From 51ea26897fcff05e2f1996614323a9798e42229a Mon Sep 17 00:00:00 2001
From: "Mark A. Miller" <mamillerpa@gmail.com>
Date: Tue, 28 Mar 2023 16:37:38 -0400
Subject: [PATCH 1/2] #95

---
 poetry.lock    | 940 ++++++++++++++++++++++++-------------------------
 pyproject.toml |   5 +-
 2 files changed, 456 insertions(+), 489 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index b1b3823..69f601c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -59,29 +59,26 @@ tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy
 
 [[package]]
 name = "babel"
-version = "2.11.0"
+version = "2.12.1"
 description = "Internationalization utilities"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "Babel-2.11.0-py3-none-any.whl", hash = "sha256:1ad3eca1c885218f6dce2ab67291178944f810a10a9b5f3cb8382a5a232b64fe"},
-    {file = "Babel-2.11.0.tar.gz", hash = "sha256:5ef4b3226b0180dedded4229651c8b0e1a3a6a2837d45a073272f313e4cf97f6"},
+    {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"},
+    {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"},
 ]
 
-[package.dependencies]
-pytz = ">=2015.7"
-
 [[package]]
 name = "beautifulsoup4"
-version = "4.11.2"
+version = "4.12.0"
 description = "Screen-scraping library"
 category = "main"
 optional = false
 python-versions = ">=3.6.0"
 files = [
-    {file = "beautifulsoup4-4.11.2-py3-none-any.whl", hash = "sha256:0e79446b10b3ecb499c1556f7e228a53e64a2bfcebd455f370d8927cb5b59e39"},
-    {file = "beautifulsoup4-4.11.2.tar.gz", hash = "sha256:bc4bdda6717de5a2987436fb8d72f45dc90dd856bdfd512a1314ce90349a0106"},
+    {file = "beautifulsoup4-4.12.0-py3-none-any.whl", hash = "sha256:2130a5ad7f513200fae61a17abb5e338ca980fa28c439c0571014bc0217e9591"},
+    {file = "beautifulsoup4-4.12.0.tar.gz", hash = "sha256:c5fceeaec29d09c84970e47c65f2f0efe57872f7cff494c9691a26ec0ff13234"},
 ]
 
 [package.dependencies]
@@ -93,29 +90,29 @@ lxml = ["lxml"]
 
 [[package]]
 name = "bioregistry"
-version = "0.5.143"
+version = "0.6.99"
 description = "Integrated registry of biological databases and nomenclatures"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "bioregistry-0.5.143-py3-none-any.whl", hash = "sha256:70e0221fae09bf3aa47799a8bfb592d42d95d6a2df4924ce10dfe40cc294150e"},
-    {file = "bioregistry-0.5.143.tar.gz", hash = "sha256:15e2beb3a7d53fa81abbf0339762fcec59f7ba5a1ac219f2c247e04c3eaa8007"},
+    {file = "bioregistry-0.6.99-py3-none-any.whl", hash = "sha256:7c30edaea11cbed1e13f64ba1debdabc12b65b70c0bc2d904b8b2ed692b9a404"},
+    {file = "bioregistry-0.6.99.tar.gz", hash = "sha256:22bc981f39c5aaa1a5430d695728a6dade6edcbfb0abbc2e42b4013a9fe4102b"},
 ]
 
 [package.dependencies]
 click = "*"
 curies = "*"
-more-click = "*"
+more-click = ">=0.1.2"
 pydantic = "*"
 pystow = ">=0.1.13"
 requests = "*"
 tqdm = "*"
 
 [package.extras]
-align = ["beautifulsoup4", "class-resolver", "defusedxml", "pyyaml", "tabulate"]
+align = ["beautifulsoup4", "class-resolver", "defusedxml", "fairsharing-client (>=0.1.0)", "pyyaml", "tabulate"]
 charts = ["matplotlib", "matplotlib-venn", "pandas", "seaborn"]
-docs = ["autodoc-pydantic", "sphinx", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme"]
+docs = ["autodoc-pydantic", "sphinx", "sphinx-autodoc-typehints (==1.21.1)", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme"]
 export = ["ndex2", "pyyaml", "rdflib", "rdflib-jsonld"]
 gha = ["more-itertools"]
 health = ["click-default-group", "pandas", "pyyaml", "tabulate"]
@@ -174,100 +171,87 @@ files = [
 
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 name = "charset-normalizer"
-version = "3.0.1"
+version = "3.1.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 category = "main"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7.0"
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+    {file = "coverage-7.2.2-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:4f68ee32d7c4164f1e2c8797535a6d0a3733355f5861e0f667e37df2d4b07140"},
+    {file = "coverage-7.2.2-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:d52f0a114b6a58305b11a5cdecd42b2e7f1ec77eb20e2b33969d702feafdd016"},
+    {file = "coverage-7.2.2-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:797aad79e7b6182cb49c08cc5d2f7aa7b2128133b0926060d0a8889ac43843be"},
+    {file = "coverage-7.2.2-cp39-cp39-win32.whl", hash = "sha256:db45eec1dfccdadb179b0f9ca616872c6f700d23945ecc8f21bb105d74b1c5fc"},
+    {file = "coverage-7.2.2-cp39-cp39-win_amd64.whl", hash = "sha256:8dbe2647bf58d2c5a6c5bcc685f23b5f371909a5624e9f5cd51436d6a9f6c6ef"},
+    {file = "coverage-7.2.2-pp37.pp38.pp39-none-any.whl", hash = "sha256:872d6ce1f5be73f05bea4df498c140b9e7ee5418bfa2cc8204e7f9b817caa968"},
+    {file = "coverage-7.2.2.tar.gz", hash = "sha256:36dd42da34fe94ed98c39887b86db9d06777b1c8f860520e21126a75507024f2"},
 ]
 
 [package.dependencies]
@@ -366,14 +350,14 @@ toml = ["tomli"]
 
 [[package]]
 name = "curies"
-version = "0.4.2"
+version = "0.4.5"
 description = "Idiomatic conversion between URIs and compact URIs (CURIEs)."
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "curies-0.4.2-py3-none-any.whl", hash = "sha256:91d6993a59270c3c280d3689e26001eb7c098d319f9a9f102c060943fa2bc44b"},
-    {file = "curies-0.4.2.tar.gz", hash = "sha256:bdf862d9320b3f0c1d4a81532b07457da5370aa72bc6189099480ac0db80a6f7"},
+    {file = "curies-0.4.5-py3-none-any.whl", hash = "sha256:73281f6616ec47c8d46d842def7a2021416c9ac10f580f9116125abf4bd2f943"},
+    {file = "curies-0.4.5.tar.gz", hash = "sha256:c01626183b520db1b4af6a1fd41ee6d02462fea4ce54d8c5a528e5782268589c"},
 ]
 
 [package.dependencies]
@@ -386,6 +370,7 @@ docs = ["sphinx", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-rtd-t
 fastapi = ["fastapi", "httpx"]
 flask = ["flask"]
 pandas = ["pandas"]
+rdflib = ["rdflib"]
 tests = ["coverage", "pytest"]
 
 [[package]]
@@ -467,14 +452,14 @@ files = [
 
 [[package]]
 name = "exceptiongroup"
-version = "1.1.0"
+version = "1.1.1"
 description = "Backport of PEP 654 (exception groups)"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "exceptiongroup-1.1.0-py3-none-any.whl", hash = "sha256:327cbda3da756e2de031a3107b81ab7b3770a602c4d16ca618298c526f4bec1e"},
-    {file = "exceptiongroup-1.1.0.tar.gz", hash = "sha256:bcb67d800a4497e1b404c2dd44fca47d3b7a5e5433dbab67f96c1a685cdfdf23"},
+    {file = "exceptiongroup-1.1.1-py3-none-any.whl", hash = "sha256:232c37c63e4f682982c8b6459f33a8981039e5fb8756b2074364e5055c498c9e"},
+    {file = "exceptiongroup-1.1.1.tar.gz", hash = "sha256:d484c3090ba2889ae2928419117447a14daf3c1231d5e30d0aae34f354f01785"},
 ]
 
 [package.extras]
@@ -482,19 +467,19 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "filelock"
-version = "3.9.0"
+version = "3.10.7"
 description = "A platform independent file lock."
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "filelock-3.9.0-py3-none-any.whl", hash = "sha256:f58d535af89bb9ad5cd4df046f741f8553a418c01a7856bf0d173bbc9f6bd16d"},
-    {file = "filelock-3.9.0.tar.gz", hash = "sha256:7b319f24340b51f55a2bf7a12ac0755a9b03e718311dac567a0f4f7fabd2f5de"},
+    {file = "filelock-3.10.7-py3-none-any.whl", hash = "sha256:bde48477b15fde2c7e5a0713cbe72721cb5a5ad32ee0b8f419907960b9d75536"},
+    {file = "filelock-3.10.7.tar.gz", hash = "sha256:892be14aa8efc01673b5ed6589dbccb95f9a8596f0507e232626155495c18105"},
 ]
 
 [package.extras]
-docs = ["furo (>=2022.12.7)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.5)"]
-testing = ["covdefaults (>=2.2.2)", "coverage (>=7.0.1)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-timeout (>=2.1)"]
+docs = ["furo (>=2022.12.7)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.2.2)", "diff-cover (>=7.5)", "pytest (>=7.2.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest-timeout (>=2.1)"]
 
 [[package]]
 name = "fqdn"
@@ -566,14 +551,14 @@ grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0dev)"]
 
 [[package]]
 name = "google-api-python-client"
-version = "2.77.0"
+version = "2.83.0"
 description = "Google API Client Library for Python"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "google-api-python-client-2.77.0.tar.gz", hash = "sha256:f18e9dbb365f0485194a8daf5d60da2cff6a80ce2c9a694efc2b279922cb3dd0"},
-    {file = "google_api_python_client-2.77.0-py2.py3-none-any.whl", hash = "sha256:42a44e9adfca6bb27540ce52348aa1d3b81e214bcc53d454a76ebfbe8eee1483"},
+    {file = "google-api-python-client-2.83.0.tar.gz", hash = "sha256:d07509f1b2d2b2427363b454db996f7a15e1751a48cfcaf28427050560dd51cf"},
+    {file = "google_api_python_client-2.83.0-py2.py3-none-any.whl", hash = "sha256:afa7fe2a5d77e8f136cdb8f40a120dd6660c2292f791c1b22734dfe786bd1dac"},
 ]
 
 [package.dependencies]
@@ -585,14 +570,14 @@ uritemplate = ">=3.0.1,<5"
 
 [[package]]
 name = "google-auth"
-version = "2.16.0"
+version = "2.17.0"
 description = "Google Authentication Library"
 category = "main"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*"
 files = [
-    {file = "google-auth-2.16.0.tar.gz", hash = "sha256:ed7057a101af1146f0554a769930ac9de506aeca4fd5af6543ebe791851a9fbd"},
-    {file = "google_auth-2.16.0-py2.py3-none-any.whl", hash = "sha256:5045648c821fb72384cdc0e82cc326df195f113a33049d9b62b74589243d2acc"},
+    {file = "google-auth-2.17.0.tar.gz", hash = "sha256:f51d26ebb3e5d723b9a7dbd310b6c88654ef1ad1fc35750d1fdba48ca4d82f52"},
+    {file = "google_auth-2.17.0-py2.py3-none-any.whl", hash = "sha256:45ba9b4b3e49406de3c5451697820694b2f6ce8a6b75bb187852fdae231dab94"},
 ]
 
 [package.dependencies]
@@ -646,14 +631,14 @@ tool = ["click (>=6.0.0)"]
 
 [[package]]
 name = "googleapis-common-protos"
-version = "1.58.0"
+version = "1.59.0"
 description = "Common protobufs used in Google APIs"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "googleapis-common-protos-1.58.0.tar.gz", hash = "sha256:c727251ec025947d545184ba17e3578840fc3a24a0516a020479edab660457df"},
-    {file = "googleapis_common_protos-1.58.0-py2.py3-none-any.whl", hash = "sha256:ca3befcd4580dab6ad49356b46bf165bb68ff4b32389f028f1abd7c10ab9519a"},
+    {file = "googleapis-common-protos-1.59.0.tar.gz", hash = "sha256:4168fcb568a826a52f23510412da405abd93f4d23ba544bb68d943b14ba3cb44"},
+    {file = "googleapis_common_protos-1.59.0-py2.py3-none-any.whl", hash = "sha256:b287dc48449d1d41af0c69f4ea26242b5ae4c3d7249a38b0984c86a4caffff1f"},
 ]
 
 [package.dependencies]
@@ -798,14 +783,14 @@ files = [
 
 [[package]]
 name = "httplib2"
-version = "0.21.0"
+version = "0.22.0"
 description = "A comprehensive HTTP client library."
 category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
-    {file = "httplib2-0.21.0-py3-none-any.whl", hash = "sha256:987c8bb3eb82d3fa60c68699510a692aa2ad9c4bd4f123e51dfb1488c14cdd01"},
-    {file = "httplib2-0.21.0.tar.gz", hash = "sha256:fc144f091c7286b82bec71bdbd9b27323ba709cc612568d3000893bfd9cb4b34"},
+    {file = "httplib2-0.22.0-py3-none-any.whl", hash = "sha256:14ae0a53c1ba8f3d37e9e27cf37eabb0fb9980f435ba405d546948b009dd64dc"},
+    {file = "httplib2-0.22.0.tar.gz", hash = "sha256:d7a10bc5ef5ab08322488bde8c726eeee5c8618723fdb399597ec58f3d82df81"},
 ]
 
 [package.dependencies]
@@ -1033,14 +1018,14 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 
 [[package]]
 name = "linkml"
-version = "1.4.4"
+version = "1.4.11"
 description = "Linked Open Data Modeling Language"
 category = "main"
 optional = false
 python-versions = ">=3.7.6,<4.0.0"
 files = [
-    {file = "linkml-1.4.4-py3-none-any.whl", hash = "sha256:82c701fd242174108ca11c18afa4e81c0d231c78ee1c3bfd33c27dfe8663ad25"},
-    {file = "linkml-1.4.4.tar.gz", hash = "sha256:5699c2e2016bc89a48cf645f462f970585bf31b88442ef56305d2e2192c30649"},
+    {file = "linkml-1.4.11-py3-none-any.whl", hash = "sha256:2811af5c6a69fb5b8acc4c85741b6aa6d17ef5579a0118a5028025d8a2480866"},
+    {file = "linkml-1.4.11.tar.gz", hash = "sha256:ac5260a0cab15b36dbf2929afc43d7bc8e8af0e198ade7ee90be1dad8fd8d743"},
 ]
 
 [package.dependencies]
@@ -1097,14 +1082,14 @@ linkml-runtime = ">=1.1.6"
 
 [[package]]
 name = "linkml-runtime"
-version = "1.4.5"
+version = "1.4.10"
 description = "Runtime environment for LinkML, the Linked open data modeling language"
 category = "main"
 optional = false
 python-versions = ">=3.7.6,<4.0.0"
 files = [
-    {file = "linkml-runtime-1.4.5.tar.gz", hash = "sha256:bdb6260dfd9b050a6edce8e72061e77e7080471d5d53e694805cb948c8c9f473"},
-    {file = "linkml_runtime-1.4.5-py3-none-any.whl", hash = "sha256:fc1149c59e038a45e5d46c677a19b5dfc15dedce3ef967eed2ee3e0958fd2e49"},
+    {file = "linkml_runtime-1.4.10-py3-none-any.whl", hash = "sha256:d0bebb2b67eecb3887d41cb61e192106eb61a06cfb25439234dbf830fac34b0c"},
+    {file = "linkml_runtime-1.4.10.tar.gz", hash = "sha256:1dd5fe05374d971fe58b0df6111c719b3bec5f87e64d80ad098e79af52e1590d"},
 ]
 
 [package.dependencies]
@@ -1141,24 +1126,24 @@ testing = ["coverage", "pyyaml"]
 
 [[package]]
 name = "markdown-it-py"
-version = "2.1.0"
+version = "2.2.0"
 description = "Python port of markdown-it. Markdown parsing, done right!"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "markdown-it-py-2.1.0.tar.gz", hash = "sha256:cf7e59fed14b5ae17c0006eff14a2d9a00ed5f3a846148153899a0224e2c07da"},
-    {file = "markdown_it_py-2.1.0-py3-none-any.whl", hash = "sha256:93de681e5c021a432c63147656fe21790bc01231e0cd2da73626f1aa3ac0fe27"},
+    {file = "markdown-it-py-2.2.0.tar.gz", hash = "sha256:7c9a5e412688bc771c67432cbfebcdd686c93ce6484913dccf06cb5a0bea35a1"},
+    {file = "markdown_it_py-2.2.0-py3-none-any.whl", hash = "sha256:5a35f8d1870171d9acc47b99612dc146129b631baf04970128b568f190d0cc30"},
 ]
 
 [package.dependencies]
 mdurl = ">=0.1,<1.0"
 
 [package.extras]
-benchmarking = ["psutil", "pytest", "pytest-benchmark (>=3.2,<4.0)"]
-code-style = ["pre-commit (==2.6)"]
-compare = ["commonmark (>=0.9.1,<0.10.0)", "markdown (>=3.3.6,<3.4.0)", "mistletoe (>=0.8.1,<0.9.0)", "mistune (>=2.0.2,<2.1.0)", "panflute (>=2.1.3,<2.2.0)"]
-linkify = ["linkify-it-py (>=1.0,<2.0)"]
+benchmarking = ["psutil", "pytest", "pytest-benchmark"]
+code-style = ["pre-commit (>=3.0,<4.0)"]
+compare = ["commonmark (>=0.9,<1.0)", "markdown (>=3.4,<4.0)", "mistletoe (>=1.0,<2.0)", "mistune (>=2.0,<3.0)", "panflute (>=2.3,<3.0)"]
+linkify = ["linkify-it-py (>=1,<3)"]
 plugins = ["mdit-py-plugins"]
 profiling = ["gprof2dot"]
 rtd = ["attrs", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
@@ -1226,14 +1211,14 @@ files = [
 
 [[package]]
 name = "mdit-py-plugins"
-version = "0.3.3"
+version = "0.3.5"
 description = "Collection of plugins for markdown-it-py"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "mdit-py-plugins-0.3.3.tar.gz", hash = "sha256:5cfd7e7ac582a594e23ba6546a2f406e94e42eb33ae596d0734781261c251260"},
-    {file = "mdit_py_plugins-0.3.3-py3-none-any.whl", hash = "sha256:36d08a29def19ec43acdcd8ba471d3ebab132e7879d442760d963f19913e04b9"},
+    {file = "mdit-py-plugins-0.3.5.tar.gz", hash = "sha256:eee0adc7195e5827e17e02d2a258a2ba159944a0748f59c5099a4a27f78fcf6a"},
+    {file = "mdit_py_plugins-0.3.5-py3-none-any.whl", hash = "sha256:ca9a0714ea59a24b2b044a1831f48d817dd0c817e84339f20e7889f392d77c4e"},
 ]
 
 [package.dependencies]
@@ -1317,30 +1302,30 @@ tests = ["coverage", "pytest"]
 
 [[package]]
 name = "myst-parser"
-version = "0.18.1"
-description = "An extended commonmark compliant parser, with bridges to docutils & sphinx."
+version = "1.0.0"
+description = "An extended [CommonMark](https://spec.commonmark.org/) compliant parser,"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "myst-parser-0.18.1.tar.gz", hash = "sha256:79317f4bb2c13053dd6e64f9da1ba1da6cd9c40c8a430c447a7b146a594c246d"},
-    {file = "myst_parser-0.18.1-py3-none-any.whl", hash = "sha256:61b275b85d9f58aa327f370913ae1bec26ebad372cc99f3ab85c8ec3ee8d9fb8"},
+    {file = "myst-parser-1.0.0.tar.gz", hash = "sha256:502845659313099542bd38a2ae62f01360e7dd4b1310f025dd014dfc0439cdae"},
+    {file = "myst_parser-1.0.0-py3-none-any.whl", hash = "sha256:69fb40a586c6fa68995e6521ac0a525793935db7e724ca9bac1d33be51be9a4c"},
 ]
 
 [package.dependencies]
 docutils = ">=0.15,<0.20"
 jinja2 = "*"
 markdown-it-py = ">=1.0.0,<3.0.0"
-mdit-py-plugins = ">=0.3.1,<0.4.0"
+mdit-py-plugins = ">=0.3.4,<0.4.0"
 pyyaml = "*"
-sphinx = ">=4,<6"
-typing-extensions = "*"
+sphinx = ">=5,<7"
 
 [package.extras]
-code-style = ["pre-commit (>=2.12,<3.0)"]
+code-style = ["pre-commit (>=3.0,<4.0)"]
 linkify = ["linkify-it-py (>=1.0,<2.0)"]
-rtd = ["ipython", "sphinx-book-theme", "sphinx-design", "sphinxcontrib.mermaid (>=0.7.1,<0.8.0)", "sphinxext-opengraph (>=0.6.3,<0.7.0)", "sphinxext-rediraffe (>=0.2.7,<0.3.0)"]
-testing = ["beautifulsoup4", "coverage[toml]", "pytest (>=6,<7)", "pytest-cov", "pytest-param-files (>=0.3.4,<0.4.0)", "pytest-regressions", "sphinx (<5.2)", "sphinx-pytest"]
+rtd = ["ipython", "pydata-sphinx-theme (==v0.13.0rc4)", "sphinx-autodoc2 (>=0.4.2,<0.5.0)", "sphinx-book-theme (==1.0.0rc2)", "sphinx-copybutton", "sphinx-design2", "sphinx-pyscript", "sphinx-tippy (>=0.3.1)", "sphinx-togglebutton", "sphinxext-opengraph (>=0.7.5,<0.8.0)", "sphinxext-rediraffe (>=0.2.7,<0.3.0)"]
+testing = ["beautifulsoup4", "coverage[toml]", "pytest (>=7,<8)", "pytest-cov", "pytest-param-files (>=0.3.4,<0.4.0)", "pytest-regressions", "sphinx-pytest"]
+testing-docutils = ["pygments", "pytest (>=7,<8)", "pytest-param-files (>=0.3.4,<0.4.0)"]
 
 [[package]]
 name = "oauthlib"
@@ -1383,14 +1368,14 @@ termcolor = "*"
 
 [[package]]
 name = "openpyxl"
-version = "3.1.1"
+version = "3.1.2"
 description = "A Python library to read/write Excel 2010 xlsx/xlsm files"
 category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
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 ]
 
 [package.dependencies]
@@ -1741,14 +1725,14 @@ shexjsg = ">=0.8.1"
 
 [[package]]
 name = "pystow"
-version = "0.4.9"
+version = "0.5.0"
 description = "Easily pick a place to store data for your python package."
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -1766,14 +1750,14 @@ xml = ["lxml"]
 
 [[package]]
 name = "pytest"
-version = "7.2.1"
+version = "7.2.2"
 description = "pytest: simple powerful testing with Python"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -1850,18 +1834,6 @@ files = [
 [package.dependencies]
 sortedcontainers = "*"
 
-[[package]]
-name = "pytz"
-version = "2022.7.1"
-description = "World timezone definitions, modern and historical"
-category = "main"
-optional = false
-python-versions = "*"
-files = [
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-]
-
 [[package]]
 name = "pyyaml"
 version = "6.0"
@@ -1929,28 +1901,25 @@ pyyaml = "*"
 
 [[package]]
 name = "rdflib"
-version = "6.2.0"
+version = "6.3.2"
 description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information."
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.7,<4.0"
 files = [
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 ]
 
 [package.dependencies]
-isodate = "*"
-pyparsing = "*"
-setuptools = "*"
+isodate = ">=0.6.0,<0.7.0"
+pyparsing = ">=2.1.0,<4"
 
 [package.extras]
-berkeleydb = ["berkeleydb"]
-dev = ["black (==22.6.0)", "flake8", "flakeheaven", "isort", "mypy", "pep8-naming", "types-setuptools"]
-docs = ["myst-parser", "sphinx (<6)", "sphinx-autodoc-typehints", "sphinxcontrib-apidoc", "sphinxcontrib-kroki"]
-html = ["html5lib"]
-networkx = ["networkx"]
-tests = ["html5lib", "pytest", "pytest-cov"]
+berkeleydb = ["berkeleydb (>=18.1.0,<19.0.0)"]
+html = ["html5lib (>=1.0,<2.0)"]
+lxml = ["lxml (>=4.3.0,<5.0.0)"]
+networkx = ["networkx (>=2.0.0,<3.0.0)"]
 
 [[package]]
 name = "rdflib-jsonld"
@@ -2128,23 +2097,6 @@ files = [
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 ]
 
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-description = "Easily download, build, install, upgrade, and uninstall Python packages"
-category = "main"
-optional = false
-python-versions = ">=3.7"
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-[package.extras]
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-
 [[package]]
 name = "shexjsg"
 version = "0.8.2"
@@ -2248,27 +2200,27 @@ pandas = ["pandas (>=1.3.5)"]
 
 [[package]]
 name = "sphinx"
-version = "5.3.0"
+version = "6.1.3"
 description = "Python documentation generator"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
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 [package.dependencies]
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 babel = ">=2.9"
 colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
-docutils = ">=0.14,<0.20"
+docutils = ">=0.18,<0.20"
 imagesize = ">=1.3"
 importlib-metadata = {version = ">=4.8", markers = "python_version < \"3.10\""}
 Jinja2 = ">=3.0"
 packaging = ">=21.0"
-Pygments = ">=2.12"
-requests = ">=2.5.0"
+Pygments = ">=2.13"
+requests = ">=2.25.0"
 snowballstemmer = ">=2.0"
 sphinxcontrib-applehelp = "*"
 sphinxcontrib-devhelp = "*"
@@ -2279,8 +2231,8 @@ sphinxcontrib-serializinghtml = ">=1.1.5"
 
 [package.extras]
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-test = ["cython", "html5lib", "pytest (>=4.6)", "typed_ast"]
+lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-simplify", "isort", "mypy (>=0.990)", "ruff", "sphinx-lint", "types-requests"]
+test = ["cython", "html5lib", "pytest (>=4.6)"]
 
 [[package]]
 name = "sphinx-click"
@@ -2369,18 +2321,18 @@ test = ["html5lib", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-jquery"
-version = "2.0.0"
+version = "4.1"
 description = "Extension to include jQuery on newer Sphinx releases"
 category = "main"
 optional = false
 python-versions = ">=2.7"
 files = [
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 ]
 
 [package.dependencies]
-setuptools = "*"
+Sphinx = ">=1.8"
 
 [[package]]
 name = "sphinxcontrib-jsmath"
@@ -2431,53 +2383,53 @@ test = ["pytest"]
 
 [[package]]
 name = "sqlalchemy"
-version = "2.0.3"
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 python-versions = ">=3.7"
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 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
+testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "8f374ed0d50f93dbfe09d717d955c41cbd986e4444625f820dadaa8366661cca"
+content-hash = "2d664d2aaf80cb3c4c3c81cb792daf8d6574ee0b5af9570a00ebd52cc829eef4"
diff --git a/pyproject.toml b/pyproject.toml
index e6a942c..c0fb2a0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,10 +12,11 @@ documentation = "https://github.com/linkml/schemasheets"
 
 [tool.poetry.dependencies]
 python = "^3.9"
-linkml = "^1.4"
+linkml = "1.4.11"
+linkml-runtime = "1.4.10"
 Jinja2 = "^3.0.3"
 ontodev-cogs = "^0.3.3"
-bioregistry = "~0.5"
+bioregistry = "0.6.99"
 
 [tool.poetry.dev-dependencies]
 pytest = "^7.2"

From 7b35dbe5c58a4cf1f9dd50885fc8bd6b574942c3 Mon Sep 17 00:00:00 2001
From: "Mark A. Miller" <mamillerpa@gmail.com>
Date: Wed, 29 Mar 2023 20:25:31 -0400
Subject: [PATCH 2/2] #95

---
 poetry.lock           | 16 ++++++++--------
 pyproject.toml        |  6 +++---
 tests/test_headers.py | 11 ++++++-----
 3 files changed, 17 insertions(+), 16 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 69f601c..c068010 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1018,14 +1018,14 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 
 [[package]]
 name = "linkml"
-version = "1.4.11"
+version = "1.5.0"
 description = "Linked Open Data Modeling Language"
 category = "main"
 optional = false
 python-versions = ">=3.7.6,<4.0.0"
 files = [
-    {file = "linkml-1.4.11-py3-none-any.whl", hash = "sha256:2811af5c6a69fb5b8acc4c85741b6aa6d17ef5579a0118a5028025d8a2480866"},
-    {file = "linkml-1.4.11.tar.gz", hash = "sha256:ac5260a0cab15b36dbf2929afc43d7bc8e8af0e198ade7ee90be1dad8fd8d743"},
+    {file = "linkml-1.5.0-py3-none-any.whl", hash = "sha256:8f8d23f7f7bd6a10a5130d28ea576f7ceccd14e123ad4c0365bb53bc58664ba0"},
+    {file = "linkml-1.5.0.tar.gz", hash = "sha256:120fac9dd5a27d3dabc5e45fdeaf0b2fe187fe5f59bf7bc0806ebb5a884e6942"},
 ]
 
 [package.dependencies]
@@ -1038,7 +1038,7 @@ jinja2 = ">=3.1.0"
 jsonasobj2 = ">=1.0.3,<2.0.0"
 jsonschema = {version = ">=4.0.0", extras = ["format"]}
 linkml-dataops = "*"
-linkml-runtime = ">=1,<2"
+linkml-runtime = ">=1.5.0"
 myst-parser = "*"
 openpyxl = "*"
 parse = "*"
@@ -1082,14 +1082,14 @@ linkml-runtime = ">=1.1.6"
 
 [[package]]
 name = "linkml-runtime"
-version = "1.4.10"
+version = "1.5.0"
 description = "Runtime environment for LinkML, the Linked open data modeling language"
 category = "main"
 optional = false
 python-versions = ">=3.7.6,<4.0.0"
 files = [
-    {file = "linkml_runtime-1.4.10-py3-none-any.whl", hash = "sha256:d0bebb2b67eecb3887d41cb61e192106eb61a06cfb25439234dbf830fac34b0c"},
-    {file = "linkml_runtime-1.4.10.tar.gz", hash = "sha256:1dd5fe05374d971fe58b0df6111c719b3bec5f87e64d80ad098e79af52e1590d"},
+    {file = "linkml_runtime-1.5.0-py3-none-any.whl", hash = "sha256:ddc3d224d9db39be2df33a02718cd75462942009454aca7f828b726129357a37"},
+    {file = "linkml_runtime-1.5.0.tar.gz", hash = "sha256:dd80aec72f6d3226b39415cf4aa8cdda482dc73fcc227f938c6fff72afd80b20"},
 ]
 
 [package.dependencies]
@@ -2785,4 +2785,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "2d664d2aaf80cb3c4c3c81cb792daf8d6574ee0b5af9570a00ebd52cc829eef4"
+content-hash = "0b39de9e9388e460a2ae4fdc48b5e8648b6682cc7981784bea272e0b3dabc59d"
diff --git a/pyproject.toml b/pyproject.toml
index c0fb2a0..53d5c1e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,11 +12,11 @@ documentation = "https://github.com/linkml/schemasheets"
 
 [tool.poetry.dependencies]
 python = "^3.9"
-linkml = "1.4.11"
-linkml-runtime = "1.4.10"
+linkml = "^1.4"
+linkml-runtime = "^1.4"
 Jinja2 = "^3.0.3"
 ontodev-cogs = "^0.3.3"
-bioregistry = "0.6.99"
+bioregistry = ">0.5.0, <0.7.0"
 
 [tool.poetry.dev-dependencies]
 pytest = "^7.2"
diff --git a/tests/test_headers.py b/tests/test_headers.py
index 1eadd68..20d2c63 100644
--- a/tests/test_headers.py
+++ b/tests/test_headers.py
@@ -45,11 +45,12 @@
          {DATATYPE: "> type", INFO: " description"},
      ]
      ),
-    (6,
-     [
-         {DATATYPE: "> metaslot.type", INFO: " description"},
-     ]
-     ),
+    # unnecessary/incompatible with the latest meta-model
+    # (6,
+    #  [
+    #      {DATATYPE: "> metaslot.type", INFO: " description"},
+    #  ]
+    #  ),
 ]
 
 def test_parse_header():