diff --git a/Makefile b/Makefile
index dcc90975..8b10c17d 100644
--- a/Makefile
+++ b/Makefile
@@ -12,6 +12,7 @@ WGET = /usr/bin/env wget --timestamping --no-verbose
 .DEFAULT_GOAL := all
 SHELL := bash
 
+RUN = poetry run
 
 .PHONY: all
 all: install format test clean
@@ -29,12 +30,12 @@ install-full:
 
 .PHONY: test
 test: install
-	poetry run python -m pytest tests
+	$(RUN) python -m pytest tests
 
 
 .PHONY: docs
 docs: install-full
-	poetry run typer src/monarch_ingest/main.py utils docs --name ingest --output docs/CLI.md
+	$(RUN) typer src/monarch_ingest/main.py utils docs --name ingest --output docs/CLI.md
 	
 
 .PHONY: clean
@@ -47,18 +48,11 @@ clean:
 
 .PHONY: lint
 lint: install-full
-	poetry run flake8 --exit-zero --max-line-length 120 src/monarch_ingest/ tests/
-	poetry run black --check --diff monarch_ingest tests
-	poetry run isort --check-only --diff monarch_ingest tests
+	$(RUN) ruff check --diff --exit-zero src/ tests/
+	$(RUN) black --check --diff -l 120 src/ tests/
 
 
 .PHONY: format
 format: install-full
-	poetry run autoflake \
-		--recursive \
-		--remove-all-unused-imports \
-		--remove-unused-variables \
-		--ignore-init-module-imports \
-		--in-place monarch_ingest tests
-	poetry run isort monarch_ingest tests
-	poetry run black monarch_ingest tests
+	$(RUN) ruff check --fix --exit-zero src/ tests/
+	$(RUN) black -l 120 src/ tests/
diff --git a/docs/Create-an-Ingest/4. Implement.md b/docs/Create-an-Ingest/4. Implement.md
index d8ebe23e..1cb7a4b3 100644
--- a/docs/Create-an-Ingest/4. Implement.md	
+++ b/docs/Create-an-Ingest/4. Implement.md	
@@ -7,7 +7,7 @@ Most Koza scripts can run in flat mode, which means that the transform code itse
 Start with the imports, and make sure to set the source_name, which will be used for communicating with the reader and writer.
 
 ```python
-from koza.cli_runner import koza_app
+from koza.cli_utils import koza_app
 from biolink.pydanticmodel_v2 import Gene
 
 # The source name is used for reading and writing
diff --git a/docs/Create-an-Ingest/5. Test.md b/docs/Create-an-Ingest/5. Test.md
index fc13f3e5..aef2be90 100644
--- a/docs/Create-an-Ingest/5. Test.md	
+++ b/docs/Create-an-Ingest/5. Test.md	
@@ -8,7 +8,7 @@ First, set up your basic fixtures, taking care to set the correct source name an
 
 ```python
 import pytest
-from koza.cli_runner import get_translation_table
+from koza.cli_utils import get_translation_table
 
 @pytest.fixture
 def tt():
diff --git a/ingest_template/example_test.py b/ingest_template/example_test.py
index 0f7f109d..d11ab6a5 100644
--- a/ingest_template/example_test.py
+++ b/ingest_template/example_test.py
@@ -1,5 +1,5 @@
 import pytest
-from koza.cli_runner import get_translation_table
+from koza.cli_utils import get_translation_table
 
 
 @pytest.fixture
diff --git a/ingest_template/source-file-template-csv.py b/ingest_template/source-file-template-csv.py
index 9e6005da..8fd0127d 100644
--- a/ingest_template/source-file-template-csv.py
+++ b/ingest_template/source-file-template-csv.py
@@ -1,7 +1,7 @@
 from typing import List
 
 from biolink.pydanticmodel_v2 import Gene
-from koza.cli_runner import koza_app
+from koza.cli_utils import koza_app
 
 # You've got 'NCBI_Gene:' and you want 'NCBIGene:'? clean it up.
 curie_cleaner = koza_app.curie_cleaner
diff --git a/ingest_template/source-file-template-json.py b/ingest_template/source-file-template-json.py
index 7a16e05b..f95e170b 100644
--- a/ingest_template/source-file-template-json.py
+++ b/ingest_template/source-file-template-json.py
@@ -7,7 +7,7 @@
     GeneToPhenotypicFeatureAssociation,
     PhenotypicFeature,
 )
-from koza.cli_runner import koza_app
+from koza.cli_utils import koza_app
 
 # include logging if necessary
 from loguru import logger
diff --git a/poetry.lock b/poetry.lock
index 2a0a3446..2d6e80f2 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -72,13 +72,13 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p
 
 [[package]]
 name = "babel"
-version = "2.14.0"
+version = "2.15.0"
 description = "Internationalization utilities"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
-    {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
+    {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"},
+    {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"},
 ]
 
 [package.extras]
@@ -107,60 +107,53 @@ lxml = ["lxml"]
 
 [[package]]
 name = "biolink-model"
-version = "0.0.0"
+version = "4.2.1"
 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"
-files = []
-develop = false
+python-versions = "<4.0,>=3.9"
+files = [
+    {file = "biolink_model-4.2.1-py3-none-any.whl", hash = "sha256:dae399cb8a81e9360300abcb1d6bf38c29efc790e8a0732dacb7d501aee84ab0"},
+    {file = "biolink_model-4.2.1.tar.gz", hash = "sha256:9defa7af163a64b98fa9dd026c3ce10523ea302ec5c2e035c4067134106915e1"},
+]
 
 [package.dependencies]
 beautifulsoup4 = ">=4.0.0"
-curies = "^0.7.4"
-prefixmaps = "^0.2.0"
-pytest = "^7.3.1"
-pyyaml = "^6.0.1"
-stringcase = "^1.2.0"
-yamllint = "^1.35.1"
-
-[package.extras]
-docs = []
-
-[package.source]
-type = "git"
-url = "https://github.com/biolink/biolink-model"
-reference = "master"
-resolved_reference = "d44c32ffef2c9141fd19d62a4a25b9ee945a5b8e"
+curies = ">=0.7.4,<0.8.0"
+prefixmaps = ">=0.2.3,<0.3.0"
+pytest = ">=8.1.1,<9.0.0"
+pyyaml = ">=6.0.1,<7.0.0"
+stringcase = ">=1.2.0,<2.0.0"
+yamllint = ">=1.35.1,<2.0.0"
 
 [[package]]
 name = "black"
-version = "24.3.0"
+version = "24.4.2"
 description = "The uncompromising code formatter."
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "black-24.3.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:9f50ea1132e2189d8dff0115ab75b65590a3e97de1e143795adb4ce317934995"},
-    {file = "black-24.3.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:e2af80566f43c85f5797365077fb64a393861a3730bd110971ab7a0c94e873e7"},
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+    {file = "black-24.4.2-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:bf10f7310db693bb62692609b397e8d67257c55f949abde4c67f9cc574492cc7"},
+    {file = "black-24.4.2-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:98e123f1d5cfd42f886624d84464f7756f60ff6eab89ae845210631714f6db94"},
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+    {file = "black-24.4.2-cp38-cp38-win_amd64.whl", hash = "sha256:b1530ae42e9d6d5b670a34db49a94115a64596bc77710b1d05e9801e62ca0a7c"},
+    {file = "black-24.4.2-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:37aae07b029fa0174d39daf02748b379399b909652a806e5708199bd93899da1"},
+    {file = "black-24.4.2-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:da33a1a5e49c4122ccdfd56cd021ff1ebc4a1ec4e2d01594fef9b6f267a9e741"},
+    {file = "black-24.4.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ef703f83fc32e131e9bcc0a5094cfe85599e7109f896fe8bc96cc402f3eb4b6e"},
+    {file = "black-24.4.2-cp39-cp39-win_amd64.whl", hash = "sha256:b9176b9832e84308818a99a561e90aa479e73c523b3f77afd07913380ae2eab7"},
+    {file = "black-24.4.2-py3-none-any.whl", hash = "sha256:d36ed1124bb81b32f8614555b34cc4259c3fbc7eec17870e8ff8ded335b58d8c"},
+    {file = "black-24.4.2.tar.gz", hash = "sha256:c872b53057f000085da66a19c55d68f6f8ddcac2642392ad3a355878406fbd4d"},
 ]
 
 [package.dependencies]
@@ -180,33 +173,33 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "bmt"
-version = "1.1.3"
+version = "1.4.1"
 description = "Biolink Model Toolkit: A Python API for working with the Biolink Model"
 optional = false
-python-versions = ">=3.9,<4.0"
+python-versions = "<4.0,>=3.9"
 files = [
-    {file = "bmt-1.1.3-py3-none-any.whl", hash = "sha256:7818da7f8debc807e80bbe181af70edb525ac3c7115bee86021607dcbaa0c372"},
-    {file = "bmt-1.1.3.tar.gz", hash = "sha256:605ebffaec269dbf335b2a3ac0da575cc5299e98cfecfac0d6eff514a317983b"},
+    {file = "bmt-1.4.1-py3-none-any.whl", hash = "sha256:94016f64cdca85a65a83c45667313ffc83da9af31a3dab7b14e868c4cb6ab0bb"},
+    {file = "bmt-1.4.1.tar.gz", hash = "sha256:deb6dd64c6a57a77e727af6629b880116858d7303ec88e90723a488fac775735"},
 ]
 
 [package.dependencies]
 deprecation = ">=2.1.0,<3.0.0"
-linkml-runtime = ">=1.5.0,<2.0.0"
+linkml-runtime = ">=1.6.3,<2.0.0"
 stringcase = ">=1.2.0,<2.0.0"
 
 [[package]]
 name = "boto3"
-version = "1.34.71"
+version = "1.34.106"
 description = "The AWS SDK for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "boto3-1.34.71-py3-none-any.whl", hash = "sha256:7ce8c9a50af2f8a159a0dd86b40011d8dfdaba35005a118e51cd3ac72dc630f1"},
-    {file = "boto3-1.34.71.tar.gz", hash = "sha256:d786e7fbe3c4152866199786468a625dc77b9f27294cd7ad4f63cd2e0c927287"},
+    {file = "boto3-1.34.106-py3-none-any.whl", hash = "sha256:d3be4e1dd5d546a001cd4da805816934cbde9d395316546e9411fec341ade5cf"},
+    {file = "boto3-1.34.106.tar.gz", hash = "sha256:6165b8cf1c7e625628ab28b32f9027064c8f5e5fca1c38d7fc228cd22069a19f"},
 ]
 
 [package.dependencies]
-botocore = ">=1.34.71,<1.35.0"
+botocore = ">=1.34.106,<1.35.0"
 jmespath = ">=0.7.1,<2.0.0"
 s3transfer = ">=0.10.0,<0.11.0"
 
@@ -215,13 +208,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "botocore"
-version = "1.34.71"
+version = "1.34.106"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "botocore-1.34.71-py3-none-any.whl", hash = "sha256:3bc9e23aee73fe6f097823d61f79a8877790436038101a83fa96c7593e8109f8"},
-    {file = "botocore-1.34.71.tar.gz", hash = "sha256:c58f9ed71af2ea53d24146187130541222d7de8c27eb87d23f15457e7b83d88b"},
+    {file = "botocore-1.34.106-py3-none-any.whl", hash = "sha256:4baf0e27c2dfc4f4d0dee7c217c716e0782f9b30e8e1fff983fce237d88f73ae"},
+    {file = "botocore-1.34.106.tar.gz", hash = "sha256:921fa5202f88c3e58fdcb4b3acffd56d65b24bca47092ee4b27aa988556c0be6"},
 ]
 
 [package.dependencies]
@@ -230,7 +223,7 @@ 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 (==0.19.19)"]
+crt = ["awscrt (==0.20.9)"]
 
 [[package]]
 name = "cachetools"
@@ -464,13 +457,13 @@ test = ["codacy-coverage", "coveralls", "dict_hash", "pytest", "pytest-cov", "ra
 
 [[package]]
 name = "curies"
-version = "0.7.8"
+version = "0.7.9"
 description = "Idiomatic conversion between URIs and compact URIs (CURIEs)."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "curies-0.7.8-py3-none-any.whl", hash = "sha256:a60b2559f08557176b0a3df1f7c47ec7cd8ae4e0695f23fc6574825d2ccd17eb"},
-    {file = "curies-0.7.8.tar.gz", hash = "sha256:d208ad40b5e40b532285c917f116001f9e887a48dda54e6eedd10e514ea6aa1a"},
+    {file = "curies-0.7.9-py3-none-any.whl", hash = "sha256:e4c5beb91642376953c94db0ee2fb5d2b011c3b16749516436114ba61442f260"},
+    {file = "curies-0.7.9.tar.gz", hash = "sha256:3b63c5fea7b0e967629a3a384b1a8c59b56c503487c1dcbacddeab59e25db4d8"},
 ]
 
 [package.dependencies]
@@ -619,16 +612,6 @@ files = [
     {file = "duckdb-0.9.2.tar.gz", hash = "sha256:3843afeab7c3fc4a4c0b53686a4cc1d9cdbdadcbb468d60fef910355ecafd447"},
 ]
 
-[[package]]
-name = "editorconfig"
-version = "0.12.4"
-description = "EditorConfig File Locator and Interpreter for Python"
-optional = false
-python-versions = "*"
-files = [
-    {file = "EditorConfig-0.12.4.tar.gz", hash = "sha256:24857fa1793917dd9ccf0c7810a07e05404ce9b823521c7dce22a4fb5d125f80"},
-]
-
 [[package]]
 name = "elastic-transport"
 version = "8.13.0"
@@ -649,13 +632,13 @@ develop = ["aiohttp", "furo", "httpx", "mock", "opentelemetry-api", "opentelemet
 
 [[package]]
 name = "elasticsearch"
-version = "8.13.0"
+version = "8.13.1"
 description = "Python client for Elasticsearch"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "elasticsearch-8.13.0-py3-none-any.whl", hash = "sha256:4aaf49253e974eb500f01136a487bdd0f09d3cafd37a0456eff6acfff0c9199b"},
-    {file = "elasticsearch-8.13.0.tar.gz", hash = "sha256:e4ebebb22d09f0ef839c26b6aa98e19ccd636bcb77f08c12b562b02cacd5e744"},
+    {file = "elasticsearch-8.13.1-py3-none-any.whl", hash = "sha256:ba2b3f8b30a7a81beae690f1cede52fbcfd29baf3ef5bb028d4fa86972feebd8"},
+    {file = "elasticsearch-8.13.1.tar.gz", hash = "sha256:1594d2d1293672db62525bc4688d86cdaf118db0f901808db28dc90ad19b81e1"},
 ]
 
 [package.dependencies]
@@ -665,6 +648,7 @@ elastic-transport = ">=8.13,<9"
 async = ["aiohttp (>=3,<4)"]
 orjson = ["orjson (>=3)"]
 requests = ["requests (>=2.4.0,<3.0.0)"]
+vectorstore-mmr = ["numpy (>=1)", "simsimd (>=3)"]
 
 [[package]]
 name = "et-xmlfile"
@@ -679,13 +663,13 @@ files = [
 
 [[package]]
 name = "exceptiongroup"
-version = "1.2.0"
+version = "1.2.1"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "exceptiongroup-1.2.0-py3-none-any.whl", hash = "sha256:4bfd3996ac73b41e9b9628b04e079f193850720ea5945fc96a08633c66912f14"},
-    {file = "exceptiongroup-1.2.0.tar.gz", hash = "sha256:91f5c769735f051a4290d52edd0858999b57e5876e9f85937691bd4c9fa3ed68"},
+    {file = "exceptiongroup-1.2.1-py3-none-any.whl", hash = "sha256:5258b9ed329c5bbdd31a309f53cbfb0b155341807f6ff7606a1e801a891b29ad"},
+    {file = "exceptiongroup-1.2.1.tar.gz", hash = "sha256:a4785e48b045528f5bfe627b6ad554ff32def154f42372786903b7abcfe1aa16"},
 ]
 
 [package.extras]
@@ -693,13 +677,13 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "filelock"
-version = "3.13.3"
+version = "3.14.0"
 description = "A platform independent file lock."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "filelock-3.13.3-py3-none-any.whl", hash = "sha256:5ffa845303983e7a0b7ae17636509bc97997d58afeafa72fb141a17b152284cb"},
-    {file = "filelock-3.13.3.tar.gz", hash = "sha256:a79895a25bbefdf55d1a2a0a80968f7dbb28edcd6d4234a0afb3f37ecde4b546"},
+    {file = "filelock-3.14.0-py3-none-any.whl", hash = "sha256:43339835842f110ca7ae60f1e1c160714c5a6afd15a2873419ab185334975c0f"},
+    {file = "filelock-3.14.0.tar.gz", hash = "sha256:6ea72da3be9b8c82afd3edcf99f2fffbb5076335a5ae4d03248bb5b6c3eae78a"},
 ]
 
 [package.extras]
@@ -720,13 +704,13 @@ files = [
 
 [[package]]
 name = "gdown"
-version = "5.1.0"
+version = "5.2.0"
 description = "Google Drive Public File/Folder Downloader"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "gdown-5.1.0-py3-none-any.whl", hash = "sha256:421530fd238fa15d41ba43219a79fdc28efe8ac11022173abad333701b77de2c"},
-    {file = "gdown-5.1.0.tar.gz", hash = "sha256:550a72dc5ca2819fe4bcc15d80d05d7c98c0b90e57256254b77d0256b9df4683"},
+    {file = "gdown-5.2.0-py3-none-any.whl", hash = "sha256:33083832d82b1101bdd0e9df3edd0fbc0e1c5f14c9d8c38d2a35bf1683b526d6"},
+    {file = "gdown-5.2.0.tar.gz", hash = "sha256:2145165062d85520a3cd98b356c9ed522c5e7984d408535409fd46f94defc787"},
 ]
 
 [package.dependencies]
@@ -736,7 +720,7 @@ requests = {version = "*", extras = ["socks"]}
 tqdm = "*"
 
 [package.extras]
-test = ["build", "mypy", "pytest", "pytest-xdist", "ruff", "twine", "types-requests"]
+test = ["build", "mypy", "pytest", "pytest-xdist", "ruff", "twine", "types-requests", "types-setuptools"]
 
 [[package]]
 name = "ghp-import"
@@ -757,13 +741,13 @@ dev = ["flake8", "markdown", "twine", "wheel"]
 
 [[package]]
 name = "google-api-core"
-version = "2.18.0"
+version = "2.19.0"
 description = "Google API client core library"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "google-api-core-2.18.0.tar.gz", hash = "sha256:62d97417bfc674d6cef251e5c4d639a9655e00c45528c4364fbfebb478ce72a9"},
-    {file = "google_api_core-2.18.0-py3-none-any.whl", hash = "sha256:5a63aa102e0049abe85b5b88cb9409234c1f70afcda21ce1e40b285b9629c1d6"},
+    {file = "google-api-core-2.19.0.tar.gz", hash = "sha256:cf1b7c2694047886d2af1128a03ae99e391108a08804f87cfd35970e49c9cd10"},
+    {file = "google_api_core-2.19.0-py3-none-any.whl", hash = "sha256:8661eec4078c35428fd3f69a2c7ee29e342896b70f01d1a1cbcb334372dd6251"},
 ]
 
 [package.dependencies]
@@ -1045,13 +1029,13 @@ test = ["objgraph", "psutil"]
 
 [[package]]
 name = "griffe"
-version = "0.42.1"
+version = "0.45.0"
 description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "griffe-0.42.1-py3-none-any.whl", hash = "sha256:7e805e35617601355edcac0d3511cedc1ed0cb1f7645e2d336ae4b05bbae7b3b"},
-    {file = "griffe-0.42.1.tar.gz", hash = "sha256:57046131384043ed078692b85d86b76568a686266cc036b9b56b704466f803ce"},
+    {file = "griffe-0.45.0-py3-none-any.whl", hash = "sha256:90fe5c90e1b0ca7dd6fee78f9009f4e01b37dbc9ab484a9b2c1578915db1e571"},
+    {file = "griffe-0.45.0.tar.gz", hash = "sha256:85cb2868d026ea51c89bdd589ad3ccc94abc5bd8d5d948e3d4450778a2a05b4a"},
 ]
 
 [package.dependencies]
@@ -1070,13 +1054,13 @@ files = [
 
 [[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]]
@@ -1108,6 +1092,17 @@ files = [
     {file = "ijson-3.2.3-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:4a3a6a2fbbe7550ffe52d151cf76065e6b89cfb3e9d0463e49a7e322a25d0426"},
     {file = "ijson-3.2.3-cp311-cp311-win32.whl", hash = "sha256:6a4db2f7fb9acfb855c9ae1aae602e4648dd1f88804a0d5cfb78c3639bcf156c"},
     {file = "ijson-3.2.3-cp311-cp311-win_amd64.whl", hash = "sha256:ccd6be56335cbb845f3d3021b1766299c056c70c4c9165fb2fbe2d62258bae3f"},
+    {file = "ijson-3.2.3-cp312-cp312-macosx_10_9_universal2.whl", hash = "sha256:055b71bbc37af5c3c5861afe789e15211d2d3d06ac51ee5a647adf4def19c0ea"},
+    {file = "ijson-3.2.3-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:c075a547de32f265a5dd139ab2035900fef6653951628862e5cdce0d101af557"},
+    {file = "ijson-3.2.3-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:457f8a5fc559478ac6b06b6d37ebacb4811f8c5156e997f0d87d708b0d8ab2ae"},
+    {file = "ijson-3.2.3-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:9788f0c915351f41f0e69ec2618b81ebfcf9f13d9d67c6d404c7f5afda3e4afb"},
+    {file = "ijson-3.2.3-cp312-cp312-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:fa234ab7a6a33ed51494d9d2197fb96296f9217ecae57f5551a55589091e7853"},
+    {file = "ijson-3.2.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bdd0dc5da4f9dc6d12ab6e8e0c57d8b41d3c8f9ceed31a99dae7b2baf9ea769a"},
+    {file = "ijson-3.2.3-cp312-cp312-musllinux_1_1_aarch64.whl", hash = "sha256:c6beb80df19713e39e68dc5c337b5c76d36ccf69c30b79034634e5e4c14d6904"},
+    {file = "ijson-3.2.3-cp312-cp312-musllinux_1_1_i686.whl", hash = "sha256:a2973ce57afb142d96f35a14e9cfec08308ef178a2c76b8b5e1e98f3960438bf"},
+    {file = "ijson-3.2.3-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:105c314fd624e81ed20f925271ec506523b8dd236589ab6c0208b8707d652a0e"},
+    {file = "ijson-3.2.3-cp312-cp312-win32.whl", hash = "sha256:ac44781de5e901ce8339352bb5594fcb3b94ced315a34dbe840b4cff3450e23b"},
+    {file = "ijson-3.2.3-cp312-cp312-win_amd64.whl", hash = "sha256:0567e8c833825b119e74e10a7c29761dc65fcd155f5d4cb10f9d3b8916ef9912"},
     {file = "ijson-3.2.3-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:eeb286639649fb6bed37997a5e30eefcacddac79476d24128348ec890b2a0ccb"},
     {file = "ijson-3.2.3-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:396338a655fb9af4ac59dd09c189885b51fa0eefc84d35408662031023c110d1"},
     {file = "ijson-3.2.3-cp36-cp36m-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:0e0243d166d11a2a47c17c7e885debf3b19ed136be2af1f5d1c34212850236ac"},
@@ -1263,13 +1258,13 @@ arrow = ">=0.15.0"
 
 [[package]]
 name = "jinja2"
-version = "3.1.3"
+version = "3.1.4"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "Jinja2-3.1.3-py3-none-any.whl", hash = "sha256:7d6d50dd97d52cbc355597bd845fabfbac3f551e1f99619e39a35ce8c370b5fa"},
-    {file = "Jinja2-3.1.3.tar.gz", hash = "sha256:ac8bd6544d4bb2c9792bf3a159e80bba8fda7f07e81bc3aed565432d5925ba90"},
+    {file = "jinja2-3.1.4-py3-none-any.whl", hash = "sha256:bc5dd2abb727a5319567b7a813e6a2e7318c39f4f487cfe6c89c6f9c7d25197d"},
+    {file = "jinja2-3.1.4.tar.gz", hash = "sha256:4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369"},
 ]
 
 [package.dependencies]
@@ -1289,20 +1284,6 @@ files = [
     {file = "jmespath-1.0.1.tar.gz", hash = "sha256:90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe"},
 ]
 
-[[package]]
-name = "jsbeautifier"
-version = "1.15.1"
-description = "JavaScript unobfuscator and beautifier."
-optional = false
-python-versions = "*"
-files = [
-    {file = "jsbeautifier-1.15.1.tar.gz", hash = "sha256:ebd733b560704c602d744eafc839db60a1ee9326e30a2a80c4adb8718adc1b24"},
-]
-
-[package.dependencies]
-editorconfig = ">=0.12.2"
-six = ">=1.13.0"
-
 [[package]]
 name = "json-flattener"
 version = "0.1.9"
@@ -1398,13 +1379,13 @@ files = [
 
 [[package]]
 name = "jsonschema"
-version = "4.21.1"
+version = "4.22.0"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jsonschema-4.21.1-py3-none-any.whl", hash = "sha256:7996507afae316306f9e2290407761157c6f78002dcf7419acb99822143d1c6f"},
-    {file = "jsonschema-4.21.1.tar.gz", hash = "sha256:85727c00279f5fa6bedbe6238d2aa6403bedd8b4864ab11207d07df3cc1b2ee5"},
+    {file = "jsonschema-4.22.0-py3-none-any.whl", hash = "sha256:ff4cfd6b1367a40e7bc6411caec72effadd3db0bbe5017de188f2d6108335802"},
+    {file = "jsonschema-4.22.0.tar.gz", hash = "sha256:5b22d434a45935119af990552c862e5d6d564e8f6601206b305a61fdf661a2b7"},
 ]
 
 [package.dependencies]
@@ -1459,13 +1440,13 @@ test = ["tox"]
 
 [[package]]
 name = "kghub-downloader"
-version = "0.3.7"
+version = "0.3.8"
 description = "Downloads and caches files for knowledge graph ETL"
 optional = false
 python-versions = "<4.0,>=3.8"
 files = [
-    {file = "kghub_downloader-0.3.7-py3-none-any.whl", hash = "sha256:c06320e79812a48e9ee88a0fba738d974fb628ee9999eaf0554245caeec85e09"},
-    {file = "kghub_downloader-0.3.7.tar.gz", hash = "sha256:36125e06bd96ebbffc3109c92c23568da55ecd9ec93f440c62ff1ed9739cd046"},
+    {file = "kghub_downloader-0.3.8-py3-none-any.whl", hash = "sha256:d8a2b6f9502d84caf700e8736f06cb82f0dfd0e06ab7ee1ee63f9e37acf90ed6"},
+    {file = "kghub_downloader-0.3.8.tar.gz", hash = "sha256:a77dd62b1a00ca0d5d6ea81dbe983c4293bb71e6a9c73c6174cb309a771fc9ce"},
 ]
 
 [package.dependencies]
@@ -1474,92 +1455,89 @@ compress-json = ">1.0,<2.0"
 elasticsearch = ">7.0,<9.0"
 gdown = ">=4.7.1"
 google-cloud-storage = ">=2.1.0,<3.0.0"
-mkdocs = ">=1.4.0,<2.0.0"
-mkdocs-material = ">=8.5.6,<9.0.0"
+mkdocs = ">=1.4"
+mkdocs-material = ">=9.5"
 mkdocstrings = {version = ">=0.20.0,<0.21.0", extras = ["python"]}
 PyYAML = ">5.0,<7.0"
 tqdm = ">=4.62.3"
-typer = ">=0.7.0,<0.8.0"
+typer = ">=0.12.3,<0.13.0"
 
 [[package]]
 name = "kgx"
-version = "0.0.0"
+version = "2.4.0"
 description = "A Python library and set of command line utilities for exchanging Knowledge Graphs (KGs) that conform to or are aligned to the Biolink Model."
 optional = false
-python-versions = "^3.9"
-files = []
-develop = false
+python-versions = "<4.0,>=3.9"
+files = [
+    {file = "kgx-2.4.0-py3-none-any.whl", hash = "sha256:51f612cb25aa47ce9a702db3902bb689f5346e27af602ba556033ded99f4e543"},
+    {file = "kgx-2.4.0.tar.gz", hash = "sha256:6b15d59d4a3057fed39b3450e5ea02611099688fc9e355682c498ea97c5413e2"},
+]
 
 [package.dependencies]
-bmt = "^1.1.0"
-cachetools = "^5.0.0"
+bmt = ">=1.4.0,<2.0.0"
+cachetools = ">=5.0.0,<6.0.0"
 Click = "*"
-deprecation = "^2.1.0"
-docker = "^6.0.0"
-docutils = "^0.18.1"
-ijson = "^3.1.3"
-inflection = "^0.5.1"
-jsonlines = "^4.0.0"
-jsonstreams = "^0.6.0"
-linkml = "^1.5.0"
-linkml-runtime = "^1.5.0"
+deprecation = ">=2.1.0,<3.0.0"
+docker = ">=6.0.0,<7.0.0"
+docutils = ">=0.18.1,<0.19.0"
+ijson = ">=3.1.3,<4.0.0"
+inflection = ">=0.5.1,<0.6.0"
+jsonlines = ">=4.0.0,<5.0.0"
+jsonstreams = ">=0.6.0,<0.7.0"
+linkml = ">=1.7.7,<2.0.0"
+linkml-runtime = ">=1.7.5,<2.0.0"
 mypy = "*"
-neo4j = "^4.4.10"
+neo4j = ">=4.4.10,<5.0.0"
 networkx = "*"
-ordered-set = "^4.0.2"
+ordered-set = ">=4.0.2,<5.0.0"
 pandas = ">1.0.3"
-prefixcommons = "^0.1.4"
-prologterms = "^0.0.6"
+prefixcommons = ">=0.1.4,<0.2.0"
+prologterms = ">=0.0.6,<0.0.7"
+pyarrow = ">=15.0.2,<16.0.0"
 pytest = "*"
-python-dateutil = "^2.8.1"
+python-dateutil = ">=2.8.1,<3.0.0"
 pyyaml = "*"
 rdflib = ">=6.0.0"
 recommonmark = "*"
 shexjsg = "*"
 SPARQLWrapper = ">=1.8.2"
 Sphinx = "*"
-stringcase = "^1.2.0"
-terminaltables = "^3.1.0"
-tox = "^4.13.0"
-validators = "^0.20.0"
-
-[package.source]
-type = "git"
-url = "https://github.com/biolink/kgx"
-reference = "master"
-resolved_reference = "8e5981697b4549b0be36ff37bf8b9f0eea06a7fc"
+stringcase = ">=1.2.0,<2.0.0"
+terminaltables = ">=3.1.0,<4.0.0"
+tox = ">=4.13.0,<5.0.0"
+validators = ">=0.20.0,<0.21.0"
 
 [[package]]
 name = "koza"
-version = "0.5.3"
+version = "0.6.0"
 description = "Data transformation framework for LinkML data models"
 optional = false
-python-versions = ">=3.9,<4.0"
+python-versions = "<4.0,>=3.9"
 files = [
-    {file = "koza-0.5.3-py3-none-any.whl", hash = "sha256:e55f209c64f2c0c3c60212afd29507cc8701ee37ff11ecb0eb11318f6087eaa8"},
-    {file = "koza-0.5.3.tar.gz", hash = "sha256:c04c64a9aa67f8b34f4cd45fdc28109b9db407653b6af5b07d9b15b5962a8867"},
+    {file = "koza-0.6.0-py3-none-any.whl", hash = "sha256:21be1eb8d8d6dd24901fe913bd3430aac472a3bc1460d84bf4e1936133a5f8a1"},
+    {file = "koza-0.6.0.tar.gz", hash = "sha256:6fbc2e693c9956df0c3fb8b8b4304baeec6bc9eb4377e85f7ec5e15228e47376"},
 ]
 
 [package.dependencies]
-linkml = ">=1.6.3"
+duckdb = "*"
+linkml = ">=1.7.8"
 loguru = "*"
 ordered-set = ">=4.1.0"
 pydantic = ">=2.4,<3.0"
 pyyaml = ">=5.0.0"
 requests = ">=2.24.0,<3.0.0"
 sssom = ">=0.4"
-typer = ">=0.7.0,<0.8.0"
-typer-cli = ">=0.0.13,<0.0.14"
+typer = ">=0.12.3"
 
 [[package]]
 name = "linkml"
-version = "1.6.3"
+version = "1.7.10"
 description = "Linked Open Data Modeling Language"
 optional = false
-python-versions = ">=3.8.1,<4.0.0"
+python-versions = "<4.0.0,>=3.8.1"
 files = [
-    {file = "linkml-1.6.3-py3-none-any.whl", hash = "sha256:2bcfa9e35b3e0d868f396fa48ede1b9e3c6016df956dd5ca92d70ff621ffc77e"},
-    {file = "linkml-1.6.3.tar.gz", hash = "sha256:2692243c9fb1c262ea83b725c70d6f537844ae7a9405101c94bccf65def6d952"},
+    {file = "linkml-1.7.10-py3-none-any.whl", hash = "sha256:bf21cce814e9d1509489f1e6e15a7e86e4f11d949490d9a7a5c3f6b5b412ec62"},
+    {file = "linkml-1.7.10.tar.gz", hash = "sha256:1c38601c3cd495e34490b8cf7277fd3674ec68dcbe9f5efcec2658093801ce91"},
 ]
 
 [package.dependencies]
@@ -1572,11 +1550,11 @@ jinja2 = ">=3.1.0"
 jsonasobj2 = ">=1.0.3,<2.0.0"
 jsonschema = {version = ">=4.0.0", extras = ["format"]}
 linkml-dataops = "*"
-linkml-runtime = ">=1.6.0"
+linkml-runtime = ">=1.7.4"
 openpyxl = "*"
 parse = "*"
 prefixcommons = ">=0.1.7"
-prefixmaps = ">=0.1.3"
+prefixmaps = ">=0.2.2"
 pydantic = ">=1.0.0,<3.0.0"
 pyjsg = ">=0.11.6"
 pyshex = ">=0.7.20"
@@ -1588,6 +1566,11 @@ requests = ">=2.22"
 sqlalchemy = ">=1.4.31"
 watchdog = ">=0.9.0"
 
+[package.extras]
+black = ["black (>=24.0.0)"]
+shacl = ["pyshacl (>=0.25.0,<0.26.0)"]
+tests = ["black (>=24.0.0)", "pyshacl (>=0.25.0,<0.26.0)"]
+
 [[package]]
 name = "linkml-dataops"
 version = "0.1.0"
@@ -1608,13 +1591,13 @@ linkml-runtime = ">=1.1.6"
 
 [[package]]
 name = "linkml-runtime"
-version = "1.6.3"
+version = "1.7.5"
 description = "Runtime environment for LinkML, the Linked open data modeling language"
 optional = false
-python-versions = ">=3.7.6,<4.0.0"
+python-versions = "<4.0,>=3.8"
 files = [
-    {file = "linkml_runtime-1.6.3-py3-none-any.whl", hash = "sha256:08f616302ce493be775104c87bd5a2ec0eb2c67624e611a3f7e28c978d08a4d1"},
-    {file = "linkml_runtime-1.6.3.tar.gz", hash = "sha256:88e3d0b776055723d187128c03527145dc1ffdc2d2a69e89f8aabce203d418a3"},
+    {file = "linkml_runtime-1.7.5-py3-none-any.whl", hash = "sha256:c58000c7c68fa97b7d76c50421a85a64e25f07eec5bcac464bc00c4cd79007a6"},
+    {file = "linkml_runtime-1.7.5.tar.gz", hash = "sha256:b31197a5398359441ae1ed43470c54377a1d08db961366dda670300dddcd71d7"},
 ]
 
 [package.dependencies]
@@ -1683,6 +1666,30 @@ files = [
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 testing = ["coverage", "pyyaml"]
 
+[[package]]
+name = "markdown-it-py"
+version = "3.0.0"
+description = "Python port of markdown-it. Markdown parsing, done right!"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "markdown-it-py-3.0.0.tar.gz", hash = "sha256:e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb"},
+    {file = "markdown_it_py-3.0.0-py3-none-any.whl", hash = "sha256:355216845c60bd96232cd8d8c40e8f9765cc86f46880e43a8fd22dc1a1a8cab1"},
+]
+
+[package.dependencies]
+mdurl = ">=0.1,<1.0"
+
+[package.extras]
+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 = ["jupyter_sphinx", "mdit-py-plugins", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
+testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
+
 [[package]]
 name = "markupsafe"
 version = "2.1.5"
@@ -1752,6 +1759,17 @@ files = [
     {file = "MarkupSafe-2.1.5.tar.gz", hash = "sha256:d283d37a890ba4c1ae73ffadf8046435c76e7bc2247bbb63c00bd1a709c6544b"},
 ]
 
+[[package]]
+name = "mdurl"
+version = "0.1.2"
+description = "Markdown URL utilities"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "mdurl-0.1.2-py3-none-any.whl", hash = "sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8"},
+    {file = "mdurl-0.1.2.tar.gz", hash = "sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba"},
+]
+
 [[package]]
 name = "mergedeep"
 version = "1.3.4"
@@ -1765,13 +1783,13 @@ files = [
 
 [[package]]
 name = "mkdocs"
-version = "1.5.3"
+version = "1.6.0"
 description = "Project documentation with Markdown."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "mkdocs-1.5.3-py3-none-any.whl", hash = "sha256:3b3a78e736b31158d64dbb2f8ba29bd46a379d0c6e324c2246c3bc3d2189cfc1"},
-    {file = "mkdocs-1.5.3.tar.gz", hash = "sha256:eb7c99214dcb945313ba30426c2451b735992c73c2e10838f76d09e39ff4d0e2"},
+    {file = "mkdocs-1.6.0-py3-none-any.whl", hash = "sha256:1eb5cb7676b7d89323e62b56235010216319217d4af5ddc543a91beb8d125ea7"},
+    {file = "mkdocs-1.6.0.tar.gz", hash = "sha256:a73f735824ef83a4f3bcb7a231dcab23f5a838f88b7efc54a0eef5fbdbc3c512"},
 ]
 
 [package.dependencies]
@@ -1779,19 +1797,19 @@ click = ">=7.0"
 colorama = {version = ">=0.4", markers = "platform_system == \"Windows\""}
 ghp-import = ">=1.0"
 jinja2 = ">=2.11.1"
-markdown = ">=3.2.1"
+markdown = ">=3.3.6"
 markupsafe = ">=2.0.1"
 mergedeep = ">=1.3.4"
+mkdocs-get-deps = ">=0.2.0"
 packaging = ">=20.5"
 pathspec = ">=0.11.1"
-platformdirs = ">=2.2.0"
 pyyaml = ">=5.1"
 pyyaml-env-tag = ">=0.1"
 watchdog = ">=2.0"
 
 [package.extras]
 i18n = ["babel (>=2.9.0)"]
-min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-import (==1.0)", "importlib-metadata (==4.3)", "jinja2 (==2.11.1)", "markdown (==3.2.1)", "markupsafe (==2.0.1)", "mergedeep (==1.3.4)", "packaging (==20.5)", "pathspec (==0.11.1)", "platformdirs (==2.2.0)", "pyyaml (==5.1)", "pyyaml-env-tag (==0.1)", "typing-extensions (==3.10)", "watchdog (==2.0)"]
+min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-import (==1.0)", "importlib-metadata (==4.4)", "jinja2 (==2.11.1)", "markdown (==3.3.6)", "markupsafe (==2.0.1)", "mergedeep (==1.3.4)", "mkdocs-get-deps (==0.2.0)", "packaging (==20.5)", "pathspec (==0.11.1)", "pyyaml (==5.1)", "pyyaml-env-tag (==0.1)", "watchdog (==2.0)"]
 
 [[package]]
 name = "mkdocs-autorefs"
@@ -1809,25 +1827,50 @@ Markdown = ">=3.3"
 markupsafe = ">=2.0.1"
 mkdocs = ">=1.1"
 
+[[package]]
+name = "mkdocs-get-deps"
+version = "0.2.0"
+description = "MkDocs extension that lists all dependencies according to a mkdocs.yml file"
+optional = false
+python-versions = ">=3.8"
+files = [
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+    {file = "mkdocs_get_deps-0.2.0.tar.gz", hash = "sha256:162b3d129c7fad9b19abfdcb9c1458a651628e4b1dea628ac68790fb3061c60c"},
+]
+
+[package.dependencies]
+mergedeep = ">=1.3.4"
+platformdirs = ">=2.2.0"
+pyyaml = ">=5.1"
+
 [[package]]
 name = "mkdocs-material"
-version = "8.5.11"
+version = "9.5.23"
 description = "Documentation that simply works"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 [package.dependencies]
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-markdown = ">=3.2"
-mkdocs = ">=1.4.0"
-mkdocs-material-extensions = ">=1.1"
-pygments = ">=2.12"
-pymdown-extensions = ">=9.4"
-requests = ">=2.26"
+babel = ">=2.10,<3.0"
+colorama = ">=0.4,<1.0"
+jinja2 = ">=3.0,<4.0"
+markdown = ">=3.2,<4.0"
+mkdocs = ">=1.6,<2.0"
+mkdocs-material-extensions = ">=1.3,<2.0"
+paginate = ">=0.5,<1.0"
+pygments = ">=2.16,<3.0"
+pymdown-extensions = ">=10.2,<11.0"
+regex = ">=2022.4"
+requests = ">=2.26,<3.0"
+
+[package.extras]
+git = ["mkdocs-git-committers-plugin-2 (>=1.1,<2.0)", "mkdocs-git-revision-date-localized-plugin (>=1.2.4,<2.0)"]
+imaging = ["cairosvg (>=2.6,<3.0)", "pillow (>=10.2,<11.0)"]
+recommended = ["mkdocs-minify-plugin (>=0.7,<1.0)", "mkdocs-redirects (>=1.2,<2.0)", "mkdocs-rss-plugin (>=1.6,<2.0)"]
 
 [[package]]
 name = "mkdocs-material-extensions"
@@ -1840,27 +1883,6 @@ files = [
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 ]
 
-[[package]]
-name = "mkdocs-mermaid2-plugin"
-version = "0.6.0"
-description = "A MkDocs plugin for including mermaid graphs in markdown sources"
-optional = false
-python-versions = ">=3.5"
-files = [
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-pymdown-extensions = ">=8.0"
-pyyaml = "*"
-requests = "*"
-setuptools = ">=18.5"
-
 [[package]]
 name = "mkdocstrings"
 version = "0.20.0"
@@ -1921,38 +1943,38 @@ test = ["codacy-coverage", "coveralls", "parameterized", "pytest", "pytest-cov",
 
 [[package]]
 name = "mypy"
-version = "1.9.0"
+version = "1.10.0"
 description = "Optional static typing for Python"
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 python-versions = ">=3.8"
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+    {file = "mypy-1.10.0.tar.gz", hash = "sha256:3d087fcbec056c4ee34974da493a826ce316947485cef3901f511848e687c131"},
 ]
 
 [package.dependencies]
@@ -1979,12 +2001,12 @@ files = [
 
 [[package]]
 name = "neo4j"
-version = "4.4.11"
+version = "4.4.12"
 description = "Neo4j Bolt driver for Python"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "neo4j-4.4.11.tar.gz", hash = "sha256:2fb4693d524e7661ed6b0ea5b4e3a6272dba2567809ecd1d63f1c896ebcfc241"},
+    {file = "neo4j-4.4.12.tar.gz", hash = "sha256:b138271400e1ef2b89738e90ae0beb96b005f7dfedd68b17c4b85ee732d54125"},
 ]
 
 [package.dependencies]
@@ -1992,20 +2014,20 @@ pytz = "*"
 
 [[package]]
 name = "networkx"
-version = "3.2.1"
+version = "3.3"
 description = "Python package for creating and manipulating graphs and networks"
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
 files = [
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+    {file = "networkx-3.3-py3-none-any.whl", hash = "sha256:28575580c6ebdaf4505b22c6256a2b9de86b316dc63ba9e93abde3d78dfdbcf2"},
+    {file = "networkx-3.3.tar.gz", hash = "sha256:0c127d8b2f4865f59ae9cb8aafcd60b5c70f3241ebd66f7defad7c4ab90126c9"},
 ]
 
 [package.extras]
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-developer = ["changelist (==0.4)", "mypy (>=1.1)", "pre-commit (>=3.2)", "rtoml"]
-doc = ["nb2plots (>=0.7)", "nbconvert (<7.9)", "numpydoc (>=1.6)", "pillow (>=9.4)", "pydata-sphinx-theme (>=0.14)", "sphinx (>=7)", "sphinx-gallery (>=0.14)", "texext (>=0.6.7)"]
-extra = ["lxml (>=4.6)", "pydot (>=1.4.2)", "pygraphviz (>=1.11)", "sympy (>=1.10)"]
+default = ["matplotlib (>=3.6)", "numpy (>=1.23)", "pandas (>=1.4)", "scipy (>=1.9,!=1.11.0,!=1.11.1)"]
+developer = ["changelist (==0.5)", "mypy (>=1.1)", "pre-commit (>=3.2)", "rtoml"]
+doc = ["myst-nb (>=1.0)", "numpydoc (>=1.7)", "pillow (>=9.4)", "pydata-sphinx-theme (>=0.14)", "sphinx (>=7)", "sphinx-gallery (>=0.14)", "texext (>=0.6.7)"]
+extra = ["lxml (>=4.6)", "pydot (>=2.0)", "pygraphviz (>=1.12)", "sympy (>=1.10)"]
 test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"]
 
 [[package]]
@@ -2092,6 +2114,16 @@ files = [
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 ]
 
+[[package]]
+name = "paginate"
+version = "0.5.6"
+description = "Divides large result sets into pages for easier browsing"
+optional = false
+python-versions = "*"
+files = [
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+]
+
 [[package]]
 name = "pandas"
 version = "2.0.3"
@@ -2198,28 +2230,29 @@ files = [
 
 [[package]]
 name = "platformdirs"
-version = "4.2.0"
-description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+version = "4.2.2"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
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 test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)"]
+type = ["mypy (>=1.8)"]
 
 [[package]]
 name = "pluggy"
-version = "1.4.0"
+version = "1.5.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -2256,13 +2289,13 @@ requests = ">=2.28.1,<3.0.0"
 
 [[package]]
 name = "prefixmaps"
-version = "0.2.2"
+version = "0.2.4"
 description = "A python library for retrieving semantic prefix maps"
 optional = false
-python-versions = ">=3.8,<4.0"
+python-versions = "<4.0,>=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -2317,6 +2350,54 @@ files = [
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 ]
 
+[[package]]
+name = "pyarrow"
+version = "15.0.2"
+description = "Python library for Apache Arrow"
+optional = false
+python-versions = ">=3.8"
+files = [
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+]
+
+[package.dependencies]
+numpy = ">=1.16.6,<2"
+
 [[package]]
 name = "pyasn1"
 version = "0.6.0"
@@ -2344,18 +2425,18 @@ pyasn1 = ">=0.4.6,<0.7.0"
 
 [[package]]
 name = "pydantic"
-version = "2.6.4"
+version = "2.7.1"
 description = "Data validation using Python type hints"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 annotated-types = ">=0.4.0"
-pydantic-core = "2.16.3"
+pydantic-core = "2.18.2"
 typing-extensions = ">=4.6.1"
 
 [package.extras]
@@ -2363,90 +2444,90 @@ email = ["email-validator (>=2.0.0)"]
 
 [[package]]
 name = "pydantic-core"
-version = "2.16.3"
-description = ""
+version = "2.18.2"
+description = "Core functionality for Pydantic validation and serialization"
 optional = false
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@@ -2454,17 +2535,16 @@ typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0"
 
 [[package]]
 name = "pygments"
-version = "2.17.2"
+version = "2.18.0"
 description = "Pygments is a syntax highlighting package written in Python."
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 windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
@@ -2484,17 +2564,17 @@ jsonasobj = ">=1.2.1"
 
 [[package]]
 name = "pymdown-extensions"
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+version = "10.8.1"
 description = "Extension pack for Python Markdown."
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 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
-markdown = ">=3.5"
+markdown = ">=3.6"
 pyyaml = "*"
 
 [package.extras]
@@ -2620,13 +2700,13 @@ test = ["pytest", "pytest-cov"]
 
 [[package]]
 name = "pytest"
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+version = "8.2.0"
 description = "pytest: simple powerful testing with Python"
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 [package.dependencies]
@@ -2634,11 +2714,11 @@ colorama = {version = "*", markers = "sys_platform == \"win32\""}
 exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
 iniconfig = "*"
 packaging = "*"
-pluggy = ">=0.12,<2.0"
-tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
+pluggy = ">=1.5,<2.0"
+tomli = {version = ">=1", markers = "python_version < \"3.11\""}
 
 [package.extras]
-testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
+dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
 [[package]]
 name = "pytest-logging"
@@ -2674,6 +2754,7 @@ description = "A pure Python implementation of the trie data structure."
 optional = false
 python-versions = "*"
 files = [
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 name = "referencing"
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 [package.dependencies]
 attrs = ">=22.2.0"
 rpds-py = ">=0.7.0"
 
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+    {file = "scipy-1.13.0.tar.gz", hash = "sha256:58569af537ea29d3f78e5abd18398459f195546bb3be23d16677fb26616cc11e"},
 ]
 
+[package.dependencies]
+numpy = ">=1.22.4,<2.3"
+
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mypy (==1.9)", "packaging (>=23.2)", "pip (>=19.1)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff (>=0.2.1)", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
-testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.2)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
+dev = ["cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy", "pycodestyle", "pydevtool", "rich-click", "ruff", "types-psutil", "typing_extensions"]
+doc = ["jupyterlite-pyodide-kernel", "jupyterlite-sphinx (>=0.12.0)", "jupytext", "matplotlib (>=3.5)", "myst-nb", "numpydoc", "pooch", "pydata-sphinx-theme (>=0.15.2)", "sphinx (>=5.0.0)", "sphinx-design (>=0.4.0)"]
+test = ["array-api-strict", "asv", "gmpy2", "hypothesis (>=6.30)", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
 
 [[package]]
 name = "sh"
@@ -3217,13 +3399,13 @@ files = [
 
 [[package]]
 name = "shellingham"
-version = "1.4.0"
+version = "1.5.4"
 description = "Tool to Detect Surrounding Shell"
 optional = false
-python-versions = "!=3.0,!=3.1,!=3.2,!=3.3,>=2.6"
+python-versions = ">=3.7"
 files = [
-    {file = "shellingham-1.4.0-py2.py3-none-any.whl", hash = "sha256:536b67a0697f2e4af32ab176c00a50ac2899c5a05e0d8e2dadac8e58888283f9"},
-    {file = "shellingham-1.4.0.tar.gz", hash = "sha256:4855c2458d6904829bd34c299f11fdeed7cfefbf8a2c522e4caea6cd76b3171e"},
+    {file = "shellingham-1.5.4-py2.py3-none-any.whl", hash = "sha256:7ecfff8f2fd72616f7481040475a65b2bf8af90a56c89140852d1120324e8686"},
+    {file = "shellingham-1.5.4.tar.gz", hash = "sha256:8dbca0739d487e5bd35ab3ca4b36e11c4078f3a234bfce294b0a0291363404de"},
 ]
 
 [[package]]
@@ -3322,20 +3504,20 @@ pandas = ["pandas (>=1.3.5)"]
 
 [[package]]
 name = "sphinx"
-version = "7.2.6"
+version = "7.3.7"
 description = "Python documentation generator"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "sphinx-7.2.6-py3-none-any.whl", hash = "sha256:1e09160a40b956dc623c910118fa636da93bd3ca0b9876a7b3df90f07d691560"},
-    {file = "sphinx-7.2.6.tar.gz", hash = "sha256:9a5160e1ea90688d5963ba09a2dcd8bdd526620edbb65c328728f1b2228d5ab5"},
+    {file = "sphinx-7.3.7-py3-none-any.whl", hash = "sha256:413f75440be4cacf328f580b4274ada4565fb2187d696a84970c23f77b64d8c3"},
+    {file = "sphinx-7.3.7.tar.gz", hash = "sha256:a4a7db75ed37531c05002d56ed6948d4c42f473a36f46e1382b0bd76ca9627bc"},
 ]
 
 [package.dependencies]
-alabaster = ">=0.7,<0.8"
+alabaster = ">=0.7.14,<0.8.0"
 babel = ">=2.9"
 colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
-docutils = ">=0.18.1,<0.21"
+docutils = ">=0.18.1,<0.22"
 imagesize = ">=1.3"
 Jinja2 = ">=3.0"
 packaging = ">=21.0"
@@ -3348,11 +3530,12 @@ sphinxcontrib-htmlhelp = ">=2.0.0"
 sphinxcontrib-jsmath = "*"
 sphinxcontrib-qthelp = "*"
 sphinxcontrib-serializinghtml = ">=1.1.9"
+tomli = {version = ">=2", markers = "python_version < \"3.11\""}
 
 [package.extras]
 docs = ["sphinxcontrib-websupport"]
-lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-simplify", "isort", "mypy (>=0.990)", "ruff", "sphinx-lint", "types-requests"]
-test = ["cython (>=3.0)", "filelock", "html5lib", "pytest (>=4.6)", "setuptools (>=67.0)"]
+lint = ["flake8 (>=3.5.0)", "importlib_metadata", "mypy (==1.9.0)", "pytest (>=6.0)", "ruff (==0.3.7)", "sphinx-lint", "tomli", "types-docutils", "types-requests"]
+test = ["cython (>=3.0)", "defusedxml (>=0.7.1)", "pytest (>=6.0)", "setuptools (>=67.0)"]
 
 [[package]]
 name = "sphinxcontrib-applehelp"
@@ -3529,13 +3712,13 @@ sqlcipher = ["sqlcipher3_binary"]
 
 [[package]]
 name = "sssom"
-version = "0.4.5"
+version = "0.4.9"
 description = "Operations on SSSOM mapping tables"
 optional = false
 python-versions = "<4.0,>=3.8"
 files = [
-    {file = "sssom-0.4.5-py3-none-any.whl", hash = "sha256:8fd582082b9b5e748f05d1831362f1af9f700837a01f1d5fca09361519657d54"},
-    {file = "sssom-0.4.5.tar.gz", hash = "sha256:753b3481083a6a62d39f11d6dc18e6038fc0edaa27929e0881e1c7fee8f8bcbe"},
+    {file = "sssom-0.4.9-py3-none-any.whl", hash = "sha256:54af580957947175dfcc96e7ce2323ea3b476eb58b6e7a2e95d8c3e10c6393f4"},
+    {file = "sssom-0.4.9.tar.gz", hash = "sha256:16674d58aa37ab82c1f6f69d317c0bdc6eedd59e8d809fcbc87f5f1e1eefdbf1"},
 ]
 
 [package.dependencies]
@@ -3543,7 +3726,7 @@ click = ">=8.1.6"
 curies = ">=0.7.3"
 deprecation = ">=2.1.0,<3.0.0"
 importlib-resources = ">=6.1.1,<7.0.0"
-linkml-runtime = ">=1.5.5"
+linkml-runtime = ">=1.7.5,<2.0.0"
 networkx = {version = ">=3.1", extras = ["networkx"]}
 pandas = ">1.0.3"
 pansql = {version = ">=0.0.1", extras = ["pansql"]}
@@ -3551,23 +3734,22 @@ pyyaml = ">=6.0.1,<7.0.0"
 rdflib = ">=6.0.0"
 scipy = {version = "*", extras = ["scipy"]}
 sparqlwrapper = ">=2.0.0"
-sssom-schema = ">=0.14.0"
+sssom-schema = ">=0.15.2,<0.16.0"
 validators = ">=0.20.0"
 
 [[package]]
 name = "sssom-schema"
-version = "0.15.0"
+version = "0.15.2"
 description = "SSSOM is a Simple Standard for Sharing Ontology Mappings."
 optional = false
-python-versions = ">=3.7.6,<4.0.0"
+python-versions = "<4.0,>=3.8"
 files = [
-    {file = "sssom_schema-0.15.0-py3-none-any.whl", hash = "sha256:0ba81a0fe76d28a2c65d65a99e0cd17d8dd08274f9735776a70c8d2f3734e901"},
-    {file = "sssom_schema-0.15.0.tar.gz", hash = "sha256:35d56ba6d0350b1e07df2789aebac9c5c70b0888bf88ec3c0592c89e9c13d228"},
+    {file = "sssom_schema-0.15.2-py3-none-any.whl", hash = "sha256:41112586160d5e57a7cfedab22dfd0c21d1e3e1a86805f7fe31918a9b664ca15"},
+    {file = "sssom_schema-0.15.2.tar.gz", hash = "sha256:c759ee8f9e4a7e5e8249b58198189b2e48e297ff31a918d4af64a89ed30938da"},
 ]
 
 [package.dependencies]
 linkml-runtime = "*"
-mkdocs-mermaid2-plugin = ">=0.6.0,<0.7.0"
 
 [[package]]
 name = "stringcase"
@@ -3603,13 +3785,13 @@ files = [
 
 [[package]]
 name = "tox"
-version = "4.14.2"
+version = "4.15.0"
 description = "tox is a generic virtualenv management and test command line tool"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "tox-4.14.2-py3-none-any.whl", hash = "sha256:2900c4eb7b716af4a928a7fdc2ed248ad6575294ed7cfae2ea41203937422847"},
-    {file = "tox-4.14.2.tar.gz", hash = "sha256:0defb44f6dafd911b61788325741cc6b2e12ea71f987ac025ad4d649f1f1a104"},
+    {file = "tox-4.15.0-py3-none-any.whl", hash = "sha256:300055f335d855b2ab1b12c5802de7f62a36d4fd53f30bd2835f6a201dda46ea"},
+    {file = "tox-4.15.0.tar.gz", hash = "sha256:7a0beeef166fbe566f54f795b4906c31b428eddafc0102ac00d20998dd1933f6"},
 ]
 
 [package.dependencies]
@@ -3630,13 +3812,13 @@ testing = ["build[virtualenv] (>=1.0.3)", "covdefaults (>=2.3)", "detect-test-po
 
 [[package]]
 name = "tqdm"
-version = "4.66.2"
+version = "4.66.4"
 description = "Fast, Extensible Progress Meter"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "tqdm-4.66.2-py3-none-any.whl", hash = "sha256:1ee4f8a893eb9bef51c6e35730cebf234d5d0b6bd112b0271e10ed7c24a02bd9"},
-    {file = "tqdm-4.66.2.tar.gz", hash = "sha256:6cd52cdf0fef0e0f543299cfc96fec90d7b8a7e88745f411ec33eb44d5ed3531"},
+    {file = "tqdm-4.66.4-py3-none-any.whl", hash = "sha256:b75ca56b413b030bc3f00af51fd2c1a1a5eac6a0c1cca83cbb37a5c52abce644"},
+    {file = "tqdm-4.66.4.tar.gz", hash = "sha256:e4d936c9de8727928f3be6079590e97d9abfe8d39a590be678eb5919ffc186bb"},
 ]
 
 [package.dependencies]
@@ -3650,39 +3832,20 @@ telegram = ["requests"]
 
 [[package]]
 name = "typer"
-version = "0.7.0"
+version = "0.12.3"
 description = "Typer, build great CLIs. Easy to code. Based on Python type hints."
 optional = false
-python-versions = ">=3.6"
-files = [
-    {file = "typer-0.7.0-py3-none-any.whl", hash = "sha256:b5e704f4e48ec263de1c0b3a2387cd405a13767d2f907f44c1a08cbad96f606d"},
-    {file = "typer-0.7.0.tar.gz", hash = "sha256:ff797846578a9f2a201b53442aedeb543319466870fbe1c701eab66dd7681165"},
-]
-
-[package.dependencies]
-click = ">=7.1.1,<9.0.0"
-
-[package.extras]
-all = ["colorama (>=0.4.3,<0.5.0)", "rich (>=10.11.0,<13.0.0)", "shellingham (>=1.3.0,<2.0.0)"]
-dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "pre-commit (>=2.17.0,<3.0.0)"]
-doc = ["cairosvg (>=2.5.2,<3.0.0)", "mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "pillow (>=9.3.0,<10.0.0)"]
-test = ["black (>=22.3.0,<23.0.0)", "coverage (>=6.2,<7.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "pytest (>=4.4.0,<8.0.0)", "pytest-cov (>=2.10.0,<5.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "pytest-xdist (>=1.32.0,<4.0.0)", "rich (>=10.11.0,<13.0.0)", "shellingham (>=1.3.0,<2.0.0)"]
-
-[[package]]
-name = "typer-cli"
-version = "0.0.13"
-description = "Run Typer scripts with completion, without having to create a package, using Typer CLI."
-optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "typer_cli-0.0.13-py3-none-any.whl", hash = "sha256:5ae0f99dce8f8f9669137a2c98eb42485cd4412e0ec225c8eb29ce8ac3378731"},
-    {file = "typer_cli-0.0.13.tar.gz", hash = "sha256:f5b85764e56fb3fe835ed008ad5bc7db4961f7bcce1f1c1698ac46b6c5d9b86f"},
+    {file = "typer-0.12.3-py3-none-any.whl", hash = "sha256:070d7ca53f785acbccba8e7d28b08dcd88f79f1fbda035ade0aecec71ca5c914"},
+    {file = "typer-0.12.3.tar.gz", hash = "sha256:49e73131481d804288ef62598d97a1ceef3058905aa536a1134f90891ba35482"},
 ]
 
 [package.dependencies]
-colorama = ">=0.4.3,<=0.5.0"
-shellingham = ">=1.3.2,<=1.4.0"
-typer = ">=0.4.0,<=0.7.0"
+click = ">=8.0.0"
+rich = ">=10.11.0"
+shellingham = ">=1.3.0"
+typing-extensions = ">=3.7.4.3"
 
 [[package]]
 name = "types-python-dateutil"
@@ -3697,13 +3860,13 @@ files = [
 
 [[package]]
 name = "typing-extensions"
-version = "4.10.0"
+version = "4.11.0"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "typing_extensions-4.10.0-py3-none-any.whl", hash = "sha256:69b1a937c3a517342112fb4c6df7e72fc39a38e7891a5730ed4985b5214b5475"},
-    {file = "typing_extensions-4.10.0.tar.gz", hash = "sha256:b0abd7c89e8fb96f98db18d86106ff1d90ab692004eb746cf6eda2682f91b3cb"},
+    {file = "typing_extensions-4.11.0-py3-none-any.whl", hash = "sha256:c1f94d72897edaf4ce775bb7558d5b79d8126906a14ea5ed1635921406c0387a"},
+    {file = "typing_extensions-4.11.0.tar.gz", hash = "sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0"},
 ]
 
 [[package]]
@@ -3766,13 +3929,13 @@ test = ["flake8 (>=2.4.0)", "isort (>=4.2.2)", "pytest (>=2.2.3)"]
 
 [[package]]
 name = "virtualenv"
-version = "20.25.1"
+version = "20.26.2"
 description = "Virtual Python Environment builder"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "virtualenv-20.25.1-py3-none-any.whl", hash = "sha256:961c026ac520bac5f69acb8ea063e8a4f071bcc9457b9c1f28f6b085c511583a"},
-    {file = "virtualenv-20.25.1.tar.gz", hash = "sha256:e08e13ecdca7a0bd53798f356d5831434afa5b07b93f0abdf0797b7a06ffe197"},
+    {file = "virtualenv-20.26.2-py3-none-any.whl", hash = "sha256:a624db5e94f01ad993d476b9ee5346fdf7b9de43ccaee0e0197012dc838a0e9b"},
+    {file = "virtualenv-20.26.2.tar.gz", hash = "sha256:82bf0f4eebbb78d36ddaee0283d43fe5736b53880b8a8cdcd37390a07ac3741c"},
 ]
 
 [package.dependencies]
@@ -3781,7 +3944,7 @@ filelock = ">=3.12.2,<4"
 platformdirs = ">=3.9.1,<5"
 
 [package.extras]
-docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
+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)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
 
 [[package]]
@@ -3842,17 +4005,17 @@ tests = ["pytest", "pytest-cov"]
 
 [[package]]
 name = "websocket-client"
-version = "1.7.0"
+version = "1.8.0"
 description = "WebSocket client for Python with low level API options"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "websocket-client-1.7.0.tar.gz", hash = "sha256:10e511ea3a8c744631d3bd77e61eb17ed09304c413ad42cf6ddfa4c7787e8fe6"},
-    {file = "websocket_client-1.7.0-py3-none-any.whl", hash = "sha256:f4c3d22fec12a2461427a29957ff07d35098ee2d976d3ba244e688b8b4057588"},
+    {file = "websocket_client-1.8.0-py3-none-any.whl", hash = "sha256:17b44cc997f5c498e809b22cdf2d9c7a9e71c02c8cc2b6c56e7c2d1239bfa526"},
+    {file = "websocket_client-1.8.0.tar.gz", hash = "sha256:3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da"},
 ]
 
 [package.extras]
-docs = ["Sphinx (>=6.0)", "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"]
 
@@ -3969,20 +4132,20 @@ dev = ["doc8", "flake8", "flake8-import-order", "rstcheck[sphinx]", "sphinx"]
 
 [[package]]
 name = "zipp"
-version = "3.18.1"
+version = "3.18.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"},
-    {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"},
+    {file = "zipp-3.18.2-py3-none-any.whl", hash = "sha256:dce197b859eb796242b0622af1b8beb0a722d52aa2f57133ead08edd5bf5374e"},
+    {file = "zipp-3.18.2.tar.gz", hash = "sha256:6278d9ddbcfb1f1089a88fde84481528b07b0e10474e09dcfe53dad4069fa059"},
 ]
 
 [package.extras]
 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)"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "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 = ">=3.10,<3.12"
-content-hash = "124411a2f853848695af9adf07d18c32ea666412954c689edf45894400daa226"
+python-versions = "^3.10"
+content-hash = "00afbdf0968eb1f108d7c3f61fb0c8509f5e4914e9d89893775d2c99e3baee96"
diff --git a/pyproject.toml b/pyproject.toml
index fccf2ab6..007ab6bb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,18 +15,16 @@ packages = [
 ]
 
 [tool.poetry.dependencies]
-python = ">=3.10,<3.12"
-# biolink-model = "^4.2.0"
-# When 4.2.0 (or any release after 4.1.6) is released, we can remove the git dependency
-biolink-model = { git = "https://github.com/biolink/biolink-model", branch = "master" }
+python = "^3.10"
+biolink-model = "^4.2.0"
 bmt = "^1.0.15"
 cat-merge = "0.2.1"
 closurizer = "0.5.1"
 kghub-downloader = "^0.3.2"
-kgx = { git = "https://github.com/biolink/kgx", branch = "master" } # ">=2.1"
-koza = ">=0.5.2"
-linkml = "1.6.3"
-linkml-solr = "0.1.5" # "^0.1.3"
+kgx = ">=2.4.0"
+koza = ">=0.6.0"
+linkml = "^1.7.8"
+linkml-solr = ">=0.1.5"
 multi-indexer = "0.0.5"
 # Other Dependencies
 botocore = "^1.31"
@@ -34,18 +32,19 @@ importlib-metadata = ">=4.6.1"
 loguru = "*"
 pydantic = "^2.5"
 sh = "^1.14.3"
-typer = "^0.7"
-typer-cli = "^0.0.13"
+typer = "^0.12"
 yamllint = "^1.35.1"
-linkml-runtime = "1.6.3"
+linkml-runtime = "^1.7.5"
+# Remove this once cat-merge fixes its pandas dependency
+pandas = "2.0.3"
 
 [tool.poetry.group.dev]
 optional = true
 
 [tool.poetry.group.dev.dependencies]
-pytest = "^7.1.1"
-mkdocs = "^1.3.0"
-mkdocs-material = "^8.2.9"
+pytest = "^8.1.1"
+mkdocs = "^1.4"
+mkdocs-material = ">=9.5"
 black = "^24.3"
 ruff = "*"
 
@@ -57,11 +56,14 @@ requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
 
 [tool.black]
-line_length = 120
+line-length = 120
 skip-string-normalization = true
 
 [tool.ruff]
 line-length = 120
 ignore = [
     "F541", # f-strings with no placeholders
-]
\ No newline at end of file
+
+]
+[tool.ruff.lint.per-file-ignores]
+"tests/**.py" = ["F811"] # redefinition of unused imports (mock_koza)
diff --git a/src/monarch_ingest/__init__.py b/src/monarch_ingest/__init__.py
index 32995380..a75eb4da 100644
--- a/src/monarch_ingest/__init__.py
+++ b/src/monarch_ingest/__init__.py
@@ -1,2 +1,3 @@
 from importlib import metadata
-__version__ = metadata.version("monarch_ingest")
\ No newline at end of file
+
+__version__ = metadata.version("monarch_ingest")
diff --git a/src/monarch_ingest/cli_utils.py b/src/monarch_ingest/cli_utils.py
index eea60384..320722c4 100644
--- a/src/monarch_ingest/cli_utils.py
+++ b/src/monarch_ingest/cli_utils.py
@@ -1,7 +1,6 @@
 import csv
 import gc
 import os
-import pkgutil
 import sys
 import tarfile
 import yaml
@@ -18,7 +17,7 @@
 from cat_merge.merge import merge
 from closurizer.closurizer import add_closure
 from kgx.cli.cli_utils import transform as kgx_transform
-from koza.cli_runner import transform_source
+from koza.cli_utils import transform_source
 from koza.model.config.source_config import OutputFormat
 from linkml_runtime.utils.formatutils import camelcase
 
@@ -192,7 +191,7 @@ def transform_phenio(
                 "primary_knowledge_source",
                 "aggregator_knowledge_source",
                 "knowledge_level",
-                "agent_type"
+                "agent_type",
             ]
         ),
         axis=1,
@@ -524,15 +523,9 @@ def do_release(dir: str = OUTPUT_DIR, kghub: bool = False):
             )
             # index files on s3 after upload
             sh.multi_indexer(
-                *f"-v --prefix https://kghub.io/kg-monarch/ -b kg-hub-public-data -r kg-monarch -x".split(
-                    " "
-                )
-            )
-            sh.gsutil(
-                *f"-q -m cp -a public-read ./index.html s3://kg-hub-public-data/kg-monarch".split(
-                    " "
-                )
+                *f"-v --prefix https://kghub.io/kg-monarch/ -b kg-hub-public-data -r kg-monarch -x".split(" ")
             )
+            sh.gsutil(*f"-q -m cp -a public-read ./index.html s3://kg-hub-public-data/kg-monarch".split(" "))
 
         logger.debug("Cleaning up files...")
         sh.rm(f"output/{release_ver}")
diff --git a/src/monarch_ingest/ingests/alliance/gene.py b/src/monarch_ingest/ingests/alliance/gene.py
index 62b9d107..2bab63fa 100644
--- a/src/monarch_ingest/ingests/alliance/gene.py
+++ b/src/monarch_ingest/ingests/alliance/gene.py
@@ -1,4 +1,4 @@
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 from source_translation import source_map
 
 from biolink_model.datamodel.pydanticmodel_v2 import Gene
@@ -48,21 +48,18 @@
         id=gene_id,
         symbol=row["symbol"],
         name=row["symbol"],
-        full_name=row["name"].replace("\r",""), # Replacement to remove stray carriage returns in XenBase files
+        full_name=row["name"].replace("\r", ""),  # Replacement to remove stray carriage returns in XenBase files
         # No place in the schema for gene type (SO term) right now
         # type=row["soTermId"],
         in_taxon=[in_taxon],
         in_taxon_label=in_taxon_label,
-        provided_by=[source]
+        provided_by=[source],
     )
 
     if row["basicGeneticEntity"]["crossReferences"]:
-        gene.xref = [
-            koza_app.curie_cleaner.clean(xref["id"])
-            for xref in row["basicGeneticEntity"]["crossReferences"]
-        ]
+        gene.xref = [koza_app.curie_cleaner.clean(xref["id"]) for xref in row["basicGeneticEntity"]["crossReferences"]]
     if "synonyms" in row["basicGeneticEntity"].keys():
         # more handling for errant carriage returns
-        gene.synonym = [synonym.replace("\r","") for synonym in row["basicGeneticEntity"]["synonyms"] ]
+        gene.synonym = [synonym.replace("\r", "") for synonym in row["basicGeneticEntity"]["synonyms"]]
 
     koza_app.write(gene)
diff --git a/src/monarch_ingest/ingests/alliance/gene_to_expression.py b/src/monarch_ingest/ingests/alliance/gene_to_expression.py
index cb6d0dd0..137f5ebf 100644
--- a/src/monarch_ingest/ingests/alliance/gene_to_expression.py
+++ b/src/monarch_ingest/ingests/alliance/gene_to_expression.py
@@ -1,7 +1,6 @@
-
 import uuid
 
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 from source_translation import source_map
 
 from biolink_model.datamodel.pydanticmodel_v2 import GeneToExpressionSiteAssociation, KnowledgeLevelEnum, AgentTypeEnum
@@ -33,22 +32,19 @@
         #       but may have an UBERON term that we can use
         # stage_term_id = get_data(row, "whenExpressed.stageUberonSlimTerm.uberonTerm")
 
-
-
         publication_ids = [get_data(row, "evidence.publicationId")]
 
         xref = get_data(row, "crossReference.id")
         if xref:
             publication_ids.append(xref)
 
-
         # Our current ingest policy is to first use a reported Anatomical structure term...
         if anatomical_entity_id:
             koza_app.write(
                 GeneToExpressionSiteAssociation(
                     id="uuid:" + str(uuid.uuid1()),
                     subject=gene_id,
-                    predicate='biolink:expressed_in',
+                    predicate="biolink:expressed_in",
                     object=anatomical_entity_id,
                     stage_qualifier=stage_term_id,
                     qualifiers=([get_data(row, "assay")] if get_data(row, "assay") else None),
@@ -56,7 +52,7 @@
                     aggregator_knowledge_source=["infores:monarchinitiative", "infores:alliancegenome"],
                     primary_knowledge_source=source,
                     knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-                    agent_type=AgentTypeEnum.manual_agent
+                    agent_type=AgentTypeEnum.manual_agent,
                 )
             )
 
@@ -67,7 +63,7 @@
                 GeneToExpressionSiteAssociation(
                     id="uuid:" + str(uuid.uuid1()),
                     subject=gene_id,
-                    predicate='biolink:expressed_in',
+                    predicate="biolink:expressed_in",
                     object=cellular_component_id,
                     stage_qualifier=stage_term_id,
                     qualifiers=([get_data(row, "assay")] if get_data(row, "assay") else None),
@@ -75,7 +71,7 @@
                     aggregator_knowledge_source=["infores:monarchinitiative", "infores:alliancegenome"],
                     primary_knowledge_source=source,
                     knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-                    agent_type=AgentTypeEnum.manual_agent
+                    agent_type=AgentTypeEnum.manual_agent,
                 )
             )
         else:
@@ -85,6 +81,4 @@
             )
 
     except Exception as exc:
-        logger.error(
-            f"Alliance gene expression ingest parsing exception for data row:\n\t'{str(row)}'\n{str(exc)}"
-        )
+        logger.error(f"Alliance gene expression ingest parsing exception for data row:\n\t'{str(row)}'\n{str(exc)}")
diff --git a/src/monarch_ingest/ingests/alliance/gene_to_phenotype.py b/src/monarch_ingest/ingests/alliance/gene_to_phenotype.py
index 5f69dba7..ee6a71c2 100644
--- a/src/monarch_ingest/ingests/alliance/gene_to_phenotype.py
+++ b/src/monarch_ingest/ingests/alliance/gene_to_phenotype.py
@@ -2,10 +2,14 @@
 
 import uuid
 
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 from source_translation import source_map
 
-from biolink_model.datamodel.pydanticmodel_v2 import GeneToPhenotypicFeatureAssociation, KnowledgeLevelEnum, AgentTypeEnum
+from biolink_model.datamodel.pydanticmodel_v2 import (
+    GeneToPhenotypicFeatureAssociation,
+    KnowledgeLevelEnum,
+    AgentTypeEnum,
+)
 
 
 from loguru import logger
@@ -42,9 +46,8 @@
             publications=[row["evidence"]["publicationId"]],
             aggregator_knowledge_source=["infores:monarchinitiative", "infores:alliancegenome"],
             primary_knowledge_source=source,
-            knowledge_level = KnowledgeLevelEnum.knowledge_assertion,
-            agent_type = AgentTypeEnum.manual_agent
-
+            knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
+            agent_type=AgentTypeEnum.manual_agent,
         )
 
         if "conditionRelations" in row.keys() and row["conditionRelations"] is not None:
diff --git a/src/monarch_ingest/ingests/alliance/publication.py b/src/monarch_ingest/ingests/alliance/publication.py
index 15554230..eadadeae 100644
--- a/src/monarch_ingest/ingests/alliance/publication.py
+++ b/src/monarch_ingest/ingests/alliance/publication.py
@@ -1,4 +1,4 @@
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 from dateutil.parser import parse, ParserError
 
 from biolink_model.datamodel.pydanticmodel_v2 import Publication
@@ -9,9 +9,7 @@
 while (row := koza_app.get_row()) is not None:
 
     # TODO: remove DOI exclusion once curie regex can handle them
-    xrefs = [
-        xref["id"] for xref in row["crossReferences"] if not xref["id"].startswith("DOI:")
-    ]
+    xrefs = [xref["id"] for xref in row["crossReferences"] if not xref["id"].startswith("DOI:")]
 
     # Parse creation date for different time formats
     creation_date = row["datePublished"]
@@ -21,10 +19,12 @@
         creation_date = None
 
     source: str
-    if 'MODReferenceTypes' in row and \
-            len(row['MODReferenceTypes']) > 0 and \
-            'source' in row['MODReferenceTypes'][0] and \
-            row['MODReferenceTypes'][0]['source'] in source_map:
+    if (
+        'MODReferenceTypes' in row
+        and len(row['MODReferenceTypes']) > 0
+        and 'source' in row['MODReferenceTypes'][0]
+        and row['MODReferenceTypes'][0]['source'] in source_map
+    ):
         source = source_map[row['MODReferenceTypes'][0]['source']]
     else:  # default source
         source = "infores:alliancegenome"
@@ -36,7 +36,7 @@
         xref=xrefs,
         type=[koza_app.translation_table.resolve_term("publication")],
         creation_date=creation_date,
-        provided_by=[source]
+        provided_by=[source],
     )
 
     if "authors" in row.keys():
diff --git a/src/monarch_ingest/ingests/bgee/gene_to_expression.py b/src/monarch_ingest/ingests/bgee/gene_to_expression.py
index e049a62f..913f5366 100644
--- a/src/monarch_ingest/ingests/bgee/gene_to_expression.py
+++ b/src/monarch_ingest/ingests/bgee/gene_to_expression.py
@@ -1,4 +1,4 @@
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 from monarch_ingest.ingests.bgee.gene_to_expression_utils import process_koza_source
 
 
diff --git a/src/monarch_ingest/ingests/bgee/gene_to_expression_utils.py b/src/monarch_ingest/ingests/bgee/gene_to_expression_utils.py
index a864d78c..36a541a8 100644
--- a/src/monarch_ingest/ingests/bgee/gene_to_expression_utils.py
+++ b/src/monarch_ingest/ingests/bgee/gene_to_expression_utils.py
@@ -8,17 +8,17 @@
 def filter_group_by_rank(rows: List, col: str, largest_n: int = 0, smallest_n: int = 0) -> List[Dict]:
     """Function to filter a group of Koza rows by values largest or smallest values in column:
 
-        Get the top and/or bottom n rows ranked based on column:
+    Get the top and/or bottom n rows ranked based on column:
 
-        Args:
-            rows (List): The Koza object to read rows from.
-            col (str): The column to perform ranking and filtering.
-            largest_n (int): The number of rows to return from the largest ranking.
-            smallest_n (int): The number of rows to return from the smallest ranking.
+    Args:
+        rows (List): The Koza object to read rows from.
+        col (str): The column to perform ranking and filtering.
+        largest_n (int): The number of rows to return from the largest ranking.
+        smallest_n (int): The number of rows to return from the smallest ranking.
 
 
-        Returns:
-            List[Dict]: Returns a list of n rows in Koza dict format sorted by rank in column.
+    Returns:
+        List[Dict]: Returns a list of n rows in Koza dict format sorted by rank in column.
     """
     df = pd.DataFrame(rows)
     largest_df = df.nlargest(largest_n, col, keep="first")
@@ -29,11 +29,11 @@ def filter_group_by_rank(rows: List, col: str, largest_n: int = 0, smallest_n: i
 def write_group(rows: List, koza_app: KozaApp):
     """Function to write a group of Koza rows to KozaApp object output:
 
-        Write list of rows in Koza format to KozaApp output:
+    Write list of rows in Koza format to KozaApp output:
 
-        Args:
-            rows (List): A list of rows to output to KozaApp.
-            koza_app (KozaApp): The KozaApp to use for output of rows.
+    Args:
+        rows (List): A list of rows to output to KozaApp.
+        koza_app (KozaApp): The KozaApp to use for output of rows.
     """
     for row in rows:
         association = GeneToExpressionSiteAssociation(
@@ -44,7 +44,8 @@ def write_group(rows: List, koza_app: KozaApp):
             primary_knowledge_source="infores:bgee",
             aggregator_knowledge_source=["infores:monarchinitiative"],
             knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-            agent_type=AgentTypeEnum.not_provided)
+            agent_type=AgentTypeEnum.not_provided,
+        )
 
         koza_app.write(association)
 
@@ -52,15 +53,15 @@ def write_group(rows: List, koza_app: KozaApp):
 def get_row_group(koza_app: KozaApp, col: str = 'Gene ID') -> Union[List, None]:
     """Function to read a group of Koza rows from a KozaApp:
 
-        Get a group of rows from KozaApp grouped on column:
+    Get a group of rows from KozaApp grouped on column:
 
-        Args:
-            koza_app (KozaApp): The Koza object to read rows from.
-            col (str): The column to group rows based on.
+    Args:
+        koza_app (KozaApp): The Koza object to read rows from.
+        col (str): The column to group rows based on.
 
 
-        Returns:
-            List/None: Returns a list of rows in Koza dict format grouped by column.
+    Returns:
+        List/None: Returns a list of rows in Koza dict format grouped by column.
     """
     if not hasattr(koza_app, 'previous_row'):
         koza_app.previous_row = koza_app.get_row()
@@ -81,11 +82,11 @@ def get_row_group(koza_app: KozaApp, col: str = 'Gene ID') -> Union[List, None]:
 def process_koza_source(koza_app: KozaApp):
     """Function to filter a group of Koza rows by values largest or smallest values in column:
 
-        Get the top and/or bottom n rows ranked based on column:
+    Get the top and/or bottom n rows ranked based on column:
 
-        Args:
-            koza_app (KozaApp): The Koza object to process for ingest.
+    Args:
+        koza_app (KozaApp): The Koza object to process for ingest.
     """
-    while(row_group := get_row_group(koza_app)) is not None:
+    while (row_group := get_row_group(koza_app)) is not None:
         rank_filtered_rows = filter_group_by_rank(row_group, col='Expression rank', smallest_n=10)
         write_group(rank_filtered_rows, koza_app)
diff --git a/src/monarch_ingest/ingests/biogrid/biogrid.py b/src/monarch_ingest/ingests/biogrid/biogrid.py
index 7137e9fa..914921ab 100644
--- a/src/monarch_ingest/ingests/biogrid/biogrid.py
+++ b/src/monarch_ingest/ingests/biogrid/biogrid.py
@@ -1,5 +1,5 @@
 import uuid
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 from biolink_model.datamodel.pydanticmodel_v2 import PairwiseGeneToGeneInteraction, KnowledgeLevelEnum, AgentTypeEnum
 from biogrid_util import get_gene_id, get_evidence, get_publication_ids
 
@@ -15,8 +15,12 @@
     publications = get_publication_ids(row['Publication Identifiers'])
 
     # Only keep interactions using NCBIGene or UniProtKB identifiers, could also filter on taxid
-    if gid_a.startswith("NCBIGene:") or gid_a.startswith("UniProtKB:") \
-            and gid_b.startswith("NCBIGene:") or gid_b.startswith("UniProtKB:"):
+    if (
+        gid_a.startswith("NCBIGene:")
+        or gid_a.startswith("UniProtKB:")
+        and gid_b.startswith("NCBIGene:")
+        or gid_b.startswith("UniProtKB:")
+    ):
         association = PairwiseGeneToGeneInteraction(
             id="uuid:" + str(uuid.uuid1()),
             subject=gid_a,
@@ -27,7 +31,7 @@
             primary_knowledge_source="infores:biogrid",
             aggregator_knowledge_source=["infores:monarchinitiative"],
             knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-            agent_type=AgentTypeEnum.not_provided
+            agent_type=AgentTypeEnum.not_provided,
         )
 
         koza_app.write(association)
diff --git a/src/monarch_ingest/ingests/biogrid/biogrid_util.py b/src/monarch_ingest/ingests/biogrid/biogrid_util.py
index 1c670cd2..34024482 100644
--- a/src/monarch_ingest/ingests/biogrid/biogrid_util.py
+++ b/src/monarch_ingest/ingests/biogrid/biogrid_util.py
@@ -1,7 +1,7 @@
 """
 Some functions to assist parsing of BioGRID fields.
 """
-from sys import stderr
+
 from typing import List, Optional
 
 from loguru import logger
@@ -14,9 +14,7 @@ def get_gene_id(raw_id: str) -> str:
     :param raw_id: str, raw BioGRID input string (a pseudo-CURIE)
     :return:
     """
-    gid = (raw_id
-           .replace("entrez gene/locuslink:", "NCBIGene:")
-           .replace("uniprot/swiss-prot:", "UniProtKB:"))
+    gid = raw_id.replace("entrez gene/locuslink:", "NCBIGene:").replace("uniprot/swiss-prot:", "UniProtKB:")
 
     return gid
 
@@ -27,14 +25,14 @@ def get_gene_id(raw_id: str) -> str:
     "two hybrid": "ECO:0000024",
     "affinity chromatography technology": "ECO:0000079",
     "genetic interference": "ECO:0000011",
-    "pull down": "ECO:0000025",   # not totally sure about this one
+    "pull down": "ECO:0000025",  # not totally sure about this one
     "enzymatic study": "ECO:0000005",
     "x-ray crystallography": "ECO:0001823",
     "far western blotting": "ECO:0000076",
     "fluorescent resonance energy transfer": "ECO:0001048",
-    "imaging technique": "ECO:0000324",   # not totally sure about this one
+    "imaging technique": "ECO:0000324",  # not totally sure about this one
     "protein complementation assay": "ECO:0006256",  # not totally sure about this one
-    "biochemical": "ECO:0000172"  # not totally sure about this one
+    "biochemical": "ECO:0000172",  # not totally sure about this one
 }
 
 
@@ -54,11 +52,13 @@ def get_evidence(methods: str) -> Optional[List[str]]:
             # databaseName:identifier(methodName)
             method = method.rstrip(")").split('(')[-1]
             if method not in EVIDENCE_CODE_MAPPINGS.keys():
-                err_msg = f"Unknown interaction detection method '{method}'. " +\
-                          "Assigning default code ECO:0000006 == 'experimental evidence', the ECO root."
+                err_msg = (
+                    f"Unknown interaction detection method '{method}'. "
+                    + "Assigning default code ECO:0000006 == 'experimental evidence', the ECO root."
+                )
                 logger.warning(err_msg)
                 EVIDENCE_CODE_MAPPINGS[method] = "ECO:0000006"
-                
+
             evidence_codes.append(EVIDENCE_CODE_MAPPINGS[method])
 
     return evidence_codes if evidence_codes else None
diff --git a/src/monarch_ingest/ingests/ctd/chemical_to_disease.py b/src/monarch_ingest/ingests/ctd/chemical_to_disease.py
index ef4821a4..a053bd0a 100644
--- a/src/monarch_ingest/ingests/ctd/chemical_to_disease.py
+++ b/src/monarch_ingest/ingests/ctd/chemical_to_disease.py
@@ -1,9 +1,12 @@
 import uuid
 
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
-from biolink_model.datamodel.pydanticmodel_v2 import ChemicalToDiseaseOrPhenotypicFeatureAssociation, \
-    KnowledgeLevelEnum, AgentTypeEnum
+from biolink_model.datamodel.pydanticmodel_v2 import (
+    ChemicalToDiseaseOrPhenotypicFeatureAssociation,
+    KnowledgeLevelEnum,
+    AgentTypeEnum,
+)
 from monarch_ingest.constants import BIOLINK_TREATS_OR_APPLIED_OR_STUDIED_TO_TREAT
 
 koza_app = get_koza_app("ctd_chemical_to_disease")
@@ -28,7 +31,7 @@
             aggregator_knowledge_source=["infores:monarchinitiative"],
             primary_knowledge_source="infores:ctd",
             knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-            agent_type=AgentTypeEnum.manual_agent
+            agent_type=AgentTypeEnum.manual_agent,
         )
 
         koza_app.write(association)
diff --git a/src/monarch_ingest/ingests/dictybase/gene.py b/src/monarch_ingest/ingests/dictybase/gene.py
index 16549bc7..a52b2bf9 100644
--- a/src/monarch_ingest/ingests/dictybase/gene.py
+++ b/src/monarch_ingest/ingests/dictybase/gene.py
@@ -1,4 +1,4 @@
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
 from biolink_model.datamodel.pydanticmodel_v2 import Gene
 
@@ -9,12 +9,11 @@
 in_taxon_label = taxon_labels[in_taxon]['label'] if in_taxon in taxon_labels else "Dictyostelium discoideum"
 
 while (row := koza_app.get_row()) is not None:
-    
+
     synonyms = []
     if row['Synonyms'] is not None:
         synonyms = row['Synonyms'].split(", ")
 
-
     gene = Gene(
         id='dictyBase:' + row['GENE ID'],
         symbol=row['Gene Name'],
@@ -23,7 +22,7 @@
         synonym=synonyms,
         in_taxon=[in_taxon],
         in_taxon_label=in_taxon_label,
-        provided_by=["infores:dictybase"]
+        provided_by=["infores:dictybase"],
     )
 
     koza_app.write(gene)
diff --git a/src/monarch_ingest/ingests/dictybase/gene_to_phenotype.py b/src/monarch_ingest/ingests/dictybase/gene_to_phenotype.py
index b4036947..6f0d7f05 100644
--- a/src/monarch_ingest/ingests/dictybase/gene_to_phenotype.py
+++ b/src/monarch_ingest/ingests/dictybase/gene_to_phenotype.py
@@ -1,11 +1,13 @@
 import uuid
-from typing import Optional, Tuple
 
-from koza.cli_runner import get_koza_app
-from monarch_ingest.ingests.dictybase.utils import parse_gene_id, parse_phenotypes
+from koza.cli_utils import get_koza_app
+from monarch_ingest.ingests.dictybase.utils import parse_phenotypes
 
-from biolink_model.datamodel.pydanticmodel_v2 import GeneToPhenotypicFeatureAssociation, KnowledgeLevelEnum, \
-    AgentTypeEnum
+from biolink_model.datamodel.pydanticmodel_v2 import (
+    GeneToPhenotypicFeatureAssociation,
+    KnowledgeLevelEnum,
+    AgentTypeEnum,
+)
 
 koza_app = get_koza_app("dictybase_gene_to_phenotype")
 
@@ -32,7 +34,7 @@
                 aggregator_knowledge_source=["infores:monarchinitiative"],
                 primary_knowledge_source="infores:dictybase",
                 knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-                agent_type=AgentTypeEnum.manual_agent
+                agent_type=AgentTypeEnum.manual_agent,
             )
 
             koza_app.write(association)
diff --git a/src/monarch_ingest/ingests/dictybase/utils.py b/src/monarch_ingest/ingests/dictybase/utils.py
index 13f00b6c..89ca872c 100644
--- a/src/monarch_ingest/ingests/dictybase/utils.py
+++ b/src/monarch_ingest/ingests/dictybase/utils.py
@@ -1,6 +1,7 @@
 """
 A few Dictybase parse utility functions
 """
+
 from typing import Optional, Tuple, Dict, List
 
 
diff --git a/src/monarch_ingest/ingests/flybase/publication_to_gene.py b/src/monarch_ingest/ingests/flybase/publication_to_gene.py
index 932f81ee..35209c4b 100644
--- a/src/monarch_ingest/ingests/flybase/publication_to_gene.py
+++ b/src/monarch_ingest/ingests/flybase/publication_to_gene.py
@@ -1,9 +1,12 @@
 import uuid
 
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
-from biolink_model.datamodel.pydanticmodel_v2 import InformationContentEntityToNamedThingAssociation, AgentTypeEnum, \
-    KnowledgeLevelEnum
+from biolink_model.datamodel.pydanticmodel_v2 import (
+    InformationContentEntityToNamedThingAssociation,
+    AgentTypeEnum,
+    KnowledgeLevelEnum,
+)
 
 koza_app = get_koza_app("flybase_publication_to_gene")
 
@@ -26,7 +29,7 @@
         aggregator_knowledge_source=["infores:monarchinitiative"],
         primary_knowledge_source="infores:flybase",
         knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-        agent_type=AgentTypeEnum.manual_agent
+        agent_type=AgentTypeEnum.manual_agent,
     )
 
     koza_app.write(association)
diff --git a/src/monarch_ingest/ingests/go/annotation.py b/src/monarch_ingest/ingests/go/annotation.py
index 3c85ca91..b73bbb02 100644
--- a/src/monarch_ingest/ingests/go/annotation.py
+++ b/src/monarch_ingest/ingests/go/annotation.py
@@ -4,16 +4,17 @@
 Gene to GO term Associations
 (to MolecularActivity, BiologicalProcess and CellularComponent)
 """
+
 import uuid
 
 from biolink_model.datamodel.pydanticmodel_v2 import KnowledgeLevelEnum, AgentTypeEnum
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
 from monarch_ingest.ingests.go.annotation_utils import (
     parse_identifiers,
     get_biolink_classes,
     lookup_predicate,
-    get_infores
+    get_infores,
 )
 from loguru import logger
 
@@ -34,9 +35,7 @@
     #      'C' == cellular_component - child of GO:0005575
     go_aspect: str = row['Aspect']
     if not (go_aspect and go_aspect.upper() in ["F", "P", "C"]):
-        logger.warning(
-            f"GAF Aspect '{str(go_aspect)}' is empty or unrecognized? Skipping record"
-        )
+        logger.warning(f"GAF Aspect '{str(go_aspect)}' is empty or unrecognized? Skipping record")
 
     else:
         # Decipher the GO Evidence Code
@@ -47,9 +46,7 @@
             eco_term = koza_app.translation_table.local_table[evidence_code]
 
         if not eco_term:
-            logger.warning(
-                f"GAF Evidence Code '{str(evidence_code)}' is empty or unrecognized? Tagging as 'ND'"
-            )
+            logger.warning(f"GAF Evidence Code '{str(evidence_code)}' is empty or unrecognized? Tagging as 'ND'")
             eco_term = "ECO:0000307"
 
         # Association predicate is normally NOT negated
@@ -85,9 +82,7 @@
         else:
             # If qualifier missing, assign a default predicate
             # a.k.a. predicate based on specified GO Aspect type
-            logger.error(
-                "GAF record is missing its qualifier...assigning default qualifier as per GO term Aspect"
-            )
+            logger.error("GAF record is missing its qualifier...assigning default qualifier as per GO term Aspect")
             if go_aspect == "F":
                 predicate = "enables"
             elif go_aspect == "P":
@@ -96,16 +91,12 @@
                 predicate = "located_in"
 
         if not predicate:
-            logger.error(
-                f"GAF Qualifier '{str(qualifier)}' is unrecognized? Skipping the record..."
-            )
+            logger.error(f"GAF Qualifier '{str(qualifier)}' is unrecognized? Skipping the record...")
 
         else:
 
             # Retrieve the GO aspect related NamedThing category-associated 'node' and Association 'edge' classes
-            go_concept_node_class, gene_go_term_association_class = get_biolink_classes(
-                go_aspect
-            )
+            go_concept_node_class, gene_go_term_association_class = get_biolink_classes(go_aspect)
 
             # actual primary knowledge source of the GOA knowledge statement
             assigned_by = get_infores(row['Assigned_By'])
@@ -122,7 +113,7 @@
                 aggregator_knowledge_source=["infores:monarchinitiative"],
                 primary_knowledge_source=assigned_by,
                 knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-                agent_type=AgentTypeEnum.manual_agent
+                agent_type=AgentTypeEnum.manual_agent,
             )
 
             # Write the captured Association out
diff --git a/src/monarch_ingest/ingests/go/annotation_utils.py b/src/monarch_ingest/ingests/go/annotation_utils.py
index f4b8a504..fd9d3c9e 100644
--- a/src/monarch_ingest/ingests/go/annotation_utils.py
+++ b/src/monarch_ingest/ingests/go/annotation_utils.py
@@ -1,6 +1,7 @@
 """
 Some Gene Ontology Annotation ingest utility functions.
 """
+
 from re import sub, IGNORECASE, compile, Pattern
 from typing import Optional, Tuple, List, Dict
 
@@ -144,6 +145,7 @@ def get_biolink_classes(go_aspect: str) -> Tuple:
     """
     return _biolink_class_by_go_aspect[go_aspect.upper()]
 
+
 #
 # See comment below
 #
diff --git a/src/monarch_ingest/ingests/hgnc/gene.py b/src/monarch_ingest/ingests/hgnc/gene.py
index 9f656a56..1504ce98 100644
--- a/src/monarch_ingest/ingests/hgnc/gene.py
+++ b/src/monarch_ingest/ingests/hgnc/gene.py
@@ -1,4 +1,4 @@
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
 from biolink_model.datamodel.pydanticmodel_v2 import Gene
 
@@ -6,7 +6,7 @@
 taxon_labels = koza_app.get_map("taxon-labels")
 
 while (row := koza_app.get_row()) is not None:
-    
+
     xref_list = []
     if row['ensembl_gene_id']:
         xref_list.append('ENSEMBL:' + row['ensembl_gene_id'])
@@ -17,7 +17,6 @@
         else:
             xref_list.append('OMIM:' + row['omim_id'])
 
-
     synonyms_list = (
         row["alias_symbol"].split("|")
         + row["alias_name"].split("|")
@@ -37,7 +36,7 @@
         synonym=synonyms_list,
         in_taxon=[in_taxon],
         in_taxon_label=in_taxon_label,
-        provided_by=["infores:hgnc"]
+        provided_by=["infores:hgnc"],
     )
 
     # Excluding pub to gene associations for now
diff --git a/src/monarch_ingest/ingests/hpoa/disease_mode_of_inheritance.py b/src/monarch_ingest/ingests/hpoa/disease_mode_of_inheritance.py
index b40b85a3..0b3d56ba 100644
--- a/src/monarch_ingest/ingests/hpoa/disease_mode_of_inheritance.py
+++ b/src/monarch_ingest/ingests/hpoa/disease_mode_of_inheritance.py
@@ -19,14 +19,18 @@
   --source src/monarch_ingest/ingests/hpoa/disease_mode_of_inheritance.yaml \
   --output-format tsv
 """
+
 from typing import List
 
 import uuid
 
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
-from biolink_model.datamodel.pydanticmodel_v2 import DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation, \
-    KnowledgeLevelEnum, AgentTypeEnum
+from biolink_model.datamodel.pydanticmodel_v2 import (
+    DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation,
+    KnowledgeLevelEnum,
+    AgentTypeEnum,
+)
 
 from loguru import logger
 
@@ -34,48 +38,48 @@
 
 while (row := koza_app.get_row()) is not None:
 
-  # Object: Actually a Genetic Inheritance (as should be specified by a suitable HPO term)
-  # TODO: perhaps load the proper (Genetic Inheritance) node concepts into the Monarch Graph (simply as Ontology terms?).
-  hpo_id = row["hpo_id"]
+    # Object: Actually a Genetic Inheritance (as should be specified by a suitable HPO term)
+    # TODO: perhaps load the proper (Genetic Inheritance) node concepts into the Monarch Graph (simply as Ontology terms?).
+    hpo_id = row["hpo_id"]
 
-  # We ignore records that don't map to a known HPO term for Genetic Inheritance
-  # (as recorded in the locally bound 'hpoa-modes-of-inheritance' table)
-  if hpo_id and hpo_id in koza_app.translation_table.local_table:
+    # We ignore records that don't map to a known HPO term for Genetic Inheritance
+    # (as recorded in the locally bound 'hpoa-modes-of-inheritance' table)
+    if hpo_id and hpo_id in koza_app.translation_table.local_table:
 
-      # Nodes
+        # Nodes
 
-      # Subject: Disease
-      disease_id = row["database_id"]
+        # Subject: Disease
+        disease_id = row["database_id"]
 
-      # Predicate (canonical direction)
-      predicate = "biolink:has_mode_of_inheritance"
+        # Predicate (canonical direction)
+        predicate = "biolink:has_mode_of_inheritance"
 
-      # Annotations
+        # Annotations
 
-      # Three letter ECO code to ECO class based on HPO documentation
-      evidence_curie = koza_app.translation_table.resolve_term(row["evidence"])
+        # Three letter ECO code to ECO class based on HPO documentation
+        evidence_curie = koza_app.translation_table.resolve_term(row["evidence"])
 
-      # Publications
-      publications_field: str = row["reference"]
-      publications: List[str] = publications_field.split(";")
+        # Publications
+        publications_field: str = row["reference"]
+        publications: List[str] = publications_field.split(";")
 
-      # Filter out some weird NCBI web endpoints
-      publications = [p for p in publications if not p.startswith("http")]
+        # Filter out some weird NCBI web endpoints
+        publications = [p for p in publications if not p.startswith("http")]
 
-      # Association/Edge
-      association = DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation(
-          id="uuid:" + str(uuid.uuid1()),
-          subject=disease_id,
-          predicate=predicate,
-          object=hpo_id,
-          publications=publications,
-          has_evidence=[evidence_curie],
-          aggregator_knowledge_source=["infores:monarchinitiative"],
-          primary_knowledge_source="infores:hpo-annotations",
-          knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-          agent_type=AgentTypeEnum.manual_agent
-      )
-      koza_app.write(association)
+        # Association/Edge
+        association = DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation(
+            id="uuid:" + str(uuid.uuid1()),
+            subject=disease_id,
+            predicate=predicate,
+            object=hpo_id,
+            publications=publications,
+            has_evidence=[evidence_curie],
+            aggregator_knowledge_source=["infores:monarchinitiative"],
+            primary_knowledge_source="infores:hpo-annotations",
+            knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
+            agent_type=AgentTypeEnum.manual_agent,
+        )
+        koza_app.write(association)
 
-  else:
-      logger.warning(f"HPOA ID field value '{str(hpo_id)}' is missing or an invalid disease mode of inheritance?")
+    else:
+        logger.warning(f"HPOA ID field value '{str(hpo_id)}' is missing or an invalid disease mode of inheritance?")
diff --git a/src/monarch_ingest/ingests/hpoa/disease_to_phenotype.py b/src/monarch_ingest/ingests/hpoa/disease_to_phenotype.py
index 974aefd3..f10acacf 100644
--- a/src/monarch_ingest/ingests/hpoa/disease_to_phenotype.py
+++ b/src/monarch_ingest/ingests/hpoa/disease_to_phenotype.py
@@ -23,17 +23,20 @@
   --source src/monarch_ingest/ingests/hpoa/disease_phenotype.yaml \
   --output-format tsv
 """
-from typing import Optional, List, Tuple
+
+from typing import Optional, List
 
 import uuid
 
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
-from biolink_model.datamodel.pydanticmodel_v2 import DiseaseToPhenotypicFeatureAssociation, KnowledgeLevelEnum, \
-    AgentTypeEnum
-from monarch_ingest.ingests.hpoa.hpoa_utils import phenotype_frequency_to_hpo_term, FrequencyHpoTerm, Frequency
+from biolink_model.datamodel.pydanticmodel_v2 import (
+    DiseaseToPhenotypicFeatureAssociation,
+    KnowledgeLevelEnum,
+    AgentTypeEnum,
+)
+from monarch_ingest.ingests.hpoa.hpoa_utils import phenotype_frequency_to_hpo_term, Frequency
 
-from loguru import logger
 
 koza_app = get_koza_app("hpoa_disease_to_phenotype")
 
@@ -63,9 +66,7 @@
     # female -> PATO:0000383
     # male -> PATO:0000384
     sex: Optional[str] = row["sex"]  # may be translated by local table
-    sex_qualifier = (
-        koza_app.translation_table.resolve_term(sex) if sex else None
-    )
+    sex_qualifier = koza_app.translation_table.resolve_term(sex) if sex else None
 
     onset = row["onset"]
 
@@ -77,13 +78,12 @@
     publications: List[str] = publications_field.split(";")
 
     # don't populate the reference with the database_id / disease id
-    publications = [p for p in publications
-                    if not p == row["database_id"]]
+    publications = [p for p in publications if not p == row["database_id"]]
 
     # Association/Edge
     association = DiseaseToPhenotypicFeatureAssociation(
         id="uuid:" + str(uuid.uuid1()),
-        subject=disease_id.replace("ORPHA:", "Orphanet:"), # match `Orphanet` as used in Mondo SSSOM
+        subject=disease_id.replace("ORPHA:", "Orphanet:"),  # match `Orphanet` as used in Mondo SSSOM
         predicate=predicate,
         negated=negated,
         object=hpo_id,
@@ -99,7 +99,6 @@
         aggregator_knowledge_source=["infores:monarchinitiative"],
         primary_knowledge_source="infores:hpo-annotations",
         knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-        agent_type=AgentTypeEnum.manual_agent
-
+        agent_type=AgentTypeEnum.manual_agent,
     )
     koza_app.write(association)
diff --git a/src/monarch_ingest/ingests/hpoa/gene_to_disease.py b/src/monarch_ingest/ingests/hpoa/gene_to_disease.py
index 69a52826..54f8cc19 100644
--- a/src/monarch_ingest/ingests/hpoa/gene_to_disease.py
+++ b/src/monarch_ingest/ingests/hpoa/gene_to_disease.py
@@ -1,8 +1,12 @@
 import uuid
 
-from biolink_model.datamodel.pydanticmodel_v2 import GeneToDiseaseAssociation, CausalGeneToDiseaseAssociation, \
-    CorrelatedGeneToDiseaseAssociation, KnowledgeLevelEnum, AgentTypeEnum
-from koza.cli_runner import get_koza_app
+from biolink_model.datamodel.pydanticmodel_v2 import (
+    CausalGeneToDiseaseAssociation,
+    CorrelatedGeneToDiseaseAssociation,
+    KnowledgeLevelEnum,
+    AgentTypeEnum,
+)
+from koza.cli_utils import get_koza_app
 
 from monarch_ingest.constants import INFORES_MONARCHINITIATIVE, BIOLINK_CAUSES
 from monarch_ingest.ingests.hpoa.hpoa_utils import get_knowledge_sources, get_predicate
@@ -16,7 +20,9 @@
 
     predicate = get_predicate(row["association_type"])
 
-    primary_knowledge_source, aggregator_knowledge_source = get_knowledge_sources(row["source"], INFORES_MONARCHINITIATIVE)
+    primary_knowledge_source, aggregator_knowledge_source = get_knowledge_sources(
+        row["source"], INFORES_MONARCHINITIATIVE
+    )
 
     if predicate == BIOLINK_CAUSES:
         association_class = CausalGeneToDiseaseAssociation
@@ -31,7 +37,7 @@
         primary_knowledge_source=primary_knowledge_source,
         aggregator_knowledge_source=aggregator_knowledge_source,
         knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-        agent_type=AgentTypeEnum.manual_agent
+        agent_type=AgentTypeEnum.manual_agent,
     )
 
     koza_app.write(association)
diff --git a/src/monarch_ingest/ingests/hpoa/gene_to_phenotype.py b/src/monarch_ingest/ingests/hpoa/gene_to_phenotype.py
index ffa820c2..1ba53908 100644
--- a/src/monarch_ingest/ingests/hpoa/gene_to_phenotype.py
+++ b/src/monarch_ingest/ingests/hpoa/gene_to_phenotype.py
@@ -4,12 +4,16 @@
   --source src/monarch_ingest/ingests/hpoa/gene_to_phenotype.yaml \
   --output-format tsv
 """
+
 import uuid
 
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
-from biolink_model.datamodel.pydanticmodel_v2 import GeneToPhenotypicFeatureAssociation, KnowledgeLevelEnum, \
-    AgentTypeEnum
+from biolink_model.datamodel.pydanticmodel_v2 import (
+    GeneToPhenotypicFeatureAssociation,
+    KnowledgeLevelEnum,
+    AgentTypeEnum,
+)
 
 koza_app = get_koza_app("hpoa_gene_to_phenotype")
 
diff --git a/src/monarch_ingest/ingests/hpoa/hpoa_utils.py b/src/monarch_ingest/ingests/hpoa/hpoa_utils.py
index 7439f02d..6e2efbf7 100644
--- a/src/monarch_ingest/ingests/hpoa/hpoa_utils.py
+++ b/src/monarch_ingest/ingests/hpoa/hpoa_utils.py
@@ -1,14 +1,21 @@
 """
 HPOA processing utility methods
 """
-from typing import Optional, List, Dict, Tuple, NamedTuple
+
+from typing import Optional, List, Dict
 
 
 from loguru import logger
 from pydantic import BaseModel
 
-from monarch_ingest.constants import INFORES_MEDGEN, INFORES_OMIM, INFORES_ORPHANET, BIOLINK_CAUSES, \
-    BIOLINK_CONTRIBUTES_TO, BIOLINK_GENE_ASSOCIATED_WITH_CONDITION
+from monarch_ingest.constants import (
+    INFORES_MEDGEN,
+    INFORES_OMIM,
+    INFORES_ORPHANET,
+    BIOLINK_CAUSES,
+    BIOLINK_CONTRIBUTES_TO,
+    BIOLINK_GENE_ASSOCIATED_WITH_CONDITION,
+)
 
 
 class FrequencyHpoTerm(BaseModel):
@@ -17,6 +24,7 @@ class FrequencyHpoTerm(BaseModel):
     lower: float
     upper: float
 
+
 class Frequency(BaseModel):
     frequency_qualifier: Optional[str] = None
     has_percentage: Optional[float] = None
@@ -25,14 +33,27 @@ class Frequency(BaseModel):
     has_total: Optional[int] = None
     # convert the fields above to pydantic field declarations
 
+
 # HPO "HP:0040279": representing the frequency of phenotypic abnormalities within a patient cohort.
 hpo_term_to_frequency: Dict = {
-    "HP:0040280": FrequencyHpoTerm(curie="HP:0040280", name="Obligate", lower=100.0, upper=100.0),  # Always present,i.e. in 100% of the cases.
-    "HP:0040281": FrequencyHpoTerm(curie="HP:0040281", name="Very frequent", lower=80.0, upper=99.0),  # Present in 80% to 99% of the cases.
-    "HP:0040282": FrequencyHpoTerm(curie="HP:0040282", name="Frequent", lower=30.0, upper=79.0),       # Present in 30% to 79% of the cases.
-    "HP:0040283": FrequencyHpoTerm(curie="HP:0040283", name="Occasional", lower=5.0, upper=29.0),      # Present in 5% to 29% of the cases.
-    "HP:0040284": FrequencyHpoTerm(curie="HP:0040284", name="Very rare", lower=1.0, upper=4.0),        # Present in 1% to 4% of the cases.
-    "HP:0040285": FrequencyHpoTerm(curie="HP:0040285", name="Excluded", lower=0.0, upper=0.0)          # Present in 0% of the cases.
+    "HP:0040280": FrequencyHpoTerm(
+        curie="HP:0040280", name="Obligate", lower=100.0, upper=100.0
+    ),  # Always present,i.e. in 100% of the cases.
+    "HP:0040281": FrequencyHpoTerm(
+        curie="HP:0040281", name="Very frequent", lower=80.0, upper=99.0
+    ),  # Present in 80% to 99% of the cases.
+    "HP:0040282": FrequencyHpoTerm(
+        curie="HP:0040282", name="Frequent", lower=30.0, upper=79.0
+    ),  # Present in 30% to 79% of the cases.
+    "HP:0040283": FrequencyHpoTerm(
+        curie="HP:0040283", name="Occasional", lower=5.0, upper=29.0
+    ),  # Present in 5% to 29% of the cases.
+    "HP:0040284": FrequencyHpoTerm(
+        curie="HP:0040284", name="Very rare", lower=1.0, upper=4.0
+    ),  # Present in 1% to 4% of the cases.
+    "HP:0040285": FrequencyHpoTerm(
+        curie="HP:0040285", name="Excluded", lower=0.0, upper=0.0
+    ),  # Present in 0% of the cases.
 }
 
 
@@ -57,21 +78,19 @@ def map_percentage_frequency_to_hpo_term(percentage_or_quotient: float) -> Optio
     return None
 
 
-def phenotype_frequency_to_hpo_term(
-        frequency_field: Optional[str]
-) -> Frequency:
+def phenotype_frequency_to_hpo_term(frequency_field: Optional[str]) -> Frequency:
     """
-Maps a raw frequency field onto HPO, for consistency. This is needed since the **phenotypes.hpoa**
-file field #8 which tracks phenotypic frequency, has a variable values. There are three allowed options for this field:
+    Maps a raw frequency field onto HPO, for consistency. This is needed since the **phenotypes.hpoa**
+    file field #8 which tracks phenotypic frequency, has a variable values. There are three allowed options for this field:
 
-1. A term-id from the HPO-sub-ontology below the term “Frequency” (HP:0040279). (since December 2016 ; before was a mixture of values). The terms for frequency are in alignment with Orphanet;
-2. A percentage value such as 17%.
-3. A count of patients affected within a cohort. For instance, 7/13 would indicate that 7 of the 13 patients with the specified disease were found to have the phenotypic abnormality referred to by the HPO term in question in the study referred to by the DB_Reference;
+    1. A term-id from the HPO-sub-ontology below the term “Frequency” (HP:0040279). (since December 2016 ; before was a mixture of values). The terms for frequency are in alignment with Orphanet;
+    2. A percentage value such as 17%.
+    3. A count of patients affected within a cohort. For instance, 7/13 would indicate that 7 of the 13 patients with the specified disease were found to have the phenotypic abnormality referred to by the HPO term in question in the study referred to by the DB_Reference;
 
-    :param frequency_field: str, raw frequency value in one of the three above forms
-    :return: Optional[FrequencyHpoTerm, float, float], raw frequency mapped to its HPO term, quotient or percentage
-             respectively (as applicable); return None if unmappable;
-             percentage and/or quotient returned are also None, if not applicable
+        :param frequency_field: str, raw frequency value in one of the three above forms
+        :return: Optional[FrequencyHpoTerm, float, float], raw frequency mapped to its HPO term, quotient or percentage
+                 respectively (as applicable); return None if unmappable;
+                 percentage and/or quotient returned are also None, if not applicable
     """
     hpo_term: Optional[FrequencyHpoTerm] = None
     quotient: Optional[float] = None
@@ -104,11 +123,13 @@ def phenotype_frequency_to_hpo_term(
         # may be None, if original field was empty or has an invalid value
         return Frequency()
 
-    return Frequency(frequency_qualifier=hpo_term.curie if hpo_term else None,
-                     has_percentage=percentage,
-                     has_quotient=quotient,
-                     has_count=has_count,
-                     has_total=has_total)
+    return Frequency(
+        frequency_qualifier=hpo_term.curie if hpo_term else None,
+        has_percentage=percentage,
+        has_quotient=quotient,
+        has_count=has_count,
+        has_total=has_total,
+    )
 
 
 def get_knowledge_sources(original_source: str, additional_source: str) -> (str, List[str]):
diff --git a/src/monarch_ingest/ingests/mgi/publication_to_gene.py b/src/monarch_ingest/ingests/mgi/publication_to_gene.py
index fce8228c..75d52311 100644
--- a/src/monarch_ingest/ingests/mgi/publication_to_gene.py
+++ b/src/monarch_ingest/ingests/mgi/publication_to_gene.py
@@ -1,15 +1,18 @@
 import uuid
 
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
-from biolink_model.datamodel.pydanticmodel_v2 import InformationContentEntityToNamedThingAssociation, AgentTypeEnum, \
-    KnowledgeLevelEnum
+from biolink_model.datamodel.pydanticmodel_v2 import (
+    InformationContentEntityToNamedThingAssociation,
+    AgentTypeEnum,
+    KnowledgeLevelEnum,
+)
 
 koza_app = get_koza_app("mgi_publication_to_gene")
 
 while (row := koza_app.get_row()) is not None:
 
-    gene_id=row["MGI Marker Accession ID"]
+    gene_id = row["MGI Marker Accession ID"]
 
     relation = koza_app.translation_table.resolve_term("mentions")
 
@@ -27,7 +30,7 @@
             aggregator_knowledge_source=["infores:monarchinitiative"],
             primary_knowledge_source="infores:mgi",
             knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-            agent_type=AgentTypeEnum.manual_agent
+            agent_type=AgentTypeEnum.manual_agent,
         )
 
         koza_app.write(association)
diff --git a/src/monarch_ingest/ingests/ncbi/gene.py b/src/monarch_ingest/ingests/ncbi/gene.py
index 9810c9b7..0b7f42c4 100644
--- a/src/monarch_ingest/ingests/ncbi/gene.py
+++ b/src/monarch_ingest/ingests/ncbi/gene.py
@@ -1,4 +1,4 @@
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
 from biolink_model.datamodel.pydanticmodel_v2 import Gene
 
@@ -6,15 +6,12 @@
 taxon_labels = koza_app.get_map("taxon-labels")
 
 # If a taxon label we need isn't in phenio's NCBITaxon subset, we can add it here
-extra_taxon_labels = {
-    'NCBITaxon:227321': 'Dictyostelium discoideum'
-}
+extra_taxon_labels = {'NCBITaxon:227321': 'Dictyostelium discoideum'}
 
 while (row := koza_app.get_row()) is not None:
 
     in_taxon = 'NCBITaxon:' + row["tax_id"]
 
-
     if in_taxon in taxon_labels:
         in_taxon_label = taxon_labels[in_taxon]['label']
     elif in_taxon in extra_taxon_labels:
@@ -30,7 +27,7 @@
         description=row["description"],
         in_taxon=[in_taxon],
         in_taxon_label=in_taxon_label,
-        provided_by=["infores:ncbi-gene"]
+        provided_by=["infores:ncbi-gene"],
     )
 
     koza_app.write(gene)
diff --git a/src/monarch_ingest/ingests/panther/genome_orthologs.py b/src/monarch_ingest/ingests/panther/genome_orthologs.py
index c3990906..7dccdca7 100644
--- a/src/monarch_ingest/ingests/panther/genome_orthologs.py
+++ b/src/monarch_ingest/ingests/panther/genome_orthologs.py
@@ -4,20 +4,18 @@
 
 import uuid
 
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
 from biolink_model.datamodel.pydanticmodel_v2 import GeneToGeneHomologyAssociation, KnowledgeLevelEnum, AgentTypeEnum
 
 from monarch_ingest.ingests.panther.orthology_utils import parse_gene, ncbitaxon_catalog
 
-from loguru import logger
 
 koza_app = get_koza_app("panther_genome_orthologs")
 
 while (row := koza_app.get_row()) is not None:
 
-    if row['Gene'].split("|")[0] in ncbitaxon_catalog \
-            and row['Ortholog'].split("|")[0] in ncbitaxon_catalog:
+    if row['Gene'].split("|")[0] in ncbitaxon_catalog and row['Ortholog'].split("|")[0] in ncbitaxon_catalog:
         try:
             # TODO: we don't current capture the taxon of the subject gene
             #       nor the object ortholog. Maybe as a qualifier in Biolink 3.0?
@@ -54,13 +52,13 @@
                 aggregator_knowledge_source=["infores:monarchinitiative"],
                 primary_knowledge_source="infores:panther",
                 knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-                agent_type=AgentTypeEnum.not_provided
+                agent_type=AgentTypeEnum.not_provided,
             )
 
             # Write the captured Association out
             koza_app.write(association)
-            
-        except RuntimeError as rte:
+
+        except RuntimeError:
             # Skip the row - not of interest or error
             # logger.debug(f"{str(rte)} in data row:\n\t'{str(row)}'")
             pass
diff --git a/src/monarch_ingest/ingests/panther/orthology_utils.py b/src/monarch_ingest/ingests/panther/orthology_utils.py
index e78818da..9b13d11c 100644
--- a/src/monarch_ingest/ingests/panther/orthology_utils.py
+++ b/src/monarch_ingest/ingests/panther/orthology_utils.py
@@ -1,12 +1,14 @@
 """
 Utility functions for Panther Orthology data processing
 """
+
 # from sys import stderr
 # from os import sep, remove
 # from tarfile import (open as tar_open, ReadError, CompressionError, TarInfo)
 # from datetime import datetime
 
-from typing import Optional, Tuple#, List
+from typing import Optional, Tuple  # , List
+
 # from io import TextIOWrapper
 
 # from loguru import logger
@@ -16,13 +18,13 @@
     #       of species - just starting with the STRING DB list + Dictyostelium
     "HUMAN": "9606",
     "MOUSE": "10090",
-    "CANLF": "9615",    # Canis lupus familiaris - domestic dog
+    "CANLF": "9615",  # Canis lupus familiaris - domestic dog
     # "FELCA": "9685",  # Felis catus - domestic cat
-    "BOVIN": "9913",    # Bos taurus - cow
-    "PIG": "9823",      # Sus scrofa - pig
+    "BOVIN": "9913",  # Bos taurus - cow
+    "PIG": "9823",  # Sus scrofa - pig
     "RAT": "10116",
     "CHICK": "9031",
-    "XENTR": "8364",   # Xenopus tropicalis - tropical clawed frog
+    "XENTR": "8364",  # Xenopus tropicalis - tropical clawed frog
     "DANRE": "7955",
     "DROME": "7227",
     "CAEEL": "6239",
@@ -32,6 +34,7 @@
     "YEAST": "4932",
 }
 
+
 def ncbitaxon_by_name(species_tag: str) -> Optional[str]:
     """
     Retrieves the NCBI Taxon ID of a given species, only if we are interested in it...
@@ -52,10 +55,10 @@ def ncbitaxon_by_name(species_tag: str) -> Optional[str]:
     "EnsemblGenome": "ENSEMBL",  # TODO: review and fix this later?
     "PomBase": "PomBase",
     "WormBase": "WB",  # Wormbase supports 'WormBase:' but alliancegenome.org and identifiers.org supports 'WB:'
-    "GeneID": "NCBIGene",          # seems to be Entrez Gene ID => map onto the NCBIGene: namespace
-    "Gene": None,                  # seems to be the gene symbol - we ignore it for now?
-    "Gene_ORFName": None,          # is the gene orf name from a transcript in Uniprot - we ignore it for now?
-    "Gene_OrderedLocusName": None  # is a gene ordered locus name - we ignore it for now?
+    "GeneID": "NCBIGene",  # seems to be Entrez Gene ID => map onto the NCBIGene: namespace
+    "Gene": None,  # seems to be the gene symbol - we ignore it for now?
+    "Gene_ORFName": None,  # is the gene orf name from a transcript in Uniprot - we ignore it for now?
+    "Gene_OrderedLocusName": None,  # is a gene ordered locus name - we ignore it for now?
 }
 
 
@@ -96,9 +99,7 @@ def parse_gene_id(gene_id_spec: str) -> Optional[str]:
         #  trapped by the RuntimeError below should answer this...)
         return f"{spec_part[1]}:{spec_part[2]}"
     else:
-        raise RuntimeError(
-            f"parse_gene_id(): Error parsing '{str(gene_id_spec)}'? Ignoring..."
-        )
+        raise RuntimeError(f"parse_gene_id(): Error parsing '{str(gene_id_spec)}'? Ignoring...")
 
 
 def parse_gene(gene_entry: str) -> Optional[Tuple[str, str]]:
@@ -114,9 +115,7 @@ def parse_gene(gene_entry: str) -> Optional[Tuple[str, str]]:
     try:
         species, gene_spec, _ = gene_entry.split("|")
     except ValueError:
-        raise RuntimeError(
-            f"parse_gene(): Gene entry field '{str(gene_entry)}' has incorrect format. Ignoring..."
-        )
+        raise RuntimeError(f"parse_gene(): Gene entry field '{str(gene_entry)}' has incorrect format. Ignoring...")
 
     # get the NCBI Taxonomic identifier
     ncbitaxon_id = ncbitaxon_by_name(species)
diff --git a/src/monarch_ingest/ingests/pombase/gene.py b/src/monarch_ingest/ingests/pombase/gene.py
index 7d107854..6761c71f 100644
--- a/src/monarch_ingest/ingests/pombase/gene.py
+++ b/src/monarch_ingest/ingests/pombase/gene.py
@@ -1,5 +1,6 @@
 from biolink_model.datamodel.pydanticmodel_v2 import Gene
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
+
 # from loguru import logger
 
 
diff --git a/src/monarch_ingest/ingests/pombase/gene_to_phenotype.py b/src/monarch_ingest/ingests/pombase/gene_to_phenotype.py
index 6cb87185..ace62407 100644
--- a/src/monarch_ingest/ingests/pombase/gene_to_phenotype.py
+++ b/src/monarch_ingest/ingests/pombase/gene_to_phenotype.py
@@ -1,9 +1,12 @@
 import uuid
 
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
-from biolink_model.datamodel.pydanticmodel_v2 import GeneToPhenotypicFeatureAssociation, KnowledgeLevelEnum, \
-    AgentTypeEnum
+from biolink_model.datamodel.pydanticmodel_v2 import (
+    GeneToPhenotypicFeatureAssociation,
+    KnowledgeLevelEnum,
+    AgentTypeEnum,
+)
 
 koza_app = get_koza_app("pombase_gene_to_phenotype")
 
@@ -22,7 +25,7 @@
         aggregator_knowledge_source=["infores:monarchinitiative"],
         primary_knowledge_source="infores:pombase",
         knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-        agent_type=AgentTypeEnum.manual_agent
+        agent_type=AgentTypeEnum.manual_agent,
     )
 
     if row["Condition"]:
diff --git a/src/monarch_ingest/ingests/reactome/chemical_to_pathway.py b/src/monarch_ingest/ingests/reactome/chemical_to_pathway.py
index eb1714af..6e08a782 100644
--- a/src/monarch_ingest/ingests/reactome/chemical_to_pathway.py
+++ b/src/monarch_ingest/ingests/reactome/chemical_to_pathway.py
@@ -1,5 +1,5 @@
 import uuid
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 from biolink_model.datamodel.pydanticmodel_v2 import ChemicalToPathwayAssociation, AgentTypeEnum, KnowledgeLevelEnum
 
 koza_app = get_koza_app("reactome_chemical_to_pathway")
@@ -31,7 +31,7 @@
             aggregator_knowledge_source=["infores:monarchinitiative"],
             primary_knowledge_source="infores:reactome",
             knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-            agent_type=AgentTypeEnum.not_provided
+            agent_type=AgentTypeEnum.not_provided,
         )
 
     koza_app.write(association)
diff --git a/src/monarch_ingest/ingests/reactome/gene_to_pathway.py b/src/monarch_ingest/ingests/reactome/gene_to_pathway.py
index 00e9e80a..825c32f4 100644
--- a/src/monarch_ingest/ingests/reactome/gene_to_pathway.py
+++ b/src/monarch_ingest/ingests/reactome/gene_to_pathway.py
@@ -1,5 +1,5 @@
 import uuid
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
 from biolink_model.datamodel.pydanticmodel_v2 import GeneToPathwayAssociation, AgentTypeEnum, KnowledgeLevelEnum
 
@@ -32,7 +32,7 @@
             aggregator_knowledge_source=["infores:monarchinitiative"],
             primary_knowledge_source="infores:reactome",
             knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-            agent_type=AgentTypeEnum.not_provided
+            agent_type=AgentTypeEnum.not_provided,
         )
 
     koza_app.write(association)
diff --git a/src/monarch_ingest/ingests/reactome/pathway.py b/src/monarch_ingest/ingests/reactome/pathway.py
index 2950b867..efc25842 100644
--- a/src/monarch_ingest/ingests/reactome/pathway.py
+++ b/src/monarch_ingest/ingests/reactome/pathway.py
@@ -1,5 +1,5 @@
 from biolink_model.datamodel.pydanticmodel_v2 import Pathway
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
 koza_app = get_koza_app('reactome_pathway')
 
@@ -21,10 +21,9 @@
             name=row["Name"],
             in_taxon=[taxon_id],
             provided_by=["infores:reactome"],
-
             # the identifier is duplicated here as a xref to become visible as
             # an external link in the entity display page of the Monarch App
-            xref=[pathway_id]
+            xref=[pathway_id],
         )
 
         koza_app.write(pathway)
diff --git a/src/monarch_ingest/ingests/rgd/publication_to_gene.py b/src/monarch_ingest/ingests/rgd/publication_to_gene.py
index cea56e2d..3825f6ce 100644
--- a/src/monarch_ingest/ingests/rgd/publication_to_gene.py
+++ b/src/monarch_ingest/ingests/rgd/publication_to_gene.py
@@ -1,9 +1,12 @@
 import uuid
 
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
-from biolink_model.datamodel.pydanticmodel_v2 import InformationContentEntityToNamedThingAssociation, AgentTypeEnum, \
-    KnowledgeLevelEnum
+from biolink_model.datamodel.pydanticmodel_v2 import (
+    InformationContentEntityToNamedThingAssociation,
+    AgentTypeEnum,
+    KnowledgeLevelEnum,
+)
 
 koza_app = get_koza_app("rgd_publication_to_gene")
 
@@ -12,7 +15,7 @@
     if not row["CURATED_REF_PUBMED_ID"]:
         koza_app.next_row()
 
-    gene_id='RGD:' + row["GENE_RGD_ID"]
+    gene_id = 'RGD:' + row["GENE_RGD_ID"]
 
     id_list = row["CURATED_REF_PUBMED_ID"].split(';')
     for each_id in id_list:
@@ -27,7 +30,7 @@
             aggregator_knowledge_source=["infores:monarchinitiative"],
             primary_knowledge_source="infores:rgd",
             knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-            agent_type=AgentTypeEnum.manual_agent
+            agent_type=AgentTypeEnum.manual_agent,
         )
 
         koza_app.write(association)
diff --git a/src/monarch_ingest/ingests/sgd/publication_to_gene.py b/src/monarch_ingest/ingests/sgd/publication_to_gene.py
index 1ad07211..a5c2face 100644
--- a/src/monarch_ingest/ingests/sgd/publication_to_gene.py
+++ b/src/monarch_ingest/ingests/sgd/publication_to_gene.py
@@ -1,9 +1,12 @@
 import uuid
 
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
-from biolink_model.datamodel.pydanticmodel_v2 import InformationContentEntityToNamedThingAssociation, AgentTypeEnum, \
-    KnowledgeLevelEnum
+from biolink_model.datamodel.pydanticmodel_v2 import (
+    InformationContentEntityToNamedThingAssociation,
+    AgentTypeEnum,
+    KnowledgeLevelEnum,
+)
 
 koza_app = get_koza_app("sgd_publication_to_gene")
 
@@ -21,7 +24,7 @@
         aggregator_knowledge_source=["infores:monarchinitiative"],
         primary_knowledge_source="infores:sgd",
         knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-        agent_type=AgentTypeEnum.manual_agent
+        agent_type=AgentTypeEnum.manual_agent,
     )
 
     koza_app.write(association)
diff --git a/src/monarch_ingest/ingests/string/protein_links.py b/src/monarch_ingest/ingests/string/protein_links.py
index e65671e2..762b482f 100644
--- a/src/monarch_ingest/ingests/string/protein_links.py
+++ b/src/monarch_ingest/ingests/string/protein_links.py
@@ -1,7 +1,7 @@
 import uuid
-from typing import Optional, List
+from typing import List
 
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
 from biolink_model.datamodel.pydanticmodel_v2 import PairwiseGeneToGeneInteraction, KnowledgeLevelEnum, AgentTypeEnum
 
@@ -13,11 +13,13 @@
 
 seen_rows = set([])
 
+
 def sorted_id_pair(row) -> str:
     sorted([row['protein1'], row['protein2']])
 
+
 while (row := koza_app.get_row()) is not None and sorted_id_pair(row) not in seen_rows:
-    
+
     entrez_2_string = koza_app.get_map('entrez_2_string')
 
     pid_a = row['protein1']
@@ -51,14 +53,12 @@ def sorted_id_pair(row) -> str:
                     subject=gene_id_a,
                     object=gene_id_b,
                     predicate="biolink:interacts_with",
-
                     # sanity check: set to 'None' if empty list
                     has_evidence=has_evidence if has_evidence else None,
-
                     aggregator_knowledge_source=["infores:monarchinitiative"],
                     primary_knowledge_source="infores:string",
                     knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-                    agent_type=AgentTypeEnum.not_provided
+                    agent_type=AgentTypeEnum.not_provided,
                 )
                 seen_rows.add(sorted_id_pair(row))
                 entities.append(association)
diff --git a/src/monarch_ingest/ingests/string/string_utils.py b/src/monarch_ingest/ingests/string/string_utils.py
index 5bbc7b94..88ecd1e6 100644
--- a/src/monarch_ingest/ingests/string/string_utils.py
+++ b/src/monarch_ingest/ingests/string/string_utils.py
@@ -46,7 +46,7 @@
     "coexpression": "ECO:0000075",
     "experimental": "ECO:0000006",
     "database": "ECO:0007636",
-    "textmining": "ECO:0007833"
+    "textmining": "ECO:0007833",
 }
 
 
@@ -57,4 +57,3 @@ def map_evidence_codes(row: Dict) -> List[str]:
             eco_mappings.append(EVIDENCE_CODE_MAPPINGS[evidence_type])
 
     return eco_mappings
-
diff --git a/src/monarch_ingest/ingests/xenbase/gene_to_phenotype.py b/src/monarch_ingest/ingests/xenbase/gene_to_phenotype.py
index 6bbf74ca..f7c86c50 100644
--- a/src/monarch_ingest/ingests/xenbase/gene_to_phenotype.py
+++ b/src/monarch_ingest/ingests/xenbase/gene_to_phenotype.py
@@ -1,11 +1,13 @@
 import uuid
 
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
 from biolink_model.datamodel.pydanticmodel_v2 import (
     Gene,
     GeneToPhenotypicFeatureAssociation,
-    PhenotypicFeature, KnowledgeLevelEnum, AgentTypeEnum
+    PhenotypicFeature,
+    KnowledgeLevelEnum,
+    AgentTypeEnum,
 )
 
 koza_app = get_koza_app("xenbase_gene_to_phenotype")
@@ -31,7 +33,7 @@
         aggregator_knowledge_source=["infores:monarchinitiative"],
         primary_knowledge_source="infores:xenbase",
         knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-        agent_type=AgentTypeEnum.manual_agent
+        agent_type=AgentTypeEnum.manual_agent,
     )
 
     if row["SOURCE"]:
diff --git a/src/monarch_ingest/ingests/xenbase/non_entrez_orthologs.py b/src/monarch_ingest/ingests/xenbase/non_entrez_orthologs.py
index 61066207..930d5b36 100644
--- a/src/monarch_ingest/ingests/xenbase/non_entrez_orthologs.py
+++ b/src/monarch_ingest/ingests/xenbase/non_entrez_orthologs.py
@@ -4,7 +4,7 @@
 
 import uuid
 
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
 from biolink_model.datamodel.pydanticmodel_v2 import GeneToGeneHomologyAssociation, AgentTypeEnum, KnowledgeLevelEnum
 
@@ -33,7 +33,7 @@
                 aggregator_knowledge_source=["infores:monarchinitiative"],
                 primary_knowledge_source="infores:xenbase",
                 knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-                agent_type=AgentTypeEnum.manual_agent
+                agent_type=AgentTypeEnum.manual_agent,
             )
 
             # Write the captured Association out
@@ -48,7 +48,7 @@
                 aggregator_knowledge_source=["infores:monarchinitiative"],
                 primary_knowledge_source="infores:xenbase",
                 knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-                agent_type=AgentTypeEnum.manual_agent
+                agent_type=AgentTypeEnum.manual_agent,
             )
 
             # Write the captured Association out
@@ -63,7 +63,7 @@
                 aggregator_knowledge_source=["infores:monarchinitiative"],
                 primary_knowledge_source="infores:xenbase",
                 knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-                agent_type=AgentTypeEnum.manual_agent
+                agent_type=AgentTypeEnum.manual_agent,
             )
 
             # Write the captured Association out
diff --git a/src/monarch_ingest/ingests/xenbase/orthologs.py b/src/monarch_ingest/ingests/xenbase/orthologs.py
index 1999447b..609a27ef 100644
--- a/src/monarch_ingest/ingests/xenbase/orthologs.py
+++ b/src/monarch_ingest/ingests/xenbase/orthologs.py
@@ -4,7 +4,7 @@
 
 import uuid
 
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
 from biolink_model.datamodel.pydanticmodel_v2 import GeneToGeneHomologyAssociation, AgentTypeEnum, KnowledgeLevelEnum
 
@@ -32,7 +32,7 @@
             aggregator_knowledge_source=["infores:monarchinitiative"],
             primary_knowledge_source="infores:xenbase",
             knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-            agent_type=AgentTypeEnum.manual_agent
+            agent_type=AgentTypeEnum.manual_agent,
         )
 
         # Write the captured Association out
diff --git a/src/monarch_ingest/ingests/xenbase/publication_to_gene.py b/src/monarch_ingest/ingests/xenbase/publication_to_gene.py
index 8ce3baae..95ee84b9 100644
--- a/src/monarch_ingest/ingests/xenbase/publication_to_gene.py
+++ b/src/monarch_ingest/ingests/xenbase/publication_to_gene.py
@@ -1,10 +1,12 @@
-
 import uuid
 
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
-from biolink_model.datamodel.pydanticmodel_v2 import InformationContentEntityToNamedThingAssociation, AgentTypeEnum, \
-    KnowledgeLevelEnum
+from biolink_model.datamodel.pydanticmodel_v2 import (
+    InformationContentEntityToNamedThingAssociation,
+    AgentTypeEnum,
+    KnowledgeLevelEnum,
+)
 
 from loguru import logger
 
@@ -23,9 +25,7 @@
 
         gene_page_id = gene_page.split(" ")[0]
         try:
-            gene_ids = map(
-                lambda id: f"Xenbase:{id}", list(genepage2gene[gene_page_id].values())
-            )
+            gene_ids = map(lambda id: f"Xenbase:{id}", list(genepage2gene[gene_page_id].values()))
         except KeyError:
             logger.debug(f"Could not locate genepage_id: {gene_page_id} in row {row}")
             continue
@@ -40,7 +40,7 @@
                 aggregator_knowledge_source=["infores:monarchinitiative"],
                 primary_knowledge_source="infores:xenbase",
                 knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-                agent_type=AgentTypeEnum.manual_agent
+                agent_type=AgentTypeEnum.manual_agent,
             )
 
             entities.append(association)
diff --git a/src/monarch_ingest/ingests/zfin/gene_to_phenotype.py b/src/monarch_ingest/ingests/zfin/gene_to_phenotype.py
index bde87fae..506c5ee4 100644
--- a/src/monarch_ingest/ingests/zfin/gene_to_phenotype.py
+++ b/src/monarch_ingest/ingests/zfin/gene_to_phenotype.py
@@ -1,10 +1,12 @@
-
 import uuid
 
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
-from biolink_model.datamodel.pydanticmodel_v2 import GeneToPhenotypicFeatureAssociation, KnowledgeLevelEnum, \
-    AgentTypeEnum
+from biolink_model.datamodel.pydanticmodel_v2 import (
+    GeneToPhenotypicFeatureAssociation,
+    KnowledgeLevelEnum,
+    AgentTypeEnum,
+)
 
 from loguru import logger
 
@@ -43,7 +45,7 @@
                 aggregator_knowledge_source=["infores:monarchinitiative"],
                 primary_knowledge_source="infores:zfin",
                 knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-                agent_type=AgentTypeEnum.manual_agent
+                agent_type=AgentTypeEnum.manual_agent,
             )
 
             koza_app.write(association)
diff --git a/src/monarch_ingest/ingests/zfin/publication_to_gene.py b/src/monarch_ingest/ingests/zfin/publication_to_gene.py
index 65246f24..1f1bf6e6 100644
--- a/src/monarch_ingest/ingests/zfin/publication_to_gene.py
+++ b/src/monarch_ingest/ingests/zfin/publication_to_gene.py
@@ -1,12 +1,13 @@
-
 import uuid
 
-from koza.cli_runner import get_koza_app
+from koza.cli_utils import get_koza_app
 
-from biolink_model.datamodel.pydanticmodel_v2 import InformationContentEntityToNamedThingAssociation, AgentTypeEnum, \
-    KnowledgeLevelEnum
+from biolink_model.datamodel.pydanticmodel_v2 import (
+    InformationContentEntityToNamedThingAssociation,
+    AgentTypeEnum,
+    KnowledgeLevelEnum,
+)
 
-from loguru import logger
 
 koza_app = get_koza_app("zfin_publication_to_gene")
 
@@ -24,7 +25,7 @@
         aggregator_knowledge_source=["infores:monarchinitiative"],
         primary_knowledge_source="infores:zfin",
         knowledge_level=KnowledgeLevelEnum.knowledge_assertion,
-        agent_type=AgentTypeEnum.manual_agent
+        agent_type=AgentTypeEnum.manual_agent,
     )
 
     koza_app.write(association)
diff --git a/src/monarch_ingest/main.py b/src/monarch_ingest/main.py
index 481eeaad..fdbb4c84 100644
--- a/src/monarch_ingest/main.py
+++ b/src/monarch_ingest/main.py
@@ -117,7 +117,7 @@ def merge(
 
     # load qc_report.yaml from output_dir
     qc_report = yaml.safe_load(open(f"{output_dir}/qc_report.yaml"))
-    edge_counts = {item["name"]: item["total_number"] for item in qc_report["edges"]}
+    # edge_counts = {item["name"]: item["total_number"] for item in qc_report["edges"]}
     # load expected count yaml
     expected_counts = yaml.safe_load(open(f"src/monarch_ingest/qc_expect.yaml"))
     error = False
@@ -138,6 +138,7 @@ def merge(
     if error:
         sys.exit(1)
 
+
 @typer_app.command()
 def closure():
     apply_closure()
diff --git a/src/monarch_ingest/maps/mimtitles.py b/src/monarch_ingest/maps/mimtitles.py
index fe41256f..1407ec69 100644
--- a/src/monarch_ingest/maps/mimtitles.py
+++ b/src/monarch_ingest/maps/mimtitles.py
@@ -1,6 +1,4 @@
-
-
-from koza.cli_runner import koza_app
+from koza.cli_utils import koza_app
 
 from loguru import logger
 
diff --git a/src/monarch_ingest/utils/export_utils.py b/src/monarch_ingest/utils/export_utils.py
index da201e0c..252fedd0 100755
--- a/src/monarch_ingest/utils/export_utils.py
+++ b/src/monarch_ingest/utils/export_utils.py
@@ -1,4 +1,3 @@
-
 """ Monarch Data Dump
 
 This script is used to dump tsv files from the
@@ -11,6 +10,7 @@
   - solr_filter_1
   - solr_filter_2
 """
+
 import json
 from json import decoder
 from enum import Enum
@@ -36,10 +36,12 @@ class OutputType(str, Enum):
 OUTPUT_TYPES = set(OutputType._member_names_)
 
 
-def export(config_file: str = "./src/monarch_ingest/data-dump-config.yaml",
-           output_dir: str = "./output/tsv/",
-           output_format: OutputType = OutputType.tsv,
-           solr_url: str = "http://localhost:8983/solr/association/select"):
+def export(
+    config_file: str = "./src/monarch_ingest/data-dump-config.yaml",
+    output_dir: str = "./output/tsv/",
+    output_format: OutputType = OutputType.tsv,
+    solr_url: str = "http://localhost:8983/solr/association/select",
+):
 
     if output_format not in OUTPUT_TYPES:
         raise ValueError(f"output format not supported, supported formats are {OUTPUT_TYPES}")
@@ -58,7 +60,7 @@ def export(config_file: str = "./src/monarch_ingest/data-dump-config.yaml",
         'json.nl': 'arrarr',
         'rows': 0,
         'facet': 'true',
-        'facet.field': 'category'
+        'facet.field': 'category',
     }
 
     solr_request = requests.get(solr_url, params=assoc_params)
@@ -103,7 +105,8 @@ def export(config_file: str = "./src/monarch_ingest/data-dump-config.yaml",
 
 
 def generate_tsv(tsv_fh, solr, filters):
-    default_fields = ','.join([
+    default_fields = ','.join(
+        [
             'subject',
             'subject_label',
             'subject_taxon',
@@ -112,19 +115,22 @@ def generate_tsv(tsv_fh, solr, filters):
             'predicate',
             'object',
             'object_label',
-            'qualifier'
-            'publications',
+            'qualifier' 'publications',
             'has_evidence',
             'primary_knowledge_source',
             'aggregator_knowledge_source',
-        ])
-    disease_to_phenotype_extra_fields = ','.join([
-        'onset_qualifier',
-        'onset_qualifier_label',
-        'frequency_qualifier',
-        'frequency_qualifier_label',
-        'sex_qualifier',
-        'sex_qualifier_label'])
+        ]
+    )
+    disease_to_phenotype_extra_fields = ','.join(
+        [
+            'onset_qualifier',
+            'onset_qualifier_label',
+            'frequency_qualifier',
+            'frequency_qualifier_label',
+            'sex_qualifier',
+            'sex_qualifier_label',
+        ]
+    )
     gene_to_gene_extra_fields = ','.join(['object_taxon', 'object_taxon_label'])
 
     golr_params = {
@@ -134,7 +140,7 @@ def generate_tsv(tsv_fh, solr, filters):
         'csv.separator': '\t',
         'csv.header': 'true',
         'csv.mv.separator': '|',
-        'fl': default_fields
+        'fl': default_fields,
     }
 
     for filter in filters:
@@ -168,11 +174,9 @@ def generate_tsv(tsv_fh, solr, filters):
             resultCount = facet_response['response']['numFound']
 
             if resultCount == 0:
-                logger.warning("No results found for {}"
-                               " with filters {}".format(tsv_fh.name, filters))
+                logger.warning("No results found for {}" " with filters {}".format(tsv_fh.name, filters))
         except decoder.JSONDecodeError:
-            logger.warning("JSONDecodeError for {}"
-                           " with filters {}".format(tsv_fh.name, filters))
+            logger.warning("JSONDecodeError for {}" " with filters {}".format(tsv_fh.name, filters))
             logger.warning("solr content: {}".format(solr_request.text))
             time.sleep(500)
 
@@ -203,16 +207,9 @@ def generate_tsv(tsv_fh, solr, filters):
 
 def generate_jsonl(fh, solr, filters):
 
-    #jsonl_writer = jsonlines.open(fh)
+    # jsonl_writer = jsonlines.open(fh)
 
-    golr_params = {
-        'q': '*:*',
-        'wt': 'json',
-        'fl': '*',
-        'fq': filters,
-        'start': 0,
-        'rows': 5000
-    }
+    golr_params = {'q': '*:*', 'wt': 'json', 'fl': '*', 'fq': filters, 'start': 0, 'rows': 5000}
 
     count_params = {
         'wt': 'json',
@@ -239,11 +236,9 @@ def generate_jsonl(fh, solr, filters):
             resultCount = facet_response['response']['numFound']
 
             if resultCount == 0:
-                logger.warning("No results found for {}"
-                               " with filters {}".format(fh.name, filters))
+                logger.warning("No results found for {}" " with filters {}".format(fh.name, filters))
         except decoder.JSONDecodeError:
-            logger.warning("JSONDecodeError for {}"
-                           " with filters {}".format(fh.name, filters))
+            logger.warning("JSONDecodeError for {}" " with filters {}".format(fh.name, filters))
             logger.warning("solr content: {}".format(solr_request.text))
             time.sleep(500)
 
@@ -284,4 +279,3 @@ def fetch_solr_doc(session, solr, params, retries=10):
 def camel_to_snake(name):
     name = re.sub('(.)([A-Z][a-z]+)', r'\1_\2', name)
     return re.sub('([a-z0-9])([A-Z])', r'\1_\2', name).lower()
-
diff --git a/src/monarch_ingest/utils/ingest_utils.py b/src/monarch_ingest/utils/ingest_utils.py
index a8a06fa7..7b1c16c6 100644
--- a/src/monarch_ingest/utils/ingest_utils.py
+++ b/src/monarch_ingest/utils/ingest_utils.py
@@ -23,7 +23,7 @@ def ingest_output_exists(source, output_dir):
     ingests = get_ingests()
 
     ingest_config = yaml.load(pkgutil.get_data("monarch_ingest", ingests[source]["config"]), UniqueIncludeLoader)
-    
+
     has_node_properties = "node_properties" in ingest_config
     has_edge_properties = "edge_properties" in ingest_config
 
diff --git a/src/monarch_ingest/utils/log_utils.py b/src/monarch_ingest/utils/log_utils.py
index 82fcd325..5ce0023c 100644
--- a/src/monarch_ingest/utils/log_utils.py
+++ b/src/monarch_ingest/utils/log_utils.py
@@ -6,21 +6,22 @@
 LOGURU_FORMAT = "<green>{time:YYYY-MM-DD_HH:mm:ss}</green> | <level>{level: <8}</level> | <cyan>{name: <16}</cyan> | <level>{message}</level>"
 LOGURU_FORMAT_SIMPLE = "{time:YYYY-MM-DD_HH:mm:ss} | {level: <8} | {name: <16} | {message}"
 
+
 def get_logger(name: Optional[str] = None, verbose: Optional[bool] = None):
     logger = loguru.logger
     logger.remove()
     logger.add(
-        sink = sys.stderr,
-        level = "INFO" if (verbose is None) else "DEBUG" if (verbose is True) else "WARNING",
-        format = LOGURU_FORMAT,
-        colorize = True,
+        sink=sys.stderr,
+        level="INFO" if (verbose is None) else "DEBUG" if (verbose is True) else "WARNING",
+        format=LOGURU_FORMAT,
+        colorize=True,
     )
     if name:
         fp = f"logs/{name}"
         logger.add(
-            sink = fp + "_{time:YYYY-MM-DD_HH-mm-ss}.log",
-            level = "DEBUG",
-            format = LOGURU_FORMAT_SIMPLE,
-            colorize = True,
+            sink=fp + "_{time:YYYY-MM-DD_HH-mm-ss}.log",
+            level="DEBUG",
+            format=LOGURU_FORMAT_SIMPLE,
+            colorize=True,
         )
-    return logger
\ No newline at end of file
+    return logger
diff --git a/tests/conftest.py b/tests/conftest.py
index 2508a212..5377e12a 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,11 +1,4 @@
-import types
-from typing import Iterable
-
 import pytest
-from koza.cli_runner import get_koza_app, get_translation_table, _set_koza_app, test_koza
-from koza.model.config.source_config import PrimaryFileConfig
-from koza.model.source import Source
-from loguru import logger
 
 
 @pytest.fixture(scope="package")
@@ -13,81 +6,18 @@ def global_table():
     return "src/monarch_ingest/translation_table.yaml"
 
 
-@pytest.fixture(scope="package")
-def mock_koza():
-    # This should be extracted out but for quick prototyping
-    def _mock_write(self, *entities):
-        if hasattr(self, '_entities'):
-            self._entities.extend(list(entities))
-        else:
-            self._entities = list(entities)
-
-    def _make_mock_koza_app(
-        name: str,
-        data: Iterable,
-        transform_code: str,
-        map_cache=None,
-        filters=None,
-        global_table=None,
-        local_table=None,
-    ):
-        mock_source_file_config = PrimaryFileConfig(
-            name=name,
-            files=[],
-            transform_code=transform_code,
-        )
-        mock_source_file = Source(mock_source_file_config)
-        mock_source_file._reader = data
-
-        _set_koza_app(
-            source=mock_source_file,
-            translation_table=get_translation_table(global_table, local_table, logger),
-            logger=logger,
-        )
-        koza = get_koza_app(name)
-
-        # TODO filter mocks
-        koza._map_cache = map_cache
-        koza.write = types.MethodType(_mock_write, koza)
-
-        return koza
-
-    def _transform(
-        name: str,
-        data: Iterable,
-        transform_code: str,
-        map_cache=None,
-        filters=None,
-        global_table=None,
-        local_table=None,
-    ):
-        koza_app = _make_mock_koza_app(
-            name,
-            data,
-            transform_code,
-            map_cache=map_cache,
-            filters=filters,
-            global_table=global_table,
-            local_table=local_table,
-        )
-        test_koza(koza_app)
-        koza_app.process_sources()
-        if not hasattr(koza_app, '_entities'):
-            koza_app._entities = []
-        return koza_app._entities
-
-    return _transform
-
 @pytest.fixture
 def taxon_label_map_cache():
-    return {"taxon-labels": {
-        "NCBITaxon:7955": {"label": "Danio rerio"},
-        "NCBITaxon:6239": {"label": "Caenorhabditis elegans"},
-        "NCBITaxon:44689": {"label": "Dictyostelium discoideum"},
-        "NCBITaxon:9606" : {"label": "Homo sapiens"},
-        "NCBITaxon:4896" : {"label": "Schizosaccharomyces pombe"},
-        "NCBITaxon:9615" : {"label": "Canis lupus familiaris"},
-        "NCBITaxon:9913" : {"label": "Bos taurus"},
-        "NCBITaxon:9823" : {"label": "Sus scrofa"},
-        "NCBITaxon:9031" : {"label": "Gallus gallus"},
-    }}
+    return {
+        "taxon-labels": {
+            "NCBITaxon:7955": {"label": "Danio rerio"},
+            "NCBITaxon:6239": {"label": "Caenorhabditis elegans"},
+            "NCBITaxon:44689": {"label": "Dictyostelium discoideum"},
+            "NCBITaxon:9606": {"label": "Homo sapiens"},
+            "NCBITaxon:4896": {"label": "Schizosaccharomyces pombe"},
+            "NCBITaxon:9615": {"label": "Canis lupus familiaris"},
+            "NCBITaxon:9913": {"label": "Bos taurus"},
+            "NCBITaxon:9823": {"label": "Sus scrofa"},
+            "NCBITaxon:9031": {"label": "Gallus gallus"},
+        }
+    }
diff --git a/tests/unit/alliance/test_alliance_gene.py b/tests/unit/alliance/test_alliance_gene.py
index 1ca221c2..267c5b0f 100644
--- a/tests/unit/alliance/test_alliance_gene.py
+++ b/tests/unit/alliance/test_alliance_gene.py
@@ -1,4 +1,5 @@
 import pytest
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
@@ -149,10 +150,9 @@ def no_name_row():
 
 @pytest.fixture
 def pax2a(mock_koza, source_name, pax2a_row, taxon_label_map_cache, script, global_table):
-    row = iter([pax2a_row])
     return mock_koza(
         source_name,
-        row,
+        pax2a_row,
         script,
         map_cache=taxon_label_map_cache,
         global_table=global_table,
@@ -161,10 +161,9 @@ def pax2a(mock_koza, source_name, pax2a_row, taxon_label_map_cache, script, glob
 
 @pytest.fixture
 def no_synonym_gene(mock_koza, source_name, no_synonym_row, taxon_label_map_cache, script, global_table):
-    row = iter([no_synonym_row])
     return mock_koza(
         source_name,
-        row,
+        no_synonym_row,
         script,
         map_cache=taxon_label_map_cache,
         global_table=global_table,
@@ -173,10 +172,9 @@ def no_synonym_gene(mock_koza, source_name, no_synonym_row, taxon_label_map_cach
 
 @pytest.fixture
 def no_name_gene(mock_koza, source_name, no_name_row, taxon_label_map_cache, script, global_table):
-    row = iter([no_name_row])
     return mock_koza(
         source_name,
-        row,
+        no_name_row,
         script,
         map_cache=taxon_label_map_cache,
         global_table=global_table,
@@ -188,10 +186,12 @@ def test_gene_information_gene(pax2a):
     gene = pax2a[0]
     assert gene
 
+
 def test_gene_taxon(pax2a):
     gene = pax2a[0]
-    assert 'NCBITaxon:7955' in gene.in_taxon
-    assert gene.in_taxon_label == 'Danio rerio'
+    assert "NCBITaxon:7955" in gene.in_taxon
+    assert gene.in_taxon_label == "Danio rerio"
+
 
 def test_gene_information_synonym(pax2a):
     gene = pax2a[0]
@@ -203,6 +203,7 @@ def test_gene_information_id(pax2a):
     gene = pax2a[0]
     assert gene.id == "ZFIN:ZDB-GENE-990415-8"
 
+
 def test_gene_information_no_synonyms(no_synonym_gene):
     gene = no_synonym_gene[0]
     assert gene.synonym is None or len(gene.synonym) == 0
diff --git a/tests/unit/alliance/test_alliance_gene_to_expression.py b/tests/unit/alliance/test_alliance_gene_to_expression.py
index 198209b2..a9a8e9d8 100644
--- a/tests/unit/alliance/test_alliance_gene_to_expression.py
+++ b/tests/unit/alliance/test_alliance_gene_to_expression.py
@@ -1,5 +1,7 @@
 import pytest
 from biolink_model.datamodel.pydanticmodel_v2 import GeneToExpressionSiteAssociation
+from koza.utils.testing_utils import mock_koza  # noqa: F401
+
 
 @pytest.fixture
 def source_name():
@@ -42,10 +44,9 @@ def rat_row():
 
 @pytest.fixture
 def rattus(rat_row, mock_koza, source_name, script, global_table):
-    rows = iter([rat_row])
     return mock_koza(
         source_name,
-        rows,
+        rat_row,
         script,
         global_table=global_table,
     )
@@ -94,10 +95,9 @@ def mgi_row():
 
 @pytest.fixture
 def mouse(mgi_row, mock_koza, source_name, script, global_table):
-    rows = iter([mgi_row])
     return mock_koza(
         source_name,
-        rows,
+        mgi_row,
         script,
         global_table=global_table,
     )
@@ -148,10 +148,9 @@ def zfin_row():
 
 @pytest.fixture
 def zebrafish(zfin_row, mock_koza, source_name, script, global_table):
-    rows = iter([zfin_row])
     return mock_koza(
         source_name,
-        rows,
+        zfin_row,
         script,
         global_table=global_table,
     )
@@ -197,10 +196,9 @@ def fly_row():
 
 @pytest.fixture
 def drosophila(fly_row, mock_koza, source_name, script, global_table):
-    rows = iter([fly_row])
     return mock_koza(
         source_name,
-        rows,
+        fly_row,
         script,
         global_table=global_table,
     )
@@ -250,10 +248,9 @@ def worm_row():
 
 @pytest.fixture
 def worm(worm_row, mock_koza, source_name, script, global_table):
-    rows = iter([worm_row])
     return mock_koza(
         source_name,
-        rows,
+        worm_row,
         script,
         global_table=global_table,
     )
@@ -294,10 +291,9 @@ def sgd_row():
 
 @pytest.fixture
 def yeast(sgd_row, mock_koza, source_name, script, global_table):
-    rows = iter([sgd_row])
     return mock_koza(
         source_name,
-        rows,
+        sgd_row,
         script,
         global_table=global_table,
     )
diff --git a/tests/unit/alliance/test_alliance_gene_to_phenotype.py b/tests/unit/alliance/test_alliance_gene_to_phenotype.py
index 49383c2d..4164f690 100644
--- a/tests/unit/alliance/test_alliance_gene_to_phenotype.py
+++ b/tests/unit/alliance/test_alliance_gene_to_phenotype.py
@@ -1,5 +1,6 @@
 import pytest
 from biolink_model.datamodel.pydanticmodel_v2 import Gene, GeneToPhenotypicFeatureAssociation, PhenotypicFeature
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
@@ -34,11 +35,9 @@ def rat_row():
 @pytest.fixture
 def rat(rat_row, mock_koza, source_name, script, map_cache, global_table):
     # First row is a gene, second is a feature and should get ignored
-    rows = iter([rat_row])
-
     return mock_koza(
         source_name,
-        rows,
+        rat_row,
         script,
         map_cache=map_cache,
         global_table=global_table,
@@ -70,11 +69,9 @@ def conditions_row(rat_row):
 
 @pytest.fixture
 def conditions_entities(conditions_row, mock_koza, source_name, script, map_cache, global_table):
-    rows = iter([conditions_row])
-
     return mock_koza(
         source_name,
-        rows,
+        conditions_row,
         script,
         map_cache=map_cache,
         global_table=global_table,
diff --git a/tests/unit/alliance/test_alliance_publication.py b/tests/unit/alliance/test_alliance_publication.py
index f9b4658e..9cff2a4f 100644
--- a/tests/unit/alliance/test_alliance_publication.py
+++ b/tests/unit/alliance/test_alliance_publication.py
@@ -1,6 +1,7 @@
 import datetime
 
 import pytest
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
@@ -47,7 +48,7 @@ def row():
 
 @pytest.mark.skip(reason="Will need to be updated for recent Biolink if used")
 def test_research_article(mock_koza, source_name, row, script, global_table):
-    entities = mock_koza(source_name, iter([row]), script, global_table=global_table)
+    entities = mock_koza(source_name, row, script, global_table=global_table)
     pub = entities[0]
     assert pub
     assert pub.id == "PMID:27653487"
@@ -75,7 +76,7 @@ def test_mesh_terms(mock_koza, source_name, row, script, global_table, mesh_term
             "referenceId": "PMID:23576957",
         },
     ]
-    entities = mock_koza(source_name, iter([row]), script, global_table=global_table)
+    entities = mock_koza(source_name, row, script, global_table=global_table)
     pub = entities[0]
     assert pub
     assert mesh_term in pub.mesh_terms
@@ -84,7 +85,7 @@ def test_mesh_terms(mock_koza, source_name, row, script, global_table, mesh_term
 @pytest.mark.skip(reason="Will need to be updated for recent Biolink if used")
 @pytest.mark.parametrize("author", ["Hong W", "Takshak A", "Osunbayo O", "Kunwar A", "Vershinin M"])
 def test_research_authors(mock_koza, source_name, row, script, global_table, author):
-    entities = mock_koza(source_name, iter([row]), script, global_table=global_table)
+    entities = mock_koza(source_name, row, script, global_table=global_table)
     pub = entities[0]
     assert author in pub.authors
 
@@ -92,7 +93,7 @@ def test_research_authors(mock_koza, source_name, row, script, global_table, aut
 @pytest.mark.skip(reason="Will need to be updated for recent Biolink if used")
 def test_single_xref(mock_koza, source_name, row, script, global_table):
     row["crossReferences"] = [row["crossReferences"][0]]
-    entities = mock_koza(source_name, iter([row]), script, global_table=global_table)
+    entities = mock_koza(source_name, row, script, global_table=global_table)
     pub = entities[0]
     assert pub.xref == ["SGD:S000185012"]
 
@@ -103,7 +104,7 @@ def test_single_xref(mock_koza, source_name, row, script, global_table):
 )
 def test_time_parser(mock_koza, source_name, row, script, global_table, creation_date):
     row["datePublished"] = creation_date
-    entities = mock_koza(source_name, iter([row]), script, global_table=global_table)
+    entities = mock_koza(source_name, row, script, global_table=global_table)
     pub = entities[0]
     d = pub.creation_date
     assert isinstance(d, datetime.date) or isinstance(d, datetime.datetime)
@@ -113,7 +114,7 @@ def test_time_parser(mock_koza, source_name, row, script, global_table, creation
 @pytest.mark.parametrize("creation_date", ["Unknown", "2016 Jul-Aug", "2003 ?%p?\b\bhP\u0007 19", "2000 Dec 14-28"])
 def test_notatime_parser(mock_koza, source_name, row, script, global_table, creation_date):
     row["datePublished"] = creation_date
-    entities = mock_koza(source_name, iter([row]), script, global_table=global_table)
+    entities = mock_koza(source_name, row, script, global_table=global_table)
     pub = entities[0]
     # assert pub.creation_date == None or isinstance(pub.creation_date, datetime.datetime)
     d = pub.creation_date
diff --git a/tests/unit/bgee/test_bgee_gene_to_expression.py b/tests/unit/bgee/test_bgee_gene_to_expression.py
index 9a5f0b0c..3946b6cb 100644
--- a/tests/unit/bgee/test_bgee_gene_to_expression.py
+++ b/tests/unit/bgee/test_bgee_gene_to_expression.py
@@ -120,10 +120,10 @@ def smallest_n() -> int:
 def test_filter_group_by_rank_short(row_group_1, filter_col, smallest_n):
     filtered_group = filter_group_by_rank(row_group_1, filter_col, smallest_n=smallest_n)
 
-    assert type(filtered_group) is list
+    assert isinstance(filtered_group, list)
     assert len(filtered_group) == 5
     for i in filtered_group:
-        assert type(i) is dict
+        assert isinstance(i, dict)
         assert i['Gene ID'] == 'ENSSSCG00000000002'
 
     filtered_group_df = pd.DataFrame(filtered_group)
@@ -134,10 +134,10 @@ def test_filter_group_by_rank_short(row_group_1, filter_col, smallest_n):
 def test_filter_group_by_rank_long(row_group_2, filter_col, smallest_n):
     filtered_group = filter_group_by_rank(row_group_2, filter_col, smallest_n=smallest_n)
 
-    assert type(filtered_group) is list
+    assert isinstance(filtered_group, list)
     assert len(filtered_group) == 10
     for i in filtered_group:
-        assert type(i) is dict
+        assert isinstance(i, dict)
         assert i['Gene ID'] == 'ENSSSCG00000000003'
 
     filtered_group_df = pd.DataFrame(filtered_group)
@@ -157,7 +157,7 @@ def test_write_group(row_group_1, bgee_mock_koza):
     prev_uuid = 0
     object_list = ['CL:0000023', 'CL:0000501', 'UBERON:0000948', 'UBERON:0005417', 'UBERON:0005418']
     for index, item in enumerate(write_result):
-        assert type(item) == GeneToExpressionSiteAssociation
+        assert isinstance(item, GeneToExpressionSiteAssociation)
         assert item.id != prev_uuid
         prev_uuid = item.id
         assert item.category == ['biolink:GeneToExpressionSiteAssociation']
@@ -169,10 +169,10 @@ def test_write_group(row_group_1, bgee_mock_koza):
 def test_get_row_group(bgee_mock_koza, row_group_1, filter_col) -> List:
     row_group = get_row_group(bgee_mock_koza)
 
-    assert type(row_group) is list
+    assert isinstance(row_group, list)
     assert len(row_group) == 5
     for i in row_group:
-        assert type(i) is dict
+        assert isinstance(i, dict)
 
     assert row_group == row_group_1
 
diff --git a/tests/unit/biogrid/test_biogrid.py b/tests/unit/biogrid/test_biogrid.py
index 474a3363..c092cfbb 100644
--- a/tests/unit/biogrid/test_biogrid.py
+++ b/tests/unit/biogrid/test_biogrid.py
@@ -1,9 +1,9 @@
 """
 Unit tests for BioGRID protein links ingest
 """
-import pytest
 
-from biolink_model.datamodel.pydanticmodel_v2 import PairwiseGeneToGeneInteraction
+import pytest
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
@@ -30,26 +30,26 @@ def basic_row():
     return {
         "ID Interactor A": "entrez gene/locuslink:6416",
         "ID Interactor B": "entrez gene/locuslink:2318",
-        "Alt IDs Interactor A": "biogrid:112315|entrez gene/locuslink:MAP2K4|uniprot/swiss-prot:P45985|" +
-                                "refseq:NP_003001|refseq:NP_001268364",
-        "Alt IDs Interactor B": "biogrid:108607|entrez gene/locuslink:FLNC|uniprot/swiss-prot:Q14315|" +
-                                "refseq:NP_001120959|refseq:NP_001449",
-        "Aliases Interactor A": "entrez gene/locuslink:JNKK1(gene name synonym)|" +
-                                "entrez gene/locuslink:MAPKK4(gene name synonym)|" +
-                                "entrez gene/locuslink:MEK4(gene name synonym)",
-        "Aliases Interactor B": "entrez gene/locuslink:ABP280A(gene name synonym)|" +
-                                "entrez gene/locuslink:FLN2(gene name synonym)|" +
-                                "entrez gene/locuslink:MFM5(gene name synonym)|" +
-                                "entrez gene/locuslink:MPD4(gene name synonym)",
+        "Alt IDs Interactor A": "biogrid:112315|entrez gene/locuslink:MAP2K4|uniprot/swiss-prot:P45985|"
+        + "refseq:NP_003001|refseq:NP_001268364",
+        "Alt IDs Interactor B": "biogrid:108607|entrez gene/locuslink:FLNC|uniprot/swiss-prot:Q14315|"
+        + "refseq:NP_001120959|refseq:NP_001449",
+        "Aliases Interactor A": "entrez gene/locuslink:JNKK1(gene name synonym)|"
+        + "entrez gene/locuslink:MAPKK4(gene name synonym)|"
+        + "entrez gene/locuslink:MEK4(gene name synonym)",
+        "Aliases Interactor B": "entrez gene/locuslink:ABP280A(gene name synonym)|"
+        + "entrez gene/locuslink:FLN2(gene name synonym)|"
+        + "entrez gene/locuslink:MFM5(gene name synonym)|"
+        + "entrez gene/locuslink:MPD4(gene name synonym)",
         "Interaction Detection Method": 'psi-mi:"MI:0018"(two hybrid)',
         "Publication 1st Author": "Marti A (1997)",
-        "Publication Identifiers":  "pubmed:9006895|pubmed:10727406",
+        "Publication Identifiers": "pubmed:9006895|pubmed:10727406",
         "Taxid Interactor A": "taxid:9606",
         "Taxid Interactor B": "taxid:9606",
         "Interaction Types": 'psi-mi:"MI:0407"(direct interaction)',
         "Source Database": 'psi-mi:"MI:0463"(biogrid)',
         "Interaction Identifiers": "biogrid:103",
-        "Confidence Values": ""
+        "Confidence Values": "",
     }
 
 
@@ -65,12 +65,7 @@ def basic_pl(mock_koza, source_name, basic_row, script, global_table):
     :param global_table:
     :return:
     """
-    return mock_koza(
-        name=source_name,
-        data=iter([basic_row]),
-        transform_code=script,
-        global_table=global_table
-    )
+    return mock_koza(name=source_name, data=basic_row, transform_code=script, global_table=global_table)
 
 
 def test_association(basic_pl):
diff --git a/tests/unit/ctd/test_ctd_chemical_to_disease.py b/tests/unit/ctd/test_ctd_chemical_to_disease.py
index d259569e..6a685806 100644
--- a/tests/unit/ctd/test_ctd_chemical_to_disease.py
+++ b/tests/unit/ctd/test_ctd_chemical_to_disease.py
@@ -1,7 +1,10 @@
 import pytest
 from biolink_model.datamodel.pydanticmodel_v2 import ChemicalToDiseaseOrPhenotypicFeatureAssociation
+from koza.utils.testing_utils import mock_koza  # noqa: F401
+
 from monarch_ingest.constants import BIOLINK_TREATS_OR_APPLIED_OR_STUDIED_TO_TREAT
 
+
 @pytest.fixture
 def source_name():
     return "ctd_chemical_to_disease"
@@ -15,20 +18,20 @@ def script():
 @pytest.fixture
 def no_direct_evidence(mock_koza, source_name, script, global_table):
     row = {
-        'ChemicalName': '10074-G5',
-        'ChemicalID': 'C534883',
-        'CasRN': '',
-        'DiseaseName': 'Adenocarcinoma',
-        'DiseaseID': 'MESH:D000230',
-        'DirectEvidence': '',
-        'InferenceGeneSymbol': 'MYC',
-        'InferenceScore': '4.08',
-        'OmimIDs': '',
-        'PubMedIDs': '26432044',
+        "ChemicalName": "10074-G5",
+        "ChemicalID": "C534883",
+        "CasRN": "",
+        "DiseaseName": "Adenocarcinoma",
+        "DiseaseID": "MESH:D000230",
+        "DirectEvidence": "",
+        "InferenceGeneSymbol": "MYC",
+        "InferenceScore": "4.08",
+        "OmimIDs": "",
+        "PubMedIDs": "26432044",
     }
     return mock_koza(
         name=source_name,
-        data=iter([row]),
+        data=row,
         transform_code=script,
         global_table=global_table,
     )
@@ -37,20 +40,20 @@ def no_direct_evidence(mock_koza, source_name, script, global_table):
 @pytest.fixture
 def marker_mechanism(mock_koza, source_name, script, global_table):
     row = {
-        'ChemicalName': '10,10-bis(4-pyridinylmethyl)-9(10H)-anthracenone',
-        'ChemicalID': 'C112297',
-        'CasRN': '',
-        'DiseaseName': 'Hyperkinesis',
-        'DiseaseID': 'MESH:D006948',
-        'DirectEvidence': 'marker/mechanism',
-        'InferenceGeneSymbol': '',
-        'InferenceScore': '',
-        'OmimIDs': '',
-        'PubMedIDs': '19098162',
+        "ChemicalName": "10,10-bis(4-pyridinylmethyl)-9(10H)-anthracenone",
+        "ChemicalID": "C112297",
+        "CasRN": "",
+        "DiseaseName": "Hyperkinesis",
+        "DiseaseID": "MESH:D006948",
+        "DirectEvidence": "marker/mechanism",
+        "InferenceGeneSymbol": "",
+        "InferenceScore": "",
+        "OmimIDs": "",
+        "PubMedIDs": "19098162",
     }
     return mock_koza(
         name=source_name,
-        data=iter([row]),
+        data=row,
         transform_code=script,
         global_table=global_table,
     )
@@ -59,20 +62,20 @@ def marker_mechanism(mock_koza, source_name, script, global_table):
 @pytest.fixture
 def therapeutic(mock_koza, source_name, script, global_table):
     row = {
-        'ChemicalName': '10,11-dihydro-10-hydroxycarbamazepine',
-        'ChemicalID': 'C039775',
-        'CasRN': '',
-        'DiseaseName': 'Epilepsy',
-        'DiseaseID': 'MESH:D004827',
-        'DirectEvidence': 'therapeutic',
-        'InferenceGeneSymbol': '',
-        'InferenceScore': '',
-        'OmimIDs': '',
-        'PubMedIDs': '17516704|123',
+        "ChemicalName": "10,11-dihydro-10-hydroxycarbamazepine",
+        "ChemicalID": "C039775",
+        "CasRN": "",
+        "DiseaseName": "Epilepsy",
+        "DiseaseID": "MESH:D004827",
+        "DirectEvidence": "therapeutic",
+        "InferenceGeneSymbol": "",
+        "InferenceScore": "",
+        "OmimIDs": "",
+        "PubMedIDs": "17516704|123",
     }
     return mock_koza(
         name=source_name,
-        data=iter([row]),
+        data=row,
         transform_code=script,
         global_table=global_table,
     )
@@ -95,7 +98,7 @@ def test_therapeutic_entities(therapeutic):
     association = [e for e in entities if isinstance(e, ChemicalToDiseaseOrPhenotypicFeatureAssociation)][0]
     assert association
     assert association.predicate == BIOLINK_TREATS_OR_APPLIED_OR_STUDIED_TO_TREAT
-    assert 'PMID:17516704' in association.publications
-    assert 'PMID:123' in association.publications
+    assert "PMID:17516704" in association.publications
+    assert "PMID:123" in association.publications
     assert association.primary_knowledge_source == "infores:ctd"
     assert "infores:monarchinitiative" in association.aggregator_knowledge_source
diff --git a/tests/unit/dictybase/test_dictybase_gene.py b/tests/unit/dictybase/test_dictybase_gene.py
index 675ce4d4..2de2c344 100644
--- a/tests/unit/dictybase/test_dictybase_gene.py
+++ b/tests/unit/dictybase/test_dictybase_gene.py
@@ -2,6 +2,7 @@
 
 import pytest
 from biolink_model.datamodel.pydanticmodel_v2 import Gene
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
@@ -25,7 +26,7 @@ def test_row_1():
     """
     :return: Test Dictybase Gene input data row.
     """
-    return {'GENE ID': 'DDB_G0269222', 'Gene Name': 'gefB', 'Synonyms': 'RasGEFB, RasGEF'}
+    return {"GENE ID": "DDB_G0269222", "Gene Name": "gefB", "Synonyms": "RasGEFB, RasGEF"}
 
 
 @pytest.fixture
@@ -44,7 +45,7 @@ def basic_dictybase_1(mock_koza, source_name, script, taxon_label_map_cache, tes
     """
     return mock_koza(
         name=source_name,
-        data=iter([test_row_1]),
+        data=test_row_1,
         transform_code=script,
         map_cache=taxon_label_map_cache,
         global_table=global_table,
@@ -59,7 +60,7 @@ def test_dictybase_ncbi_mapped_gene_ingest(basic_dictybase_1):
     assert entity[0].id == "dictyBase:DDB_G0269222"
     assert entity[0].symbol == "gefB"
     assert entity[0].name == "gefB"
-    assert 'RasGEFB' in entity[0].synonym
-    assert 'RasGEF' in entity[0].synonym
+    assert "RasGEFB" in entity[0].synonym
+    assert "RasGEF" in entity[0].synonym
     assert "NCBITaxon:44689" in entity[0].in_taxon
     assert "infores:dictybase" in entity[0].provided_by
diff --git a/tests/unit/dictybase/test_dictybase_gene_to_phenotype.py b/tests/unit/dictybase/test_dictybase_gene_to_phenotype.py
index e5431c35..d85e1db9 100644
--- a/tests/unit/dictybase/test_dictybase_gene_to_phenotype.py
+++ b/tests/unit/dictybase/test_dictybase_gene_to_phenotype.py
@@ -2,6 +2,7 @@
 
 import pytest
 from biolink_model.datamodel.pydanticmodel_v2 import GeneToPhenotypicFeatureAssociation
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 from monarch_ingest.ingests.dictybase.utils import parse_phenotypes
 
@@ -108,7 +109,7 @@ def basic_dictybase_1(mock_koza, source_name, script, test_row_1, global_table,
     :return: mock_koza application
     """
     return mock_koza(
-        name=source_name, data=iter([test_row_1]), transform_code=script, global_table=global_table, map_cache=map_cache
+        name=source_name, data=test_row_1, transform_code=script, global_table=global_table, map_cache=map_cache
     )
 
 
@@ -164,7 +165,7 @@ def basic_dictybase_2(mock_koza, source_name, script, test_row_2, global_table,
     :return: mock_koza application
     """
     return mock_koza(
-        name=source_name, data=iter([test_row_2]), transform_code=script, global_table=global_table, map_cache=map_cache
+        name=source_name, data=test_row_2, transform_code=script, global_table=global_table, map_cache=map_cache
     )
 
 
diff --git a/tests/unit/flybase/test_flybase_publication_to_gene.py b/tests/unit/flybase/test_flybase_publication_to_gene.py
index b9524d4f..80f2f24c 100644
--- a/tests/unit/flybase/test_flybase_publication_to_gene.py
+++ b/tests/unit/flybase/test_flybase_publication_to_gene.py
@@ -1,4 +1,5 @@
 import pytest
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 # This name must match the ingest name in the transform code
@@ -29,7 +30,7 @@ def basic_row():
 def basic_g2p(mock_koza, source_name, basic_row, script, global_table):
     return mock_koza(
         source_name,
-        iter([basic_row]),
+        basic_row,
         script,
         global_table=global_table,
     )
@@ -46,10 +47,10 @@ def test_association(basic_g2p):
 
 @pytest.fixture
 def basic_g2p_without_pmid(mock_koza, source_name, basic_row, script, global_table):
-    basic_row['PubMed_id'] = None
+    basic_row["PubMed_id"] = None
     return mock_koza(
         source_name,
-        iter([basic_row]),
+        basic_row,
         script,
         global_table=global_table,
     )
diff --git a/tests/unit/go/test_go_annotation.py b/tests/unit/go/test_go_annotation.py
index 59449d2e..376e7019 100644
--- a/tests/unit/go/test_go_annotation.py
+++ b/tests/unit/go/test_go_annotation.py
@@ -6,6 +6,7 @@
 
 import pytest
 from biolink_model.datamodel.pydanticmodel_v2 import Association
+from koza.utils.testing_utils import mock_koza  # noqa: F401  # noqa: F401
 from loguru import logger
 
 from monarch_ingest.ingests.go.annotation_utils import parse_identifiers
@@ -97,23 +98,23 @@ def test_rows():
         },
         # Multiple taxa
         {
-            'DB': 'WB',
-            'DB_Object_ID': 'WBGene00000013',
-            'DB_Object_Symbol': 'abf-2',
-            'Qualifier': 'involved_in',
-            'GO_ID': 'GO:0050830',
-            'DB_Reference': 'WB_REF:WBPaper00045314|PMID:24882217',
-            'Evidence_Code': 'IEP',
-            'With_or_From': '',
-            'Aspect': 'P',
-            'DB_Object_Name': '',
-            'DB_Object_Synonym': 'C50F2.10|C50F2.e',
-            'DB_Object_Type': 'gene',
-            'Taxon': 'taxon:6239|taxon:46170',
-            'Date': '20140827',
-            'Assigned_By': 'WB',
-            'Annotation_Extension': '',
-            'Gene_Product_Form_ID': '',
+            "DB": "WB",
+            "DB_Object_ID": "WBGene00000013",
+            "DB_Object_Symbol": "abf-2",
+            "Qualifier": "involved_in",
+            "GO_ID": "GO:0050830",
+            "DB_Reference": "WB_REF:WBPaper00045314|PMID:24882217",
+            "Evidence_Code": "IEP",
+            "With_or_From": "",
+            "Aspect": "P",
+            "DB_Object_Name": "",
+            "DB_Object_Synonym": "C50F2.10|C50F2.e",
+            "DB_Object_Type": "gene",
+            "Taxon": "taxon:6239|taxon:46170",
+            "Date": "20140827",
+            "Assigned_By": "WB",
+            "Annotation_Extension": "",
+            "Gene_Product_Form_ID": "",
         },
         # Test default qualifier override for molecular function
         {
@@ -316,7 +317,7 @@ def basic_go(mock_koza, source_name, test_rows, script, global_table, local_tabl
     """
     return mock_koza(
         name=source_name,
-        data=iter(test_rows),
+        data=test_rows,
         transform_code=script,
         global_table=global_table,
         local_table=local_table,
@@ -470,28 +471,28 @@ def test_association(basic_go):
 @pytest.fixture
 def mgi_entities(mock_koza, source_name, script, global_table, local_table):
     row = {
-        'DB': 'MGI',
-        'DB_Object_ID': 'MGI:1918911',
-        'DB_Object_Symbol': '0610005C13Rik',
-        'Qualifier': 'enables',
-        'GO_ID': 'GO:0003674',
-        'DB_Reference': 'MGI:MGI:2156816|GO_REF:0000015',
-        'Evidence_Code': 'ND',
-        'With_or_From': '',
-        'Aspect': 'F',
-        'DB_Object_Name': 'RIKEN cDNA 0610005C13 gene',
-        'DB_Object_Synonym': '',
-        'DB_Object_Type': 'gene',
-        'Taxon': 'taxon:10090',
-        'Date': '20200917',
-        'Assigned_By': 'MGI',
-        'Annotation_Extension': '',
-        'Gene_Product_Form_ID': '',
+        "DB": "MGI",
+        "DB_Object_ID": "MGI:1918911",
+        "DB_Object_Symbol": "0610005C13Rik",
+        "Qualifier": "enables",
+        "GO_ID": "GO:0003674",
+        "DB_Reference": "MGI:MGI:2156816|GO_REF:0000015",
+        "Evidence_Code": "ND",
+        "With_or_From": "",
+        "Aspect": "F",
+        "DB_Object_Name": "RIKEN cDNA 0610005C13 gene",
+        "DB_Object_Synonym": "",
+        "DB_Object_Type": "gene",
+        "Taxon": "taxon:10090",
+        "Date": "20200917",
+        "Assigned_By": "MGI",
+        "Annotation_Extension": "",
+        "Gene_Product_Form_ID": "",
     }
 
     return mock_koza(
         name=source_name,
-        data=iter([row]),
+        data=row,
         transform_code=script,
         global_table=global_table,
         local_table=local_table,
diff --git a/tests/unit/hgnc/test_hgnc_gene.py b/tests/unit/hgnc/test_hgnc_gene.py
index 84fe02a6..70629d8c 100644
--- a/tests/unit/hgnc/test_hgnc_gene.py
+++ b/tests/unit/hgnc/test_hgnc_gene.py
@@ -1,4 +1,5 @@
 import pytest
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
@@ -29,7 +30,7 @@ def gene_row():
 
 @pytest.fixture
 def pax2a(mock_koza, source_name, gene_row, script, taxon_label_map_cache, global_table):
-    row = iter([gene_row])
+    row = gene_row
     return mock_koza(
         source_name,
         row,
@@ -48,13 +49,13 @@ def test_gene(pax2a):
 def test_gene_information_synonym(pax2a):
     gene = pax2a[0]
     assert gene.synonym
-    assert gene.synonym == ['ACF', 'ASP', 'ACF64', 'ACF65', 'APOBEC1CF', '', '', '']
+    assert gene.synonym == ["ACF", "ASP", "ACF64", "ACF65", "APOBEC1CF", "", "", ""]
 
 
 def test_gene_information_xref(pax2a):
     gene = pax2a[0]
     assert gene.xref
-    assert gene.xref == ['ENSEMBL:ENSG00000148584', 'OMIM:618199']
+    assert gene.xref == ["ENSEMBL:ENSG00000148584", "OMIM:618199"]
 
 
 # Commenting out publication ingests at least temporarily
diff --git a/tests/unit/hpoa/test_hpoa_disease_mode_of_inheritance.py b/tests/unit/hpoa/test_hpoa_disease_mode_of_inheritance.py
index f0682519..476afaa1 100644
--- a/tests/unit/hpoa/test_hpoa_disease_mode_of_inheritance.py
+++ b/tests/unit/hpoa/test_hpoa_disease_mode_of_inheritance.py
@@ -1,27 +1,25 @@
 import pytest
 from biolink_model.datamodel.pydanticmodel_v2 import DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
 def d2moi_entities(mock_koza, global_table):
-    row = iter(
-        [
-            {
-                "database_id": "OMIM:300425",
-                "disease_name": "Autism susceptibility, X-linked 1",
-                "qualifier": "",
-                "hpo_id": "HP:0001417",
-                "reference": "OMIM:300425",
-                "evidence": "IEA",
-                "onset": "",
-                "frequency": "",
-                "sex": "",
-                "modifier": "",
-                "aspect": "I",  # assert 'Inheritance' test record
-                "biocuration": "HPO:iea[2009-02-17]",
-            }
-        ]
-    )
+    row = {
+        "database_id": "OMIM:300425",
+        "disease_name": "Autism susceptibility, X-linked 1",
+        "qualifier": "",
+        "hpo_id": "HP:0001417",
+        "reference": "OMIM:300425",
+        "evidence": "IEA",
+        "onset": "",
+        "frequency": "",
+        "sex": "",
+        "modifier": "",
+        "aspect": "I",  # assert 'Inheritance' test record
+        "biocuration": "HPO:iea[2009-02-17]",
+    }
+
     return mock_koza(
         name="hpoa_disease_mode_of_inheritance",
         data=row,
diff --git a/tests/unit/hpoa/test_hpoa_disease_phenotype.py b/tests/unit/hpoa/test_hpoa_disease_phenotype.py
index 6aa88401..acf984d5 100644
--- a/tests/unit/hpoa/test_hpoa_disease_phenotype.py
+++ b/tests/unit/hpoa/test_hpoa_disease_phenotype.py
@@ -1,27 +1,24 @@
 import pytest
 from biolink_model.datamodel.pydanticmodel_v2 import DiseaseToPhenotypicFeatureAssociation
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
 def d2pf_entities_1(mock_koza, global_table):
-    row = iter(
-        [
-            {
-                "database_id": "OMIM:614856",
-                "disease_name": "Osteogenesis imperfecta, type XIII",
-                "qualifier": "NOT",
-                "hpo_id": "HP:0000343",
-                "reference": "OMIM:614856",
-                "evidence": "TAS",
-                "onset": "HP:0003593",
-                "frequency": "1/1",
-                "sex": "FEMALE",
-                "modifier": "",
-                "aspect": "C",  # assert 'Clinical' test record
-                "biocuration": "HPO:skoehler[2012-11-16]",
-            }
-        ]
-    )
+    row = {
+        "database_id": "OMIM:614856",
+        "disease_name": "Osteogenesis imperfecta, type XIII",
+        "qualifier": "NOT",
+        "hpo_id": "HP:0000343",
+        "reference": "OMIM:614856",
+        "evidence": "TAS",
+        "onset": "HP:0003593",
+        "frequency": "1/1",
+        "sex": "FEMALE",
+        "modifier": "",
+        "aspect": "C",  # assert 'Clinical' test record
+        "biocuration": "HPO:skoehler[2012-11-16]",
+    }
     return mock_koza(
         name="hpoa_disease_to_phenotype",
         data=row,
@@ -47,31 +44,27 @@ def test_disease_to_phenotype_transform_1(d2pf_entities_1):
     assert association.has_total == 1
     assert association.has_quotient == 1.0  # '1/1' implies Always present, i.e. in 100% of the cases.
     assert association.has_percentage == 100.0
-    assert association.frequency_qualifier is None # No implied frequency qualifier based on the '1/1' ratio.
+    assert association.frequency_qualifier is None  # No implied frequency qualifier based on the '1/1' ratio.
     assert association.primary_knowledge_source == "infores:hpo-annotations"
     assert "infores:monarchinitiative" in association.aggregator_knowledge_source
 
 
 @pytest.fixture
 def d2pf_entities_2(mock_koza, global_table):
-    row = iter(
-        [
-            {
-                "database_id": "OMIM:117650",
-                "disease_name": "Cerebrocostomandibular syndrome",
-                "qualifier": "",
-                "hpo_id": "HP:0001249",
-                "reference": "OMIM:117650",
-                "evidence": "TAS",
-                "onset": "",
-                "frequency": "50%",
-                "sex": "",
-                "modifier": "",
-                "aspect": "P",
-                "biocuration": "HPO:probinson[2009-02-17]",
-            }
-        ]
-    )
+    row = {
+        "database_id": "OMIM:117650",
+        "disease_name": "Cerebrocostomandibular syndrome",
+        "qualifier": "",
+        "hpo_id": "HP:0001249",
+        "reference": "OMIM:117650",
+        "evidence": "TAS",
+        "onset": "",
+        "frequency": "50%",
+        "sex": "",
+        "modifier": "",
+        "aspect": "P",
+        "biocuration": "HPO:probinson[2009-02-17]",
+    }
     return mock_koza(
         name="hpoa_disease_to_phenotype",
         data=row,
@@ -95,31 +88,27 @@ def test_disease_to_phenotype_transform_2(d2pf_entities_2):
     assert not association.onset_qualifier
     assert association.has_percentage == 50.0  # '50%' implies Present in 30% to 79% of the cases.
     assert association.has_quotient == 0.5
-    assert association.frequency_qualifier is None # No implied frequency qualifier based on the '50%' ratio.
+    assert association.frequency_qualifier is None  # No implied frequency qualifier based on the '50%' ratio.
     assert association.primary_knowledge_source == "infores:hpo-annotations"
     assert "infores:monarchinitiative" in association.aggregator_knowledge_source
 
 
 @pytest.fixture
 def d2pf_entities_3(mock_koza, global_table):
-    row = iter(
-        [
-            {
-                "database_id": "OMIM:117650",
-                "disease_name": "Cerebrocostomandibular syndrome",
-                "qualifier": "",
-                "hpo_id": "HP:0001545",
-                "reference": "OMIM:117650;PMID:12345",
-                "evidence": "TAS",
-                "onset": "",
-                "frequency": "HP:0040283",
-                "sex": "",
-                "modifier": "",
-                "aspect": "P",
-                "biocuration": "HPO:skoehler[2017-07-13]",
-            }
-        ]
-    )
+    row = {
+        "database_id": "OMIM:117650",
+        "disease_name": "Cerebrocostomandibular syndrome",
+        "qualifier": "",
+        "hpo_id": "HP:0001545",
+        "reference": "OMIM:117650;PMID:12345",
+        "evidence": "TAS",
+        "onset": "",
+        "frequency": "HP:0040283",
+        "sex": "",
+        "modifier": "",
+        "aspect": "P",
+        "biocuration": "HPO:skoehler[2017-07-13]",
+    }
     return mock_koza(
         name="hpoa_disease_to_phenotype",
         data=row,
@@ -153,24 +142,20 @@ def test_disease_to_phenotype_transform_3(d2pf_entities_3):
 
 @pytest.fixture
 def d2pf_frequency_fraction_entities(mock_koza, global_table, d2pf_entities_1):
-    row = iter(
-        [
-            {
-                "database_id": "OMIM:117650",
-                "disease_name": "Cerebrocostomandibular syndrome",
-                "qualifier": "",
-                "hpo_id": "HP:0001545",
-                "reference": "OMIM:117650",
-                "evidence": "TAS",
-                "onset": "",
-                "frequency": "3/20",
-                "sex": "",
-                "modifier": "",
-                "aspect": "P",
-                "biocuration": "HPO:skoehler[2017-07-13]",
-            }
-        ]
-    )
+    row = {
+        "database_id": "OMIM:117650",
+        "disease_name": "Cerebrocostomandibular syndrome",
+        "qualifier": "",
+        "hpo_id": "HP:0001545",
+        "reference": "OMIM:117650",
+        "evidence": "TAS",
+        "onset": "",
+        "frequency": "3/20",
+        "sex": "",
+        "modifier": "",
+        "aspect": "P",
+        "biocuration": "HPO:skoehler[2017-07-13]",
+    }
     return mock_koza(
         name="hpoa_disease_to_phenotype",
         data=row,
@@ -179,12 +164,16 @@ def d2pf_frequency_fraction_entities(mock_koza, global_table, d2pf_entities_1):
         local_table="./src/monarch_ingest/ingests/hpoa/hpoa-translation.yaml",
     )
 
+
 def test_disease_to_phenotype_transform_frequency_fraction(d2pf_frequency_fraction_entities):
     assert d2pf_frequency_fraction_entities
     assert len(d2pf_frequency_fraction_entities) == 1
-    association = [entity for entity in d2pf_frequency_fraction_entities if isinstance(entity, DiseaseToPhenotypicFeatureAssociation)][0]
+    association = [
+        entity
+        for entity in d2pf_frequency_fraction_entities
+        if isinstance(entity, DiseaseToPhenotypicFeatureAssociation)
+    ][0]
     assert association.has_count == 3
     assert association.has_total == 20
     assert association.has_quotient == 0.15
     assert association.has_percentage == 15.0
-
diff --git a/tests/unit/hpoa/test_hpoa_gene_to_disease.py b/tests/unit/hpoa/test_hpoa_gene_to_disease.py
index 587f2ea8..8f209ef8 100644
--- a/tests/unit/hpoa/test_hpoa_gene_to_disease.py
+++ b/tests/unit/hpoa/test_hpoa_gene_to_disease.py
@@ -1,7 +1,8 @@
 from typing import List
 
 import pytest
-from biolink_model.datamodel.pydanticmodel_v2 import GeneToDiseaseAssociation, CausalGeneToDiseaseAssociation
+from biolink_model.datamodel.pydanticmodel_v2 import CausalGeneToDiseaseAssociation
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 from monarch_ingest.constants import (
     BIOLINK_CAUSES,
@@ -66,7 +67,7 @@ def row():
 def basic_g2d_entities(mock_koza, row):
     return mock_koza(
         name="hpoa_gene_to_disease",
-        data=iter([row]),
+        data=row,
         transform_code="./src/monarch_ingest/ingests/hpoa/gene_to_disease.py",
     )
 
diff --git a/tests/unit/hpoa/test_hpoa_gene_to_phenotype.py b/tests/unit/hpoa/test_hpoa_gene_to_phenotype.py
index 3420f789..ab2fdd0b 100644
--- a/tests/unit/hpoa/test_hpoa_gene_to_phenotype.py
+++ b/tests/unit/hpoa/test_hpoa_gene_to_phenotype.py
@@ -1,5 +1,6 @@
 import pytest
 from biolink_model.datamodel.pydanticmodel_v2 import GeneToPhenotypicFeatureAssociation
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
@@ -43,7 +44,7 @@ def basic_hpoa(mock_koza, source_name, script, test_row):
 
     :return: mock_koza application
     """
-    return mock_koza(name=source_name, data=iter([test_row]), transform_code=script)
+    return mock_koza(name=source_name, data=test_row, transform_code=script)
 
 
 @pytest.mark.parametrize("cls", [GeneToPhenotypicFeatureAssociation])
diff --git a/tests/unit/hpoa/test_hpoa_utils.py b/tests/unit/hpoa/test_hpoa_utils.py
index da25e347..aa510e26 100644
--- a/tests/unit/hpoa/test_hpoa_utils.py
+++ b/tests/unit/hpoa/test_hpoa_utils.py
@@ -1,15 +1,13 @@
 """
 Tests of HPOA Utils methods
 """
-from typing import Optional, Tuple
 
 import pytest
 
 from monarch_ingest.ingests.hpoa.hpoa_utils import (
     FrequencyHpoTerm,
     get_hpo_term,
-    map_percentage_frequency_to_hpo_term,
-    phenotype_frequency_to_hpo_term, Frequency,
+    phenotype_frequency_to_hpo_term,
 )
 
 
@@ -44,7 +42,7 @@ def test_get_hpo_term():
         ("HP:0040282", "HP:0040282", None, None, None, None),
         ("HP:0040281", "HP:0040281", None, None, None, None),
         ("HP:0040280", "HP:0040280", None, None, None, None),
-    ]
+    ],
 )
 def test_frequency_result(raw_value, frequency_qualifier, percentage, quotient, count, total):
     frequency = phenotype_frequency_to_hpo_term(raw_value)
diff --git a/tests/unit/mgi/test_mgi_publication_to_gene.py b/tests/unit/mgi/test_mgi_publication_to_gene.py
index e1a6a7fe..dc92d00a 100644
--- a/tests/unit/mgi/test_mgi_publication_to_gene.py
+++ b/tests/unit/mgi/test_mgi_publication_to_gene.py
@@ -1,5 +1,6 @@
 import pytest
 from biolink_model.datamodel.pydanticmodel_v2 import InformationContentEntityToNamedThingAssociation
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 pubmed_ids = "11217851|12466851|18163442|21267068|19213785|27357688|27914912|21873635|31504408"
 markers = "Cbe1|Smrp1"
@@ -30,7 +31,7 @@ def basic_row():
 def basic_entities(mock_koza, source_name, basic_row, script, global_table):
     return mock_koza(
         source_name,
-        iter([basic_row]),
+        basic_row,
         script,
         global_table=global_table,
     )
diff --git a/tests/unit/ncbi/test_ncbi_gene.py b/tests/unit/ncbi/test_ncbi_gene.py
index 99b356f6..2f31ff75 100644
--- a/tests/unit/ncbi/test_ncbi_gene.py
+++ b/tests/unit/ncbi/test_ncbi_gene.py
@@ -1,4 +1,5 @@
 import pytest
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
@@ -24,7 +25,7 @@ def gene_row():
 
 @pytest.fixture
 def gene_entities(mock_koza, source_name, gene_row, script, taxon_label_map_cache, global_table):
-    row = iter([gene_row])
+    row = gene_row
     return mock_koza(
         source_name,
         row,
diff --git a/tests/unit/panther/test_genome_orthologs.py b/tests/unit/panther/test_genome_orthologs.py
index cebf0cd6..01937ffd 100644
--- a/tests/unit/panther/test_genome_orthologs.py
+++ b/tests/unit/panther/test_genome_orthologs.py
@@ -1,7 +1,9 @@
 """
 Unit tests for Panther Gene Orthology relationships ingest
 """
+
 import pytest
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
@@ -140,7 +142,7 @@ def well_behaved_record_1(mock_koza, source_name, script, global_table):
     }
     return mock_koza(
         name=source_name,
-        data=iter([row]),
+        data=row,
         transform_code=script,
         global_table=global_table,
     )
@@ -162,7 +164,7 @@ def well_behaved_record_2(mock_koza, source_name, script, global_table):
     }
     return mock_koza(
         name=source_name,
-        data=iter([row]),
+        data=row,
         transform_code=script,
         global_table=global_table,
     )
@@ -185,7 +187,7 @@ def well_behaved_record_3(mock_koza, source_name, script, global_table):
     }
     return mock_koza(
         name=source_name,
-        data=iter([row]),
+        data=row,
         transform_code=script,
         global_table=global_table,
     )
@@ -207,7 +209,7 @@ def well_behaved_flybase_record(mock_koza, source_name, script, global_table):
     }
     return mock_koza(
         name=source_name,
-        data=iter([row]),
+        data=row,
         transform_code=script,
         global_table=global_table,
     )
@@ -230,7 +232,7 @@ def well_behaved_wormbase_record(mock_koza, source_name, script, global_table):
     }
     return mock_koza(
         name=source_name,
-        data=iter([row]),
+        data=row,
         transform_code=script,
         global_table=global_table,
     )
@@ -253,7 +255,7 @@ def well_behaved_pombase_record(mock_koza, source_name, script, global_table):
     }
     return mock_koza(
         name=source_name,
-        data=iter([row]),
+        data=row,
         transform_code=script,
         global_table=global_table,
     )
@@ -275,7 +277,7 @@ def odd_mgi_gene_id_record(mock_koza, source_name, script, global_table):
     }
     return mock_koza(
         name=source_name,
-        data=iter([row]),
+        data=row,
         transform_code=script,
         global_table=global_table,
     )
@@ -297,7 +299,7 @@ def pig_gene_id_record(mock_koza, source_name, script, global_table):
     }
     return mock_koza(
         name=source_name,
-        data=iter([row]),
+        data=row,
         transform_code=script,
         global_table=global_table,
     )
@@ -319,7 +321,7 @@ def aspergillus_gene_id_record(mock_koza, source_name, script, global_table):
     }
     return mock_koza(
         name=source_name,
-        data=iter([row]),
+        data=row,
         transform_code=script,
         global_table=global_table,
     )
@@ -342,7 +344,7 @@ def aardvark_is_not_a_species_record(mock_koza, source_name, script, global_tabl
     }
     return mock_koza(
         name=source_name,
-        data=iter([row]),
+        data=row,
         transform_code=script,
         global_table=global_table,
     )
@@ -364,7 +366,7 @@ def empty_gene_record(mock_koza, source_name, script, global_table):
     }
     return mock_koza(
         name=source_name,
-        data=iter([row]),
+        data=row,
         transform_code=script,
         global_table=global_table,
     )
@@ -386,7 +388,7 @@ def ill_formed_gene_spec_string(mock_koza, source_name, script, global_table):
     }
     return mock_koza(
         name=source_name,
-        data=iter([row]),
+        data=row,
         transform_code=script,
         global_table=global_table,
     )
@@ -409,7 +411,7 @@ def gene_prefix_gene_spec_string(mock_koza, source_name, script, global_table):
     }
     return mock_koza(
         name=source_name,
-        data=iter([row]),
+        data=row,
         transform_code=script,
         global_table=global_table,
     )
@@ -431,7 +433,7 @@ def geneid_prefix_gene_spec_string(mock_koza, source_name, script, global_table)
     }
     return mock_koza(
         name=source_name,
-        data=iter([row]),
+        data=row,
         transform_code=script,
         global_table=global_table,
     )
@@ -455,7 +457,7 @@ def gene_orfname_prefix_gene_spec_string(mock_koza, source_name, script, global_
     }
     return mock_koza(
         name=source_name,
-        data=iter([row]),
+        data=row,
         transform_code=script,
         global_table=global_table,
     )
@@ -479,7 +481,7 @@ def gene_orderedlocusname_prefix_gene_spec_string(mock_koza, source_name, script
     }
     return mock_koza(
         name=source_name,
-        data=iter([row]),
+        data=row,
         transform_code=script,
         global_table=global_table,
     )
@@ -506,7 +508,7 @@ def test_gene_orderedlocusname_gene_spec_string(gene_orderedlocusname_prefix_gen
 #     }
 #     return mock_koza(
 #         name=source_name,
-#         data=iter([row]),
+#         data=row,
 #         transform_code=script,
 #         global_table=global_table,
 #     )
diff --git a/tests/unit/pombase/test_pombase_gene.py b/tests/unit/pombase/test_pombase_gene.py
index e5fa3750..c500be9a 100644
--- a/tests/unit/pombase/test_pombase_gene.py
+++ b/tests/unit/pombase/test_pombase_gene.py
@@ -1,4 +1,5 @@
 import pytest
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
@@ -16,12 +17,13 @@ def gene_information_entities(mock_koza, taxon_label_map_cache, global_table):
 
     return mock_koza(
         "pombase_gene",
-        iter([row]),
+        row,
         "./src/monarch_ingest/ingests/pombase/gene.py",
         map_cache=taxon_label_map_cache,
         global_table=global_table,
     )
 
+
 @pytest.fixture
 def gene_entity_no_name(mock_koza, taxon_label_map_cache, global_table):
     row = {
@@ -37,7 +39,7 @@ def gene_entity_no_name(mock_koza, taxon_label_map_cache, global_table):
 
     return mock_koza(
         "pombase_gene",
-        iter([row]),
+        row,
         "./src/monarch_ingest/ingests/pombase/gene.py",
         map_cache=taxon_label_map_cache,
         global_table=global_table,
@@ -65,8 +67,9 @@ def test_gene_xref(gene_information_entities):
     gene = gene_information_entities[0]
     assert "UniProtKB:Q9US52" in gene.xref
 
+
 def test_gene_systematic_id_as_name(gene_entity_no_name):
     gene = gene_entity_no_name[0]
     assert gene.name == "SPAC1002.06c"
     assert gene.full_name == "SPAC1002.06c"
-    assert gene.symbol == "SPAC1002.06c"
\ No newline at end of file
+    assert gene.symbol == "SPAC1002.06c"
diff --git a/tests/unit/pombase/test_pombase_gene_to_phenotype.py b/tests/unit/pombase/test_pombase_gene_to_phenotype.py
index 8096b666..6d956017 100644
--- a/tests/unit/pombase/test_pombase_gene_to_phenotype.py
+++ b/tests/unit/pombase/test_pombase_gene_to_phenotype.py
@@ -1,35 +1,32 @@
 import pytest
 from biolink_model.datamodel.pydanticmodel_v2 import Gene, GeneToPhenotypicFeatureAssociation, PhenotypicFeature
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
 def entities(mock_koza, global_table):
-    row = iter(
-        [
-            {
-                "Database name": "PomBase",
-                "Gene systematic ID": "SPAC24B11.06c",
-                "FYPO ID": "FYPO:0004058",
-                "Allele description": "",
-                "Expression": "",
-                "Parental strain": "972 h-",
-                "Strain name (background)": "",
-                "Genotype description": "",
-                "Gene name": "sty1",
-                "Allele name": "sty1delta",
-                "Allele synonym": "",
-                "Allele type": "deletion",
-                "Evidence": "cell growth assay evidence",
-                "Condition": "",
-                "Penetrance": "",
-                "Severity": "FYPO_EXT:0000001",
-                "Extension": "",
-                "Reference": "PMID:19436749",
-                "Taxon": "4896",
-                "Date": "2014-11-21",
-            }
-        ]
-    )
+    row = {
+        "Database name": "PomBase",
+        "Gene systematic ID": "SPAC24B11.06c",
+        "FYPO ID": "FYPO:0004058",
+        "Allele description": "",
+        "Expression": "",
+        "Parental strain": "972 h-",
+        "Strain name (background)": "",
+        "Genotype description": "",
+        "Gene name": "sty1",
+        "Allele name": "sty1delta",
+        "Allele synonym": "",
+        "Allele type": "deletion",
+        "Evidence": "cell growth assay evidence",
+        "Condition": "",
+        "Penetrance": "",
+        "Severity": "FYPO_EXT:0000001",
+        "Extension": "",
+        "Reference": "PMID:19436749",
+        "Taxon": "4896",
+        "Date": "2014-11-21",
+    }
 
     return mock_koza(
         name="pombase_gene_to_phenotype",
diff --git a/tests/unit/reactome/test_reactome_chemical_to_pathway.py b/tests/unit/reactome/test_reactome_chemical_to_pathway.py
index e0ace31b..1b941de4 100644
--- a/tests/unit/reactome/test_reactome_chemical_to_pathway.py
+++ b/tests/unit/reactome/test_reactome_chemical_to_pathway.py
@@ -1,4 +1,5 @@
 import pytest
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
@@ -26,7 +27,7 @@ def basic_row():
 
 @pytest.fixture
 def basic_g2p(mock_koza, source_name, basic_row, script, global_table, local_table):
-    return mock_koza(source_name, iter([basic_row]), script, global_table=global_table, local_table=local_table)
+    return mock_koza(source_name, basic_row, script, global_table=global_table, local_table=local_table)
 
 
 def test_association(basic_g2p):
diff --git a/tests/unit/reactome/test_reactome_gene_to_pathway.py b/tests/unit/reactome/test_reactome_gene_to_pathway.py
index ca398d42..bd0dd5b8 100644
--- a/tests/unit/reactome/test_reactome_gene_to_pathway.py
+++ b/tests/unit/reactome/test_reactome_gene_to_pathway.py
@@ -1,4 +1,5 @@
 import pytest
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
@@ -31,7 +32,7 @@ def basic_row():
 
 @pytest.fixture
 def basic_g2p(mock_koza, source_name, basic_row, script, global_table, local_table):
-    return mock_koza(source_name, iter([basic_row]), script, global_table=global_table, local_table=local_table)
+    return mock_koza(source_name, basic_row, script, global_table=global_table, local_table=local_table)
 
 
 def test_association(basic_g2p):
diff --git a/tests/unit/reactome/test_reactome_pathway.py b/tests/unit/reactome/test_reactome_pathway.py
index d71add40..23428e2b 100644
--- a/tests/unit/reactome/test_reactome_pathway.py
+++ b/tests/unit/reactome/test_reactome_pathway.py
@@ -1,4 +1,5 @@
 import pytest
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
@@ -26,7 +27,7 @@ def basic_row():
 
 @pytest.fixture
 def basic_g2p(mock_koza, source_name, basic_row, script, global_table, local_table):
-    return mock_koza(source_name, iter([basic_row]), script, global_table=global_table, local_table=local_table)
+    return mock_koza(source_name, basic_row, script, global_table=global_table, local_table=local_table)
 
 
 def test_pathway_id(basic_g2p):
diff --git a/tests/unit/rgd/test_rgd_publication_to_gene.py b/tests/unit/rgd/test_rgd_publication_to_gene.py
index fd99bf07..f68a9f10 100644
--- a/tests/unit/rgd/test_rgd_publication_to_gene.py
+++ b/tests/unit/rgd/test_rgd_publication_to_gene.py
@@ -1,4 +1,5 @@
 import pytest
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 # This name must match the ingest name in the transform code
@@ -27,7 +28,7 @@ def basic_row():
 def basic_g2p(mock_koza, source_name, basic_row, script, global_table):
     return mock_koza(
         source_name,
-        iter([basic_row]),
+        basic_row,
         script,
         global_table=global_table,
     )
diff --git a/tests/unit/sgd/test_sgd_publication_to_gene.py b/tests/unit/sgd/test_sgd_publication_to_gene.py
index 41cb8ab3..b1ea23cf 100644
--- a/tests/unit/sgd/test_sgd_publication_to_gene.py
+++ b/tests/unit/sgd/test_sgd_publication_to_gene.py
@@ -1,4 +1,5 @@
 import pytest
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
@@ -23,7 +24,7 @@ def basic_row():
 def basic_g2p(mock_koza, source_name, basic_row, script, global_table):
     return mock_koza(
         source_name,
-        iter([basic_row]),
+        basic_row,
         script,
         global_table=global_table,
     )
diff --git a/tests/unit/string/test_string_protein_links.py b/tests/unit/string/test_string_protein_links.py
index 60400bfa..88b6d2af 100644
--- a/tests/unit/string/test_string_protein_links.py
+++ b/tests/unit/string/test_string_protein_links.py
@@ -1,8 +1,10 @@
 """
 Unit tests for STRING protein links ingest
 """
+
 import pytest
 from biolink_model.datamodel.pydanticmodel_v2 import PairwiseGeneToGeneInteraction
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
@@ -29,8 +31,8 @@ def map_cache():
     entrez_2_string = {
         "10090.ENSMUSP00000000001": {"entrez": "14679"},
         "10090.ENSMUSP00000020316": {"entrez": "56480"},
-        "9606.ENSP00000349467": {'entrez': '801|805|808'},
-        "9606.ENSP00000000233": {'entrez': '123|381'},
+        "9606.ENSP00000349467": {"entrez": "801|805|808"},
+        "9606.ENSP00000000233": {"entrez": "123|381"},
     }
     return {"entrez_2_string": entrez_2_string}
 
@@ -53,6 +55,7 @@ def basic_row():
         "combined_score": "183",
     }
 
+
 @pytest.fixture
 def inverse_duplicate_rows():
     return [
@@ -79,9 +82,10 @@ def inverse_duplicate_rows():
             "database": "0",
             "textmining": "67",
             "combined_score": "183",
-        }
+        },
     ]
 
+
 @pytest.fixture
 def basic_pl(mock_koza, source_name, basic_row, script, global_table, map_cache):
     """
@@ -97,12 +101,13 @@ def basic_pl(mock_koza, source_name, basic_row, script, global_table, map_cache)
     """
     return mock_koza(
         name=source_name,
-        data=iter([basic_row]),
+        data=basic_row,
         transform_code=script,
         global_table=global_table,
         map_cache=map_cache,
     )
 
+
 @pytest.fixture
 def duplicate_row_entities(mock_koza, source_name, inverse_duplicate_rows, script, global_table, map_cache):
     """
@@ -118,12 +123,13 @@ def duplicate_row_entities(mock_koza, source_name, inverse_duplicate_rows, scrip
     """
     return mock_koza(
         name=source_name,
-        data=iter(inverse_duplicate_rows),
+        data=inverse_duplicate_rows,
         transform_code=script,
         global_table=global_table,
         map_cache=map_cache,
     )
 
+
 # def test_proteins(basic_pl):
 #     gene_a = basic_pl[0]
 #     assert gene_a
@@ -154,8 +160,8 @@ def duplicate_row_entities(mock_koza, source_name, inverse_duplicate_rows, scrip
 #     assert "NCBITaxon:10090" in gene_b.in_taxon
 
 #     assert gene_b.source == "infores:entrez"
-INCLUDED_ECO_CODES = ['ECO:0000075', 'ECO:0000006', 'ECO:0007833']
-EXCLUDED_ECO_CODES = ['ECO:0000044', 'ECO:0000124', 'ECO:0000080', 'ECO:0007636']
+INCLUDED_ECO_CODES = ["ECO:0000075", "ECO:0000006", "ECO:0007833"]
+EXCLUDED_ECO_CODES = ["ECO:0000044", "ECO:0000124", "ECO:0000080", "ECO:0007636"]
 
 
 def test_association(basic_pl):
@@ -174,16 +180,16 @@ def test_association(basic_pl):
 @pytest.fixture
 def multigene_row():
     return {
-        'protein1': '9606.ENSP00000000233',
-        'protein2': '9606.ENSP00000349467',
-        'neighborhood': '0',
-        'fusion': '0',
-        'cooccurence': '332',
-        'coexpression': '62',
-        'experimental': '77',
-        'database': '0',
-        'textmining': '101',
-        'combined_score': 410,
+        "protein1": "9606.ENSP00000000233",
+        "protein2": "9606.ENSP00000349467",
+        "neighborhood": "0",
+        "fusion": "0",
+        "cooccurence": "332",
+        "coexpression": "62",
+        "experimental": "77",
+        "database": "0",
+        "textmining": "101",
+        "combined_score": 410,
     }
 
 
@@ -191,7 +197,7 @@ def multigene_row():
 def multigene_entities(mock_koza, source_name, multigene_row, script, global_table, map_cache):
     return mock_koza(
         name=source_name,
-        data=iter([multigene_row]),
+        data=multigene_row,
         transform_code=script,
         map_cache=map_cache,
         global_table=global_table,
@@ -204,8 +210,9 @@ def test_multigene_associations(multigene_entities):
     ]
     assert len(associations) == 6
 
+
 def test_duplicates_are_removed(duplicate_row_entities):
     associations = [
         association for association in duplicate_row_entities if isinstance(association, PairwiseGeneToGeneInteraction)
     ]
-    assert len(associations) == 1
\ No newline at end of file
+    assert len(associations) == 1
diff --git a/tests/unit/xenbase/test_xenbase_gene_to_phenotype.py b/tests/unit/xenbase/test_xenbase_gene_to_phenotype.py
index dfaa54ec..dcbee63a 100644
--- a/tests/unit/xenbase/test_xenbase_gene_to_phenotype.py
+++ b/tests/unit/xenbase/test_xenbase_gene_to_phenotype.py
@@ -1,30 +1,27 @@
 import pytest
 from biolink_model.datamodel.pydanticmodel_v2 import Gene, GeneToPhenotypicFeatureAssociation, PhenotypicFeature
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
 def entities(
     mock_koza,
 ):
-    row = iter(
-        [
-            {
-                "SUBJECT": "Xenbase:XB-GENE-1000632",
-                "SUBJECT_LABEL": "dctn2",
-                "SUBJECT_TAXON": "NCBITaxon:8364",
-                "SUBJECT_TAXON_LABEL": "Xla",
-                "OBJECT": "XPO:0102358",
-                "OBJECT_LABEL": "abnormal tail morphology",
-                "RELATION": "RO_0002200",
-                "RELATION_LABEL": "has_phenotype",
-                "EVIDENCE": "",
-                "EVIDENCE_LABEL": "",
-                "SOURCE": "PMID:17112317",
-                "IS_DEFINED_BY": "",
-                "QUALIFIER": "",
-            }
-        ]
-    )
+    row = {
+        "SUBJECT": "Xenbase:XB-GENE-1000632",
+        "SUBJECT_LABEL": "dctn2",
+        "SUBJECT_TAXON": "NCBITaxon:8364",
+        "SUBJECT_TAXON_LABEL": "Xla",
+        "OBJECT": "XPO:0102358",
+        "OBJECT_LABEL": "abnormal tail morphology",
+        "RELATION": "RO_0002200",
+        "RELATION_LABEL": "has_phenotype",
+        "EVIDENCE": "",
+        "EVIDENCE_LABEL": "",
+        "SOURCE": "PMID:17112317",
+        "IS_DEFINED_BY": "",
+        "QUALIFIER": "",
+    }
     return mock_koza("xenbase_gene_to_phenotype", row, "./src/monarch_ingest/ingests/xenbase/gene_to_phenotype.py")
 
 
diff --git a/tests/unit/xenbase/test_xenbase_non_entrez_orthologs.py b/tests/unit/xenbase/test_xenbase_non_entrez_orthologs.py
index 728313db..b6c55b8f 100644
--- a/tests/unit/xenbase/test_xenbase_non_entrez_orthologs.py
+++ b/tests/unit/xenbase/test_xenbase_non_entrez_orthologs.py
@@ -1,8 +1,10 @@
 """
 Unit tests for Xenbase Gene Orthology relationships ingest
 """
+
 import pytest
 from biolink_model.datamodel.pydanticmodel_v2 import GeneToGeneHomologyAssociation
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
@@ -24,12 +26,12 @@ def script():
 @pytest.fixture
 def ne_orthology_records(mock_koza, source_name, script):
     row = {
-        'Xenbase': "XB-GENE-6485390",
-        'OMIM': "614812",
-        'MGI': "1891834",
-        'ZFIN': "ZDB-GENE-070705-255",
+        "Xenbase": "XB-GENE-6485390",
+        "OMIM": "614812",
+        "MGI": "1891834",
+        "ZFIN": "ZDB-GENE-070705-255",
     }
-    return mock_koza(name=source_name, data=iter([row]), transform_code=script)
+    return mock_koza(name=source_name, data=row, transform_code=script)
 
 
 def test_ne_orthology_records(ne_orthology_records):
diff --git a/tests/unit/xenbase/test_xenbase_orthologs.py b/tests/unit/xenbase/test_xenbase_orthologs.py
index 6ecd8157..71cecced 100644
--- a/tests/unit/xenbase/test_xenbase_orthologs.py
+++ b/tests/unit/xenbase/test_xenbase_orthologs.py
@@ -1,8 +1,10 @@
 """
 Unit tests for Xenbase Gene Orthology relationships ingest
 """
+
 import pytest
 from biolink_model.datamodel.pydanticmodel_v2 import GeneToGeneHomologyAssociation
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
@@ -31,7 +33,7 @@ def orthology_record(mock_koza, source_name, script, global_table):
     }
     return mock_koza(
         name=source_name,
-        data=iter([row]),
+        data=row,
         transform_code=script,
         global_table=global_table,
     )
diff --git a/tests/unit/xenbase/test_xenbase_publication_to_gene.py b/tests/unit/xenbase/test_xenbase_publication_to_gene.py
index d66430d2..84479138 100644
--- a/tests/unit/xenbase/test_xenbase_publication_to_gene.py
+++ b/tests/unit/xenbase/test_xenbase_publication_to_gene.py
@@ -1,20 +1,18 @@
 import pytest
 from biolink_model.datamodel.pydanticmodel_v2 import Gene, InformationContentEntityToNamedThingAssociation, Publication
-from koza.cli_runner import get_translation_table
+from koza.cli_utils import get_translation_table
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 from loguru import logger
 
 
 @pytest.fixture
 def gene_literature_entities(mock_koza, global_table):
-    row = iter(
-        [
-            {
-                "xb_article": "XB-ART-1",
-                "pmid": "16938438",
-                "gene_pages": "XB-GENEPAGE-487723 nog,XB-GENEPAGE-490377 msx1,XB-GENEPAGE-481828 bmp2,XB-GENEPAGE-483057 bmp4,XB-GENEPAGE-480982 fgf8,XB-GENEPAGE-6045068 hspa1l,XB-GENEPAGE-485625 hsp70",
-            }
-        ]
-    )
+    row = {
+        "xb_article": "XB-ART-1",
+        "pmid": "16938438",
+        "gene_pages": "XB-GENEPAGE-487723 nog,XB-GENEPAGE-490377 msx1,XB-GENEPAGE-481828 bmp2,XB-GENEPAGE-483057 bmp4,XB-GENEPAGE-480982 fgf8,XB-GENEPAGE-6045068 hspa1l,XB-GENEPAGE-485625 hsp70",
+    }
+
     map_cache = {
         "genepage-2-gene": {
             "XB-GENEPAGE-487723": {
@@ -54,7 +52,7 @@ def gene_literature_entities(mock_koza, global_table):
             },
         }
     }
-    get_translation_table("src/monarch_ingest/translation_table.yaml", None, logger),
+    (get_translation_table("src/monarch_ingest/translation_table.yaml", None, logger),)
 
     return mock_koza(
         name="xenbase_publication_to_gene",
diff --git a/tests/unit/zfin/test_zfin_gene_to_phenotype.py b/tests/unit/zfin/test_zfin_gene_to_phenotype.py
index fb6881b4..c7354830 100644
--- a/tests/unit/zfin/test_zfin_gene_to_phenotype.py
+++ b/tests/unit/zfin/test_zfin_gene_to_phenotype.py
@@ -1,4 +1,5 @@
 import pytest
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
@@ -56,7 +57,7 @@ def basic_row():
 def basic_g2p(mock_koza, source_name, basic_row, script, map_cache, global_table):
     return mock_koza(
         source_name,
-        iter([basic_row]),
+        basic_row,
         script,
         map_cache=map_cache,
         global_table=global_table,
@@ -96,7 +97,7 @@ def test_association(basic_g2p):
 
 #     return mock_koza(
 #         source_name,
-#         iter([basic_row]),
+#         basic_row,
 #         script,
 #         map_cache=map_cache,
 #         global_table=global_table,
@@ -123,7 +124,7 @@ def test_association(basic_g2p):
 
 #     return mock_koza(
 #         source_name,
-#         iter([basic_row]),
+#         basic_row,
 #         script,
 #         map_cache=map_cache,
 #         global_table=global_table,
@@ -140,7 +141,7 @@ def test_excluded_tags(mock_koza, source_name, basic_row, script, map_cache, tag
     basic_row["Phenotype Tag"] = tag
     entities = mock_koza(
         source_name,
-        iter([basic_row]),
+        basic_row,
         script,
         map_cache=map_cache,
         global_table=global_table,
@@ -153,7 +154,7 @@ def test_included_tags(mock_koza, source_name, basic_row, script, map_cache, tag
     basic_row["Phenotype Tag"] = tag
     entities = mock_koza(
         source_name,
-        iter([basic_row]),
+        basic_row,
         script,
         map_cache=map_cache,
         global_table=global_table,
diff --git a/tests/unit/zfin/test_zfin_publication_to_gene.py b/tests/unit/zfin/test_zfin_publication_to_gene.py
index b99711b8..0d3e96f3 100644
--- a/tests/unit/zfin/test_zfin_publication_to_gene.py
+++ b/tests/unit/zfin/test_zfin_publication_to_gene.py
@@ -1,5 +1,6 @@
 import pytest
 from biolink_model.datamodel.pydanticmodel_v2 import InformationContentEntityToNamedThingAssociation
+from koza.utils.testing_utils import mock_koza  # noqa: F401
 
 
 @pytest.fixture
@@ -17,7 +18,7 @@ def basic_row():
 def basic_entities(mock_koza, basic_row, global_table):
     return mock_koza(
         "zfin_publication_to_gene",
-        iter([basic_row]),
+        basic_row,
         "./src/monarch_ingest/ingests/zfin/publication_to_gene.py",
         global_table=global_table,
     )