
 ]
 
 [package.dependencies]
@@ -4252,23 +4842,23 @@ urllib3 = ">=1.16"
 
 [[package]]
 name = "neo4j"
-version = "5.28.1"
+version = "6.1.0"
 description = "Neo4j Bolt driver for Python"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.10"
 groups = ["main"]
 files = [
-    {file = "neo4j-5.28.1-py3-none-any.whl", hash = "sha256:6755ef9e5f4e14b403aef1138fb6315b120631a0075c138b5ddb2a06b87b09fd"},
-    {file = "neo4j-5.28.1.tar.gz", hash = "sha256:ae8e37a1d895099062c75bc359b2cce62099baac7be768d0eba7180c1298e214"},
+    {file = "neo4j-6.1.0-py3-none-any.whl", hash = "sha256:3bd93941f3a3559af197031157220af9fd71f4f93a311db687bd69ffa417b67d"},
+    {file = "neo4j-6.1.0.tar.gz", hash = "sha256:b5dde8c0d8481e7b6ae3733569d990dd3e5befdc5d452f531ad1884ed3500b84"},
 ]
 
 [package.dependencies]
 pytz = "*"
 
 [package.extras]
-numpy = ["numpy (>=1.7.0,<3.0.0)"]
-pandas = ["numpy (>=1.7.0,<3.0.0)", "pandas (>=1.1.0,<3.0.0)"]
-pyarrow = ["pyarrow (>=1.0.0)"]
+numpy = ["numpy (>=1.21.2,<3.0.0)"]
+pandas = ["numpy (>=1.21.2,<3.0.0)", "pandas (>=1.1.0,<3.0.0)"]
+pyarrow = ["pyarrow (>=6.0.0,<23.0.0)"]
 
 [[package]]
 name = "nest-asyncio"
@@ -4305,23 +4895,49 @@ test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"]
 
 [[package]]
 name = "networkx"
-version = "3.5"
+version = "3.6"
 description = "Python package for creating and manipulating graphs and networks"
 optional = false
 python-versions = ">=3.11"
 groups = ["main"]
-markers = "python_version >= \"3.11\""
+markers = "python_version >= \"3.14\""
+files = [
+    {file = "networkx-3.6-py3-none-any.whl", hash = "sha256:cdb395b105806062473d3be36458d8f1459a4e4b98e236a66c3a48996e07684f"},
+    {file = "networkx-3.6.tar.gz", hash = "sha256:285276002ad1f7f7da0f7b42f004bcba70d381e936559166363707fdad3d72ad"},
+]
+
+[package.extras]
+benchmarking = ["asv", "virtualenv"]
+default = ["matplotlib (>=3.8)", "numpy (>=1.25)", "pandas (>=2.0)", "scipy (>=1.11.2)"]
+developer = ["mypy (>=1.15)", "pre-commit (>=4.1)"]
+doc = ["intersphinx-registry", "myst-nb (>=1.1)", "numpydoc (>=1.8.0)", "pillow (>=10)", "pydata-sphinx-theme (>=0.16)", "sphinx (>=8.0)", "sphinx-gallery (>=0.18)", "texext (>=0.6.7)"]
+example = ["cairocffi (>=1.7)", "contextily (>=1.6)", "igraph (>=0.11)", "iplotx (>=0.9.0)", "momepy (>=0.7.2)", "osmnx (>=2.0.0)", "scikit-learn (>=1.5)", "seaborn (>=0.13)"]
+extra = ["lxml (>=4.6)", "pydot (>=3.0.1)", "pygraphviz (>=1.14)", "sympy (>=1.10)"]
+release = ["build (>=0.10)", "changelist (==0.5)", "twine (>=4.0)", "wheel (>=0.40)"]
+test = ["pytest (>=7.2)", "pytest-cov (>=4.0)", "pytest-xdist (>=3.0)"]
+test-extras = ["pytest-mpl", "pytest-randomly"]
+
+[[package]]
+name = "networkx"
+version = "3.6.1"
+description = "Python package for creating and manipulating graphs and networks"
+optional = false
+python-versions = "!=3.14.1,>=3.11"
+groups = ["main"]
+markers = "python_version <= \"3.13\" and python_version >= \"3.11\""
 files = [
-    {file = "networkx-3.5-py3-none-any.whl", hash = "sha256:0030d386a9a06dee3565298b4a734b68589749a544acbb6c412dc9e2489ec6ec"},
-    {file = "networkx-3.5.tar.gz", hash = "sha256:d4c6f9cf81f52d69230866796b82afbccdec3db7ae4fbd1b65ea750feed50037"},
+    {file = "networkx-3.6.1-py3-none-any.whl", hash = "sha256:d47fbf302e7d9cbbb9e2555a0d267983d2aa476bac30e90dfbe5669bd57f3762"},
+    {file = "networkx-3.6.1.tar.gz", hash = "sha256:26b7c357accc0c8cde558ad486283728b65b6a95d85ee1cd66bafab4c8168509"},
 ]
 
 [package.extras]
+benchmarking = ["asv", "virtualenv"]
 default = ["matplotlib (>=3.8)", "numpy (>=1.25)", "pandas (>=2.0)", "scipy (>=1.11.2)"]
 developer = ["mypy (>=1.15)", "pre-commit (>=4.1)"]
 doc = ["intersphinx-registry", "myst-nb (>=1.1)", "numpydoc (>=1.8.0)", "pillow (>=10)", "pydata-sphinx-theme (>=0.16)", "sphinx (>=8.0)", "sphinx-gallery (>=0.18)", "texext (>=0.6.7)"]
-example = ["cairocffi (>=1.7)", "contextily (>=1.6)", "igraph (>=0.11)", "momepy (>=0.7.2)", "osmnx (>=2.0.0)", "scikit-learn (>=1.5)", "seaborn (>=0.13)"]
+example = ["cairocffi (>=1.7)", "contextily (>=1.6)", "igraph (>=0.11)", "iplotx (>=0.9.0)", "momepy (>=0.7.2)", "osmnx (>=2.0.0)", "scikit-learn (>=1.5)", "seaborn (>=0.13)"]
 extra = ["lxml (>=4.6)", "pydot (>=3.0.1)", "pygraphviz (>=1.14)", "sympy (>=1.10)"]
+release = ["build (>=0.10)", "changelist (==0.5)", "twine (>=4.0)", "wheel (>=0.40)"]
 test = ["pytest (>=7.2)", "pytest-cov (>=4.0)", "pytest-xdist (>=3.0)"]
 test-extras = ["pytest-mpl", "pytest-randomly"]
 
@@ -4349,39 +4965,39 @@ tests = ["coverage[toml]", "pytest"]
 
 [[package]]
 name = "nodeenv"
-version = "1.9.1"
+version = "1.10.0"
 description = "Node.js virtual environment builder"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 groups = ["dev"]
 files = [
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+    {file = "nodeenv-1.10.0-py2.py3-none-any.whl", hash = "sha256:5bb13e3eed2923615535339b3c620e76779af4cb4c6a90deccc9e36b274d3827"},
+    {file = "nodeenv-1.10.0.tar.gz", hash = "sha256:996c191ad80897d076bdfba80a41994c2b47c68e224c542b48feba42ba00f8bb"},
 ]
 
 [[package]]
 name = "notebook"
-version = "7.4.4"
+version = "7.5.5"
 description = "Jupyter Notebook - A web-based notebook environment for interactive computing"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 groups = ["dev"]
 files = [
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-    {file = "notebook-7.4.4.tar.gz", hash = "sha256:392fd501e266f2fb3466c6fcd3331163a2184968cb5c5accf90292e01dfe528c"},
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 jupyter-server = ">=2.4.0,<3"
-jupyterlab = ">=4.4.4,<4.5"
-jupyterlab-server = ">=2.27.1,<3"
+jupyterlab = ">=4.5.6,<4.6"
+jupyterlab-server = ">=2.28.0,<3"
 notebook-shim = ">=0.2,<0.3"
 tornado = ">=6.2.0"
 
 [package.extras]
 dev = ["hatch", "pre-commit"]
 docs = ["myst-parser", "nbsphinx", "pydata-sphinx-theme", "sphinx (>=1.3.6)", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"]
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+test = ["importlib-resources (>=5.0) ; python_version < \"3.10\"", "ipykernel", "jupyter-server[test] (>=2.4.0,<3)", "jupyterlab-server[test] (>=2.28.0,<3)", "nbval", "pytest (>=7.0)", "pytest-console-scripts", "pytest-timeout", "pytest-tornasync", "requests"]
 
 [[package]]
 name = "notebook-shim"
@@ -4498,19 +5114,20 @@ semsimian = ["semsimian (>=0.2.18)"]
 
 [[package]]
 name = "obographs"
-version = "0.0.8"
+version = "0.0.10"
 description = "A python data model for OBO Graphs"
 optional = false
 python-versions = ">=3.10"
 groups = ["main"]
 files = [
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 ]
 
 [package.dependencies]
 curies = ">=0.10.19"
 pydantic = "*"
+pystow = "*"
 typing-extensions = "*"
 
 [[package]]
@@ -4533,14 +5150,14 @@ dev = ["pre-commit", "pytest"]
 
 [[package]]
 name = "ols-client"
-version = "0.1.4"
+version = "0.2.1"
 description = "A client to the EBI Ontology Lookup Service"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.10"
 groups = ["main"]
 files = [
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+    {file = "ols_client-0.2.1.tar.gz", hash = "sha256:c5078446f025e2fbe24a1a2bbb924d7372216ca05e7ff11dba87aa7721be008a"},
 ]
 
 [package.dependencies]
@@ -4551,29 +5168,27 @@ pystow = "*"
 requests = "*"
 
 [package.extras]
-docs = ["sphinx", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme"]
-tests = ["coverage", "pytest"]
+similarity = ["numpy", "scikit-learn"]
 
 [[package]]
 name = "ontoportal-client"
-version = "0.0.4"
-description = "A client to BioPortal and other OntoPortal instances."
+version = "0.0.9"
+description = "A client to BioPortal and other OntoPortal instances"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.10"
 groups = ["main"]
 files = [
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 ]
 
 [package.dependencies]
+class-resolver = "*"
 pystow = "*"
+requests = "*"
+tqdm = "*"
 typing-extensions = "*"
 
-[package.extras]
-docs = ["sphinx", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-rtd-theme"]
-tests = ["coverage", "pytest", "unittest-templates"]
-
 [[package]]
 name = "openai"
 version = "0.28.1"
@@ -4634,6 +5249,7 @@ description = "A decorator to automatically detect mismatch when overriding a me
 optional = false
 python-versions = ">=3.6"
 groups = ["dev"]
+markers = "python_version < \"3.12\""
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@@ -4641,73 +5257,86 @@ files = [
 
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-version = "25.0"
+version = "26.1"
 description = "Core utilities for Python packages"
 optional = false
 python-versions = ">=3.8"
 groups = ["main", "dev", "docs"]
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 python-versions = ">=3.9"
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 [package.dependencies]
 numpy = [
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     {version = ">=1.22.4", markers = "python_version < \"3.11\""},
-    {version = ">=1.23.2", markers = "python_version == \"3.11\""},
 ]
 python-dateutil = ">=2.8.2"
 pytz = ">=2020.1"
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 test = ["hypothesis (>=6.46.1)", "pytest (>=7.3.2)", "pytest-xdist (>=2.2.0)"]
 xml = ["lxml (>=4.9.2)"]
 
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+    {file = "pandas-3.0.2-cp314-cp314t-macosx_10_15_x86_64.whl", hash = "sha256:140f0cffb1fa2524e874dde5b477d9defe10780d8e9e220d259b2c0874c89d9d"},
+    {file = "pandas-3.0.2-cp314-cp314t-macosx_11_0_arm64.whl", hash = "sha256:ae37e833ff4fed0ba352f6bdd8b73ba3ab3256a85e54edfd1ab51ae40cca0af8"},
+    {file = "pandas-3.0.2-cp314-cp314t-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:4d888a5c678a419a5bb41a2a93818e8ed9fd3172246555c0b37b7cc27027effd"},
+    {file = "pandas-3.0.2-cp314-cp314t-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:b444dc64c079e84df91baa8bf613d58405645461cabca929d9178f2cd392398d"},
+    {file = "pandas-3.0.2-cp314-cp314t-musllinux_1_2_aarch64.whl", hash = "sha256:4544c7a54920de8eeacaa1466a6b7268ecfbc9bc64ab4dbb89c6bbe94d5e0660"},
+    {file = "pandas-3.0.2-cp314-cp314t-musllinux_1_2_x86_64.whl", hash = "sha256:734be7551687c00fbd760dc0522ed974f82ad230d4a10f54bf51b80d44a08702"},
+    {file = "pandas-3.0.2-cp314-cp314t-win_amd64.whl", hash = "sha256:57a07209bebcbcf768d2d13c9b78b852f9a15978dac41b9e6421a81ad4cdd276"},
+    {file = "pandas-3.0.2-cp314-cp314t-win_arm64.whl", hash = "sha256:5371b72c2d4d415d08765f32d689217a43227484e81b2305b52076e328f6f482"},
+    {file = "pandas-3.0.2.tar.gz", hash = "sha256:f4753e73e34c8d83221ba58f232433fca2748be8b18dbca02d242ed153945043"},
+]
+
+[package.dependencies]
+numpy = {version = ">=1.26.0", markers = "python_version < \"3.14\""}
+python-dateutil = ">=2.8.2"
+tzdata = {version = "*", markers = "sys_platform == \"win32\" or sys_platform == \"emscripten\""}
+
+[package.extras]
+all = ["PyQt5 (>=5.15.9)", "SQLAlchemy (>=2.0.36)", "adbc-driver-postgresql (>=1.2.0)", "adbc-driver-sqlite (>=1.2.0)", "beautifulsoup4 (>=4.12.3)", "bottleneck (>=1.4.2)", "fastparquet (>=2024.11.0)", "fsspec (>=2024.10.0)", "gcsfs (>=2024.10.0)", "html5lib (>=1.1)", "hypothesis (>=6.116.0)", "jinja2 (>=3.1.5)", "lxml (>=5.3.0)", "matplotlib (>=3.9.3)", "numba (>=0.60.0)", "numexpr (>=2.10.2)", "odfpy (>=1.4.1)", "openpyxl (>=3.1.5)", "psycopg2 (>=2.9.10)", "pyarrow (>=13.0.0)", "pyiceberg (>=0.8.1)", "pymysql (>=1.1.1)", "pyreadstat (>=1.2.8)", "pytest (>=8.3.4)", "pytest-xdist (>=3.6.1)", "python-calamine (>=0.3.0)", "pytz (>=2024.2)", "pyxlsb (>=1.0.10)", "qtpy (>=2.4.2)", "s3fs (>=2024.10.0)", "scipy (>=1.14.1)", "tables (>=3.10.1)", "tabulate (>=0.9.0)", "xarray (>=2024.10.0)", "xlrd (>=2.0.1)", "xlsxwriter (>=3.2.0)", "zstandard (>=0.23.0)"]
+aws = ["s3fs (>=2024.10.0)"]
+clipboard = ["PyQt5 (>=5.15.9)", "qtpy (>=2.4.2)"]
+compression = ["zstandard (>=0.23.0)"]
+computation = ["scipy (>=1.14.1)", "xarray (>=2024.10.0)"]
+excel = ["odfpy (>=1.4.1)", "openpyxl (>=3.1.5)", "python-calamine (>=0.3.0)", "pyxlsb (>=1.0.10)", "xlrd (>=2.0.1)", "xlsxwriter (>=3.2.0)"]
+feather = ["pyarrow (>=13.0.0)"]
+fss = ["fsspec (>=2024.10.0)"]
+gcp = ["gcsfs (>=2024.10.0)"]
+hdf5 = ["tables (>=3.10.1)"]
+html = ["beautifulsoup4 (>=4.12.3)", "html5lib (>=1.1)", "lxml (>=5.3.0)"]
+iceberg = ["pyiceberg (>=0.8.1)"]
+mysql = ["SQLAlchemy (>=2.0.36)", "pymysql (>=1.1.1)"]
+output-formatting = ["jinja2 (>=3.1.5)", "tabulate (>=0.9.0)"]
+parquet = ["pyarrow (>=13.0.0)"]
+performance = ["bottleneck (>=1.4.2)", "numba (>=0.60.0)", "numexpr (>=2.10.2)"]
+plot = ["matplotlib (>=3.9.3)"]
+postgresql = ["SQLAlchemy (>=2.0.36)", "adbc-driver-postgresql (>=1.2.0)", "psycopg2 (>=2.9.10)"]
+pyarrow = ["pyarrow (>=13.0.0)"]
+spss = ["pyreadstat (>=1.2.8)"]
+sql-other = ["SQLAlchemy (>=2.0.36)", "adbc-driver-postgresql (>=1.2.0)", "adbc-driver-sqlite (>=1.2.0)"]
+test = ["hypothesis (>=6.116.0)", "pytest (>=8.3.4)", "pytest-xdist (>=3.6.1)"]
+timezone = ["pytz (>=2024.2)"]
+xml = ["lxml (>=5.3.0)"]
+
 [[package]]
 name = "pandocfilters"
 version = "1.5.1"
@@ -4750,23 +5469,6 @@ files = [
     {file = "pandocfilters-1.5.1.tar.gz", hash = "sha256:002b4a555ee4ebc03f8b66307e287fa492e4a77b4ea14d3f934328297bb4939e"},
 ]
 
-[[package]]
-name = "pansql"
-version = "0.0.1"
-description = "sqldf for pandas"
-optional = false
-python-versions = "*"
-groups = ["main"]
-files = [
-    {file = "pansql-0.0.1-py3-none-any.whl", hash = "sha256:0c49d8c23e418ac065af767ed350c544c0d6d96dc04e2faa1f8b37851d404988"},
-    {file = "pansql-0.0.1.tar.gz", hash = "sha256:61091112442c5d663ea5c042b6327a9b6b94c6687831677dddda46f292532e29"},
-]
-
-[package.dependencies]
-numpy = "*"
-pandas = "*"
-sqlalchemy = "*"
-
 [[package]]
 name = "parameterized"
 version = "0.8.1"
@@ -4784,66 +5486,91 @@ dev = ["jinja2"]
 
 [[package]]
 name = "paramiko"
-version = "3.5.1"
+version = "4.0.0"
 description = "SSH2 protocol library"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.9"
 groups = ["s3"]
 files = [
-    {file = "paramiko-3.5.1-py3-none-any.whl", hash = "sha256:43b9a0501fc2b5e70680388d9346cf252cfb7d00b0667c39e80eb43a408b8f61"},
-    {file = "paramiko-3.5.1.tar.gz", hash = "sha256:b2c665bc45b2b215bd7d7f039901b14b067da00f3a11e6640995fd58f2664822"},
+    {file = "paramiko-4.0.0-py3-none-any.whl", hash = "sha256:0e20e00ac666503bf0b4eda3b6d833465a2b7aff2e2b3d79a8bba5ef144ee3b9"},
+    {file = "paramiko-4.0.0.tar.gz", hash = "sha256:6a25f07b380cc9c9a88d2b920ad37167ac4667f8d9886ccebd8f90f654b5d69f"},
 ]
 
 [package.dependencies]
 bcrypt = ">=3.2"
 cryptography = ">=3.3"
+invoke = ">=2.0"
 pynacl = ">=1.5"
 
 [package.extras]
-all = ["gssapi (>=1.4.1) ; platform_system != \"Windows\"", "invoke (>=2.0)", "pyasn1 (>=0.1.7)", "pywin32 (>=2.1.8) ; platform_system == \"Windows\""]
 gssapi = ["gssapi (>=1.4.1) ; platform_system != \"Windows\"", "pyasn1 (>=0.1.7)", "pywin32 (>=2.1.8) ; platform_system == \"Windows\""]
-invoke = ["invoke (>=2.0)"]
 
 [[package]]
 name = "parse"
-version = "1.20.2"
+version = "1.21.1"
 description = "parse() is the opposite of format()"
 optional = false
 python-versions = "*"
 groups = ["main"]
 files = [
-    {file = "parse-1.20.2-py2.py3-none-any.whl", hash = "sha256:967095588cb802add9177d0c0b6133b5ba33b1ea9007ca800e526f42a85af558"},
-    {file = "parse-1.20.2.tar.gz", hash = "sha256:b41d604d16503c79d81af5165155c0b20f6c8d6c559efa66b4b695c3e5a0a0ce"},
+    {file = "parse-1.21.1-py2.py3-none-any.whl", hash = "sha256:55339ca698019815df3b8e8b550e5933933527e623b0cdf1ca2f404da35ffb47"},
+    {file = "parse-1.21.1.tar.gz", hash = "sha256:825e1a88e9d9fb481b8d2ca709c6195558b6eaa97c559ad3a9a20aa2d12815a3"},
 ]
 
 [[package]]
 name = "parso"
-version = "0.8.4"
+version = "0.8.6"
 description = "A Python Parser"
 optional = false
 python-versions = ">=3.6"
 groups = ["dev"]
 files = [
-    {file = "parso-0.8.4-py2.py3-none-any.whl", hash = "sha256:a418670a20291dacd2dddc80c377c5c3791378ee1e8d12bffc35420643d43f18"},
-    {file = "parso-0.8.4.tar.gz", hash = "sha256:eb3a7b58240fb99099a345571deecc0f9540ea5f4dd2fe14c2a99d6b281ab92d"},
+    {file = "parso-0.8.6-py2.py3-none-any.whl", hash = "sha256:2c549f800b70a5c4952197248825584cb00f033b29c692671d3bf08bf380baff"},
+    {file = "parso-0.8.6.tar.gz", hash = "sha256:2b9a0332696df97d454fa67b81618fd69c35a7b90327cbe6ba5c92d2c68a7bfd"},
 ]
 
 [package.extras]
-qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
+qa = ["flake8 (==5.0.4)", "types-setuptools (==67.2.0.1)", "zuban (==0.5.1)"]
 testing = ["docopt", "pytest"]
 
+[[package]]
+name = "path"
+version = "17.1.1"
+description = "A module wrapper for os.path"
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
+files = [
+    {file = "path-17.1.1-py3-none-any.whl", hash = "sha256:ec7e136df29172e5030dd07e037d55f676bdb29d15bfa09b80da29d07d3b9303"},
+    {file = "path-17.1.1.tar.gz", hash = "sha256:2dfcbfec8b4d960f3469c52acf133113c2a8bf12ac7b98d629fa91af87248d42"},
+]
+
+[package.extras]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
+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 = ["appdirs", "more_itertools", "packaging", "pygments", "pytest (>=6,!=8.1.*)", "pywin32 ; platform_system == \"Windows\" and python_version < \"3.12\"", "types-pywin32"]
+type = ["pytest-mypy"]
+
 [[package]]
 name = "pathspec"
-version = "0.12.1"
+version = "1.0.4"
 description = "Utility library for gitignore style pattern matching of file paths."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 groups = ["main"]
 files = [
-    {file = "pathspec-0.12.1-py3-none-any.whl", hash = "sha256:a0d503e138a4c123b27490a4f7beda6a01c6f288df0e4a8b79c7eb0dc7b4cc08"},
-    {file = "pathspec-0.12.1.tar.gz", hash = "sha256:a482d51503a1ab33b1c67a6c3813a26953dbdc71c31dacaef9a838c4e29f5712"},
+    {file = "pathspec-1.0.4-py3-none-any.whl", hash = "sha256:fb6ae2fd4e7c921a165808a552060e722767cfa526f99ca5156ed2ce45a5c723"},
+    {file = "pathspec-1.0.4.tar.gz", hash = "sha256:0210e2ae8a21a9137c0d470578cb0e595af87edaa6ebf12ff176f14a02e0e645"},
 ]
 
+[package.extras]
+hyperscan = ["hyperscan (>=0.7)"]
+optional = ["typing-extensions (>=4)"]
+re2 = ["google-re2 (>=1.1)"]
+tests = ["pytest (>=9)", "typing-extensions (>=4.15)"]
+
 [[package]]
 name = "pexpect"
 version = "4.9.0"
@@ -4862,33 +5589,28 @@ ptyprocess = ">=0.5"
 
 [[package]]
 name = "pip"
-version = "25.1.1"
+version = "26.0.1"
 description = "The PyPA recommended tool for installing Python packages."
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
 files = [
-    {file = "pip-25.1.1-py3-none-any.whl", hash = "sha256:2913a38a2abf4ea6b64ab507bd9e967f3b53dc1ede74b01b0931e1ce548751af"},
-    {file = "pip-25.1.1.tar.gz", hash = "sha256:3de45d411d308d5054c2168185d8da7f9a2cd753dbac8acbfa88a8909ecd9077"},
+    {file = "pip-26.0.1-py3-none-any.whl", hash = "sha256:bdb1b08f4274833d62c1aa29e20907365a2ceb950410df15fc9521bad440122b"},
+    {file = "pip-26.0.1.tar.gz", hash = "sha256:c4037d8a277c89b320abe636d59f91e6d0922d08a05b60e85e53b296613346d8"},
 ]
 
 [[package]]
 name = "platformdirs"
-version = "4.3.8"
+version = "4.9.6"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 groups = ["main", "dev"]
 files = [
-    {file = "platformdirs-4.3.8-py3-none-any.whl", hash = "sha256:ff7059bb7eb1179e2685604f4aaf157cfd9535242bd23742eadc3c13542139b4"},
-    {file = "platformdirs-4.3.8.tar.gz", hash = "sha256:3d512d96e16bcb959a814c9f348431070822a6496326a4be0911c40b5a74c2bc"},
+    {file = "platformdirs-4.9.6-py3-none-any.whl", hash = "sha256:e61adb1d5e5cb3441b4b7710bea7e4c12250ca49439228cc1021c00dcfac0917"},
+    {file = "platformdirs-4.9.6.tar.gz", hash = "sha256:3bfa75b0ad0db84096ae777218481852c0ebc6c727b3168c1b9e0118e458cf0a"},
 ]
 
-[package.extras]
-docs = ["furo (>=2024.8.6)", "proselint (>=0.14)", "sphinx (>=8.1.3)", "sphinx-autodoc-typehints (>=3)"]
-test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=8.3.4)", "pytest-cov (>=6)", "pytest-mock (>=3.14)"]
-type = ["mypy (>=1.14.1)"]
-
 [[package]]
 name = "pluggy"
 version = "1.6.0"
@@ -4927,14 +5649,14 @@ tests = ["coverage-conditional-plugin (>=0.9.0)", "portalocker[redis]", "pytest
 
 [[package]]
 name = "pre-commit"
-version = "4.2.0"
+version = "4.5.1"
 description = "A framework for managing and maintaining multi-language pre-commit hooks."
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 groups = ["dev"]
 files = [
-    {file = "pre_commit-4.2.0-py2.py3-none-any.whl", hash = "sha256:a009ca7205f1eb497d10b845e52c838a98b6cdd2102a6c8e4540e94ee75c58bd"},
-    {file = "pre_commit-4.2.0.tar.gz", hash = "sha256:601283b9757afd87d40c4c4a9b2b5de9637a8ea02eaff7adc2d0fb4e04841146"},
+    {file = "pre_commit-4.5.1-py2.py3-none-any.whl", hash = "sha256:3b3afd891e97337708c1674210f8eba659b52a38ea5f822ff142d10786221f77"},
+    {file = "pre_commit-4.5.1.tar.gz", hash = "sha256:eb545fcff725875197837263e977ea257a402056661f09dae08e4b149b030a61"},
 ]
 
 [package.dependencies]
@@ -4980,14 +5702,14 @@ pyyaml = ">=5.3.1"
 
 [[package]]
 name = "prettytable"
-version = "3.16.0"
+version = "3.17.0"
 description = "A simple Python library for easily displaying tabular data in a visually appealing ASCII table format"
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 groups = ["dev", "s3"]
 files = [
-    {file = "prettytable-3.16.0-py3-none-any.whl", hash = "sha256:b5eccfabb82222f5aa46b798ff02a8452cf530a352c31bddfa29be41242863aa"},
-    {file = "prettytable-3.16.0.tar.gz", hash = "sha256:3c64b31719d961bf69c9a7e03d0c1e477320906a98da63952bc6698d6164ff57"},
+    {file = "prettytable-3.17.0-py3-none-any.whl", hash = "sha256:aad69b294ddbe3e1f95ef8886a060ed1666a0b83018bbf56295f6f226c43d287"},
+    {file = "prettytable-3.17.0.tar.gz", hash = "sha256:59f2590776527f3c9e8cf9fe7b66dd215837cca96a9c39567414cbc632e8ddb0"},
 ]
 
 [package.dependencies]
@@ -5010,29 +5732,31 @@ files = [
 
 [[package]]
 name = "prometheus-client"
-version = "0.22.1"
+version = "0.25.0"
 description = "Python client for the Prometheus monitoring system."
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
 files = [
-    {file = "prometheus_client-0.22.1-py3-none-any.whl", hash = "sha256:cca895342e308174341b2cbf99a56bef291fbc0ef7b9e5412a0f26d653ba7094"},
-    {file = "prometheus_client-0.22.1.tar.gz", hash = "sha256:190f1331e783cf21eb60bca559354e0a4d4378facecf78f5428c39b675d20d28"},
+    {file = "prometheus_client-0.25.0-py3-none-any.whl", hash = "sha256:d5aec89e349a6ec230805d0df882f3807f74fd6c1a2fa86864e3c2279059fed1"},
+    {file = "prometheus_client-0.25.0.tar.gz", hash = "sha256:5e373b75c31afb3c86f1a52fa1ad470c9aace18082d39ec0d2f918d11cc9ba28"},
 ]
 
 [package.extras]
+aiohttp = ["aiohttp"]
+django = ["django"]
 twisted = ["twisted"]
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.51"
+version = "3.0.52"
 description = "Library for building powerful interactive command lines in Python"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
 files = [
-    {file = "prompt_toolkit-3.0.51-py3-none-any.whl", hash = "sha256:52742911fde84e2d423e2f9a4cf1de7d7ac4e51958f648d9540e0fb8db077b07"},
-    {file = "prompt_toolkit-3.0.51.tar.gz", hash = "sha256:931a162e3b27fc90c86f1b48bb1fb2c528c2761475e57c9c06de13311c7b54ed"},
+    {file = "prompt_toolkit-3.0.52-py3-none-any.whl", hash = "sha256:9aac639a3bbd33284347de5ad8d68ecc044b91a762dc39b7c21095fcd6a19955"},
+    {file = "prompt_toolkit-3.0.52.tar.gz", hash = "sha256:28cde192929c8e7321de85de1ddbe736f1375148b02f2e17edd840042b1be855"},
 ]
 
 [package.dependencies]
@@ -5040,287 +5764,300 @@ wcwidth = "*"
 
 [[package]]
 name = "pronto"
-version = "2.7.0"
+version = "2.7.3"
 description = "Python frontend to ontologies."
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
 files = [
-    {file = "pronto-2.7.0-py3-none-any.whl", hash = "sha256:da4fb4a6fd67ed7958cc3fc02ad0360ef81e48d2282b8e3fb9715209fcc64952"},
-    {file = "pronto-2.7.0.tar.gz", hash = "sha256:8454b89094f20eb74b3dadfd23d09ac3722a47d40c6ef3f6a1b462bc3faa030b"},
+    {file = "pronto-2.7.3-py3-none-any.whl", hash = "sha256:c7e225a39ddaca2771e46d6b3511ae851d1440b6a96e455aa7eb2bbbb459b8be"},
+    {file = "pronto-2.7.3.tar.gz", hash = "sha256:101effc2cc5de4269d0754e10c3c574181b8e5ba8cc615dea530b61a8cbd5046"},
 ]
 
 [package.dependencies]
 chardet = ">=5.0,<6.0"
-fastobo = ">=0.13.0,<0.14.0"
+fastobo = ">=0.13.0,<0.15.0"
 networkx = ">=2.3,<4.0"
 python-dateutil = ">=2.8,<3.0"
 
 [[package]]
 name = "propcache"
-version = "0.3.2"
+version = "0.4.1"
 description = "Accelerated property cache"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
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 [[package]]
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 [[package]]
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+version = "0.6.3"
 description = "Pure-Python implementation of ASN.1 types and DER/BER/CER codecs (X.208)"
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 python-versions = ">=3.8"
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 ]
 
 [[package]]
@@ -5429,47 +6166,47 @@ pyasn1 = ">=0.6.1,<0.7.0"
 
 [[package]]
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+version = "26.2.16"
 description = "ISO country, subdivision, language, currency and script definitions and their translations"
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+python-versions = ">=3.10"
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 [[package]]
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-typing-extensions = ">=4.12.2"
-typing-inspection = ">=0.4.0"
+pydantic-core = "2.46.2"
+typing-extensions = ">=4.14.1"
+typing-inspection = ">=0.4.2"
 
 [package.extras]
 email = ["email-validator (>=2.0.0)"]
@@ -5477,126 +6214,147 @@ timezone = ["tzdata ; python_version >= \"3.9\" and platform_system == \"Windows
 
 [[package]]
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-version = "2.33.2"
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+version = "2.11.1"
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 typing-extensions = "*"
 
 [package.extras]
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 semver = ["semver (>=3.0.2)"]
+uuid-utils = ["uuid-utils (>=0.6.0) ; python_version < \"3.14\""]
 
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 name = "pydantic-settings"
-version = "2.10.1"
+version = "2.13.1"
 description = "Settings management using Pydantic"
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 [[package]]
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+version = "2.20.0"
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 [package.dependencies]
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+requests = "*"
+
+[[package]]
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+python-versions = ">=3.6"
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+    {file = "pynacl-1.6.2-cp38-abi3-win32.whl", hash = "sha256:5811c72b473b2f38f7e2a3dc4f8642e3a3e9b5e7317266e4ced1fba85cae41aa"},
+    {file = "pynacl-1.6.2-cp38-abi3-win_amd64.whl", hash = "sha256:62985f233210dee6548c223301b6c25440852e13d59a8b81490203c3227c5ba0"},
+    {file = "pynacl-1.6.2-cp38-abi3-win_arm64.whl", hash = "sha256:834a43af110f743a754448463e8fd61259cd4ab5bbedcf70f9dabad1d28a394c"},
+    {file = "pynacl-1.6.2.tar.gz", hash = "sha256:018494d6d696ae03c7e656e5e74cdfd8ea1326962cc401bcf018f1ed8436811c"},
+]
+
+[package.dependencies]
+cffi = {version = ">=2.0.0", markers = "platform_python_implementation != \"PyPy\" and python_version >= \"3.9\""}
+
+[package.extras]
+docs = ["sphinx (<7)", "sphinx_rtd_theme"]
+tests = ["hypothesis (>=3.27.0)", "pytest (>=7.4.0)", "pytest-cov (>=2.10.1)", "pytest-xdist (>=3.5.0)"]
+
+[[package]]
+name = "pyobo"
+version = "0.12.16"
+description = "A python package for handling and generating OBO"
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+markers = "python_version == \"3.10\""
+files = [
+    {file = "pyobo-0.12.16-py3-none-any.whl", hash = "sha256:b71cb48502c0d77c06ecfaf309b51238a9349348b0d77b80835c72dfc7cdd14d"},
+    {file = "pyobo-0.12.16.tar.gz", hash = "sha256:7362cff95b78e0b3baa3723b4eb96a85c18e882b1f94fa6f53ee6f8ce87e3399"},
 ]
 
 [package.dependencies]
-cffi = ">=1.4.1"
+bioregistry = ">=0.12.30"
+bioversions = ">=0.8.243"
+cachier = "*"
+chembl-downloader = "*"
+class-resolver = ">=0.6.0"
+click = "*"
+clinicaltrials-downloader = ">=0.0.2"
+curies = ">=0.10.17"
+curies-processing = ">=0.1.6"
+drugbank-downloader = "*"
+humanize = "*"
+more-click = ">=0.0.2"
+more-itertools = "*"
+networkx = ">=3.4"
+nih-reporter-downloader = ">=0.0.1"
+obographs = ">=0.0.8"
+obonet = ">=0.3.0"
+pandas = "*"
+pydantic = ">=2.0"
+pyperclip = "*"
+pystow = ">=0.7.5"
+python-dateutil = "*"
+pytz = "*"
+pyyaml = "*"
+rdflib = "*"
+requests = "*"
+robot-obo-tool = "*"
+ror-downloader = ">=0.0.4"
+ssslm = ">=0.0.13"
+sssom-pydantic = ">=0.2.0"
+tabulate = "*"
+tqdm = "*"
+typing-extensions = "*"
+umls-downloader = ">=0.1.3"
+zenodo-client = ">=0.4.1"
 
 [package.extras]
-docs = ["sphinx (>=1.6.5)", "sphinx-rtd-theme"]
-tests = ["hypothesis (>=3.27.0)", "pytest (>=3.2.1,!=3.3.0)"]
+drugcentral = ["psycopg2-binary"]
+gilda = ["ssslm[gilda]"]
+gilda-slim = ["ssslm[gilda-slim]"]
+grape = ["embiggen", "ensmallen", "grape"]
+pid = ["protmapper"]
+pykeen = ["pykeen"]
+scispacy = ["scipy (<1.11) ; python_full_version < \"3.13.0\"", "scispacy ; python_full_version < \"3.13.0\"", "spacy ; python_full_version < \"3.13.0\""]
+sources = ["pyobo[drugcentral,pid]"]
 
 [[package]]
 name = "pyobo"
-version = "0.12.4"
+version = "0.12.18"
 description = "A python package for handling and generating OBO"
 optional = false
-python-versions = ">=3.10"
+python-versions = ">=3.11"
 groups = ["main"]
+markers = "python_version >= \"3.11\""
 files = [
-    {file = "pyobo-0.12.4-py3-none-any.whl", hash = "sha256:7883de83b547b67bcfa5d8140ba48175460e47b97718bb6b7423236377d0335a"},
-    {file = "pyobo-0.12.4.tar.gz", hash = "sha256:e61d45c974568c886493c85d98df6eca9f86a25e928e38e69d513be18ac32afd"},
+    {file = "pyobo-0.12.18-py3-none-any.whl", hash = "sha256:b6a2cd8acb98b78ff524d6c15936cce6f5349ce14d88e7729f9a2962db4891da"},
+    {file = "pyobo-0.12.18.tar.gz", hash = "sha256:7942902994858f9b56f2272269aa7fcde7c6ec42473d24f382854c7df38a4b6a"},
 ]
 
 [package.dependencies]
-bioontologies = ">=0.7.2"
-bioregistry = ">=0.12.7"
-bioversions = ">=0.8.0"
+bioregistry = ">=0.12.30"
+bioversions = ">=0.8.243"
 cachier = "*"
 chembl-downloader = "*"
 class-resolver = ">=0.6.0"
 click = "*"
 clinicaltrials-downloader = ">=0.0.2"
 curies = ">=0.10.17"
-curies-processing = ">=0.1.0"
+curies-processing = ">=0.1.6"
 drugbank-downloader = "*"
 humanize = "*"
 more-click = ">=0.0.2"
@@ -5726,59 +6577,77 @@ nih-reporter-downloader = ">=0.0.1"
 obographs = ">=0.0.8"
 obonet = ">=0.3.0"
 pandas = "*"
-protmapper = "*"
-psycopg2-binary = "*"
 pydantic = ">=2.0"
-pystow = ">=0.7.0"
+pyperclip = "*"
+pystow = ">=0.7.28"
 python-dateutil = "*"
+pytz = "*"
 pyyaml = "*"
 rdflib = "*"
 requests = "*"
+robot-obo-tool = "*"
+ror-downloader = ">=0.0.4"
 ssslm = ">=0.0.13"
+sssom-pydantic = ">=0.2.0"
 tabulate = "*"
 tqdm = "*"
 typing-extensions = "*"
 umls-downloader = ">=0.1.3"
-zenodo-client = ">=0.3.6"
+zenodo-client = ">=0.4.1"
 
 [package.extras]
-gilda = ["ssslm[gilda]"]
+drugcentral = ["psycopg2-binary"]
+gilda = ["ssslm[gilda-slim]"]
 gilda-slim = ["ssslm[gilda-slim]"]
+pid = ["protmapper"]
+sources = ["protmapper", "psycopg2-binary"]
 
 [[package]]
 name = "pyparsing"
-version = "3.2.3"
-description = "pyparsing module - Classes and methods to define and execute parsing grammars"
+version = "3.3.2"
+description = "pyparsing - Classes and methods to define and execute parsing grammars"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
 files = [
-    {file = "pyparsing-3.2.3-py3-none-any.whl", hash = "sha256:a749938e02d6fd0b59b356ca504a24982314bb090c383e3cf201c95ef7e2bfcf"},
-    {file = "pyparsing-3.2.3.tar.gz", hash = "sha256:b9c13f1ab8b3b542f72e28f634bad4de758ab3ce4546e4301970ad6fa77c38be"},
+    {file = "pyparsing-3.3.2-py3-none-any.whl", hash = "sha256:850ba148bd908d7e2411587e247a1e4f0327839c40e2e5e6d05a007ecc69911d"},
+    {file = "pyparsing-3.3.2.tar.gz", hash = "sha256:c777f4d763f140633dcb6d8a3eda953bf7a214dc4eff598413c070bcdc117cbc"},
 ]
 
 [package.extras]
 diagrams = ["jinja2", "railroad-diagrams"]
 
+[[package]]
+name = "pyperclip"
+version = "1.11.0"
+description = "A cross-platform clipboard module for Python. (Only handles plain text for now.)"
+optional = false
+python-versions = "*"
+groups = ["main"]
+files = [
+    {file = "pyperclip-1.11.0-py3-none-any.whl", hash = "sha256:299403e9ff44581cb9ba2ffeed69c7aa96a008622ad0c46cb575ca75b5b84273"},
+    {file = "pyperclip-1.11.0.tar.gz", hash = "sha256:244035963e4428530d9e3a6101a1ef97209c6825edab1567beac148ccc1db1b6"},
+]
+
 [[package]]
 name = "pyproject-api"
-version = "1.9.1"
+version = "1.10.0"
 description = "API to interact with the python pyproject.toml based projects"
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 groups = ["main", "dev"]
 files = [
-    {file = "pyproject_api-1.9.1-py3-none-any.whl", hash = "sha256:7d6238d92f8962773dd75b5f0c4a6a27cce092a14b623b811dba656f3b628948"},
-    {file = "pyproject_api-1.9.1.tar.gz", hash = "sha256:43c9918f49daab37e302038fc1aed54a8c7a91a9fa935d00b9a485f37e0f5335"},
+    {file = "pyproject_api-1.10.0-py3-none-any.whl", hash = "sha256:8757c41a79c0f4ab71b99abed52b97ecf66bd20b04fa59da43b5840bac105a09"},
+    {file = "pyproject_api-1.10.0.tar.gz", hash = "sha256:40c6f2d82eebdc4afee61c773ed208c04c19db4c4a60d97f8d7be3ebc0bbb330"},
 ]
 
 [package.dependencies]
 packaging = ">=25"
-tomli = {version = ">=2.2.1", markers = "python_version < \"3.11\""}
+tomli = {version = ">=2.3", markers = "python_version < \"3.11\""}
 
 [package.extras]
-docs = ["furo (>=2024.8.6)", "sphinx-autodoc-typehints (>=3.2)"]
-testing = ["covdefaults (>=2.3)", "pytest (>=8.3.5)", "pytest-cov (>=6.1.1)", "pytest-mock (>=3.14)", "setuptools (>=80.3.1)"]
+docs = ["furo (>=2025.9.25)", "sphinx-autodoc-typehints (>=3.5.1)"]
+testing = ["covdefaults (>=2.3)", "pytest (>=8.4.2)", "pytest-cov (>=7)", "pytest-mock (>=3.15.1)", "setuptools (>=80.9)"]
 
 [[package]]
 name = "pyshex"
@@ -5838,17 +6707,17 @@ files = [
 
 [[package]]
 name = "pysolr"
-version = "3.10.0"
+version = "3.11.0"
 description = "Lightweight Python client for Apache Solr"
 optional = false
-python-versions = "*"
+python-versions = ">=3.10"
 groups = ["main"]
 files = [
-    {file = "pysolr-3.10.0.tar.gz", hash = "sha256:127b4a2dd169234acb1586643a6cd1e3e94b917921e69bf569d7b2a2aa0ef409"},
+    {file = "pysolr-3.11.0.tar.gz", hash = "sha256:bbd0e7467835316880f994b55386c9bc3c146733c17d85a3fed317755976c40a"},
 ]
 
 [package.dependencies]
-requests = ">=2.9.1"
+requests = ">=2.32.5"
 setuptools = "*"
 
 [package.extras]
@@ -5856,47 +6725,51 @@ solrcloud = ["kazoo (>=2.5.0)"]
 
 [[package]]
 name = "pystow"
-version = "0.7.1"
+version = "0.8.3"
 description = "Easily pick a place to store data for your Python code"
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 groups = ["main"]
 files = [
-    {file = "pystow-0.7.1-py3-none-any.whl", hash = "sha256:ea5b08f670a9126e368f719b29c02414a7480c13c30efec03d5cdfa69fb929f6"},
-    {file = "pystow-0.7.1.tar.gz", hash = "sha256:ad0605f378b1b9ea0e57feb0f198df25717ee9d29596a643a8d00492e21cd62a"},
+    {file = "pystow-0.8.3-py3-none-any.whl", hash = "sha256:022cc481b77d02b2df746f778a6d5014f3ed7b3abed96aacf46bc4333d61d2b6"},
+    {file = "pystow-0.8.3.tar.gz", hash = "sha256:90d927cfaa6172aaa0677005763b32f98ee5d9e0c4f243fc02943a90c08f2b98"},
 ]
 
 [package.dependencies]
-click = "*"
-requests = "*"
+bs4 = {version = "*", optional = true, markers = "extra == \"bs4\""}
+requests = {version = "*", optional = true, markers = "extra == \"bs4\""}
 tqdm = "*"
 typing-extensions = "*"
 
 [package.extras]
 aws = ["boto3"]
-docs = ["sphinx (>=8)", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme (>=3.0)"]
+bs4 = ["bs4", "requests"]
+cli = ["click"]
 pandas = ["pandas"]
+pydantic = ["pydantic"]
+ratelimit = ["ratelimit", "requests"]
 rdf = ["rdflib"]
-tests = ["coverage[toml]", "pytest", "requests-file"]
+requests = ["requests"]
 xml = ["lxml"]
+yaml = ["pyyaml"]
 
 [[package]]
 name = "pytest"
-version = "8.4.1"
+version = "9.0.3"
 description = "pytest: simple powerful testing with Python"
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 groups = ["main", "dev"]
 files = [
-    {file = "pytest-8.4.1-py3-none-any.whl", hash = "sha256:539c70ba6fcead8e78eebbf1115e8b589e7565830d7d006a8723f19ac8a0afb7"},
-    {file = "pytest-8.4.1.tar.gz", hash = "sha256:7c67fd69174877359ed9371ec3af8a3d2b04741818c51e5e99cc1742251fa93c"},
+    {file = "pytest-9.0.3-py3-none-any.whl", hash = "sha256:2c5efc453d45394fdd706ade797c0a81091eccd1d6e4bccfcd476e2b8e0ab5d9"},
+    {file = "pytest-9.0.3.tar.gz", hash = "sha256:b86ada508af81d19edeb213c681b1d48246c1a91d304c6c81a427674c17eb91c"},
 ]
 
 [package.dependencies]
 colorama = {version = ">=0.4", markers = "sys_platform == \"win32\""}
 exceptiongroup = {version = ">=1", markers = "python_version < \"3.11\""}
-iniconfig = ">=1"
-packaging = ">=20"
+iniconfig = ">=1.0.1"
+packaging = ">=22"
 pluggy = ">=1.5,<2"
 pygments = ">=2.7.2"
 tomli = {version = ">=1", markers = "python_version < \"3.11\""}
@@ -5933,16 +6806,36 @@ files = [
 [package.dependencies]
 six = ">=1.5"
 
+[[package]]
+name = "python-discovery"
+version = "1.2.2"
+description = "Python interpreter discovery"
+optional = false
+python-versions = ">=3.8"
+groups = ["main", "dev"]
+files = [
+    {file = "python_discovery-1.2.2-py3-none-any.whl", hash = "sha256:e1ae95d9af875e78f15e19aed0c6137ab1bb49c200f21f5061786490c9585c7a"},
+    {file = "python_discovery-1.2.2.tar.gz", hash = "sha256:876e9c57139eb757cb5878cbdd9ae5379e5d96266c99ef731119e04fffe533bb"},
+]
+
+[package.dependencies]
+filelock = ">=3.15.4"
+platformdirs = ">=4.3.6,<5"
+
+[package.extras]
+docs = ["furo (>=2025.12.19)", "sphinx (>=9.1)", "sphinx-autodoc-typehints (>=3.6.3)", "sphinxcontrib-mermaid (>=2)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.5.4)", "pytest (>=8.3.5)", "pytest-mock (>=3.14)", "setuptools (>=75.1)"]
+
 [[package]]
 name = "python-dotenv"
-version = "1.1.1"
+version = "1.2.2"
 description = "Read key-value pairs from a .env file and set them as environment variables"
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 groups = ["main"]
 files = [
-    {file = "python_dotenv-1.1.1-py3-none-any.whl", hash = "sha256:31f23644fe2602f88ff55e1f5c79ba497e01224ee7737937930c448e4d0e24dc"},
-    {file = "python_dotenv-1.1.1.tar.gz", hash = "sha256:a8a6399716257f45be6a007360200409fce5cda2661e3dec71d23dc15f6189ab"},
+    {file = "python_dotenv-1.2.2-py3-none-any.whl", hash = "sha256:1d8214789a24de455a8b8bd8ae6fe3c6b69a5e3d64aa8a8e5d68e694bbcb285a"},
+    {file = "python_dotenv-1.2.2.tar.gz", hash = "sha256:2c371a91fbd7ba082c2c1dc1f8bf89ca22564a087c2c287cd9b662adde799cf3"},
 ]
 
 [package.extras]
@@ -5950,289 +6843,292 @@ cli = ["click (>=5.0)"]
 
 [[package]]
 name = "python-json-logger"
-version = "3.3.0"
+version = "4.1.0"
 description = "JSON Log Formatter for the Python Logging Package"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.10"
 groups = ["dev"]
 files = [
-    {file = "python_json_logger-3.3.0-py3-none-any.whl", hash = "sha256:dd980fae8cffb24c13caf6e158d3d61c0d6d22342f932cb6e9deedab3d35eec7"},
-    {file = "python_json_logger-3.3.0.tar.gz", hash = "sha256:12b7e74b17775e7d565129296105bbe3910842d9d0eb083fc83a6a617aa8df84"},
+    {file = "python_json_logger-4.1.0-py3-none-any.whl", hash = "sha256:132994765cf75bf44554be9aa49b06ef2345d23661a96720262716438141b6b2"},
+    {file = "python_json_logger-4.1.0.tar.gz", hash = "sha256:b396b9e3ed782b09ff9d6e4f1683d46c83ad0d35d2e407c09a9ebbf038f88195"},
 ]
 
 [package.extras]
-dev = ["backports.zoneinfo ; python_version < \"3.9\"", "black", "build", "freezegun", "mdx_truly_sane_lists", "mike", "mkdocs", "mkdocs-awesome-pages-plugin", "mkdocs-gen-files", "mkdocs-literate-nav", "mkdocs-material (>=8.5)", "mkdocstrings[python]", "msgspec ; implementation_name != \"pypy\"", "mypy", "orjson ; implementation_name != \"pypy\"", "pylint", "pytest", "tzdata", "validate-pyproject[all]"]
-
-[[package]]
-name = "python-keycloak"
-version = "5.6.0"
-description = "python-keycloak is a Python package providing access to the Keycloak API."
-optional = false
-python-versions = "<4.0,>=3.9"
-groups = ["main"]
-files = [
-    {file = "python_keycloak-5.6.0-py3-none-any.whl", hash = "sha256:d9f1a44d28e0cba424ab27b9c867974dcd68a13afea53a21a001af927ffb03cd"},
-    {file = "python_keycloak-5.6.0.tar.gz", hash = "sha256:dcc966605a0a60e9c21a679d7c8f732ffd5ed52ed785a615a863de6bd19e5eaa"},
-]
-
-[package.dependencies]
-aiofiles = ">=24.1.0"
-async-property = ">=0.2.2"
-deprecation = ">=2.1.0"
-httpx = ">=0.23.2"
-jwcrypto = ">=1.5.4"
-requests = ">=2.20.0"
-requests-toolbelt = ">=0.6.0"
+dev = ["black", "build", "freezegun", "mdx_truly_sane_lists", "mike", "mkdocs", "mkdocs-awesome-pages-plugin", "mkdocs-gen-files", "mkdocs-literate-nav", "mkdocs-material (>=8.5)", "mkdocstrings[python]", "msgspec ; implementation_name != \"pypy\"", "mypy", "orjson ; implementation_name != \"pypy\"", "pylint", "pytest", "tzdata", "validate-pyproject[all]"]
 
 [[package]]
 name = "python-sql"
-version = "1.6.0"
+version = "1.8.1"
 description = "Library to write SQL queries"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.9"
 groups = ["dev"]
 files = [
-    {file = "python_sql-1.6.0-py3-none-any.whl", hash = "sha256:e20b1feb4791c69d95669d6a4acbb4002c08cc37c17df998a651e2631b37697d"},
-    {file = "python_sql-1.6.0.tar.gz", hash = "sha256:5b34a124e8ad74c53acd97248684b5bfbb4538388f6676662981a327183ec36c"},
+    {file = "python_sql-1.8.1-py3-none-any.whl", hash = "sha256:5d2091a2c9cb7684930e68eeccc8251c51dc95332126c6173d07c85c2587e8ff"},
+    {file = "python_sql-1.8.1.tar.gz", hash = "sha256:9cdf51e802276fe5bc981f5b222dbc612b952c0e3f91c95ede7efdffe75770b0"},
 ]
 
 [[package]]
 name = "python-ulid"
-version = "3.0.0"
+version = "3.1.0"
 description = "Universally unique lexicographically sortable identifier"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
 files = [
-    {file = "python_ulid-3.0.0-py3-none-any.whl", hash = "sha256:e4c4942ff50dbd79167ad01ac725ec58f924b4018025ce22c858bfcff99a5e31"},
-    {file = "python_ulid-3.0.0.tar.gz", hash = "sha256:e50296a47dc8209d28629a22fc81ca26c00982c78934bd7766377ba37ea49a9f"},
+    {file = "python_ulid-3.1.0-py3-none-any.whl", hash = "sha256:e2cdc979c8c877029b4b7a38a6fba3bc4578e4f109a308419ff4d3ccf0a46619"},
+    {file = "python_ulid-3.1.0.tar.gz", hash = "sha256:ff0410a598bc5f6b01b602851a3296ede6f91389f913a5d5f8c496003836f636"},
 ]
 
 [package.extras]
 pydantic = ["pydantic (>=2.0)"]
 
-[[package]]
-name = "pytrie"
-version = "0.4.0"
-description = "A pure Python implementation of the trie data structure."
-optional = false
-python-versions = "*"
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 [package.extras]
 socks = ["PySocks (>=1.5.6,!=1.5.7)"]
-use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
+use-chardet-on-py3 = ["chardet (>=3.0.2,<8)"]
 
 [[package]]
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+version = "1.3.1"
 description = "A persistent cache for python requests"
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 python-versions = ">=3.8"
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 [package.dependencies]
@@ -6377,15 +7275,12 @@ attrs = ">=21.2"
 cattrs = ">=22.2"
 platformdirs = ">=2.5"
 requests = ">=2.22"
-url-normalize = ">=1.4"
+url-normalize = ">=2.0"
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-json = ["ujson (>=5.4)"]
 mongodb = ["pymongo (>=3)"]
 redis = ["redis (>=3)"]
 security = ["itsdangerous (>=2.0)"]
@@ -6474,378 +7369,259 @@ files = [
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 ]
 
+[[package]]
+name = "rfc3987-syntax"
+version = "1.1.0"
+description = "Helper functions to syntactically validate strings according to RFC 3987."
+optional = false
+python-versions = ">=3.9"
+groups = ["dev"]
+files = [
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+
+[package.extras]
+testing = ["pytest (>=8.3.5)"]
+
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 [package.extras]
 jupyter = ["ipywidgets (>=7.5.1,<9)"]
 
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-name = "roman-numerals-py"
-version = "3.1.0"
+name = "robot-obo-tool"
+version = "0.0.1"
+description = "A wrapper around ROBOT"
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
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-[package.extras]
-lint = ["mypy (==1.15.0)", "pyright (==1.1.394)", "ruff (==0.9.7)"]
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-version = "1.3.1"
-description = "Sniff out which async library your code is running under"
-optional = false
-python-versions = ">=3.7"
-groups = ["main", "dev"]
-files = [
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-
 [[package]]
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 version = "3.0.1"
@@ -6965,28 +7728,16 @@ files = [
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-description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set"
-optional = false
-python-versions = "*"
-groups = ["main"]
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-]
-
 [[package]]
 name = "soupsieve"
-version = "2.7"
+version = "2.8.3"
 description = "A modern CSS selector implementation for Beautiful Soup."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 groups = ["main", "dev"]
 files = [
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@@ -7066,28 +7817,28 @@ test = ["cython (>=3.0)", "defusedxml (>=0.7.1)", "pytest (>=8.0)", "setuptools
 
 [[package]]
 name = "sphinx"
-version = "8.2.3"
+version = "9.0.4"
 description = "Python documentation generator"
 optional = false
 python-versions = ">=3.11"
 groups = ["main", "docs"]
-markers = "python_version >= \"3.11\""
+markers = "python_version == \"3.11\""
 files = [
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 packaging = ">=23.0"
 Pygments = ">=2.17"
 requests = ">=2.30.0"
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 snowballstemmer = ">=2.2"
 sphinxcontrib-applehelp = ">=1.0.7"
 sphinxcontrib-devhelp = ">=1.0.6"
@@ -7096,10 +7847,37 @@ sphinxcontrib-jsmath = ">=1.0.1"
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+optional = false
+python-versions = ">=3.12"
+groups = ["main", "docs"]
+markers = "python_version >= \"3.12\""
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+docutils = ">=0.21,<0.23"
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@@ -7123,14 +7901,14 @@ testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8.0.1)",
 
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+version = "6.2.0"
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+python-versions = ">=3.10"
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 [package.dependencies]
@@ -7138,21 +7916,25 @@ click = ">=8.0"
 docutils = "*"
 sphinx = ">=4.0"
 
+[package.extras]
+docs = ["reno"]
+test = ["pytest", "pytest-cov"]
+
 [[package]]
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-sphinx = ">=6,<9"
+docutils = ">0.18,<0.23"
+sphinx = ">=6,<10"
 sphinxcontrib-jquery = ">=4,<5"
 
 [package.extras]
@@ -7275,73 +8057,79 @@ test = ["pytest"]
 
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+version = "2.0.49"
 description = "Database Abstraction Library"
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 typing-extensions = ">=4.6.0"
 
 [package.extras]
@@ -7460,30 +8248,30 @@ tui = ["trogon"]
 
 [[package]]
 name = "sqlparse"
-version = "0.5.3"
+version = "0.5.5"
 description = "A non-validating SQL parser."
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.extras]
-dev = ["build", "hatch"]
+dev = ["build"]
 doc = ["sphinx"]
 
 [[package]]
 name = "ssslm"
-version = "0.0.17"
+version = "0.1.3"
 description = "A simple standard for sharing literal mappings"
 optional = false
 python-versions = ">=3.10"
 groups = ["main"]
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 ]
 
 [package.dependencies]
@@ -7491,59 +8279,100 @@ click = "*"
 curies = "*"
 pydantic = "*"
 pydantic-extra-types = {version = "*", extras = ["pycountry"]}
-pystow = ">=0.7.1"
+pystow = ">=0.7.3"
 tqdm = "*"
 
 [package.extras]
 gilda = ["gilda", "nltk", "pystow"]
+gilda-default = ["boto3"]
 gilda-slim = ["gilda-slim", "nltk", "pystow"]
-pandas = ["pandas"]
+gliner = ["gliner"]
+ontology = ["bioregistry"]
+pandas = ["numpy (>=2.0.0)", "pandas"]
+rdflib = ["rdflib"]
+scispacy = ["numpy (<2.0) ; python_full_version < \"3.11.0\"", "scispacy ; python_full_version < \"3.11.0\"", "spacy ; python_full_version < \"3.11.0\""]
 web = ["fastapi", "uvicorn"]
 
 [[package]]
 name = "sssom"
-version = "0.4.16"
+version = "0.4.18"
 description = "Operations on SSSOM mapping tables"
 optional = false
-python-versions = "<4.0.0,>=3.9"
+python-versions = "<4.0.0,>=3.10"
 groups = ["main"]
 files = [
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+    {file = "sssom-0.4.18.tar.gz", hash = "sha256:af1338f32f80e2d71df8faa8b51d5d4b79e23b0508af4c7d89a288f1520d2490"},
 ]
 
 [package.dependencies]
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-curies = ">=0.10.18"
-deprecation = ">=2.1.0,<3.0.0"
-importlib-resources = ">=6.1.1,<7.0.0"
+curies = ">=0.10.23"
+deprecation = ">=2.1.0"
 linkml = ">1.7.10"
-linkml-runtime = ">=1.7.5,<2.0.0"
-networkx = {version = ">=3.1", extras = ["networkx"]}
+linkml-runtime = ">=1.7.5"
+packaging = ">=20.0"
 pandas = ">1.0.3"
-pansql = {version = ">=0.0.1", extras = ["pansql"]}
-pyyaml = ">=6.0.1,<7.0.0"
-rdflib = ">=6.0.0"
-scipy = {version = "*", extras = ["scipy"]}
+pyyaml = ">=6.0.1"
+rdflib = ">=7.1.3"
 sparqlwrapper = ">=2.0.0"
-sssom-schema = ">=1.0.0,<2.0.0"
+sssom-schema = "1.1.0a3"
 validators = ">=0.20.0"
 
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+scipy = ["scipy"]
+
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+description = "Pydantic models for SSSOM"
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
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+
+[package.extras]
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+wikidata = ["bioregistry", "quickstatements-client (>=0.1.2)", "wikidata-client"]
+
 [[package]]
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 linkml-runtime = "*"
 
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 [[package]]
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 version = "0.6.3"
@@ -7577,14 +8406,14 @@ files = [
 
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 [package.extras]
@@ -7592,14 +8421,14 @@ widechars = ["wcwidth"]
 
 [[package]]
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+version = "9.1.4"
 description = "Retry code until it succeeds"
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 [package.extras]
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+markers = {main = "python_version == \"3.10\"", dev = "python_version < \"3.15\"", docs = "python_version == \"3.10\""}
 
 [[package]]
 name = "tornado"
-version = "6.5.1"
+version = "6.5.5"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
 files = [
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-    {file = "tornado-6.5.1.tar.gz", hash = "sha256:84ceece391e8eb9b2b95578db65e920d2a61070260594819589609ba9bc6308c"},
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+    {file = "tornado-6.5.5-cp39-abi3-win_amd64.whl", hash = "sha256:6443a794ba961a9f619b1ae926a2e900ac20c34483eea67be4ed8f1e58d3ef7b"},
+    {file = "tornado-6.5.5-cp39-abi3-win_arm64.whl", hash = "sha256:2c9a876e094109333f888539ddb2de4361743e5d21eece20688e3e351e4990a6"},
+    {file = "tornado-6.5.5.tar.gz", hash = "sha256:192b8f3ea91bd7f1f50c06955416ed76c6b72f96779b962f07f911b91e8d30e9"},
 ]
 
 [[package]]
@@ -7754,14 +8596,14 @@ test = ["devpi-process (>=1.0.2)", "pytest (>=8.3.4)", "pytest-mock (>=3.14)"]
 
 [[package]]
 name = "tqdm"
-version = "4.67.1"
+version = "4.67.3"
 description = "Fast, Extensible Progress Meter"
 optional = false
 python-versions = ">=3.7"
 groups = ["main"]
 files = [
-    {file = "tqdm-4.67.1-py3-none-any.whl", hash = "sha256:26445eca388f82e72884e0d580d5464cd801a3ea01e63e5601bdff9ba6a48de2"},
-    {file = "tqdm-4.67.1.tar.gz", hash = "sha256:f8aef9c52c08c13a65f30ea34f4e5aac3fd1a34959879d7e59e63027286627f2"},
+    {file = "tqdm-4.67.3-py3-none-any.whl", hash = "sha256:ee1e4c0e59148062281c49d80b25b67771a127c85fc9676d3be5f243206826bf"},
+    {file = "tqdm-4.67.3.tar.gz", hash = "sha256:7d825f03f89244ef73f1d4ce193cb1774a8179fd96f31d7e1dcde62092b960bb"},
 ]
 
 [package.dependencies]
@@ -7808,29 +8650,18 @@ rich = ">=10.11.0"
 shellingham = ">=1.3.0"
 typing-extensions = ">=3.7.4.3"
 
-[[package]]
-name = "types-python-dateutil"
-version = "2.9.0.20250516"
-description = "Typing stubs for python-dateutil"
-optional = false
-python-versions = ">=3.9"
-groups = ["main", "dev"]
-files = [
-    {file = "types_python_dateutil-2.9.0.20250516-py3-none-any.whl", hash = "sha256:2b2b3f57f9c6a61fba26a9c0ffb9ea5681c9b83e69cd897c6b5f668d9c0cab93"},
-    {file = "types_python_dateutil-2.9.0.20250516.tar.gz", hash = "sha256:13e80d6c9c47df23ad773d54b2826bd52dbbb41be87c3f339381c1700ad21ee5"},
-]
-
 [[package]]
 name = "typing-extensions"
-version = "4.14.0"
+version = "4.15.0"
 description = "Backported and Experimental Type Hints for Python 3.9+"
 optional = false
 python-versions = ">=3.9"
-groups = ["main", "dev"]
+groups = ["main", "dev", "s3"]
 files = [
-    {file = "typing_extensions-4.14.0-py3-none-any.whl", hash = "sha256:a1514509136dd0b477638fc68d6a91497af5076466ad0fa6c338e44e359944af"},
-    {file = "typing_extensions-4.14.0.tar.gz", hash = "sha256:8676b788e32f02ab42d9e7c61324048ae4c6d844a399eebace3d4979d75ceef4"},
+    {file = "typing_extensions-4.15.0-py3-none-any.whl", hash = "sha256:f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548"},
+    {file = "typing_extensions-4.15.0.tar.gz", hash = "sha256:0cea48d173cc12fa28ecabc3b837ea3cf6f38c6d1136f85cbaaf598984861466"},
 ]
+markers = {s3 = "python_version == \"3.10\""}
 
 [[package]]
 name = "typing-inspect"
@@ -7850,14 +8681,14 @@ typing-extensions = ">=3.7.4"
 
 [[package]]
 name = "typing-inspection"
-version = "0.4.1"
+version = "0.4.2"
 description = "Runtime typing introspection tools"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
 files = [
-    {file = "typing_inspection-0.4.1-py3-none-any.whl", hash = "sha256:389055682238f53b04f7badcb49b989835495a96700ced5dab2d8feae4b26f51"},
-    {file = "typing_inspection-0.4.1.tar.gz", hash = "sha256:6ae134cc0203c33377d43188d4064e9b357dba58cff3185f22924610e70a9d28"},
+    {file = "typing_inspection-0.4.2-py3-none-any.whl", hash = "sha256:4ed1cacbdc298c220f1bd249ed5287caa16f34d44ef4e9c3d0cbad5b521545e7"},
+    {file = "typing_inspection-0.4.2.tar.gz", hash = "sha256:ba561c48a67c5958007083d386c3295464928b01faa735ab8547c5692e87f464"},
 ]
 
 [package.dependencies]
@@ -7865,14 +8696,14 @@ typing-extensions = ">=4.12.0"
 
 [[package]]
 name = "tzdata"
-version = "2025.2"
+version = "2026.1"
 description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
-groups = ["main"]
+groups = ["main", "dev"]
 files = [
-    {file = "tzdata-2025.2-py2.py3-none-any.whl", hash = "sha256:1a403fada01ff9221ca8044d701868fa132215d84beb92242d9acd2147f667a8"},
-    {file = "tzdata-2025.2.tar.gz", hash = "sha256:b60a638fcc0daffadf82fe0f57e53d06bdec2f36c4df66280ae79bce6bd6f2b9"},
+    {file = "tzdata-2026.1-py2.py3-none-any.whl", hash = "sha256:4b1d2be7ac37ceafd7327b961aa3a54e467efbdb563a23655fbfe0d39cfc42a9"},
+    {file = "tzdata-2026.1.tar.gz", hash = "sha256:67658a1903c75917309e753fdc349ac0efd8c27db7a0cb406a25be4840f87f98"},
 ]
 
 [[package]]
@@ -7934,21 +8765,21 @@ dev = ["mypy", "pre-commit", "pytest", "pytest-cov", "pytest-socket", "ruff"]
 
 [[package]]
 name = "urllib3"
-version = "2.5.0"
+version = "2.6.3"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=3.9"
 groups = ["main", "dev", "docs", "s3"]
 files = [
-    {file = "urllib3-2.5.0-py3-none-any.whl", hash = "sha256:e6b01673c0fa6a13e374b50871808eb3bf7046c4b125b216f6bf1cc604cff0dc"},
-    {file = "urllib3-2.5.0.tar.gz", hash = "sha256:3fc47733c7e419d4bc3f6b3dc2b4f890bb743906a30d56ba4a5bfa4bbff92760"},
+    {file = "urllib3-2.6.3-py3-none-any.whl", hash = "sha256:bf272323e553dfb2e87d9bfd225ca7b0f467b919d7bbd355436d3fd37cb0acd4"},
+    {file = "urllib3-2.6.3.tar.gz", hash = "sha256:1b62b6884944a57dbe321509ab94fd4d3b307075e0c2eae991ac71ee15ad38ed"},
 ]
 
 [package.extras]
-brotli = ["brotli (>=1.0.9) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\""]
+brotli = ["brotli (>=1.2.0) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=1.2.0.0) ; platform_python_implementation != \"CPython\""]
 h2 = ["h2 (>=4,<5)"]
 socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
-zstd = ["zstandard (>=0.18.0)"]
+zstd = ["backports-zstd (>=1.0.0) ; python_version < \"3.14\""]
 
 [[package]]
 name = "validators"
@@ -7969,24 +8800,22 @@ test = ["flake8 (>=2.4.0)", "isort (>=4.2.2)", "pytest (>=2.2.3)"]
 
 [[package]]
 name = "virtualenv"
-version = "20.31.2"
+version = "21.2.4"
 description = "Virtual Python Environment builder"
 optional = false
 python-versions = ">=3.8"
 groups = ["main", "dev"]
 files = [
-    {file = "virtualenv-20.31.2-py3-none-any.whl", hash = "sha256:36efd0d9650ee985f0cad72065001e66d49a6f24eb44d98980f630686243cf11"},
-    {file = "virtualenv-20.31.2.tar.gz", hash = "sha256:e10c0a9d02835e592521be48b332b6caee6887f332c111aa79a09b9e79efc2af"},
+    {file = "virtualenv-21.2.4-py3-none-any.whl", hash = "sha256:29d21e941795206138d0f22f4e45ff7050e5da6c6472299fb7103318763861ac"},
+    {file = "virtualenv-21.2.4.tar.gz", hash = "sha256:b294ef68192638004d72524ce7ef303e9d0cf5a44c95ce2e54a7500a6381cada"},
 ]
 
 [package.dependencies]
 distlib = ">=0.3.7,<1"
-filelock = ">=3.12.2,<4"
+filelock = {version = ">=3.24.2,<4", markers = "python_version >= \"3.10\""}
 platformdirs = ">=3.9.1,<5"
-
-[package.extras]
-docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
-test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8) ; platform_python_implementation == \"PyPy\" or platform_python_implementation == \"GraalVM\" or platform_python_implementation == \"CPython\" and sys_platform == \"win32\" and python_version >= \"3.13\"", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10) ; platform_python_implementation == \"CPython\""]
+python-discovery = ">=1.2.2"
+typing-extensions = {version = ">=4.13.2", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "watchdog"
@@ -8030,26 +8859,26 @@ watchmedo = ["PyYAML (>=3.10)"]
 
 [[package]]
 name = "wcwidth"
-version = "0.2.13"
+version = "0.6.0"
 description = "Measures the displayed width of unicode strings in a terminal"
 optional = false
-python-versions = "*"
+python-versions = ">=3.8"
 groups = ["dev", "s3"]
 files = [
-    {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"},
-    {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"},
+    {file = "wcwidth-0.6.0-py3-none-any.whl", hash = "sha256:1a3a1e510b553315f8e146c54764f4fb6264ffad731b3d78088cdb1478ffbdad"},
+    {file = "wcwidth-0.6.0.tar.gz", hash = "sha256:cdc4e4262d6ef9a1a57e018384cbeb1208d8abbc64176027e2c2455c81313159"},
 ]
 
 [[package]]
 name = "webcolors"
-version = "24.11.1"
+version = "25.10.0"
 description = "A library for working with the color formats defined by HTML and CSS."
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 groups = ["main", "dev"]
 files = [
-    {file = "webcolors-24.11.1-py3-none-any.whl", hash = "sha256:515291393b4cdf0eb19c155749a096f779f7d909f7cceea072791cb9095b92e9"},
-    {file = "webcolors-24.11.1.tar.gz", hash = "sha256:ecb3d768f32202af770477b8b65f318fa4f566c22948673a977b00d589dd80f6"},
+    {file = "webcolors-25.10.0-py3-none-any.whl", hash = "sha256:032c727334856fc0b968f63daa252a1ac93d33db2f5267756623c210e57a4f1d"},
+    {file = "webcolors-25.10.0.tar.gz", hash = "sha256:62abae86504f66d0f6364c2a8520de4a0c47b80c03fc3a5f1815fedbef7c19bf"},
 ]
 
 [[package]]
@@ -8066,20 +8895,37 @@ files = [
 
 [[package]]
 name = "websocket-client"
-version = "1.8.0"
+version = "1.9.0"
 description = "WebSocket client for Python with low level API options"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 groups = ["main", "dev"]
 files = [
-    {file = "websocket_client-1.8.0-py3-none-any.whl", hash = "sha256:17b44cc997f5c498e809b22cdf2d9c7a9e71c02c8cc2b6c56e7c2d1239bfa526"},
-    {file = "websocket_client-1.8.0.tar.gz", hash = "sha256:3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da"},
+    {file = "websocket_client-1.9.0-py3-none-any.whl", hash = "sha256:af248a825037ef591efbf6ed20cc5faa03d3b47b9e5a2230a529eeee1c1fc3ef"},
+    {file = "websocket_client-1.9.0.tar.gz", hash = "sha256:9e813624b6eb619999a97dc7958469217c3176312b3a16a4bd1bc7e08a46ec98"},
 ]
 
 [package.extras]
-docs = ["Sphinx (>=6.0)", "myst-parser (>=2.0.0)", "sphinx-rtd-theme (>=1.1.0)"]
+docs = ["Sphinx (>=6.0)", "myst-parser (>=2.0.0)", "sphinx_rtd_theme (>=1.1.0)"]
 optional = ["python-socks", "wsaccel"]
-test = ["websockets"]
+test = ["pytest", "websockets"]
+
+[[package]]
+name = "wikidata-client"
+version = "0.0.4"
+description = "Interact with Wikidata programmatically"
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+markers = "python_version >= \"3.14\" or python_version == \"3.10\""
+files = [
+    {file = "wikidata_client-0.0.4-py3-none-any.whl", hash = "sha256:5390fe6a63926e2b7354c44ae1a6c6c481ed26ceb0a82b66fff95bf242b201b7"},
+    {file = "wikidata_client-0.0.4.tar.gz", hash = "sha256:ea6862191d8b78dcb9edbc4b2dad8ff24310e42d76cd129066b1020402c070c5"},
+]
+
+[package.dependencies]
+click = "*"
+requests = "*"
 
 [[package]]
 name = "win32-setctime"
@@ -8099,205 +8945,243 @@ dev = ["black (>=19.3b0) ; python_version >= \"3.6\"", "pytest (>=4.6.2)"]
 
 [[package]]
 name = "wrapt"
-version = "1.17.2"
+version = "2.1.2"
 description = "Module for decorators, wrappers and monkey patching."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
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 [package.dependencies]
@@ -8307,38 +9191,35 @@ propcache = ">=0.2.1"
 
 [[package]]
 name = "zenodo-client"
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-description = "A wrapper for the Zenodo API."
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+description = "A wrapper for the Zenodo API"
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-python-versions = ">=3.9"
+python-versions = ">=3.10"
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 ]
 
 [package.dependencies]
 click = "*"
-more_click = "*"
+more-click = "*"
 pydantic = ">=2"
 pystow = ">=0.4.9"
 requests = "*"
-typing_extensions = "*"
-
-[package.extras]
-docs = ["sphinx (>=8.0)", "sphinx-click", "sphinx-rtd-theme (>=3.0)"]
-tests = ["coverage", "pytest"]
+tqdm = "*"
+typing-extensions = "*"
 
 [[package]]
 name = "zipp"
-version = "3.23.0"
+version = "3.23.1"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
 files = [
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 [package.extras]