From 14939405d035b9c662434e16014c9610984ed5ff Mon Sep 17 00:00:00 2001
From: Peter Van Dyken <pvandyk2@uwo.ca>
Date: Tue, 16 Apr 2024 17:40:01 -0400
Subject: [PATCH] Prevent installation of docutils==0.21.1

Unable to be installed by poetry due to a malformed upload to pypi

See https://github.com/python-poetry/poetry/issues/9293
---
 poetry.lock    | 1557 ++++++++++++++++++++++++++++--------------------
 pyproject.toml |   14 +-
 2 files changed, 921 insertions(+), 650 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 873560ba..09b82fa8 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -25,6 +25,28 @@ files = [
 [package.dependencies]
 typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""}
 
+[[package]]
+name = "anyio"
+version = "4.3.0"
+description = "High level compatibility layer for multiple asynchronous event loop implementations"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "anyio-4.3.0-py3-none-any.whl", hash = "sha256:048e05d0f6caeed70d731f3db756d35dcc1f35747c8c403364a8332c630441b8"},
+    {file = "anyio-4.3.0.tar.gz", hash = "sha256:f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6"},
+]
+
+[package.dependencies]
+exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""}
+idna = ">=2.8"
+sniffio = ">=1.1"
+typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""}
+
+[package.extras]
+doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
+test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"]
+trio = ["trio (>=0.23)"]
+
 [[package]]
 name = "appdirs"
 version = "1.4.4"
@@ -125,13 +147,13 @@ lxml = ["lxml"]
 
 [[package]]
 name = "bids-validator"
-version = "1.14.0"
+version = "1.14.5"
 description = "Validator for the Brain Imaging Data Structure"
 optional = false
-python-versions = "*"
+python-versions = ">=3.8"
 files = [
-    {file = "bids-validator-1.14.0.tar.gz", hash = "sha256:33b0f865c1aa3e39fb92518df163fa6b79478d1aa102af52fd53704a5ef2ea46"},
-    {file = "bids_validator-1.14.0-py3-none-any.whl", hash = "sha256:bab89f97a8d833235562cf0f3ac981bfca71acf2793a6c12a8af631c29ee0b8f"},
+    {file = "bids-validator-1.14.5.tar.gz", hash = "sha256:4d721bd5f7fb0fa68cfbc2f9178ecee43beea69d529f846797e190694744827a"},
+    {file = "bids_validator-1.14.5-py3-none-any.whl", hash = "sha256:9b5cb66b7c07924789486ea0aadc92c43a91ee427cb540f0bb4dc9b89397dbdf"},
 ]
 
 [[package]]
@@ -155,13 +177,13 @@ all = ["coverage", "docopt", "mock", "nexus-sdk", "oyaml", "pytest", "pytest-run
 
 [[package]]
 name = "certifi"
-version = "2023.11.17"
+version = "2024.2.2"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"},
-    {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"},
+    {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"},
+    {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"},
 ]
 
 [[package]]
@@ -326,19 +348,19 @@ files = [
 
 [[package]]
 name = "copier"
-version = "9.1.1"
+version = "9.2.0"
 description = "A library for rendering project templates."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "copier-9.1.1-py3-none-any.whl", hash = "sha256:d6983127a7d1af7970bf8d5a50948ca6057a592a87ed4b39eaf6a86b8746fa2a"},
-    {file = "copier-9.1.1.tar.gz", hash = "sha256:1127771e33d00453bdc716ab314b06c11bd0925815ab1e1010c03278d7934ebd"},
+    {file = "copier-9.2.0-py3-none-any.whl", hash = "sha256:62682ce8cd78db1006feafe2c815d59d5069efa4c2009017f3c63780d977f6de"},
+    {file = "copier-9.2.0.tar.gz", hash = "sha256:4ed9012579923955d3fc61d049568907fabe6d9a47e5f871236c6aae0b7472f1"},
 ]
 
 [package.dependencies]
 colorama = ">=0.4.6"
-decorator = ">=5.1.1"
 dunamai = {version = ">=1.7.0", markers = "python_version < \"4\""}
+eval-type-backport = {version = ">=0.1.3,<0.2.0", markers = "python_version < \"3.10\""}
 funcy = ">=1.17"
 jinja2 = ">=3.1.3"
 jinja2-ansible-filters = ">=1.3.1"
@@ -348,69 +370,68 @@ plumbum = ">=1.6.9"
 pydantic = ">=2.4.2"
 pygments = ">=2.7.1"
 pyyaml = ">=5.3.1"
-pyyaml-include = ">=1.2"
 questionary = ">=1.8.1"
 typing-extensions = {version = ">=3.7.4,<5.0.0", markers = "python_version < \"3.9\""}
 
 [[package]]
 name = "coverage"
-version = "7.4.1"
+version = "7.4.4"
 description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "coverage-7.4.4.tar.gz", hash = "sha256:c901df83d097649e257e803be22592aedfd5182f07b3cc87d640bbb9afd50f49"},
 ]
 
 [package.dependencies]
@@ -453,17 +474,6 @@ files = [
     {file = "datrie-0.8.2.tar.gz", hash = "sha256:525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d"},
 ]
 
-[[package]]
-name = "decorator"
-version = "5.1.1"
-description = "Decorators for Humans"
-optional = false
-python-versions = ">=3.5"
-files = [
-    {file = "decorator-5.1.1-py3-none-any.whl", hash = "sha256:b8c3f85900b9dc423225913c5aace94729fe1fa9763b38939a95226f02d37186"},
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-]
-
 [[package]]
 name = "distlib"
 version = "0.3.8"
@@ -487,13 +497,13 @@ files = [
 
 [[package]]
 name = "docstring-parser"
-version = "0.15"
+version = "0.16"
 description = "Parse Python docstrings in reST, Google and Numpydoc format"
 optional = false
 python-versions = ">=3.6,<4.0"
 files = [
-    {file = "docstring_parser-0.15-py3-none-any.whl", hash = "sha256:d1679b86250d269d06a99670924d6bce45adc00b08069dae8c47d98e89b667a9"},
-    {file = "docstring_parser-0.15.tar.gz", hash = "sha256:48ddc093e8b1865899956fcc03b03e66bb7240c310fac5af81814580c55bf682"},
+    {file = "docstring_parser-0.16-py3-none-any.whl", hash = "sha256:bf0a1387354d3691d102edef7ec124f219ef639982d096e26e3b60aeffa90637"},
+    {file = "docstring_parser-0.16.tar.gz", hash = "sha256:538beabd0af1e2db0146b6bd3caa526c35a34d61af9fd2887f3a8a27a739aa6e"},
 ]
 
 [[package]]
@@ -520,18 +530,32 @@ files = [
 
 [[package]]
 name = "dunamai"
-version = "1.19.0"
+version = "1.20.0"
 description = "Dynamic version generation"
 optional = false
-python-versions = ">=3.5,<4.0"
+python-versions = ">=3.5"
 files = [
-    {file = "dunamai-1.19.0-py3-none-any.whl", hash = "sha256:1ed948676bbf0812bfaafe315a134634f8d6eb67138513c75aa66e747404b9c6"},
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+    {file = "dunamai-1.20.0-py3-none-any.whl", hash = "sha256:a2185c227351a52a013c7d7a695d3f3cb6625c3eed14a5295adbbcc7e2f7f8d4"},
+    {file = "dunamai-1.20.0.tar.gz", hash = "sha256:c3f1ee64a1e6cc9ebc98adafa944efaccd0db32482d2177e59c1ff6bdf23cd70"},
 ]
 
 [package.dependencies]
 packaging = ">=20.9"
 
+[[package]]
+name = "eval-type-backport"
+version = "0.1.3"
+description = "Like `typing._eval_type`, but lets older Python versions use newer typing features."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "eval_type_backport-0.1.3-py3-none-any.whl", hash = "sha256:519d2a993b3da286df9f90e17f503f66435106ad870cf26620c5720e2158ddf2"},
+    {file = "eval_type_backport-0.1.3.tar.gz", hash = "sha256:d83ee225331dfa009493cec1f3608a71550b515ee4749abe78da14e3c5e314f5"},
+]
+
+[package.extras]
+tests = ["pytest"]
+
 [[package]]
 name = "exceptiongroup"
 version = "1.2.0"
@@ -548,13 +572,13 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "execnet"
-version = "2.0.2"
+version = "2.1.1"
 description = "execnet: rapid multi-Python deployment"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "execnet-2.0.2-py3-none-any.whl", hash = "sha256:88256416ae766bc9e8895c76a87928c0012183da3cc4fc18016e6f050e025f41"},
-    {file = "execnet-2.0.2.tar.gz", hash = "sha256:cc59bc4423742fd71ad227122eb0dd44db51efb3dc4095b45ac9a08c770096af"},
+    {file = "execnet-2.1.1-py3-none-any.whl", hash = "sha256:26dee51f1b80cebd6d0ca8e74dd8745419761d3bef34163928cbebbdc4749fdc"},
+    {file = "execnet-2.1.1.tar.gz", hash = "sha256:5189b52c6121c24feae288166ab41b32549c7e2348652736540b9e6e7d4e72e3"},
 ]
 
 [package.extras]
@@ -576,18 +600,18 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc
 
 [[package]]
 name = "filelock"
-version = "3.13.1"
+version = "3.13.4"
 description = "A platform independent file lock."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "filelock-3.13.1-py3-none-any.whl", hash = "sha256:57dbda9b35157b05fb3e58ee91448612eb674172fab98ee235ccb0b5bee19a1c"},
-    {file = "filelock-3.13.1.tar.gz", hash = "sha256:521f5f56c50f8426f5e03ad3b281b490a87ef15bc6c526f168290f0c7148d44e"},
+    {file = "filelock-3.13.4-py3-none-any.whl", hash = "sha256:404e5e9253aa60ad457cae1be07c0f0ca90a63931200a47d9b6a6af84fd7b45f"},
+    {file = "filelock-3.13.4.tar.gz", hash = "sha256:d13f466618bfde72bd2c18255e269f72542c6e70e7bac83a0232d6b1cc5c8cf4"},
 ]
 
 [package.extras]
-docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.24)"]
-testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)"]
+docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8.0.1)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)"]
 typing = ["typing-extensions (>=4.8)"]
 
 [[package]]
@@ -659,30 +683,31 @@ smmap = ">=3.0.1,<6"
 
 [[package]]
 name = "gitpython"
-version = "3.1.41"
+version = "3.1.43"
 description = "GitPython is a Python library used to interact with Git repositories"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "GitPython-3.1.41-py3-none-any.whl", hash = "sha256:c36b6634d069b3f719610175020a9aed919421c87552185b085e04fbbdb10b7c"},
-    {file = "GitPython-3.1.41.tar.gz", hash = "sha256:ed66e624884f76df22c8e16066d567aaa5a37d5b5fa19db2c6df6f7156db9048"},
+    {file = "GitPython-3.1.43-py3-none-any.whl", hash = "sha256:eec7ec56b92aad751f9912a73404bc02ba212a23adb2c7098ee668417051a1ff"},
+    {file = "GitPython-3.1.43.tar.gz", hash = "sha256:35f314a9f878467f5453cc1fee295c3e18e52f1b99f10f6cf5b1682e968a9e7c"},
 ]
 
 [package.dependencies]
 gitdb = ">=4.0.1,<5"
 
 [package.extras]
-test = ["black", "coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock", "mypy", "pre-commit", "pytest (>=7.3.1)", "pytest-cov", "pytest-instafail", "pytest-mock", "pytest-sugar", "sumtypes"]
+doc = ["sphinx (==4.3.2)", "sphinx-autodoc-typehints", "sphinx-rtd-theme", "sphinxcontrib-applehelp (>=1.0.2,<=1.0.4)", "sphinxcontrib-devhelp (==1.0.2)", "sphinxcontrib-htmlhelp (>=2.0.0,<=2.0.1)", "sphinxcontrib-qthelp (==1.0.3)", "sphinxcontrib-serializinghtml (==1.1.5)"]
+test = ["coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock", "mypy", "pre-commit", "pytest (>=7.3.1)", "pytest-cov", "pytest-instafail", "pytest-mock", "pytest-sugar", "typing-extensions"]
 
 [[package]]
 name = "graphlib-backport"
-version = "1.0.3"
+version = "1.1.0"
 description = "Backport of the Python 3.9 graphlib module for Python 3.6+"
 optional = false
 python-versions = ">=3.6,<4.0"
 files = [
-    {file = "graphlib_backport-1.0.3-py3-none-any.whl", hash = "sha256:24246967b9e7e6a91550bc770e6169585d35aa32790258579a8a3899a8c18fde"},
-    {file = "graphlib_backport-1.0.3.tar.gz", hash = "sha256:7bb8fc7757b8ae4e6d8000a26cd49e9232aaa9a3aa57edb478474b8424bfaae2"},
+    {file = "graphlib_backport-1.1.0-py3-none-any.whl", hash = "sha256:eccacf9f2126cdf89ce32a6018c88e1ecd3e4898a07568add6e1907a439055ba"},
+    {file = "graphlib_backport-1.1.0.tar.gz", hash = "sha256:00a7888b21e5393064a133209cb5d3b3ef0a2096cf023914c9d778dff5644125"},
 ]
 
 [[package]]
@@ -756,6 +781,17 @@ files = [
 docs = ["Sphinx", "furo"]
 test = ["objgraph", "psutil"]
 
+[[package]]
+name = "h11"
+version = "0.14.0"
+description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "h11-0.14.0-py3-none-any.whl", hash = "sha256:e3fe4ac4b851c468cc8363d500db52c2ead036020723024a109d37346efaa761"},
+    {file = "h11-0.14.0.tar.gz", hash = "sha256:8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d"},
+]
+
 [[package]]
 name = "humanfriendly"
 version = "10.0"
@@ -772,13 +808,13 @@ pyreadline3 = {version = "*", markers = "sys_platform == \"win32\" and python_ve
 
 [[package]]
 name = "hypothesis"
-version = "6.97.4"
+version = "6.100.1"
 description = "A library for property-based testing"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "hypothesis-6.97.4-py3-none-any.whl", hash = "sha256:9069fe3fb18d9b7dd218bd69ab50bbc66426819dfac7cc7168ba85034d98a4df"},
-    {file = "hypothesis-6.97.4.tar.gz", hash = "sha256:28ff724fa81ccc55f64f0f1eb06e4a75db6a195fe0857e9b3184cf4ff613a103"},
+    {file = "hypothesis-6.100.1-py3-none-any.whl", hash = "sha256:3dacf6ec90e8d14aaee02cde081ac9a17d5b70105e45e6ac822db72052c0195b"},
+    {file = "hypothesis-6.100.1.tar.gz", hash = "sha256:ebff09d7fa4f1fb6a855a812baf17e578b4481b7b70ec6d96496210d1a4c6c35"},
 ]
 
 [package.dependencies]
@@ -787,9 +823,10 @@ exceptiongroup = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 sortedcontainers = ">=2.1.0,<3.0.0"
 
 [package.extras]
-all = ["backports.zoneinfo (>=0.2.1)", "black (>=19.10b0)", "click (>=7.0)", "django (>=3.2)", "dpcontracts (>=0.4)", "lark (>=0.10.1)", "libcst (>=0.3.16)", "numpy (>=1.17.3)", "pandas (>=1.1)", "pytest (>=4.6)", "python-dateutil (>=1.4)", "pytz (>=2014.1)", "redis (>=3.0.0)", "rich (>=9.0.0)", "tzdata (>=2023.4)"]
+all = ["backports.zoneinfo (>=0.2.1)", "black (>=19.10b0)", "click (>=7.0)", "crosshair-tool (>=0.0.54)", "django (>=3.2)", "dpcontracts (>=0.4)", "hypothesis-crosshair (>=0.0.2)", "lark (>=0.10.1)", "libcst (>=0.3.16)", "numpy (>=1.17.3)", "pandas (>=1.1)", "pytest (>=4.6)", "python-dateutil (>=1.4)", "pytz (>=2014.1)", "redis (>=3.0.0)", "rich (>=9.0.0)", "tzdata (>=2024.1)"]
 cli = ["black (>=19.10b0)", "click (>=7.0)", "rich (>=9.0.0)"]
 codemods = ["libcst (>=0.3.16)"]
+crosshair = ["crosshair-tool (>=0.0.54)", "hypothesis-crosshair (>=0.0.2)"]
 dateutil = ["python-dateutil (>=1.4)"]
 django = ["django (>=3.2)"]
 dpcontracts = ["dpcontracts (>=0.4)"]
@@ -800,17 +837,17 @@ pandas = ["pandas (>=1.1)"]
 pytest = ["pytest (>=4.6)"]
 pytz = ["pytz (>=2014.1)"]
 redis = ["redis (>=3.0.0)"]
-zoneinfo = ["backports.zoneinfo (>=0.2.1)", "tzdata (>=2023.4)"]
+zoneinfo = ["backports.zoneinfo (>=0.2.1)", "tzdata (>=2024.1)"]
 
 [[package]]
 name = "identify"
-version = "2.5.33"
+version = "2.5.35"
 description = "File identification library for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "identify-2.5.33-py2.py3-none-any.whl", hash = "sha256:d40ce5fcd762817627670da8a7d8d8e65f24342d14539c59488dc603bf662e34"},
-    {file = "identify-2.5.33.tar.gz", hash = "sha256:161558f9fe4559e1557e1bff323e8631f6a0e4837f7497767c1782832f16b62d"},
+    {file = "identify-2.5.35-py2.py3-none-any.whl", hash = "sha256:c4de0081837b211594f8e877a6b4fad7ca32bbfc1a9307fdd61c28bfe923f13e"},
+    {file = "identify-2.5.35.tar.gz", hash = "sha256:10a7ca245cfcd756a554a7288159f72ff105ad233c7c4b9c6f0f4d108f5f6791"},
 ]
 
 [package.extras]
@@ -818,13 +855,13 @@ license = ["ukkonen"]
 
 [[package]]
 name = "idna"
-version = "3.6"
+version = "3.7"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
 python-versions = ">=3.5"
 files = [
-    {file = "idna-3.6-py3-none-any.whl", hash = "sha256:c05567e9c24a6b9faaa835c4821bad0590fbb9d5779e7caa6e1cc4978e7eb24f"},
-    {file = "idna-3.6.tar.gz", hash = "sha256:9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca"},
+    {file = "idna-3.7-py3-none-any.whl", hash = "sha256:82fee1fc78add43492d3a1898bfa6d8a904cc97d8427f683ed8e798d07761aa0"},
+    {file = "idna-3.7.tar.gz", hash = "sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc"},
 ]
 
 [[package]]
@@ -840,32 +877,32 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "7.0.1"
+version = "7.1.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_metadata-7.0.1-py3-none-any.whl", hash = "sha256:4805911c3a4ec7c3966410053e9ec6a1fecd629117df5adee56dfc9432a1081e"},
-    {file = "importlib_metadata-7.0.1.tar.gz", hash = "sha256:f238736bb06590ae52ac1fab06a3a9ef1d8dce2b7a35b5ab329371d6c8f5d2cc"},
+    {file = "importlib_metadata-7.1.0-py3-none-any.whl", hash = "sha256:30962b96c0c223483ed6cc7280e7f0199feb01a0e40cfae4d4450fc6fab1f570"},
+    {file = "importlib_metadata-7.1.0.tar.gz", hash = "sha256:b78938b926ee8d5f020fc4772d487045805a55ddbad2ecf21c6d60938dc7fcd2"},
 ]
 
 [package.dependencies]
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
-testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)", "pytest-ruff"]
+testing = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
 
 [[package]]
 name = "importlib-resources"
-version = "6.1.1"
+version = "6.4.0"
 description = "Read resources from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_resources-6.1.1-py3-none-any.whl", hash = "sha256:e8bf90d8213b486f428c9c39714b920041cb02c184686a3dee24905aaa8105d6"},
-    {file = "importlib_resources-6.1.1.tar.gz", hash = "sha256:3893a00122eafde6894c59914446a512f728a0c1a45f9bb9b63721b6bacf0b4a"},
+    {file = "importlib_resources-6.4.0-py3-none-any.whl", hash = "sha256:50d10f043df931902d4194ea07ec57960f66a80449ff867bfe782b4c486ba78c"},
+    {file = "importlib_resources-6.4.0.tar.gz", hash = "sha256:cdb2b453b8046ca4e3798eb1d84f3cce1446a0e8e7b5ef4efb600f19fc398145"},
 ]
 
 [package.dependencies]
@@ -873,7 +910,7 @@ zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-ruff", "zipp (>=3.17)"]
+testing = ["jaraco.test (>=5.4)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)", "zipp (>=3.17)"]
 
 [[package]]
 name = "iniconfig"
@@ -987,13 +1024,13 @@ referencing = ">=0.31.0"
 
 [[package]]
 name = "jupyter-core"
-version = "5.7.1"
+version = "5.7.2"
 description = "Jupyter core package. A base package on which Jupyter projects rely."
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "jupyter_core-5.7.2.tar.gz", hash = "sha256:aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9"},
 ]
 
 [package.dependencies]
@@ -1003,21 +1040,25 @@ traitlets = ">=5.3"
 
 [package.extras]
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"]
-test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"]
+test = ["ipykernel", "pre-commit", "pytest (<8)", "pytest-cov", "pytest-timeout"]
 
 [[package]]
 name = "lazy-loader"
-version = "0.3"
-description = "lazy_loader"
+version = "0.4"
+description = "Makes it easy to load subpackages and functions on demand."
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "lazy_loader-0.4.tar.gz", hash = "sha256:47c75182589b91a4e1a85a136c074285a5ad4d9f39c63e0d7fb76391c4574cd1"},
 ]
 
+[package.dependencies]
+packaging = "*"
+
 [package.extras]
-lint = ["pre-commit (>=3.3)"]
+dev = ["changelist (==0.5)"]
+lint = ["pre-commit (==3.7.0)"]
 test = ["pytest (>=7.4)", "pytest-cov (>=4.1)"]
 
 [[package]]
@@ -1061,71 +1102,71 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
 [[package]]
 name = "markupsafe"
-version = "2.1.4"
+version = "2.1.5"
 description = "Safely add untrusted strings to HTML/XML markup."
 optional = false
 python-versions = ">=3.7"
 files = [
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 [[package]]
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 [package.extras]
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 pytz = ">=2020.1"
 tzdata = ">=2022.7"
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 plot = ["matplotlib (>=3.6.3)"]
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-version = "1.4.2"
+version = "1.4.3"
 description = "The smartest command line arguments parser in the world"
 optional = false
 python-versions = "*"
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 [[package]]
@@ -1638,13 +1680,13 @@ ssh = ["paramiko"]
 
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 description = "A task runner that works well with poetry."
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 typing-extensions = ">=4.6.1"
 
 [package.extras]
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 ]
 
 [package.dependencies]
@@ -1896,13 +1938,13 @@ typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0"
 
 [[package]]
 name = "pyfakefs"
-version = "5.3.5"
+version = "5.4.1"
 description = "pyfakefs implements a fake file system that mocks the Python file system modules."
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [[package]]
@@ -1922,13 +1964,13 @@ windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "pyparsing"
-version = "3.1.1"
+version = "3.1.2"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
 optional = false
 python-versions = ">=3.6.8"
 files = [
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 ]
 
 [package.extras]
@@ -1947,13 +1989,13 @@ files = [
 
 [[package]]
 name = "pyright"
-version = "1.1.349"
+version = "1.1.358"
 description = "Command line wrapper for pyright"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -2007,13 +2049,13 @@ histogram = ["pygal", "pygaljs"]
 
 [[package]]
 name = "pytest-cov"
-version = "4.1.0"
+version = "5.0.0"
 description = "Pytest plugin for measuring coverage."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -2021,21 +2063,21 @@ coverage = {version = ">=5.2.1", extras = ["toml"]}
 pytest = ">=4.6"
 
 [package.extras]
-testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
+testing = ["fields", "hunter", "process-tests", "pytest-xdist", "virtualenv"]
 
 [[package]]
 name = "pytest-mock"
-version = "3.12.0"
+version = "3.14.0"
 description = "Thin-wrapper around the mock package for easier use with pytest"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
-pytest = ">=5.0"
+pytest = ">=6.2.5"
 
 [package.extras]
 dev = ["pre-commit", "pytest-asyncio", "tox"]
@@ -2076,13 +2118,13 @@ testing = ["filelock"]
 
 [[package]]
 name = "python-dateutil"
-version = "2.8.2"
+version = "2.9.0.post0"
 description = "Extensions to the standard Python datetime module"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -2090,13 +2132,13 @@ six = ">=1.5"
 
 [[package]]
 name = "pytz"
-version = "2023.4"
+version = "2024.1"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [[package]]
@@ -2181,23 +2223,6 @@ files = [
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 ]
 
-[[package]]
-name = "pyyaml-include"
-version = "1.3.2"
-description = "Extending PyYAML with a custom constructor for including YAML files within YAML files"
-optional = false
-python-versions = ">=3.7"
-files = [
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-]
-
-[package.dependencies]
-PyYAML = ">=6.0,<7.0"
-
-[package.extras]
-toml = ["toml"]
-
 [[package]]
 name = "questionary"
 version = "2.0.1"
@@ -2214,13 +2239,13 @@ prompt_toolkit = ">=2.0,<=3.0.36"
 
 [[package]]
 name = "referencing"
-version = "0.33.0"
+version = "0.34.0"
 description = "JSON Referencing + Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -2250,22 +2275,20 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "requests-mock"
-version = "1.11.0"
+version = "1.12.1"
 description = "Mock out responses from the requests package"
 optional = false
-python-versions = "*"
+python-versions = ">=3.5"
 files = [
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 ]
 
 [package.dependencies]
-requests = ">=2.3,<3"
-six = "*"
+requests = ">=2.22,<3"
 
 [package.extras]
 fixture = ["fixtures"]
-test = ["fixtures", "mock", "purl", "pytest", "requests-futures", "sphinx", "testtools"]
 
 [[package]]
 name = "reretry"
@@ -2280,121 +2303,121 @@ files = [
 
 [[package]]
 name = "rpds-py"
-version = "0.17.1"
+version = "0.18.0"
 description = "Python bindings to Rust's persistent data structures (rpds)"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [[package]]
 name = "simplejson"
@@ -2705,24 +2728,28 @@ files = [
 
 [[package]]
 name = "smart-open"
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 description = "Utils for streaming large files (S3, HDFS, GCS, Azure Blob Storage, gzip, bz2...)"
 optional = false
-python-versions = ">=3.6,<4.0"
+python-versions = "<4.0,>=3.7"
 files = [
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 ]
 
+[package.dependencies]
+wrapt = "*"
+
 [package.extras]
-all = ["azure-common", "azure-core", "azure-storage-blob", "boto3", "google-cloud-storage (>=2.6.0)", "paramiko", "requests"]
+all = ["azure-common", "azure-core", "azure-storage-blob", "boto3", "google-cloud-storage (>=2.6.0)", "paramiko", "requests", "zstandard"]
 azure = ["azure-common", "azure-core", "azure-storage-blob"]
 gcs = ["google-cloud-storage (>=2.6.0)"]
 http = ["requests"]
 s3 = ["boto3"]
 ssh = ["paramiko"]
-test = ["azure-common", "azure-core", "azure-storage-blob", "boto3", "google-cloud-storage (>=2.6.0)", "moto[server]", "paramiko", "pytest", "pytest-rerunfailures", "requests", "responses"]
+test = ["azure-common", "azure-core", "azure-storage-blob", "boto3", "google-cloud-storage (>=2.6.0)", "moto[server]", "paramiko", "pytest", "pytest-rerunfailures", "requests", "responses", "zstandard"]
 webhdfs = ["requests"]
+zst = ["zstandard"]
 
 [[package]]
 name = "smmap"
@@ -2777,6 +2804,17 @@ messaging = ["slacker"]
 pep = ["eido", "peppy"]
 reports = ["pygments"]
 
+[[package]]
+name = "sniffio"
+version = "1.3.1"
+description = "Sniff out which async library your code is running under"
+optional = false
+python-versions = ">=3.7"
+files = [
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+    {file = "sniffio-1.3.1.tar.gz", hash = "sha256:f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc"},
+]
+
 [[package]]
 name = "snowballstemmer"
 version = "2.2.0"
@@ -2881,6 +2919,28 @@ sphinx = "*"
 [package.extras]
 test = ["pytest", "pytest-cov"]
 
+[[package]]
+name = "sphinx-autobuild"
+version = "2024.4.16"
+description = "Rebuild Sphinx documentation on changes, with hot reloading in the browser."
+optional = false
+python-versions = ">=3.9"
+files = [
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+    {file = "sphinx_autobuild-2024.4.16.tar.gz", hash = "sha256:1c0ed37a1970eed197f9c5a66d65759e7c4e4cba7b5a5d77940752bf1a59f2c7"},
+]
+
+[package.dependencies]
+colorama = "*"
+sphinx = "*"
+starlette = ">=0.35"
+uvicorn = ">=0.25"
+watchfiles = ">=0.20"
+websockets = ">=11"
+
+[package.extras]
+test = ["pytest (>=6)"]
+
 [[package]]
 name = "sphinx-basic-ng"
 version = "1.0.0b2"
@@ -3057,60 +3117,60 @@ test = ["pytest"]
 
 [[package]]
 name = "sqlalchemy"
-version = "2.0.25"
+version = "2.0.29"
 description = "Database Abstraction Library"
 optional = false
 python-versions = ">=3.7"
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 [package.dependencies]
@@ -3142,6 +3202,24 @@ postgresql-psycopgbinary = ["psycopg[binary] (>=3.0.7)"]
 pymysql = ["pymysql"]
 sqlcipher = ["sqlcipher3_binary"]
 
+[[package]]
+name = "starlette"
+version = "0.37.2"
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+optional = false
+python-versions = ">=3.8"
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+
+[package.extras]
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+
 [[package]]
 name = "stopit"
 version = "1.1.2"
@@ -3238,70 +3316,70 @@ files = [
 
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 python-versions = ">=2"
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 python-versions = ">=3.6"
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 runtime-strict = ["jaraco.windows (==3.9.1)", "pydantic (<2.0)"]
 tests = ["coverage (>=4.3.4)", "coverage (>=4.5)", "coverage (>=5.3.1)", "coverage (>=5.3.1)", "coverage (>=5.3.1)", "coverage (>=6.1.1)", "coverage (>=6.1.1)", "coverage (>=6.1.1)", "coverage (>=6.1.1)", "coverage (>=7.3.0)", "pytest (>=4.6.0)", "pytest (>=4.6.0)", "pytest (>=4.6.0,<=4.6.11)", "pytest (>=4.6.0,<=4.6.11)", "pytest (>=4.6.0,<=6.1.2)", "pytest (>=6.2.5)", "pytest-cov (>=2.8.1)", "pytest-cov (>=2.8.1)", "pytest-cov (>=2.9.0)", "pytest-cov (>=3.0.0)", "pytest-timeout (>=1.4.2)", "requests (>=2.25.1)", "xdoctest (>=1.1.2)"]
@@ -3311,13 +3389,13 @@ types-strict = ["autoflake (==1.4)", "mypy", "yapf (==0.32.0)"]
 
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 name = "urllib3"
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+version = "2.2.1"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.extras]
@@ -3326,15 +3404,34 @@ h2 = ["h2 (>=4,<5)"]
 socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
 zstd = ["zstandard (>=0.18.0)"]
 
+[[package]]
+name = "uvicorn"
+version = "0.29.0"
+description = "The lightning-fast ASGI server."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "uvicorn-0.29.0-py3-none-any.whl", hash = "sha256:2c2aac7ff4f4365c206fd773a39bf4ebd1047c238f8b8268ad996829323473de"},
+    {file = "uvicorn-0.29.0.tar.gz", hash = "sha256:6a69214c0b6a087462412670b3ef21224fa48cae0e452b5883e8e8bdfdd11dd0"},
+]
+
+[package.dependencies]
+click = ">=7.0"
+h11 = ">=0.8"
+typing-extensions = {version = ">=4.0", markers = "python_version < \"3.11\""}
+
+[package.extras]
+standard = ["colorama (>=0.4)", "httptools (>=0.5.0)", "python-dotenv (>=0.13)", "pyyaml (>=5.1)", "uvloop (>=0.14.0,!=0.15.0,!=0.15.1)", "watchfiles (>=0.13)", "websockets (>=10.4)"]
+
 [[package]]
 name = "virtualenv"
-version = "20.25.0"
+version = "20.25.1"
 description = "Virtual Python Environment builder"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "virtualenv-20.25.0-py3-none-any.whl", hash = "sha256:4238949c5ffe6876362d9c0180fc6c3a824a7b12b80604eeb8085f2ed7460de3"},
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+    {file = "virtualenv-20.25.1-py3-none-any.whl", hash = "sha256:961c026ac520bac5f69acb8ea063e8a4f071bcc9457b9c1f28f6b085c511583a"},
+    {file = "virtualenv-20.25.1.tar.gz", hash = "sha256:e08e13ecdca7a0bd53798f356d5831434afa5b07b93f0abdf0797b7a06ffe197"},
 ]
 
 [package.dependencies]
@@ -3346,6 +3443,93 @@ platformdirs = ">=3.9.1,<5"
 docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "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)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
 
+[[package]]
+name = "watchfiles"
+version = "0.21.0"
+description = "Simple, modern and high performance file watching and code reload in python."
+optional = false
+python-versions = ">=3.8"
+files = [
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+]
+
+[package.dependencies]
+anyio = ">=3.0.0"
+
 [[package]]
 name = "wcwidth"
 version = "0.2.13"
@@ -3357,6 +3541,87 @@ files = [
     {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"},
 ]
 
+[[package]]
+name = "websockets"
+version = "12.0"
+description = "An implementation of the WebSocket Protocol (RFC 6455 & 7692)"
+optional = false
+python-versions = ">=3.8"
+files = [
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+    {file = "websockets-12.0.tar.gz", hash = "sha256:81df9cbcbb6c260de1e007e58c011bfebe2dafc8435107b0537f393dd38c8b1b"},
+]
+
 [[package]]
 name = "wrapt"
 version = "1.16.0"
@@ -3454,20 +3719,20 @@ pyyaml = ">=6.0,<7.0"
 
 [[package]]
 name = "zipp"
-version = "3.17.0"
+version = "3.18.1"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
-    {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
+    {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"},
+    {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8,<4.0"
-content-hash = "757f6259ffdcf629d6d88520124a8444a71298186e65a02e86536f8703203dea"
+content-hash = "5c75d3085ce1d46686416d4a287133ac777485d553822f56dd63965a0de5fd6f"
diff --git a/pyproject.toml b/pyproject.toml
index 31ff332b..c4bfd87d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -71,11 +71,14 @@ jinja2-time = ">=0.2.0"
 requests = ">=2.31.0"
 ruamel-yaml = ">=0.17.2"
 lazy-loader = ">=0.3"
+# Docutils is a requirement of snakemake, for snakebids otherwise it is merely a doc
+# dependency. Can't do 0.21 with poetry because of https://github.com/python-poetry/poetry/issues/9293
+docutils = "!=0.21.1"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.0.0"
 pytest-mock = "^3.7.0"
-poethepoet = "^0.24.0"
+poethepoet = "^0.25.1"
 pre-commit = "^3.0.0"
 # need custom fork of mkinit to handle .pyi files. PR to main repo pending
 # a mkinit dep has the 'platform_system == "Windows"' as a marker on an incompatible dependeny
@@ -93,8 +96,8 @@ pytest-xdist = "^3.3.1"
 pytest-split = "^0.8.1"
 tomli = "^2.0.1"
 requests-mock = "^1.11.0"
-pytest-cov = "^4.1.0"
-docstring-parser = "^0.15"
+pytest-cov = "^5.0"
+docstring-parser = "^0.16"
 
 
 [tool.poetry.group.docs.dependencies]
@@ -106,7 +109,10 @@ furo = "^2023.9.10"
 sphinx-copybutton = "^0.5.2"
 sphinx-reredirects = "^0.1.3"
 sphinx-design = "^0.5.0"
-sphinx-autobuild = "^2021.3.14"
+sphinx-autobuild = [
+    { version = "^2021.03.14", python = "3.8" },
+    { version = "^2024.02.04", python = ">=3.9" },
+]
 
 [tool.poetry.scripts]
 snakebids = "snakebids.admin:main"