From 66f392617bb3b0f1fb76cf6eb28747ef0f5a985c Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Fri, 30 Sep 2022 15:53:50 -0700
Subject: [PATCH 1/2] update dependencies

---
 poetry.lock    | 1142 ++++++++++++++++++++++++++++++++++++++++--------
 pyproject.toml |    2 +-
 2 files changed, 958 insertions(+), 186 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index c77f7dc..47f4b6d 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,6 +1,6 @@
 [[package]]
 name = "aiohttp"
-version = "3.8.1"
+version = "3.8.3"
 description = "Async http client/server framework (asyncio)"
 category = "main"
 optional = false
@@ -92,14 +92,6 @@ cffi = ">=1.0.1"
 dev = ["pytest", "cogapp", "pre-commit", "wheel"]
 tests = ["pytest"]
 
-[[package]]
-name = "argparse"
-version = "1.4.0"
-description = "Python command-line parsing library"
-category = "main"
-optional = false
-python-versions = "*"
-
 [[package]]
 name = "asttokens"
 version = "2.0.8"
@@ -112,7 +104,7 @@ python-versions = "*"
 six = "*"
 
 [package.extras]
-test = ["pytest", "astroid (<=2.5.3)"]
+test = ["astroid (<=2.5.3)", "pytest"]
 
 [[package]]
 name = "async-timeout"
@@ -180,7 +172,7 @@ lxml = ["lxml"]
 
 [[package]]
 name = "bioregistry"
-version = "0.5.87"
+version = "0.5.114"
 description = "Integrated registry of biological databases and nomenclatures"
 category = "main"
 optional = false
@@ -201,7 +193,7 @@ charts = ["matplotlib", "matplotlib-venn", "seaborn", "pandas"]
 docs = ["sphinx", "sphinx-rtd-theme", "sphinx-click", "sphinx-autodoc-typehints", "sphinx-automodapi", "autodoc-pydantic"]
 export = ["pyyaml", "rdflib", "rdflib-jsonld", "ndex2"]
 gha = ["more-itertools"]
-health = ["click-default-group", "pandas", "tabulate"]
+health = ["click-default-group", "pandas", "tabulate", "pyyaml"]
 tests = ["coverage", "pytest", "more-itertools"]
 web = ["pyyaml", "rdflib", "rdflib-jsonld", "flask", "flasgger", "bootstrap-flask (<=2.0.0)", "markdown"]
 
@@ -223,7 +215,7 @@ dev = ["build (==0.8.0)", "flake8 (==4.0.1)", "hashin (==0.17.0)", "pip-tools (=
 
 [[package]]
 name = "certifi"
-version = "2022.6.15"
+version = "2022.9.24"
 description = "Python package for providing Mozilla's CA Bundle."
 category = "main"
 optional = false
@@ -383,6 +375,14 @@ python-versions = "*"
 [package.dependencies]
 packaging = "*"
 
+[[package]]
+name = "distlib"
+version = "0.3.6"
+description = "Distribution utilities"
+category = "main"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "docopt"
 version = "0.6.2"
@@ -417,15 +417,18 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "executing"
-version = "1.0.0"
+version = "1.1.0"
 description = "Get the currently executing AST node of a frame, and other information"
 category = "dev"
 optional = false
 python-versions = "*"
 
+[package.extras]
+tests = ["rich", "littleutils", "pytest", "asttokens"]
+
 [[package]]
 name = "fastjsonschema"
-version = "2.16.1"
+version = "2.16.2"
 description = "Fastest Python implementation of JSON schema"
 category = "dev"
 optional = false
@@ -442,6 +445,18 @@ category = "main"
 optional = false
 python-versions = ">=3.7"
 
+[[package]]
+name = "filelock"
+version = "3.8.0"
+description = "A platform independent file lock."
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[package.extras]
+docs = ["furo (>=2022.6.21)", "sphinx (>=5.1.1)", "sphinx-autodoc-typehints (>=1.19.1)"]
+testing = ["covdefaults (>=2.2)", "coverage (>=6.4.2)", "pytest (>=7.1.2)", "pytest-cov (>=3)", "pytest-timeout (>=2.1)"]
+
 [[package]]
 name = "frozenlist"
 version = "1.3.1"
@@ -548,7 +563,7 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "idna"
-version = "3.3"
+version = "3.4"
 description = "Internationalized Domain Names in Applications (IDNA)"
 category = "main"
 optional = false
@@ -603,7 +618,7 @@ python-versions = "*"
 
 [[package]]
 name = "ipykernel"
-version = "6.15.2"
+version = "6.16.0"
 description = "IPython Kernel for Jupyter"
 category = "dev"
 optional = false
@@ -627,7 +642,7 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest-cov", "pytest-timeout", "p
 
 [[package]]
 name = "ipython"
-version = "8.4.0"
+version = "8.5.0"
 description = "IPython: Productive Interactive Computing"
 category = "dev"
 optional = false
@@ -642,7 +657,7 @@ jedi = ">=0.16"
 matplotlib-inline = "*"
 pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""}
 pickleshare = "*"
-prompt-toolkit = ">=2.0.0,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.1.0"
+prompt-toolkit = ">3.0.1,<3.1.0"
 pygments = ">=2.4.0"
 stack-data = "*"
 traitlets = ">=5"
@@ -794,7 +809,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "jsonschema"
-version = "4.15.0"
+version = "4.16.0"
 description = "An implementation of JSON Schema validation for Python"
 category = "main"
 optional = false
@@ -935,7 +950,7 @@ regex = ["regex"]
 
 [[package]]
 name = "linkml"
-version = "1.3.0"
+version = "1.3.5"
 description = "Linked Open Data Modeling Language"
 category = "main"
 optional = false
@@ -943,20 +958,20 @@ python-versions = ">=3.7.6,<4.0.0"
 
 [package.dependencies]
 antlr4-python3-runtime = ">=4.9.0,<4.10"
-argparse = ">=1.4.0"
 click = ">=7.0"
 graphviz = ">=0.10.1"
 hbreader = "*"
 isodate = ">=0.6.0"
-jinja2 = "*"
+jinja2 = ">=3.1.0"
 jsonasobj2 = ">=1.0.3,<2.0.0"
 jsonschema = ">=3.0.1"
 linkml-dataops = "*"
-linkml-runtime = ">=1.3.0,<2.0.0"
+linkml-runtime = ">=1.3,<1.4"
 myst-parser = "*"
 openpyxl = "*"
 parse = "*"
 prefixcommons = ">=0.1.7"
+prefixmaps = ">=0.1.3,<0.2.0"
 pydantic = "*"
 pyjsg = ">=0.11.6"
 pyshex = ">=0.7.20"
@@ -967,6 +982,7 @@ rdflib = ">=6.0.0"
 requests = ">=2.22"
 sphinx-click = "*"
 sqlalchemy = ">=1.4.31"
+tox = ">=3.25.1,<4.0.0"
 watchdog = ">=0.9.0"
 
 [package.extras]
@@ -1077,19 +1093,19 @@ traitlets = "*"
 
 [[package]]
 name = "mdit-py-plugins"
-version = "0.3.0"
+version = "0.3.1"
 description = "Collection of plugins for markdown-it-py"
 category = "main"
 optional = false
-python-versions = "~=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
 markdown-it-py = ">=1.0.0,<3.0.0"
 
 [package.extras]
-code_style = ["pre-commit (==2.6)"]
-rtd = ["myst-parser (>=0.14.0,<0.15.0)", "sphinx-book-theme (>=0.1.0,<0.2.0)"]
-testing = ["coverage", "pytest (>=3.6,<4)", "pytest-cov", "pytest-regressions"]
+testing = ["pytest-regressions", "pytest-cov", "pytest", "coverage"]
+rtd = ["sphinx-book-theme (>=0.1.0,<0.2.0)", "myst-parser (>=0.16.1,<0.17.0)", "attrs"]
+code_style = ["pre-commit"]
 
 [[package]]
 name = "mdurl"
@@ -1117,21 +1133,21 @@ python-versions = "*"
 
 [[package]]
 name = "mkdocs"
-version = "1.3.1"
+version = "1.4.0"
 description = "Project documentation with Markdown."
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
-click = ">=3.3"
+click = ">=7.0"
 ghp-import = ">=1.0"
-importlib-metadata = ">=4.3"
-Jinja2 = ">=2.10.2"
+importlib-metadata = {version = ">=4.3", markers = "python_version < \"3.10\""}
+Jinja2 = ">=2.11.1"
 Markdown = ">=3.2.1,<3.4"
 mergedeep = ">=1.3.4"
 packaging = ">=20.5"
-PyYAML = ">=3.10"
+PyYAML = ">=5.1"
 pyyaml-env-tag = ">=0.1"
 watchdog = ">=2.0"
 
@@ -1167,17 +1183,17 @@ python-versions = "*"
 
 [[package]]
 name = "myst-parser"
-version = "0.18.0"
+version = "0.18.1"
 description = "An extended commonmark compliant parser, with bridges to docutils & sphinx."
 category = "main"
 optional = false
 python-versions = ">=3.7"
 
 [package.dependencies]
-docutils = ">=0.15,<0.19"
+docutils = ">=0.15,<0.20"
 jinja2 = "*"
 markdown-it-py = ">=1.0.0,<3.0.0"
-mdit-py-plugins = ">=0.3.0,<0.4.0"
+mdit-py-plugins = ">=0.3.1,<0.4.0"
 pyyaml = "*"
 sphinx = ">=4,<6"
 typing-extensions = "*"
@@ -1186,11 +1202,11 @@ typing-extensions = "*"
 code_style = ["pre-commit (>=2.12,<3.0)"]
 linkify = ["linkify-it-py (>=1.0,<2.0)"]
 rtd = ["ipython", "sphinx-book-theme", "sphinx-design", "sphinxext-rediraffe (>=0.2.7,<0.3.0)", "sphinxcontrib.mermaid (>=0.7.1,<0.8.0)", "sphinxext-opengraph (>=0.6.3,<0.7.0)"]
-testing = ["beautifulsoup4", "coverage", "pytest (>=6,<7)", "pytest-cov", "pytest-regressions", "pytest-param-files (>=0.3.4,<0.4.0)", "sphinx-pytest"]
+testing = ["beautifulsoup4", "coverage", "pytest (>=6,<7)", "pytest-cov", "pytest-regressions", "pytest-param-files (>=0.3.4,<0.4.0)", "sphinx-pytest", "sphinx (<5.2)"]
 
 [[package]]
 name = "nbclient"
-version = "0.6.7"
+version = "0.6.8"
 description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
 category = "dev"
 optional = false
@@ -1244,7 +1260,7 @@ webpdf = ["pyppeteer (>=1,<1.1)"]
 
 [[package]]
 name = "nbformat"
-version = "5.4.0"
+version = "5.6.1"
 description = "The Jupyter Notebook format"
 category = "dev"
 optional = false
@@ -1257,11 +1273,11 @@ jupyter-core = "*"
 traitlets = ">=5.1"
 
 [package.extras]
-test = ["check-manifest", "testpath", "pytest", "pre-commit"]
+test = ["check-manifest", "pep440", "pre-commit", "pytest", "testpath"]
 
 [[package]]
 name = "nest-asyncio"
-version = "1.5.5"
+version = "1.5.6"
 description = "Patch asyncio to allow nested event loops"
 category = "dev"
 optional = false
@@ -1325,7 +1341,7 @@ docopt = ">=0.6.2"
 
 [[package]]
 name = "numpy"
-version = "1.23.2"
+version = "1.23.3"
 description = "NumPy is the fundamental package for array computing with Python."
 category = "main"
 optional = false
@@ -1350,7 +1366,7 @@ viz = ["pygraphviz"]
 
 [[package]]
 name = "oaklib"
-version = "0.1.38"
+version = "0.1.43"
 description = "Ontology Access Kit: Python library for common ontology operations over a variety of backends"
 category = "main"
 optional = false
@@ -1368,6 +1384,7 @@ lark = ">=1.1.2,<2.0.0"
 linkml-runtime = ">=1.2.15,<2.0.0"
 networkx = ">=2.7.1,<3.0.0"
 nxontology = ">=0.4.0,<0.5.0"
+ols-client = ">=0.1.1,<0.2.0"
 ontoportal-client = "0.0.3"
 prefixmaps = ">=0.1.2,<0.2.0"
 pronto = ">=2.5.0,<3.0.0"
@@ -1376,12 +1393,31 @@ ratelimit = ">=2.2.1,<3.0.0"
 semsql = ">=0.1.6,<0.2.0"
 SPARQLWrapper = "*"
 SQLAlchemy = ">=1.4.32,<2.0.0"
-sssom = ">=0.3.11,<0.4.0"
+sssom = ">=0.3.16,<0.4.0"
 sssom-schema = ">=0.9.3,<0.10.0"
 
 [package.extras]
 gilda = ["gilda (>=0.10.1,<0.11.0)"]
 
+[[package]]
+name = "ols-client"
+version = "0.1.2"
+description = "A client to the EBI Ontology Lookup Service"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+class-resolver = "*"
+click = "*"
+more-click = "*"
+pystow = "*"
+requests = "*"
+
+[package.extras]
+tests = ["coverage", "pytest"]
+docs = ["sphinx-automodapi", "sphinx-autodoc-typehints", "sphinx-click", "sphinx-rtd-theme", "sphinx"]
+
 [[package]]
 name = "ontoportal-client"
 version = "0.0.3"
@@ -1422,7 +1458,7 @@ pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
 
 [[package]]
 name = "pandas"
-version = "1.4.4"
+version = "1.5.0"
 description = "Powerful data structures for data analysis, time series, and statistics"
 category = "main"
 optional = false
@@ -1430,16 +1466,14 @@ python-versions = ">=3.8"
 
 [package.dependencies]
 numpy = [
-    {version = ">=1.18.5", markers = "platform_machine != \"aarch64\" and platform_machine != \"arm64\" and python_version < \"3.10\""},
-    {version = ">=1.19.2", markers = "platform_machine == \"aarch64\" and python_version < \"3.10\""},
-    {version = ">=1.20.0", markers = "platform_machine == \"arm64\" and python_version < \"3.10\""},
     {version = ">=1.21.0", markers = "python_version >= \"3.10\""},
+    {version = ">=1.20.3", markers = "python_version < \"3.10\""},
 ]
 python-dateutil = ">=2.8.1"
 pytz = ">=2020.1"
 
 [package.extras]
-test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"]
+test = ["pytest-xdist (>=1.31)", "pytest (>=6.0)", "hypothesis (>=5.5.3)"]
 
 [[package]]
 name = "pandasql"
@@ -1472,18 +1506,18 @@ typing-inspect = ">=0.6.0"
 wrapt = "*"
 
 [package.extras]
-all = ["black", "dask", "geopandas", "shapely", "pyspark", "frictionless", "pyyaml (>=5.1)", "fastapi", "hypothesis (>=5.41.1)", "ray (<=1.7.0)", "modin", "scipy", "pandas-stubs"]
-dask = ["dask"]
-fastapi = ["fastapi"]
-geopandas = ["geopandas", "shapely"]
-hypotheses = ["scipy"]
-io = ["pyyaml (>=5.1)", "black", "frictionless"]
-modin = ["modin", "ray (<=1.7.0)", "dask"]
-modin-dask = ["modin", "dask"]
-modin-ray = ["modin", "ray (<=1.7.0)"]
-mypy = ["pandas-stubs"]
-pyspark = ["pyspark"]
 strategies = ["hypothesis (>=5.41.1)"]
+pyspark = ["pyspark"]
+mypy = ["pandas-stubs"]
+modin-ray = ["ray (<=1.7.0)", "modin"]
+modin-dask = ["dask", "modin"]
+modin = ["dask", "ray (<=1.7.0)", "modin"]
+io = ["frictionless", "black", "pyyaml (>=5.1)"]
+hypotheses = ["scipy"]
+geopandas = ["shapely", "geopandas"]
+fastapi = ["fastapi"]
+dask = ["dask"]
+all = ["pandas-stubs", "scipy", "modin", "ray (<=1.7.0)", "hypothesis (>=5.41.1)", "fastapi", "pyyaml (>=5.1)", "frictionless", "pyspark", "shapely", "geopandas", "dask", "black"]
 
 [[package]]
 name = "pandocfilters"
@@ -1532,11 +1566,23 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "platformdirs"
+version = "2.5.2"
+description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[package.extras]
+docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)", "sphinx (>=4)"]
+test = ["appdirs (==1.4.4)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)", "pytest (>=6)"]
+
 [[package]]
 name = "pluggy"
 version = "1.0.0"
 description = "plugin and hook calling mechanisms for python"
-category = "dev"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 
@@ -1565,13 +1611,14 @@ requests = ">=2.28.1,<3.0.0"
 
 [[package]]
 name = "prefixmaps"
-version = "0.1.2"
+version = "0.1.3"
 description = ""
 category = "main"
 optional = false
-python-versions = ">=3.8,<4.0"
+python-versions = ">=3.7.6,<4.0.0"
 
 [package.dependencies]
+importlib-metadata = ">=4.12.0,<5.0.0"
 PyYAML = ">=6.0,<7.0"
 
 [[package]]
@@ -1652,7 +1699,7 @@ tests = ["pytest"]
 name = "py"
 version = "1.11.0"
 description = "library with cross-python path, ini-parsing, io, code, log facilities"
-category = "dev"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
@@ -1845,7 +1892,7 @@ python-versions = "*"
 
 [[package]]
 name = "pywinpty"
-version = "2.0.7"
+version = "2.0.8"
 description = "Pseudo terminal support for Windows from Python."
 category = "dev"
 optional = false
@@ -1872,7 +1919,7 @@ pyyaml = "*"
 
 [[package]]
 name = "pyzmq"
-version = "23.2.1"
+version = "24.0.1"
 description = "Python bindings for 0MQ"
 category = "dev"
 optional = false
@@ -2274,7 +2321,7 @@ test = ["pytest"]
 
 [[package]]
 name = "sqlalchemy"
-version = "1.4.40"
+version = "1.4.41"
 description = "Database Abstraction Library"
 category = "main"
 optional = false
@@ -2374,7 +2421,7 @@ linkml-runtime = ">=1.1.24,<2.0.0"
 
 [[package]]
 name = "stack-data"
-version = "0.5.0"
+version = "0.5.1"
 description = "Extract data from python stack frames and tracebacks for informative displays"
 category = "dev"
 optional = false
@@ -2398,7 +2445,7 @@ python-versions = "*"
 
 [[package]]
 name = "terminado"
-version = "0.15.0"
+version = "0.16.0"
 description = "Tornado websocket backend for the Xterm.js Javascript terminal emulator library."
 category = "dev"
 optional = false
@@ -2431,13 +2478,13 @@ test = ["pytest", "pytest-cov", "pytest-flake8", "pytest-isort", "coverage"]
 name = "tomli"
 version = "2.0.1"
 description = "A lil' TOML parser"
-category = "dev"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 
 [[package]]
 name = "tomlkit"
-version = "0.11.4"
+version = "0.11.5"
 description = "Style preserving TOML library"
 category = "main"
 optional = false
@@ -2451,6 +2498,28 @@ category = "dev"
 optional = false
 python-versions = ">= 3.7"
 
+[[package]]
+name = "tox"
+version = "3.26.0"
+description = "tox is a generic virtualenv management and test command line tool"
+category = "main"
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+
+[package.dependencies]
+colorama = {version = ">=0.4.1", markers = "platform_system == \"Windows\""}
+filelock = ">=3.0.0"
+packaging = ">=14"
+pluggy = ">=0.12.0"
+py = ">=1.4.17"
+six = ">=1.14.0"
+tomli = {version = ">=2.0.1", markers = "python_version >= \"3.7\" and python_version < \"3.11\""}
+virtualenv = ">=16.0.0,<20.0.0 || >20.0.0,<20.0.1 || >20.0.1,<20.0.2 || >20.0.2,<20.0.3 || >20.0.3,<20.0.4 || >20.0.4,<20.0.5 || >20.0.5,<20.0.6 || >20.0.6,<20.0.7 || >20.0.7"
+
+[package.extras]
+docs = ["pygments-github-lexers (>=0.0.5)", "sphinx (>=2.0.0)", "sphinxcontrib-autoprogram (>=0.1.5)", "towncrier (>=18.5.0)"]
+testing = ["flaky (>=3.4.0)", "freezegun (>=0.3.11)", "pytest (>=4.0.0)", "pytest-cov (>=2.5.1)", "pytest-mock (>=1.10.0)", "pytest-randomly (>=1.0.0)", "psutil (>=5.6.1)", "pathlib2 (>=2.3.3)"]
+
 [[package]]
 name = "tqdm"
 version = "4.64.1"
@@ -2470,7 +2539,7 @@ telegram = ["requests"]
 
 [[package]]
 name = "traitlets"
-version = "5.3.0"
+version = "5.4.0"
 description = ""
 category = "dev"
 optional = false
@@ -2526,6 +2595,23 @@ decorator = ">=3.4.0"
 [package.extras]
 test = ["pytest (>=2.2.3)", "flake8 (>=2.4.0)", "isort (>=4.2.2)"]
 
+[[package]]
+name = "virtualenv"
+version = "20.16.5"
+description = "Virtual Python Environment builder"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+distlib = ">=0.3.5,<1"
+filelock = ">=3.4.1,<4"
+platformdirs = ">=2.4,<3"
+
+[package.extras]
+docs = ["proselint (>=0.13)", "sphinx (>=5.1.1)", "sphinx-argparse (>=0.3.1)", "sphinx-rtd-theme (>=1)", "towncrier (>=21.9)"]
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+]
 yarl = []
 zipp = []
diff --git a/pyproject.toml b/pyproject.toml
index 5134a66..5d75996 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,7 +12,7 @@ packages = [
 
 [tool.poetry.dependencies]
 python = "^3.9"
-linkml = "1.3.0"
+linkml = "^1.3.0"
 mkdocs = "^1.2.3"
 pandas = "^1.3.5"
 python-dateutil = "^2.8.2"

From 47c46385796e786f3f78f6a5a9b086557fe09a72 Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Fri, 30 Sep 2022 16:31:01 -0700
Subject: [PATCH 2/2] fixing tests

---
 poetry.lock                                          | 12 ++++++------
 pyproject.toml                                       |  6 +++---
 .../test_bioportal_schema_annotator.py               |  4 ++--
 tests/test_annotators/test_lov_schema_annotator.py   |  2 +-
 tests/test_annotators/test_schema_enricher.py        |  2 +-
 5 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 47f4b6d..27ebb76 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1490,8 +1490,8 @@ sqlalchemy = "*"
 
 [[package]]
 name = "pandera"
-version = "0.11.0"
-description = "A light-weight and flexible data validation and testing tool for dataframes."
+version = "0.12.0"
+description = "A light-weight and flexible data validation and testing tool for statistical data objects."
 category = "main"
 optional = false
 python-versions = ">=3.8"
@@ -1507,8 +1507,8 @@ wrapt = "*"
 
 [package.extras]
 strategies = ["hypothesis (>=5.41.1)"]
-pyspark = ["pyspark"]
-mypy = ["pandas-stubs"]
+pyspark = ["pyspark (>=3.2.0)"]
+mypy = ["pandas-stubs (<=1.4.3.220807)"]
 modin-ray = ["ray (<=1.7.0)", "modin"]
 modin-dask = ["dask", "modin"]
 modin = ["dask", "ray (<=1.7.0)", "modin"]
@@ -1517,7 +1517,7 @@ hypotheses = ["scipy"]
 geopandas = ["shapely", "geopandas"]
 fastapi = ["fastapi"]
 dask = ["dask"]
-all = ["pandas-stubs", "scipy", "modin", "ray (<=1.7.0)", "hypothesis (>=5.41.1)", "fastapi", "pyyaml (>=5.1)", "frictionless", "pyspark", "shapely", "geopandas", "dask", "black"]
+all = ["pyyaml (>=5.1)", "geopandas", "shapely", "ray (<=1.7.0)", "pyspark (>=3.2.0)", "modin", "scipy", "hypothesis (>=5.41.1)", "fastapi", "pandas-stubs (<=1.4.3.220807)", "black", "dask", "frictionless"]
 
 [[package]]
 name = "pandocfilters"
@@ -2686,7 +2686,7 @@ mariadb = []
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.9"
-content-hash = "07962e529f940e6cb225c712c374a12fa0010055d72aced8dea117a68b440ca9"
+content-hash = "d6477184cf64bdca2c5263a49054b41b228236a30403cb570acd873268b1d294"
 
 [metadata.files]
 aiohttp = []
diff --git a/pyproject.toml b/pyproject.toml
index 5d75996..0d86766 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,7 +12,7 @@ packages = [
 
 [tool.poetry.dependencies]
 python = "^3.9"
-linkml = "^1.3.0"
+linkml = "^1.3.5"
 mkdocs = "^1.2.3"
 pandas = "^1.3.5"
 python-dateutil = "^2.8.2"
@@ -24,8 +24,8 @@ psycopg2-binary = "^2.9.2"
 strsimpy = "^0.2.1"
 requests = "^2.26.0"
 bioregistry = "^0.5.87"
-oaklib = "^0.1.38"
-pandera = "^0.11.0"
+oaklib = "^0.1.43"
+pandera = "^0.12.0"
 tomlkit = "^0.11.4"
 inflect = "^6.0.0"
 
diff --git a/tests/test_annotators/test_bioportal_schema_annotator.py b/tests/test_annotators/test_bioportal_schema_annotator.py
index 86f4a3d..6ae2505 100644
--- a/tests/test_annotators/test_bioportal_schema_annotator.py
+++ b/tests/test_annotators/test_bioportal_schema_annotator.py
@@ -4,7 +4,7 @@
 from linkml.utils.schema_builder import SchemaBuilder
 from linkml_runtime.dumpers import yaml_dumper
 from linkml_runtime.linkml_model import SchemaDefinition, EnumDefinition, PermissibleValue
-from oaklib.implementations import BioportalImplementation
+from oaklib.implementations import BioPortalImplementation
 
 from schema_automator.annotators.schema_annotator import SchemaAnnotator
 
@@ -22,7 +22,7 @@ class BioPortalSchemaAnnotatorTestCase(unittest.TestCase):
 
     def setUp(self) -> None:
         try:
-            impl = BioportalImplementation()
+            impl = BioPortalImplementation()
             if impl.api_key:
                 self.annotator = SchemaAnnotator(impl, curie_only=True, mine_descriptions=True)
             else:
diff --git a/tests/test_annotators/test_lov_schema_annotator.py b/tests/test_annotators/test_lov_schema_annotator.py
index c8fea48..650d406 100644
--- a/tests/test_annotators/test_lov_schema_annotator.py
+++ b/tests/test_annotators/test_lov_schema_annotator.py
@@ -8,7 +8,7 @@
 from linkml_runtime.dumpers import yaml_dumper
 from linkml_runtime.linkml_model import SchemaDefinition, EnumDefinition, PermissibleValue
 from oaklib import OntologyResource
-from oaklib.implementations import BioportalImplementation
+from oaklib.implementations import BioPortalImplementation
 from oaklib.implementations.sparql.lov_implementation import LovImplementation
 from oaklib.selector import get_implementation_from_shorthand
 
diff --git a/tests/test_annotators/test_schema_enricher.py b/tests/test_annotators/test_schema_enricher.py
index f3f83b1..cdc3a70 100644
--- a/tests/test_annotators/test_schema_enricher.py
+++ b/tests/test_annotators/test_schema_enricher.py
@@ -6,7 +6,7 @@
 from linkml.utils.schema_builder import SchemaBuilder
 from linkml_runtime.dumpers import yaml_dumper
 from linkml_runtime.linkml_model import SchemaDefinition, EnumDefinition, PermissibleValue
-from oaklib.implementations import BioportalImplementation
+from oaklib.implementations import BioPortalImplementation
 from oaklib.selector import get_implementation_from_shorthand
 
 from schema_automator.annotators.schema_annotator import SchemaAnnotator